Statistics Researchhttp://hdl.handle.net/10023/1002017-06-23T22:23:27Z2017-06-23T22:23:27ZAutomatic generation of generalised regular factorial designsKobilinsky, AndréMonod, HervéBailey, R. A.http://hdl.handle.net/10023/110252017-06-19T23:15:39Z2017-09-01T00:00:00ZThe R package planor enables the user to search for, and construct, factorial designs satisfying given conditions. The user specifies the factors and their numbers of levels, the factorial terms which are assumed to be non-zero, and the subset of those which are to be estimated. Both block and treatment factors can be allowed for, and they may have either fixed or random effects, as well as hierarchy relationships. The designs are generalised regular designs, which means that each one is constructed by using a design key and that the underlying theory is that of finite abelian groups. The main theoretical results and algorithms on which planor is based are developed and illustrated, with the emphasis on mathematical rather than programming details. Sections 3–5 are dedicated to the elementary case, when the numbers of levels of all factors are powers of the same prime. The ineligible factorial terms associated with users’ specifications are defined and it is shown how they can be used to search for a design key by a backtrack algorithm. Then the results are extended to the case when different primes are involved, by making use of the Sylow decomposition of finite abelian groups. The proposed approach provides a unified framework for a wide range of factorial designs.
Open Access for this article was paid for by the French Research Agency (ANR), project Escapade (ANR-12-AGRO-0003).
2017-09-01T00:00:00ZKobilinsky, AndréMonod, HervéBailey, R. A.The R package planor enables the user to search for, and construct, factorial designs satisfying given conditions. The user specifies the factors and their numbers of levels, the factorial terms which are assumed to be non-zero, and the subset of those which are to be estimated. Both block and treatment factors can be allowed for, and they may have either fixed or random effects, as well as hierarchy relationships. The designs are generalised regular designs, which means that each one is constructed by using a design key and that the underlying theory is that of finite abelian groups. The main theoretical results and algorithms on which planor is based are developed and illustrated, with the emphasis on mathematical rather than programming details. Sections 3–5 are dedicated to the elementary case, when the numbers of levels of all factors are powers of the same prime. The ineligible factorial terms associated with users’ specifications are defined and it is shown how they can be used to search for a design key by a backtrack algorithm. Then the results are extended to the case when different primes are involved, by making use of the Sylow decomposition of finite abelian groups. The proposed approach provides a unified framework for a wide range of factorial designs.On the correspondence from Bayesian log-linear modelling to logistic regression modelling with g-priorsPapathomas, Michailhttp://hdl.handle.net/10023/108542017-06-18T01:32:16Z2017-05-18T00:00:00ZConsider a set of categorical variables where at least one of them is binary. The log-linear model that describes the counts in the resulting contingency table implies a specific logistic regression model, with the binary variable as the outcome. Within the Bayesian framework, the g-prior and mixtures of g-priors are commonly assigned to the parameters of a generalized linear model. We prove that assigning a g-prior (or a mixture of g-priors) to the parameters of a certain log-linear model designates a g-prior (or a mixture of g-priors) on the parameters of the corresponding logistic regression. By deriving an asymptotic result, and with numerical illustrations, we demonstrate that when a g-prior is adopted, this correspondence extends to the posterior distribution of the model parameters. Thus, it is valid to translate inferences from fitting a log-linear model to inferences within the logistic regression framework, with regard to the presence of main effects and interaction terms.
2017-05-18T00:00:00ZPapathomas, MichailConsider a set of categorical variables where at least one of them is binary. The log-linear model that describes the counts in the resulting contingency table implies a specific logistic regression model, with the binary variable as the outcome. Within the Bayesian framework, the g-prior and mixtures of g-priors are commonly assigned to the parameters of a generalized linear model. We prove that assigning a g-prior (or a mixture of g-priors) to the parameters of a certain log-linear model designates a g-prior (or a mixture of g-priors) on the parameters of the corresponding logistic regression. By deriving an asymptotic result, and with numerical illustrations, we demonstrate that when a g-prior is adopted, this correspondence extends to the posterior distribution of the model parameters. Thus, it is valid to translate inferences from fitting a log-linear model to inferences within the logistic regression framework, with regard to the presence of main effects and interaction terms.Estimating Key Largo woodrat abundance using spatially explicit capture–recapture and trapping point transectsPotts, Joanne MarieBuckland, Stephen TerrenceThomas, LenSavage, Annehttp://hdl.handle.net/10023/106252017-04-25T08:58:53Z2016-04-17T00:00:00ZThe Key Largo woodrat (Neotoma floridana smalli) is an endangered rodent with a restricted geographic range and small population size. Establishing an efficient monitoring program of its abundance has been problematic; previous trapping designs have not worked well because the species is sparsely distributed. We compared Key Largo woodrat abundance estimates in Key Largo, Florida, USA, obtained using trapping point transects (TPT) and spatially explicit capture–recapture (SECR) based on statistical properties, survey effort, practicality, and cost. Both methods combine aspects of distance sampling with capture–recapture, but TPT relies on radiotracking individuals to estimate detectability and SECR relies on repeat capture information to estimate densities of home ranges. Abundance estimates using TPT in the spring of 2007 and 2008 were 333 woodrats (CV = 0.46) and 696 (CV = 0.43), respectively. Abundance estimates using SECR in the spring, summer, and winter of 2007 were 97 (CV = 0.31), 334 (CV = 0.26), and 433 (CV = 0.20) animals, respectively. Trapping point transects used approximately 960 person-hours and 1,010 trap-nights/season. Spatially explicit capture–recapture used approximately 500 person-hours and 6,468 trap-nights/season. Significant time was saved in the SECR survey by setting large numbers of traps close together, minimizing time walking between traps. Trapping point transects were practical to implement in the field, and valuable auxiliary information on Key Largo woodrat behavior was obtained via radiocollaring. In this particular study, detectability of the woodrat using TPT was very low and consequently the SECR method was more efficient. Both methods require a substantial investment in survey effort to detect any change in abundance because of large uncertainty in estimates.
JMP was funded by Disney's Animal Programs, the US Fish and Wildlife Service and University of St Andrews.
2016-04-17T00:00:00ZPotts, Joanne MarieBuckland, Stephen TerrenceThomas, LenSavage, AnneThe Key Largo woodrat (Neotoma floridana smalli) is an endangered rodent with a restricted geographic range and small population size. Establishing an efficient monitoring program of its abundance has been problematic; previous trapping designs have not worked well because the species is sparsely distributed. We compared Key Largo woodrat abundance estimates in Key Largo, Florida, USA, obtained using trapping point transects (TPT) and spatially explicit capture–recapture (SECR) based on statistical properties, survey effort, practicality, and cost. Both methods combine aspects of distance sampling with capture–recapture, but TPT relies on radiotracking individuals to estimate detectability and SECR relies on repeat capture information to estimate densities of home ranges. Abundance estimates using TPT in the spring of 2007 and 2008 were 333 woodrats (CV = 0.46) and 696 (CV = 0.43), respectively. Abundance estimates using SECR in the spring, summer, and winter of 2007 were 97 (CV = 0.31), 334 (CV = 0.26), and 433 (CV = 0.20) animals, respectively. Trapping point transects used approximately 960 person-hours and 1,010 trap-nights/season. Spatially explicit capture–recapture used approximately 500 person-hours and 6,468 trap-nights/season. Significant time was saved in the SECR survey by setting large numbers of traps close together, minimizing time walking between traps. Trapping point transects were practical to implement in the field, and valuable auxiliary information on Key Largo woodrat behavior was obtained via radiocollaring. In this particular study, detectability of the woodrat using TPT was very low and consequently the SECR method was more efficient. Both methods require a substantial investment in survey effort to detect any change in abundance because of large uncertainty in estimates.Assigning stranded bottlenose dolphins to source stocks using stable isotope ratios following the Deepwater Horizon oil spillHohn, A. A.Thomas, L.Carmichael, R. H.Litz, J.Clemons-Chevis, C.Shippee, S. F.Sinclair, C.Smith, S.Speakman, T. R.Tumlin, M. C.Zolman, E. S.http://hdl.handle.net/10023/105882017-06-18T01:58:32Z2017-01-31T00:00:00ZThe potential for stranded dolphins to serve as a tool for monitoring free-ranging populations would be enhanced if their stocks of origin were known. We used stable isotopes of carbon, nitrogen, and sulfur from skin to assign stranded bottlenose dolphins Tursiops truncatus to different habitats, as a proxy for stocks (demographically independent populations), following the Deepwater Horizon oil spill. Model results from biopsy samples collected from dolphins from known habitats (n = 205) resulted in an 80.5% probability of correct assignment. These results were applied to data from stranded dolphins (n = 217), resulting in predicted assignment probabilities of 0.473, 0.172, and 0.355 to Estuarine, Barrier Island (BI), and Coastal stocks, respectively. Differences were found west and east of the Mississippi River, with more Coastal dolphins stranding in western Louisiana and more Estuarine dolphins stranding in Mississippi. Within the Estuarine East Stock, 2 groups were identified, one predominantly associated with Mississippi and Alabama estuaries and another with western Florida. δ15N values were higher in stranded samples for both Estuarine and BI stocks, potentially indicating nutritional stress. High probabilities of correct assignment of the biopsy samples indicate predictable variation in stable isotopes and fidelity to habitat. The power of δ34S to discriminate habitats relative to salinity was essential. Stable isotopes may provide guidance regarding where additional testing is warranted to confirm demographic independence and aid in determining the source habitat of stranded dolphins, thus increasing the value of biological data collected from stranded individuals.
2017-01-31T00:00:00ZHohn, A. A.Thomas, L.Carmichael, R. H.Litz, J.Clemons-Chevis, C.Shippee, S. F.Sinclair, C.Smith, S.Speakman, T. R.Tumlin, M. C.Zolman, E. S.The potential for stranded dolphins to serve as a tool for monitoring free-ranging populations would be enhanced if their stocks of origin were known. We used stable isotopes of carbon, nitrogen, and sulfur from skin to assign stranded bottlenose dolphins Tursiops truncatus to different habitats, as a proxy for stocks (demographically independent populations), following the Deepwater Horizon oil spill. Model results from biopsy samples collected from dolphins from known habitats (n = 205) resulted in an 80.5% probability of correct assignment. These results were applied to data from stranded dolphins (n = 217), resulting in predicted assignment probabilities of 0.473, 0.172, and 0.355 to Estuarine, Barrier Island (BI), and Coastal stocks, respectively. Differences were found west and east of the Mississippi River, with more Coastal dolphins stranding in western Louisiana and more Estuarine dolphins stranding in Mississippi. Within the Estuarine East Stock, 2 groups were identified, one predominantly associated with Mississippi and Alabama estuaries and another with western Florida. δ15N values were higher in stranded samples for both Estuarine and BI stocks, potentially indicating nutritional stress. High probabilities of correct assignment of the biopsy samples indicate predictable variation in stable isotopes and fidelity to habitat. The power of δ34S to discriminate habitats relative to salinity was essential. Stable isotopes may provide guidance regarding where additional testing is warranted to confirm demographic independence and aid in determining the source habitat of stranded dolphins, thus increasing the value of biological data collected from stranded individuals.Quantifying injury to common bottlenose dolphins from the Deepwater Horizon oil spill using an age-, sex- and class-structured population modelSchwacke, Lori H.Thomas, LenWells, Randall S.McFee, Wayne E.Hohn, Aleta A.Mullin, Keith D.Zolman, Eric S.Quigley, Brian M.Rowles, Teri K.Schwacke, John H.http://hdl.handle.net/10023/105872017-06-18T01:58:31Z2017-01-31T00:00:00ZField studies documented increased mortality, adverse health effects, and reproductive failure in common bottlenose dolphins Tursiops truncatus following the Deepwater Horizon (DWH) oil spill. In order to determine the appropriate type and amount of restoration needed to compensate for losses, the overall extent of injuries to dolphins had to be quantified. Simply counting dead individuals does not consider long-term impacts to populations, such as the loss of future reproductive potential from mortality of females, or the chronic health effects that continue to compromise survival long after acute effects subside. Therefore, we constructed a sex- and agestructured model of population growth and included additional class structure to represent dolphins exposed and unexposed to DWH oil. The model was applied for multiple stocks to predict injured population trajectories using estimates of post-spill survival and reproductive rates. Injured trajectories were compared to baseline trajectories that were expected had the DWH incident not occurred. Two principal measures of injury were computed: (1) lost cetacean years (LCY); the difference between baseline and injured population size, summed over the modeled time period, and (2) time to recovery; the number of years for the stock to recover to within 95% of baseline. For the dolphin stock in Barataria Bay, Louisiana, the estimated LCY was substantial: 30 347 LCY (95% CI: 11 511 to 89 746). Estimated time to recovery was 39 yr (95% CI: 24 to 80). Similar recovery timelines were predicted for stocks in the Mississippi River Delta, Mississippi Sound, Mobile Bay and the Northern Coastal Stock.
2017-01-31T00:00:00ZSchwacke, Lori H.Thomas, LenWells, Randall S.McFee, Wayne E.Hohn, Aleta A.Mullin, Keith D.Zolman, Eric S.Quigley, Brian M.Rowles, Teri K.Schwacke, John H.Field studies documented increased mortality, adverse health effects, and reproductive failure in common bottlenose dolphins Tursiops truncatus following the Deepwater Horizon (DWH) oil spill. In order to determine the appropriate type and amount of restoration needed to compensate for losses, the overall extent of injuries to dolphins had to be quantified. Simply counting dead individuals does not consider long-term impacts to populations, such as the loss of future reproductive potential from mortality of females, or the chronic health effects that continue to compromise survival long after acute effects subside. Therefore, we constructed a sex- and agestructured model of population growth and included additional class structure to represent dolphins exposed and unexposed to DWH oil. The model was applied for multiple stocks to predict injured population trajectories using estimates of post-spill survival and reproductive rates. Injured trajectories were compared to baseline trajectories that were expected had the DWH incident not occurred. Two principal measures of injury were computed: (1) lost cetacean years (LCY); the difference between baseline and injured population size, summed over the modeled time period, and (2) time to recovery; the number of years for the stock to recover to within 95% of baseline. For the dolphin stock in Barataria Bay, Louisiana, the estimated LCY was substantial: 30 347 LCY (95% CI: 11 511 to 89 746). Estimated time to recovery was 39 yr (95% CI: 24 to 80). Similar recovery timelines were predicted for stocks in the Mississippi River Delta, Mississippi Sound, Mobile Bay and the Northern Coastal Stock.Where were they from? Modelling the source stock of dolphins stranded after the Deepwater Horizon oil spill using genetic and stable isotope dataThomas, L.Booth, C. G.Rosel, P. E.Hohn, A.Litz, J.Schwacke, L. H.http://hdl.handle.net/10023/105862017-06-18T01:58:30Z2017-01-31T00:00:00ZUnderstanding the source stock of common bottlenose dolphins Tursiops truncatus that stranded in the northern Gulf of Mexico subsequent to the Deepwater Horizon oil spill was essential to accurately quantify injury and apportion individuals to the appropriate stock. The aim of this study, part of the Natural Resource Damage Assessment (NRDA), was to estimate the proportion of the 932 recorded strandings between May 2010 and June 2014 that came from coastal versus bay, sound and estuary (BSE) stocks. Four sources of relevant information were available on overlapping subsets totaling 336 (39%) of the strandings: genetic stock assignment, stable isotope ratios, photo-ID and individual genetic-ID. We developed a hierarchical Bayesian model for combining these sources that weighted each data source for each stranding according to a measure of estimated precision: the effective sample size (ESS). The photo- and genetic-ID data were limited and considered to potentially introduce biases, so these data sources were excluded from analyses used in the NRDA. Estimates were calculated separately in 3 regions: East (of the Mississippi outflow), West (of the Mississippi outflow through Vermilion Bay, Louisiana) and Western Louisiana (west of Vermilion Bay to the Texas-Louisiana border); the estimated proportions of coastal strandings were, respectively 0.215 (95% CI: 0.169-0.263), 0.016 (0.036-0.099) and 0.622 (0.487-0.803). This method represents a general approach for integrating multiple sources of information that have differing uncertainties.
2017-01-31T00:00:00ZThomas, L.Booth, C. G.Rosel, P. E.Hohn, A.Litz, J.Schwacke, L. H.Understanding the source stock of common bottlenose dolphins Tursiops truncatus that stranded in the northern Gulf of Mexico subsequent to the Deepwater Horizon oil spill was essential to accurately quantify injury and apportion individuals to the appropriate stock. The aim of this study, part of the Natural Resource Damage Assessment (NRDA), was to estimate the proportion of the 932 recorded strandings between May 2010 and June 2014 that came from coastal versus bay, sound and estuary (BSE) stocks. Four sources of relevant information were available on overlapping subsets totaling 336 (39%) of the strandings: genetic stock assignment, stable isotope ratios, photo-ID and individual genetic-ID. We developed a hierarchical Bayesian model for combining these sources that weighted each data source for each stranding according to a measure of estimated precision: the effective sample size (ESS). The photo- and genetic-ID data were limited and considered to potentially introduce biases, so these data sources were excluded from analyses used in the NRDA. Estimates were calculated separately in 3 regions: East (of the Mississippi outflow), West (of the Mississippi outflow through Vermilion Bay, Louisiana) and Western Louisiana (west of Vermilion Bay to the Texas-Louisiana border); the estimated proportions of coastal strandings were, respectively 0.215 (95% CI: 0.169-0.263), 0.016 (0.036-0.099) and 0.622 (0.487-0.803). This method represents a general approach for integrating multiple sources of information that have differing uncertainties.Survival, density, and abundance of common bottlenose dolphins in Barataria Bay (USA) following the Deepwater Horizon oil spillMcDonald, Trent L.Hornsby, Fawn E.Speakman, Todd R.Zolman, Eric S.Mullin, Keith D.Sinclair, CarrieRosel, Patricia E.Thomas, LenSchwacke, Lori H.http://hdl.handle.net/10023/105802017-06-18T01:58:23Z2017-01-31T00:00:00ZTo assess potential impacts of the Deepwater Horizon oil spill in April 2010, we conducted boat-based photo-identification surveys for common bottlenose dolphins Tursiops truncatus in Barataria Bay, Louisiana, USA (~230 km2, located 167 km WNW of the spill center). Crews logged 838 h of survey effort along pre-defined routes on 10 occasions between late June 2010 and early May 2014. We applied a previously unpublished spatial version of the robust design capture-recapture model to estimate survival and density. This model used photo locations to estimate density in the absence of study area boundaries and to separate mortality from permanent emigration. To estimate abundance, we applied density estimates to saltwater (salinity > ~8 ppt) areas of the bay where telemetry data suggested that dolphins reside. Annual dolphin survival varied between 0.80 and 0.85 (95% CIs varied from 0.77 to 0.90) over 3 yr following the Deepwater Horizon spill. In 2 non-oiled bays (in Florida and North Carolina), historic survival averages approximately 0.95. From June to November 2010, abundance increased from 1300 (95% CI ± ~130) to 3100 (95% CI ± ~400), then declined and remained between ~1600 and ~2400 individuals until spring 2013. In fall 2013 and spring 2014, abundance increased again to approximately 3100 individuals. Dolphin abundance prior to the spill was unknown, but we hypothesize that some dolphins moved out of the sampled area, probably northward into marshes, prior to initiation of our surveys in late June 2010, and later immigrated back into the sampled area.
2017-01-31T00:00:00ZMcDonald, Trent L.Hornsby, Fawn E.Speakman, Todd R.Zolman, Eric S.Mullin, Keith D.Sinclair, CarrieRosel, Patricia E.Thomas, LenSchwacke, Lori H.To assess potential impacts of the Deepwater Horizon oil spill in April 2010, we conducted boat-based photo-identification surveys for common bottlenose dolphins Tursiops truncatus in Barataria Bay, Louisiana, USA (~230 km2, located 167 km WNW of the spill center). Crews logged 838 h of survey effort along pre-defined routes on 10 occasions between late June 2010 and early May 2014. We applied a previously unpublished spatial version of the robust design capture-recapture model to estimate survival and density. This model used photo locations to estimate density in the absence of study area boundaries and to separate mortality from permanent emigration. To estimate abundance, we applied density estimates to saltwater (salinity > ~8 ppt) areas of the bay where telemetry data suggested that dolphins reside. Annual dolphin survival varied between 0.80 and 0.85 (95% CIs varied from 0.77 to 0.90) over 3 yr following the Deepwater Horizon spill. In 2 non-oiled bays (in Florida and North Carolina), historic survival averages approximately 0.95. From June to November 2010, abundance increased from 1300 (95% CI ± ~130) to 3100 (95% CI ± ~400), then declined and remained between ~1600 and ~2400 individuals until spring 2013. In fall 2013 and spring 2014, abundance increased again to approximately 3100 individuals. Dolphin abundance prior to the spill was unknown, but we hypothesize that some dolphins moved out of the sampled area, probably northward into marshes, prior to initiation of our surveys in late June 2010, and later immigrated back into the sampled area.Delphinid echolocation click detection probability on near-seafloor sensorsFrasier, Kaitlin E.Wiggins, Sean M.Harris, DanielleMarques, Tiago A.Thomas, LenHildebrand, John A.http://hdl.handle.net/10023/105122017-06-18T01:46:09Z2016-09-01T00:00:00ZThe probability of detecting echolocating delphinids on a near-seafloor sensor was estimated using two Monte Carlo simulation methods. One method estimated the probability of detecting a single click (cue counting); the other estimated the probability of detecting a group of delphinids (group counting). Echolocation click beam pattern and source level assumptions strongly influenced detectability predictions by the cue counting model. Group detectability was also influenced by assumptions about group behaviors. Model results were compared to in situ recordings of encounters with Risso's dolphin (Grampus griseus) and presumed pantropical spotted dolphin (Stenella attenuata) from a near-seafloor four-channel tracking sensor deployed in the Gulf of Mexico (25.537°N 84.632°W, depth 1220 m). Horizontal detection range, received level and estimated source level distributions from localized encounters were compared with the model predictions. Agreement between in situ results and model predictions suggests that simulations can be used to estimate detection probabilities when direct distance estimation is not available.
Funding for HARP data collection and analysis was provided by the Natural Resource Damage Assessment partners (20105138) and the Center for the Integrated Modeling and Analysis of the Gulf Ecosystem (C-IMAGE) Consortium of the BP/Gulf of Mexico Research Initiative (SA 12-10/GoMRI-007). The analyses and opinions expressed are those of the authors and not necessarily those of the funding entities. This research was made possible by a grant from The Gulf of Mexico Research Initiative/C-IMAGE II.
2016-09-01T00:00:00ZFrasier, Kaitlin E.Wiggins, Sean M.Harris, DanielleMarques, Tiago A.Thomas, LenHildebrand, John A.The probability of detecting echolocating delphinids on a near-seafloor sensor was estimated using two Monte Carlo simulation methods. One method estimated the probability of detecting a single click (cue counting); the other estimated the probability of detecting a group of delphinids (group counting). Echolocation click beam pattern and source level assumptions strongly influenced detectability predictions by the cue counting model. Group detectability was also influenced by assumptions about group behaviors. Model results were compared to in situ recordings of encounters with Risso's dolphin (Grampus griseus) and presumed pantropical spotted dolphin (Stenella attenuata) from a near-seafloor four-channel tracking sensor deployed in the Gulf of Mexico (25.537°N 84.632°W, depth 1220 m). Horizontal detection range, received level and estimated source level distributions from localized encounters were compared with the model predictions. Agreement between in situ results and model predictions suggests that simulations can be used to estimate detection probabilities when direct distance estimation is not available.A simulation approach to assessing environmental risk of sound exposure to marine mammalsDonovan, Carl R.Harris, Catriona M.Milazzo, LorenzoHarwood, JohnMarshall, LauraWilliams, Robhttp://hdl.handle.net/10023/103822017-06-18T01:42:23Z2017-04-01T00:00:00ZIntense underwater sounds caused by military sonar, seismic surveys, and pile driving can harm acoustically sensitive marine mammals. Many jurisdictions require such activities to undergo marine mammal impact assessments to guide mitigation. However, the ability to assess impacts in a rigorous, quantitative way is hindered by large knowledge gaps concerning hearing ability, sensitivity, and behavioral responses to noise exposure. We describe a simulation-based framework, called SAFESIMM (Statistical Algorithms For Estimating the Sonar Influence on Marine Megafauna), that can be used to calculate the numbers of agents (animals) likely to be affected by intense underwater sounds. We illustrate the simulation framework using two species that are likely to be affected by marine renewable energy developments in UK waters: gray seal (Halichoerus grypus) and harbor porpoise (Phocoena phocoena). We investigate three sources of uncertainty: How sound energy is perceived by agents with differing hearing abilities; how agents move in response to noise (i.e., the strength and directionality of their evasive movements); and the way in which these responses may interact with longer term constraints on agent movement. The estimate of received sound exposure level (SEL) is influenced most strongly by the weighting function used to account for the specie's presumed hearing ability. Strongly directional movement away from the sound source can cause modest reductions (~5 dB) in SEL over the short term (periods of less than 10 days). Beyond 10 days, the way in which agents respond to noise exposure has little or no effect on SEL, unless their movements are constrained by natural boundaries. Most experimental studies of noise impacts have been short-term. However, data are needed on long-term effects because uncertainty about predicted SELs accumulates over time. Synthesis and applications. Simulation frameworks offer a powerful way to explore, understand, and estimate effects of cumulative sound exposure on marine mammals and to quantify associated levels of uncertainty. However, they can often require subjective decisions that have important consequences for management recommendations, and the basis for these decisions must be clearly described.
2017-04-01T00:00:00ZDonovan, Carl R.Harris, Catriona M.Milazzo, LorenzoHarwood, JohnMarshall, LauraWilliams, RobIntense underwater sounds caused by military sonar, seismic surveys, and pile driving can harm acoustically sensitive marine mammals. Many jurisdictions require such activities to undergo marine mammal impact assessments to guide mitigation. However, the ability to assess impacts in a rigorous, quantitative way is hindered by large knowledge gaps concerning hearing ability, sensitivity, and behavioral responses to noise exposure. We describe a simulation-based framework, called SAFESIMM (Statistical Algorithms For Estimating the Sonar Influence on Marine Megafauna), that can be used to calculate the numbers of agents (animals) likely to be affected by intense underwater sounds. We illustrate the simulation framework using two species that are likely to be affected by marine renewable energy developments in UK waters: gray seal (Halichoerus grypus) and harbor porpoise (Phocoena phocoena). We investigate three sources of uncertainty: How sound energy is perceived by agents with differing hearing abilities; how agents move in response to noise (i.e., the strength and directionality of their evasive movements); and the way in which these responses may interact with longer term constraints on agent movement. The estimate of received sound exposure level (SEL) is influenced most strongly by the weighting function used to account for the specie's presumed hearing ability. Strongly directional movement away from the sound source can cause modest reductions (~5 dB) in SEL over the short term (periods of less than 10 days). Beyond 10 days, the way in which agents respond to noise exposure has little or no effect on SEL, unless their movements are constrained by natural boundaries. Most experimental studies of noise impacts have been short-term. However, data are needed on long-term effects because uncertainty about predicted SELs accumulates over time. Synthesis and applications. Simulation frameworks offer a powerful way to explore, understand, and estimate effects of cumulative sound exposure on marine mammals and to quantify associated levels of uncertainty. However, they can often require subjective decisions that have important consequences for management recommendations, and the basis for these decisions must be clearly described.The classification of partition homogeneous groups with applications to semigroup theoryAndré, JorgeAraúo, JoāoCameron, Peter Jephsonhttp://hdl.handle.net/10023/102282017-04-25T08:48:46Z2016-04-15T00:00:00ZLet λ=(λ1,λ2,...) be a partition of n, a sequence of positive integers in non-increasing order with sum n. Let Ω:={1,...,n}. An ordered partition P=(A1,A2,...) of Ω has type λ if |Ai|=λi.Following Martin and Sagan, we say that G is λ-transitive if, for any two ordered partitions P=(A1,A2,...) and Q=(B1,B2,...) of Ω of type λ, there exists g ∈ G with Aig=Bi for all i. A group G is said to be λ-homogeneous if, given two ordered partitions P and Q as above, inducing the sets P'={A1,A2,...} and Q'={B1,B2,...}, there exists g ∈ G such that P'g=Q'. Clearly a λ-transitive group is λ-homogeneous.The first goal of this paper is to classify the λ-homogeneous groups (Theorems 1.1 and 1.2). The second goal is to apply this classification to a problem in semigroup theory.Let Tn and Sn denote the transformation monoid and the symmetric group on Ω, respectively. Fix a group H<=Sn. Given a non-invertible transformation a in Tn-Sn and a group G<=Sn, we say that (a,G) is an H-pair if the semigroups generated by {a} ∪ H and {a} ∪ G contain the same non-units, that is, {a,G}\G= {a,H}\H. Using the classification of the λ-homogeneous groups we classify all the Sn-pairs (Theorem 1.8). For a multitude of transformation semigroups this theorem immediately implies a description of their automorphisms, congruences, generators and other relevant properties (Theorem 8.5). This topic involves both group theory and semigroup theory; we have attempted to include enough exposition to make the paper self-contained for researchers in both areas. The paper finishes with a number of open problems on permutation and linear groups.
2016-04-15T00:00:00ZAndré, JorgeAraúo, JoāoCameron, Peter JephsonLet λ=(λ1,λ2,...) be a partition of n, a sequence of positive integers in non-increasing order with sum n. Let Ω:={1,...,n}. An ordered partition P=(A1,A2,...) of Ω has type λ if |Ai|=λi.Following Martin and Sagan, we say that G is λ-transitive if, for any two ordered partitions P=(A1,A2,...) and Q=(B1,B2,...) of Ω of type λ, there exists g ∈ G with Aig=Bi for all i. A group G is said to be λ-homogeneous if, given two ordered partitions P and Q as above, inducing the sets P'={A1,A2,...} and Q'={B1,B2,...}, there exists g ∈ G such that P'g=Q'. Clearly a λ-transitive group is λ-homogeneous.The first goal of this paper is to classify the λ-homogeneous groups (Theorems 1.1 and 1.2). The second goal is to apply this classification to a problem in semigroup theory.Let Tn and Sn denote the transformation monoid and the symmetric group on Ω, respectively. Fix a group H<=Sn. Given a non-invertible transformation a in Tn-Sn and a group G<=Sn, we say that (a,G) is an H-pair if the semigroups generated by {a} ∪ H and {a} ∪ G contain the same non-units, that is, {a,G}\G= {a,H}\H. Using the classification of the λ-homogeneous groups we classify all the Sn-pairs (Theorem 1.8). For a multitude of transformation semigroups this theorem immediately implies a description of their automorphisms, congruences, generators and other relevant properties (Theorem 8.5). This topic involves both group theory and semigroup theory; we have attempted to include enough exposition to make the paper self-contained for researchers in both areas. The paper finishes with a number of open problems on permutation and linear groups.An assessment of the population of cotton-top tamarins (Saguinus oedipus) and their habitat in ColombiaSavage, AnneThomas, LenFeilen, Katie L.Kidney, DarrenSoto, Luis H.Pearson, MackenzieMedina, Felix S.Emeris, GermanGuillen, Rosamira R.http://hdl.handle.net/10023/101002017-06-18T01:52:54Z2016-12-28T00:00:00ZNumerous animals have declining populations due to habitat loss, illegal wildlife trade, and climate change. The cotton-top tamarin (Saguinus oedipus) is a Critically Endangered primate species, endemic to northwest Colombia, threatened by deforestation and illegal trade. In order to assess the current state of this species, we analyzed changes in the population of cotton-top tamarins and its habitat from 2005 to 2012. We used a tailor-made "lure strip transect" method to survey 43 accessible forest parcels that represent 30% of the species' range. Estimated population size in the surveyed region was approximately 2,050 in 2005 and 1,900 in 2012, with a coefficient of variation of approximately 10%. The estimated population change between surveys was -7% (a decline of approximately 1.3% per year) suggesting a relatively stable population. If densities of inaccessible forest parcels are similar to those of surveyed samples, the estimated population of cotton-top tamarins in the wild in 2012 was 6,946 individuals. We also recorded little change in the amount of suitable habitat for cotton-top tamarins between sample periods: in 2005, 18% of surveyed forest was preferred habitat for cotton-top tamarins, while in 2012, 17% percent was preferred. We attribute the relatively stable population of this Critically Endangered species to increased conservation efforts of Proyecto Tití, conservation NGOs, and the Colombian government. Due to continued threats to cotton-top tamarins and their habitat such as agriculture and urban expansion, ongoing conservation efforts are needed to ensure the long-term survival of cotton-top tamarins in Colombia.
2016-12-28T00:00:00ZSavage, AnneThomas, LenFeilen, Katie L.Kidney, DarrenSoto, Luis H.Pearson, MackenzieMedina, Felix S.Emeris, GermanGuillen, Rosamira R.Numerous animals have declining populations due to habitat loss, illegal wildlife trade, and climate change. The cotton-top tamarin (Saguinus oedipus) is a Critically Endangered primate species, endemic to northwest Colombia, threatened by deforestation and illegal trade. In order to assess the current state of this species, we analyzed changes in the population of cotton-top tamarins and its habitat from 2005 to 2012. We used a tailor-made "lure strip transect" method to survey 43 accessible forest parcels that represent 30% of the species' range. Estimated population size in the surveyed region was approximately 2,050 in 2005 and 1,900 in 2012, with a coefficient of variation of approximately 10%. The estimated population change between surveys was -7% (a decline of approximately 1.3% per year) suggesting a relatively stable population. If densities of inaccessible forest parcels are similar to those of surveyed samples, the estimated population of cotton-top tamarins in the wild in 2012 was 6,946 individuals. We also recorded little change in the amount of suitable habitat for cotton-top tamarins between sample periods: in 2005, 18% of surveyed forest was preferred habitat for cotton-top tamarins, while in 2012, 17% percent was preferred. We attribute the relatively stable population of this Critically Endangered species to increased conservation efforts of Proyecto Tití, conservation NGOs, and the Colombian government. Due to continued threats to cotton-top tamarins and their habitat such as agriculture and urban expansion, ongoing conservation efforts are needed to ensure the long-term survival of cotton-top tamarins in Colombia.On optimality and construction of circular repeated-measurements designsBailey, Rosemary AnneCameron, Peter JephsonFilipiak, KatarzynaKunert, JoachimMarkiewicz, Augustynhttp://hdl.handle.net/10023/100922017-04-25T08:48:58Z2017-01-01T00:00:00ZThe aim of this paper is to characterize and construct universally optimal designs among the class of circular repeated-measurements designs when the parameters do not permit balance for carry-over effects. It is shown that some circular weakly neighbour balanced designs defined by Filipiak and Markiewicz (2012) are universally optimal repeated-measurements designs. These results extend the work of Magda (1980), Kunert (1984b) and Filipiak and Markiewicz (2012).
2017-01-01T00:00:00ZBailey, Rosemary AnneCameron, Peter JephsonFilipiak, KatarzynaKunert, JoachimMarkiewicz, AugustynThe aim of this paper is to characterize and construct universally optimal designs among the class of circular repeated-measurements designs when the parameters do not permit balance for carry-over effects. It is shown that some circular weakly neighbour balanced designs defined by Filipiak and Markiewicz (2012) are universally optimal repeated-measurements designs. These results extend the work of Magda (1980), Kunert (1984b) and Filipiak and Markiewicz (2012).Estimability of variance components when all model matrices commuteBailey, Rosemary AnneFerreira, Sandra S.Ferreira, DarioNunes, Celiahttp://hdl.handle.net/10023/99832017-04-25T08:45:22Z2016-03-01T00:00:00ZThis paper deals with estimability of variance components in mixed models when all model matrices commute. In this situation, it is well known that the best linear unbiased estimators of fixed effects are the ordinary least squares estimators. If, in addition, the family of possible variance-covariance matrices forms an orthogonal block structure, then there are the same number of variance components as strata, and the variance components are all estimable if and only if there are non-zero residual degrees of freedom in each stratum. We investigate the case where the family of possible variance-covariance matrices, while still commutative, no longer forms an orthogonal block structure. Now the variance components may or may not all be estimable, but there is no clear link with residual degrees of freedom. Whether or not they are all estimable, there may or may not be uniformly best unbiased quadratic estimators of those that are estimable. Examples are given to demonstrate all four possibilities.
This work was partially supported by national funds of FCT - Foundation for Science and Technology under UID/MAT/00212/2013.
2016-03-01T00:00:00ZBailey, Rosemary AnneFerreira, Sandra S.Ferreira, DarioNunes, CeliaThis paper deals with estimability of variance components in mixed models when all model matrices commute. In this situation, it is well known that the best linear unbiased estimators of fixed effects are the ordinary least squares estimators. If, in addition, the family of possible variance-covariance matrices forms an orthogonal block structure, then there are the same number of variance components as strata, and the variance components are all estimable if and only if there are non-zero residual degrees of freedom in each stratum. We investigate the case where the family of possible variance-covariance matrices, while still commutative, no longer forms an orthogonal block structure. Now the variance components may or may not all be estimable, but there is no clear link with residual degrees of freedom. Whether or not they are all estimable, there may or may not be uniformly best unbiased quadratic estimators of those that are estimable. Examples are given to demonstrate all four possibilities.Extinction is imminent for Mexico’s endemic porpoise unless fishery bycatch is eliminatedTaylor, Barbara L.Rojas-Bracho, LorenzoMoore, JeffreyJaramillo-Legorreta, ArmandoVer Hoef, Jay M.Cardenas-Hinojosa, GustavoNieto-Garcia, EdwynaBarlow, JayGerrodette, TimTregenza, NicholasThomas, LenHammond, Philip S.http://hdl.handle.net/10023/99382017-06-18T01:42:37Z2016-12-05T00:00:00ZThe number of Mexico’s endemic porpoise, the vaquita (Phocoena sinus), is collapsing primarily due to bycatch in illegal gillnets set for totoaba (Totoaba macdonaldi), an endangered fish whose swim bladders are exported to China. Previous research estimated that vaquitas declined from about 567 to 245 individuals between 1997 and 2008. Acoustic monitoring between 2011 and 2015 showed a decline of 34%/year. Here, we combine visual line transect and passive acoustic data collected simultaneously in a robust spatial analysis to estimate that only 59 (95% Bayesian Credible Interval [CRI] 22 – 145) vaquita remained as of autumn 2015, a decrease since 1997 of 92% (95% CRI 80%-97%). Risk analysis suggests that if the current, temporary gillnet ban is maintained and effectively enforced, vaquitas could recover to 2008 population levels by 2050. Otherwise, the species is likely to be extinct within a decade.
Primary funding was by Secretaria del Medio Ambiente y Recursos Naturales (Secretario R. Pacchiano). Mexican support was from SEMARNAT, CONABIO, CONANP, PROFEPA, SEMAR, and WWF-Mexico. US support from NOAA-Fisheries-SWFSC and The Marine Mammal Center.
2016-12-05T00:00:00ZTaylor, Barbara L.Rojas-Bracho, LorenzoMoore, JeffreyJaramillo-Legorreta, ArmandoVer Hoef, Jay M.Cardenas-Hinojosa, GustavoNieto-Garcia, EdwynaBarlow, JayGerrodette, TimTregenza, NicholasThomas, LenHammond, Philip S.The number of Mexico’s endemic porpoise, the vaquita (Phocoena sinus), is collapsing primarily due to bycatch in illegal gillnets set for totoaba (Totoaba macdonaldi), an endangered fish whose swim bladders are exported to China. Previous research estimated that vaquitas declined from about 567 to 245 individuals between 1997 and 2008. Acoustic monitoring between 2011 and 2015 showed a decline of 34%/year. Here, we combine visual line transect and passive acoustic data collected simultaneously in a robust spatial analysis to estimate that only 59 (95% Bayesian Credible Interval [CRI] 22 – 145) vaquita remained as of autumn 2015, a decrease since 1997 of 92% (95% CRI 80%-97%). Risk analysis suggests that if the current, temporary gillnet ban is maintained and effectively enforced, vaquitas could recover to 2008 population levels by 2050. Otherwise, the species is likely to be extinct within a decade.Passive acoustic monitoring of the decline of Mexico's critically endangered vaquitaJaramillo-Legorreta, ArmandoCardenas-Hinojosa, GustavoNieto-Garcia, EdwynaRojas-Bracho, LorenzoHoef, Jay VerMoore, JeffreyTregenza, NicholasBarlow, JayGerrodette, TimThomas, LenTaylor, Barbarahttp://hdl.handle.net/10023/99372017-06-18T01:39:05Z2017-02-01T00:00:00ZThe vaquita (Phocoena sinus) is the world's most endangered marine mammal with ≈245 individuals remaining in 2008. This species of porpoise is endemic to the northern Gulf of California, Mexico, and has historically suffered population declines from unsustainable bycatch in gillnets. An illegal gillnet fishery for an endangered fish, the totoaba (Totoaba macdonaldi), has recently resurged throughout the vaquita's range. The secretive but lucrative wildlife trade with China for totoaba swim bladders has probably increased vaquita bycatch mortality, but by an unknown amount. Precise population monitoring by visual surveys is difficult because vaquitas are inherently hard to see and have now become so rare that sighting rates are very low. However, their echolocation clicks can be identified readily on specialized acoustic detectors. Acoustic detections on an array of 46 moored detectors indicate that vaquita acoustic activity declined by 80% between 2011 and 2015 in the central part of the species’ range. Statistical models estimate an annual rate of decline of 34% (95% Bayesian Credible Interval -48% to -21%). Based on preliminary acoustic monitoring results from 2011–2014 the Government of Mexico enacted and is enforcing an emergency 2-year ban of gillnets throughout the species’ range to prevent extinction, at a cost of $74 million USD to compensate fishers. Developing precise acoustic monitoring methods proved critical to exposing the severity of vaquitas’ decline and emphasizes the need for continual monitoring to effectively manage critically endangered species.
Different institutions and agencies have provided funding during the development and implementation of the acoustic monitoring program.
2017-02-01T00:00:00ZJaramillo-Legorreta, ArmandoCardenas-Hinojosa, GustavoNieto-Garcia, EdwynaRojas-Bracho, LorenzoHoef, Jay VerMoore, JeffreyTregenza, NicholasBarlow, JayGerrodette, TimThomas, LenTaylor, BarbaraThe vaquita (Phocoena sinus) is the world's most endangered marine mammal with ≈245 individuals remaining in 2008. This species of porpoise is endemic to the northern Gulf of California, Mexico, and has historically suffered population declines from unsustainable bycatch in gillnets. An illegal gillnet fishery for an endangered fish, the totoaba (Totoaba macdonaldi), has recently resurged throughout the vaquita's range. The secretive but lucrative wildlife trade with China for totoaba swim bladders has probably increased vaquita bycatch mortality, but by an unknown amount. Precise population monitoring by visual surveys is difficult because vaquitas are inherently hard to see and have now become so rare that sighting rates are very low. However, their echolocation clicks can be identified readily on specialized acoustic detectors. Acoustic detections on an array of 46 moored detectors indicate that vaquita acoustic activity declined by 80% between 2011 and 2015 in the central part of the species’ range. Statistical models estimate an annual rate of decline of 34% (95% Bayesian Credible Interval -48% to -21%). Based on preliminary acoustic monitoring results from 2011–2014 the Government of Mexico enacted and is enforcing an emergency 2-year ban of gillnets throughout the species’ range to prevent extinction, at a cost of $74 million USD to compensate fishers. Developing precise acoustic monitoring methods proved critical to exposing the severity of vaquitas’ decline and emphasizes the need for continual monitoring to effectively manage critically endangered species.The challenges of analyzing behavioral response study data : an overview of the MOCHA (Multi-study OCean acoustics Human effects Analysis) projectHarris, Catriona MThomas, LenSadykova, DinaraDe Ruiter, Stacy LynnTyack, Peter LloydSouthall, Brandon L.Read, Andrew J.Miller, Patrickhttp://hdl.handle.net/10023/99232017-04-25T09:21:14Z2016-01-01T00:00:00ZThis paper describes the MOCHA project which aims to develop novel approaches for the analysis of data collected during Behavioral Response Studies (BRSs). BRSs are experiments aimed at directly quantifying the effects of controlled dosages of natural or anthropogenic stimuli (typically sound) on marine mammal behavior. These experiments typically result in low sample size, relative to variability, and so we are looking at a number of studies in combination to maximize the gain from each one. We describe a suite of analytical tools applied to BRS data on beaked whales, including a simulation study aimed at informing future experimental design.
Date of Acceptance:
2016-01-01T00:00:00ZHarris, Catriona MThomas, LenSadykova, DinaraDe Ruiter, Stacy LynnTyack, Peter LloydSouthall, Brandon L.Read, Andrew J.Miller, PatrickThis paper describes the MOCHA project which aims to develop novel approaches for the analysis of data collected during Behavioral Response Studies (BRSs). BRSs are experiments aimed at directly quantifying the effects of controlled dosages of natural or anthropogenic stimuli (typically sound) on marine mammal behavior. These experiments typically result in low sample size, relative to variability, and so we are looking at a number of studies in combination to maximize the gain from each one. We describe a suite of analytical tools applied to BRS data on beaked whales, including a simulation study aimed at informing future experimental design.String C-groups as transitive subgroups of SnCameron, Peter JephsonFernandes, Maria ElisaLeemans, DimitriMixer, Markhttp://hdl.handle.net/10023/97942017-04-25T08:43:57Z2016-02-01T00:00:00ZIf Γ is a string C-group which is isomorphic to a transitive subgroup of the symmetric group Sn (other than Sn and the alternating group An), then the rank of Γ is at most n/2+1, with finitely many exceptions (which are classified). It is conjectured that only the symmetric group has to be excluded.
2016-02-01T00:00:00ZCameron, Peter JephsonFernandes, Maria ElisaLeemans, DimitriMixer, MarkIf Γ is a string C-group which is isomorphic to a transitive subgroup of the symmetric group Sn (other than Sn and the alternating group An), then the rank of Γ is at most n/2+1, with finitely many exceptions (which are classified). It is conjectured that only the symmetric group has to be excluded.Habitat complexity in aquatic microcosms affects processes driven by detrivoresFlores, LoreaBailey, R. A.Elosegi, ArturoLarrañaga, AitorReiss, Juliahttp://hdl.handle.net/10023/97492017-06-18T01:48:03Z2016-11-01T00:00:00ZHabitat complexity can influence predation rates (e.g. by providing refuge) but other ecosystem processes and species interactions might also be modulated by the properties of habitat structure. Here, we focussed on how complexity of artificial habitat (plastic plants), in microcosms, influenced short-term processes driven by three aquatic detritivores. The effects of habitat complexity on leaf decomposition, production of fine organic matter and pH levels were explored by measuring complexity in three ways: 1. as the presence vs. absence of habitat structure; 2. as the amount of structure (3 or 4.5 g of plastic plants); and 3. as the spatial configuration of structures (measured as fractal dimension). The experiment also addressed potential interactions among the consumers by running all possible species combinations. In the experimental microcosms, habitat complexity influenced how species performed, especially when comparing structure present vs. structure absent. Treatments with structure showed higher fine particulate matter production and lower pH compared to treatments without structures and this was probably due to higher digestion and respiration when structures were present. When we explored the effects of the different complexity levels, we found that the amount of structure added explained more than the fractal dimension of the structures. We give a detailed overview of the experimental design, statistical models and R codes, because our statistical analysis can be applied to other study systems (and disciplines such as restoration ecology). We further make suggestions of how to optimise statistical power when artificially assembling, and analysing, ‘habitat complexity’ by not confounding complexity with the amount of structure added. In summary, this study highlights the importance of habitat complexity for energy flow and the maintenance of ecosystem processes in aquatic ecosystems.
LF was supported in part by the Spanish Ministry of Economy and Competitiveness through the project SCARCE Consolider-Ingenio CSD2009-00065.
2016-11-01T00:00:00ZFlores, LoreaBailey, R. A.Elosegi, ArturoLarrañaga, AitorReiss, JuliaHabitat complexity can influence predation rates (e.g. by providing refuge) but other ecosystem processes and species interactions might also be modulated by the properties of habitat structure. Here, we focussed on how complexity of artificial habitat (plastic plants), in microcosms, influenced short-term processes driven by three aquatic detritivores. The effects of habitat complexity on leaf decomposition, production of fine organic matter and pH levels were explored by measuring complexity in three ways: 1. as the presence vs. absence of habitat structure; 2. as the amount of structure (3 or 4.5 g of plastic plants); and 3. as the spatial configuration of structures (measured as fractal dimension). The experiment also addressed potential interactions among the consumers by running all possible species combinations. In the experimental microcosms, habitat complexity influenced how species performed, especially when comparing structure present vs. structure absent. Treatments with structure showed higher fine particulate matter production and lower pH compared to treatments without structures and this was probably due to higher digestion and respiration when structures were present. When we explored the effects of the different complexity levels, we found that the amount of structure added explained more than the fractal dimension of the structures. We give a detailed overview of the experimental design, statistical models and R codes, because our statistical analysis can be applied to other study systems (and disciplines such as restoration ecology). We further make suggestions of how to optimise statistical power when artificially assembling, and analysing, ‘habitat complexity’ by not confounding complexity with the amount of structure added. In summary, this study highlights the importance of habitat complexity for energy flow and the maintenance of ecosystem processes in aquatic ecosystems.Effects of a scientific echo sounder on the behavior of short-finned pilot whales (Globicephala macrorhynchus)Quick, NicolaScott-Hayward, LindesaySadykova, DinaraNowacek, DougRead, Andrewhttp://hdl.handle.net/10023/95552017-06-18T01:44:40Z2016-09-26T00:00:00ZActive echo sounding devices are often employed for commercial or scientific purposes in the foraging habitats of marine mammals. We conducted an experiment off Cape Hatteras, North Carolina, USA, to assess whether the behavior of short-finned pilot whales (Globicephala macrorhynchus) changed when exposed to an EK60 scientific echo sounder. We attached digital acoustic recording tags (DTAGs) to nine individuals, five of which were exposed. A hidden Markov model to characterize diving states with and without exposure provided no evidence for a change in foraging behavior. However, generalized estimating equations to model changes in heading variance over the entire tag record under all experimental conditions showed a consistent increase in heading variance during exposure over all values of depth and pitch. This suggests that regardless of behavioral state, the whales changed their heading more frequently when the echo sounder was active. This response could represent increased vigilance in which whales maintained awareness of echo sounder location by increasing their heading variance and provides the first quantitative analysis on reactions of cetaceans to a scientific echo sounder.
This work was supported by award RC-2154 from the Strategic Environmental Research and Development Program and funding from the Naval Facilities Engineering Command Atlantic and NOAA Fisheries, Southeast Region.
2016-09-26T00:00:00ZQuick, NicolaScott-Hayward, LindesaySadykova, DinaraNowacek, DougRead, AndrewActive echo sounding devices are often employed for commercial or scientific purposes in the foraging habitats of marine mammals. We conducted an experiment off Cape Hatteras, North Carolina, USA, to assess whether the behavior of short-finned pilot whales (Globicephala macrorhynchus) changed when exposed to an EK60 scientific echo sounder. We attached digital acoustic recording tags (DTAGs) to nine individuals, five of which were exposed. A hidden Markov model to characterize diving states with and without exposure provided no evidence for a change in foraging behavior. However, generalized estimating equations to model changes in heading variance over the entire tag record under all experimental conditions showed a consistent increase in heading variance during exposure over all values of depth and pitch. This suggests that regardless of behavioral state, the whales changed their heading more frequently when the echo sounder was active. This response could represent increased vigilance in which whales maintained awareness of echo sounder location by increasing their heading variance and provides the first quantitative analysis on reactions of cetaceans to a scientific echo sounder.Lengths of words in transformation semigroups generated by digraphsCameron, P. J.Castillo-Ramirez, A.Gadouleau, M.Mitchell, J. D.http://hdl.handle.net/10023/92772017-06-18T01:32:48Z2017-02-01T00:00:00ZGiven a simple digraph D on n vertices (with n≥2), there is a natural construction of a semigroup of transformations ⟨D⟩. For any edge (a, b) of D, let a→b be the idempotent of rank n−1 mapping a to b and fixing all vertices other than a; then, define ⟨D⟩ to be the semigroup generated by a→b for all (a,b)∈E(D). For α∈⟨D⟩, let ℓ(D,α) be the minimal length of a word in E(D) expressing α. It is well known that the semigroup Singn of all transformations of rank at most n−1 is generated by its idempotents of rank n−1. When D=Kn is the complete undirected graph, Howie and Iwahori, independently, obtained a formula to calculate ℓ(Kn,α), for any α∈⟨Kn⟩=Singn; however, no analogous non-trivial results are known when D≠Kn. In this paper, we characterise all simple digraphs D such that either ℓ(D,α) is equal to Howie–Iwahori’s formula for all α∈⟨D⟩, or ℓ(D,α)=n−fix(α) for all α∈⟨D⟩, or ℓ(D,α)=n−rk(α) for all α∈⟨D⟩. We also obtain bounds for ℓ(D,α) when D is an acyclic digraph or a strong tournament (the latter case corresponds to a smallest generating set of idempotents of rank n−1 of Singn). We finish the paper with a list of conjectures and open problems
The second and third authors were supported by the EPSRC grant EP/K033956/1.
2017-02-01T00:00:00ZCameron, P. J.Castillo-Ramirez, A.Gadouleau, M.Mitchell, J. D.Given a simple digraph D on n vertices (with n≥2), there is a natural construction of a semigroup of transformations ⟨D⟩. For any edge (a, b) of D, let a→b be the idempotent of rank n−1 mapping a to b and fixing all vertices other than a; then, define ⟨D⟩ to be the semigroup generated by a→b for all (a,b)∈E(D). For α∈⟨D⟩, let ℓ(D,α) be the minimal length of a word in E(D) expressing α. It is well known that the semigroup Singn of all transformations of rank at most n−1 is generated by its idempotents of rank n−1. When D=Kn is the complete undirected graph, Howie and Iwahori, independently, obtained a formula to calculate ℓ(Kn,α), for any α∈⟨Kn⟩=Singn; however, no analogous non-trivial results are known when D≠Kn. In this paper, we characterise all simple digraphs D such that either ℓ(D,α) is equal to Howie–Iwahori’s formula for all α∈⟨D⟩, or ℓ(D,α)=n−fix(α) for all α∈⟨D⟩, or ℓ(D,α)=n−rk(α) for all α∈⟨D⟩. We also obtain bounds for ℓ(D,α) when D is an acyclic digraph or a strong tournament (the latter case corresponds to a smallest generating set of idempotents of rank n−1 of Singn). We finish the paper with a list of conjectures and open problemsModeling the aggregated exposure and responses of bowhead whales Balaena mysticetus to multiple sources of anthropogenic underwater soundEllison, William T.Racca, RobertoClark, Christopher W.Streever, BillFrankel, Adam S.Fleishman, EricaAngliss, RobynBerger, JoelKetten, DarleneGuerra, MelaniaLeu, MatthiasMcKenna, MeganSformo, ToddSouthall, BrandonSuydam, RobertThomas, Lenhttp://hdl.handle.net/10023/92592017-04-25T09:05:47Z2016-05-02T00:00:00ZPotential responses of marine mammals to anthropogenic underwater sound are usually assessed by researchers and regulators on the basis of exposure to a single, relatively loud sound source. However, marine mammals typically receive sounds from multiple, dynamic sources. We developed a method to aggregate modeled sounds from multiple sources and estimate the sound levels received by individuals. To illustrate the method, we modeled the sound fields of 9 sources associated with oil development and estimated the sound received over 47 d by a population of 10 000 simulated bowhead whales Balaena mysticetus on their annual migration through the Alaskan Beaufort Sea. Empirical data were sufficient to parameterize simulations of the distribution of individual whales over time and their range of movement patterns. We ran 2 simulations to estimate the sound exposure history and distances traveled by bowhead whales: one in which they could change their movement paths (avert) in response to set levels of sound and one in which they could not avert. When animals could not avert, about 2% of the simulated population was exposed to root mean square (rms) sound pressure levels (SPL) ≥ 180 dB re 1 mu Pa, a level that regulators in the U.S. often associate with injury. When animals could avert from sound levels that regulators often associate with behavioral disturbance (rms SPL > 160 dB re 1 μPa), <1% of the simulated population was exposed to levels associated with injury. Nevertheless, many simulated bowhead whales received sound levels considerably above ambient throughout their migration. Our method enables estimates of the aggregated level of sound to which populations are exposed over extensive areas and time periods.
This work was supported in part by a contract between BP Exploration (Alaska) Inc. and the University of California, Santa Barbara (E.F.), and by the North Slope Borough.
2016-05-02T00:00:00ZEllison, William T.Racca, RobertoClark, Christopher W.Streever, BillFrankel, Adam S.Fleishman, EricaAngliss, RobynBerger, JoelKetten, DarleneGuerra, MelaniaLeu, MatthiasMcKenna, MeganSformo, ToddSouthall, BrandonSuydam, RobertThomas, LenPotential responses of marine mammals to anthropogenic underwater sound are usually assessed by researchers and regulators on the basis of exposure to a single, relatively loud sound source. However, marine mammals typically receive sounds from multiple, dynamic sources. We developed a method to aggregate modeled sounds from multiple sources and estimate the sound levels received by individuals. To illustrate the method, we modeled the sound fields of 9 sources associated with oil development and estimated the sound received over 47 d by a population of 10 000 simulated bowhead whales Balaena mysticetus on their annual migration through the Alaskan Beaufort Sea. Empirical data were sufficient to parameterize simulations of the distribution of individual whales over time and their range of movement patterns. We ran 2 simulations to estimate the sound exposure history and distances traveled by bowhead whales: one in which they could change their movement paths (avert) in response to set levels of sound and one in which they could not avert. When animals could not avert, about 2% of the simulated population was exposed to root mean square (rms) sound pressure levels (SPL) ≥ 180 dB re 1 mu Pa, a level that regulators in the U.S. often associate with injury. When animals could avert from sound levels that regulators often associate with behavioral disturbance (rms SPL > 160 dB re 1 μPa), <1% of the simulated population was exposed to levels associated with injury. Nevertheless, many simulated bowhead whales received sound levels considerably above ambient throughout their migration. Our method enables estimates of the aggregated level of sound to which populations are exposed over extensive areas and time periods.PReMiuM : an R package for profile regression mixture models using Dirichlet processesLiverani, SilviaHastie, DavidAzizi, LamiaePapathomas, MichailRichardson, Sylviahttp://hdl.handle.net/10023/89312017-04-25T08:48:20Z2015-03-20T00:00:00ZPReMiuM is a recently developed R package for Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership (Molitor, Papathomas, Jerrett, and Richardson 2010). The package allows binary, categorical, count and continuous response, as well as continuous and discrete covariates. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to tting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection.
2015-03-20T00:00:00ZLiverani, SilviaHastie, DavidAzizi, LamiaePapathomas, MichailRichardson, SylviaPReMiuM is a recently developed R package for Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership (Molitor, Papathomas, Jerrett, and Richardson 2010). The package allows binary, categorical, count and continuous response, as well as continuous and discrete covariates. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to tting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection.Avoidance of wind farms by harbour seals is limited to pile driving activitiesRussell, Deborah J. F.Hastie, Gordon D.Thompson, DavidJanik, Vincent M.Hammond, Philip S.Scott-Hayward, Lindesay A. S.Matthiopoulos, JasonJones, Esther L.McConnell, Bernie J.http://hdl.handle.net/10023/88562017-06-18T01:32:15Z2016-12-01T00:00:00Z1. As part of global efforts to reduce dependence on carbon-based energy sources there has been a rapid increase in the installation of renewable energy devices. The installation and operation of these devices can result in conflicts with wildlife. In the marine environment, mammals may avoid wind farms that are under construction or operating. Such avoidance may lead to more time spent travelling or displacement from key habitats. A paucity of data on at-sea movements of marine mammals around wind farms limits our understanding of the nature of their potential impacts. 2. Here, we present the results of a telemetry study on harbour seals Phoca vitulina in The Wash, south-east England, an area where wind farms are being constructed using impact pile driving. We investigated whether seals avoid wind farms during operation, construction in its entirety, or during piling activity. The study was carried out using historical telemetry data collected prior to any wind farm development and telemetry data collected in 2012 during the construction of one wind farm and the operation of another. 3. Within an operational wind farm, there was a close-to-significant increase in seal usage compared to prior to wind farm development. However, the wind farm was at the edge of a large area of increased usage, so the presence of the wind farm was unlikely to be the cause. 4. There was no significant displacement during construction as a whole. However, during piling, seal usage (abundance) was significantly reduced up to 25 km from the piling activity; within 25 km of the centre of the wind farm, there was a 19 to 83% (95% confidence intervals) decrease in usage compared to during breaks in piling, equating to a mean estimated displacement of 440 individuals. This amounts to significant displacement starting from predicted received levels of between 166 and 178 dB re 1 μPa(p·p). Displacement was limited to piling activity; within 2 h of cessation of pile driving, seals were distributed as per the non-piling scenario. 5. Synthesis and applications. Our spatial and temporal quantification of avoidance of wind farms by harbour seals is critical to reduce uncertainty and increase robustness in environmental impact assessments of future developments. Specifically, the results will allow policymakers to produce industry guidance on the likelihood of displacement of seals in response to pile driving; the relationship between sound levels and avoidance rates; and the duration of any avoidance, thus allowing far more accurate environmental assessments to be carried out during the consenting process. Further, our results can be used to inform mitigation strategies in terms of both the sound levels likely to cause displacement and what temporal patterns of piling would minimize the magnitude of the energetic impacts of displacement.
DJFR, GH, VMJ and BM were funded by the UK Department of Energy and Climate Change (DECC) as part of their Offshore Energy Strategic Environmental Assessment programme. DT and GH were also funded by NERC/Defra EBAO NE/J004243/1. ELJ was funded under Scottish Government grant MMSS001/01. This work was also supported by National Capability funding from the Natural Environment Research Council to SMRU (grant no. SMRU1001). Tags and their deployment in the Thames in 2006 and The Wash were funded by DECC. Tags and their deployment in the Thames in 2012 were commissioned by Zoological Society London, with funding from BBC Wildlife Fund and Sita Trust.
2016-12-01T00:00:00ZRussell, Deborah J. F.Hastie, Gordon D.Thompson, DavidJanik, Vincent M.Hammond, Philip S.Scott-Hayward, Lindesay A. S.Matthiopoulos, JasonJones, Esther L.McConnell, Bernie J.1. As part of global efforts to reduce dependence on carbon-based energy sources there has been a rapid increase in the installation of renewable energy devices. The installation and operation of these devices can result in conflicts with wildlife. In the marine environment, mammals may avoid wind farms that are under construction or operating. Such avoidance may lead to more time spent travelling or displacement from key habitats. A paucity of data on at-sea movements of marine mammals around wind farms limits our understanding of the nature of their potential impacts. 2. Here, we present the results of a telemetry study on harbour seals Phoca vitulina in The Wash, south-east England, an area where wind farms are being constructed using impact pile driving. We investigated whether seals avoid wind farms during operation, construction in its entirety, or during piling activity. The study was carried out using historical telemetry data collected prior to any wind farm development and telemetry data collected in 2012 during the construction of one wind farm and the operation of another. 3. Within an operational wind farm, there was a close-to-significant increase in seal usage compared to prior to wind farm development. However, the wind farm was at the edge of a large area of increased usage, so the presence of the wind farm was unlikely to be the cause. 4. There was no significant displacement during construction as a whole. However, during piling, seal usage (abundance) was significantly reduced up to 25 km from the piling activity; within 25 km of the centre of the wind farm, there was a 19 to 83% (95% confidence intervals) decrease in usage compared to during breaks in piling, equating to a mean estimated displacement of 440 individuals. This amounts to significant displacement starting from predicted received levels of between 166 and 178 dB re 1 μPa(p·p). Displacement was limited to piling activity; within 2 h of cessation of pile driving, seals were distributed as per the non-piling scenario. 5. Synthesis and applications. Our spatial and temporal quantification of avoidance of wind farms by harbour seals is critical to reduce uncertainty and increase robustness in environmental impact assessments of future developments. Specifically, the results will allow policymakers to produce industry guidance on the likelihood of displacement of seals in response to pile driving; the relationship between sound levels and avoidance rates; and the duration of any avoidance, thus allowing far more accurate environmental assessments to be carried out during the consenting process. Further, our results can be used to inform mitigation strategies in terms of both the sound levels likely to cause displacement and what temporal patterns of piling would minimize the magnitude of the energetic impacts of displacement.An efficient acoustic density estimation method with human detectors applied to gibbons in CambodiaKidney, DarrenRawson, Benjamin M.Borchers, David LouisStevenson, BenMarques, Tiago A.Thomas, Lenhttp://hdl.handle.net/10023/88422017-06-18T01:34:10Z2016-05-19T00:00:00ZSome animal species are hard to see but easy to hear. Standard visual methods for estimating population density for such species are often ineffective or inefficient, but methods based on passive acoustics show more promise. We develop spatially explicit capture-recapture (SECR) methods for territorial vocalising species, in which humans act as an acoustic detector array. We use SECR and estimated bearing data from a single-occasion acoustic survey of a gibbon population in northeastern Cambodia to estimate the density of calling groups. The properties of the estimator are assessed using a simulation study, in which a variety of survey designs are also investigated. We then present a new form of the SECR likelihood for multi-occasion data which accounts for the stochastic availability of animals. In the context of gibbon surveys this allows model-based estimation of the proportion of groups that produce territorial vocalisations on a given day, thereby enabling the density of groups, instead of the density of calling groups, to be estimated. We illustrate the performance of this new estimator by simulation. We show that it is possible to estimate density reliably from human acoustic detections of visually cryptic species using SECR methods. For gibbon surveys we also show that incorporating observers' estimates of bearings to detected groups substantially improves estimator performance. Using the new form of the SECR likelihood we demonstrate that estimates of availability, in addition to population density and detection function parameters, can be obtained from multi-occasion data, and that the detection function parameters are not confounded with the availability parameter. This acoustic SECR method provides a means of obtaining reliable density estimates for territorial vocalising species. It is also efficient in terms of data requirements since it only requires routine survey data. We anticipate that the low-tech field requirements will make this method an attractive option in many situations where populations can be surveyed acoustically by humans.
D. Kidney was supported by an Engineering and Physical Sciences Research Council (EPSRC) Doctoral Training Grant studentship (EPSRC grant EP/P505097/1). B. Stevenson was supported by a studentship jointly funded by the University of St Andrews and EPSRC, through the National Centre for Statistical Ecology (EPSRC grant EP/I000917/1).
2016-05-19T00:00:00ZKidney, DarrenRawson, Benjamin M.Borchers, David LouisStevenson, BenMarques, Tiago A.Thomas, LenSome animal species are hard to see but easy to hear. Standard visual methods for estimating population density for such species are often ineffective or inefficient, but methods based on passive acoustics show more promise. We develop spatially explicit capture-recapture (SECR) methods for territorial vocalising species, in which humans act as an acoustic detector array. We use SECR and estimated bearing data from a single-occasion acoustic survey of a gibbon population in northeastern Cambodia to estimate the density of calling groups. The properties of the estimator are assessed using a simulation study, in which a variety of survey designs are also investigated. We then present a new form of the SECR likelihood for multi-occasion data which accounts for the stochastic availability of animals. In the context of gibbon surveys this allows model-based estimation of the proportion of groups that produce territorial vocalisations on a given day, thereby enabling the density of groups, instead of the density of calling groups, to be estimated. We illustrate the performance of this new estimator by simulation. We show that it is possible to estimate density reliably from human acoustic detections of visually cryptic species using SECR methods. For gibbon surveys we also show that incorporating observers' estimates of bearings to detected groups substantially improves estimator performance. Using the new form of the SECR likelihood we demonstrate that estimates of availability, in addition to population density and detection function parameters, can be obtained from multi-occasion data, and that the detection function parameters are not confounded with the availability parameter. This acoustic SECR method provides a means of obtaining reliable density estimates for territorial vocalising species. It is also efficient in terms of data requirements since it only requires routine survey data. We anticipate that the low-tech field requirements will make this method an attractive option in many situations where populations can be surveyed acoustically by humans.Gauging allowable harm limits to cumulative, sub-lethal effects of human activities on wildlife : a case-study approach using two whale populationsWilliams, RobThomas, LenAshe, ErinClark, Christopher W.Hammond, Philip S.http://hdl.handle.net/10023/87162017-06-18T01:34:04Z2016-08-01T00:00:00ZAs sublethal human pressures on marine wildlife and their habitats increase and interact in complex ways, there is a pressing need for methods to quantify cumulative impacts of these stressors on populations, and policy decisions about allowable harm limits. Few studies quantify population consequences of individual stressors, and fewer quantify synergistic effects. Incorporating all sources of uncertainty can cause predictions to span the range from negligible to catastrophic. Two places were identified to bound this problem through energetic mechanisms that reduce prey available to individuals. First, the US Marine Mammal Protection Act's Potential Biological Removal (PBR) equation was used as a placeholder allowable harm limit to represent the number of animals that can be removed annually without depleting a population below agreed-upon management targets. That rephrased the research question from, “How big could cumulative impacts be?” to “How big would cumulative impacts have to be to exceed an agreed-upon threshold?” Secondly, two data-rich case studies, namely Gulf of Maine humpback and northeast Pacific resident killer whales, were used as examples to parameterize the weakest link, namely between prey availability and demography. Given no additional information, the model predicted that human activities need only reduce prey available to the killer whale population by ~10% to cause a population-level take, through reduced fecundity and/or survival, equivalent to PBR. By contrast, in the humpback population, reduction in prey availability of ~50% was needed to cause a similar, PBR-sized effect. The paper describes an approach – results are merely illustrative. The two case studies differ in prey specialization, life history, and, no doubt, proximity to carrying capacity. This method of inverting the problem refocuses discussions around what the level of prey depletion – via competition with commercial fisheries, displacement from feeding areas through noise-generating activities, or acoustic masking of signals used to detect prey – would have to occur to exceed allowable harm limits set for lethal takes in fisheries or other, more easily quantifiable, human activities.
Rob Williams was supported by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme (Project CONCEAL, FP7, PIIF-GA-2009-253407).
2016-08-01T00:00:00ZWilliams, RobThomas, LenAshe, ErinClark, Christopher W.Hammond, Philip S.As sublethal human pressures on marine wildlife and their habitats increase and interact in complex ways, there is a pressing need for methods to quantify cumulative impacts of these stressors on populations, and policy decisions about allowable harm limits. Few studies quantify population consequences of individual stressors, and fewer quantify synergistic effects. Incorporating all sources of uncertainty can cause predictions to span the range from negligible to catastrophic. Two places were identified to bound this problem through energetic mechanisms that reduce prey available to individuals. First, the US Marine Mammal Protection Act's Potential Biological Removal (PBR) equation was used as a placeholder allowable harm limit to represent the number of animals that can be removed annually without depleting a population below agreed-upon management targets. That rephrased the research question from, “How big could cumulative impacts be?” to “How big would cumulative impacts have to be to exceed an agreed-upon threshold?” Secondly, two data-rich case studies, namely Gulf of Maine humpback and northeast Pacific resident killer whales, were used as examples to parameterize the weakest link, namely between prey availability and demography. Given no additional information, the model predicted that human activities need only reduce prey available to the killer whale population by ~10% to cause a population-level take, through reduced fecundity and/or survival, equivalent to PBR. By contrast, in the humpback population, reduction in prey availability of ~50% was needed to cause a similar, PBR-sized effect. The paper describes an approach – results are merely illustrative. The two case studies differ in prey specialization, life history, and, no doubt, proximity to carrying capacity. This method of inverting the problem refocuses discussions around what the level of prey depletion – via competition with commercial fisheries, displacement from feeding areas through noise-generating activities, or acoustic masking of signals used to detect prey – would have to occur to exceed allowable harm limits set for lethal takes in fisheries or other, more easily quantifiable, human activities.Randomization-based models for multitiered experiments : I. a chain of randomizationsBailey, Rosemary AnneBrien, C. J.http://hdl.handle.net/10023/86362017-04-25T08:42:36Z2016-06-01T00:00:00ZWe derive randomization-based models for experiments with a chain of randomizations. Estimation theory for these models leads to formulae for the estimators of treatment effects, their standard errors, and expected mean squares in the analysis of variance. We discuss the practicalities in fitting these models and outline the difficulties that can occur, many of which do not arise in two-tiered experiments.
2016-06-01T00:00:00ZBailey, Rosemary AnneBrien, C. J.We derive randomization-based models for experiments with a chain of randomizations. Estimation theory for these models leads to formulae for the estimators of treatment effects, their standard errors, and expected mean squares in the analysis of variance. We discuss the practicalities in fitting these models and outline the difficulties that can occur, many of which do not arise in two-tiered experiments.Tracking marine mammals in 3D using electronic tag dataLaplanche, C.Marques, T.A.Thomas, L.http://hdl.handle.net/10023/85912016-12-09T15:30:34Z2015-09-01T00:00:00Z1. Information about at-depth behaviour of marine mammals is fundamental yet very hard to obtain from direct visual observation. Animal-borne multisensor electronic tags provide a unique window of observation into such behaviours. 2. Electronic tag sensors allow the estimation of the animal's 3-dimensional (3D) orientation, depth and speed. Using tag flow noise level to provide an estimate of animal speed, we extend existing approaches of 3D track reconstruction by allowing the direction of movement to differ from that of the animal's longitudinal axis. 3. Data are processed by a hierarchical Bayesian model that allows processing of multisource data, accounting for measurement errors and testing hypotheses about animal movement by comparing models. 4. We illustrate the approach by reconstructing the 3D track of a 52-min deep dive of a Blainville's beaked whale Mesoplodon densirostris adult male fit with a digital tag (DTAG) in the Bahamas. At depth, the whale alternated regular movements at large speed (>1·5 m s-1) and more complex movements at lower speed (<1·5 m s-1) with diﬀerences between movement and longitudinal axis directions of up to 28°. The reconstructed 3D track agrees closely with independent acoustic-based localizations. 5. The approach is potentially applicable to study the underwater behaviour (e.g. response to anthropogenic disturbances) of a wide variety of species of marine mammals ﬁtted with triaxial magnetometer and accelerometer tags.
Date of Acceptance: 05/03/2015
2015-09-01T00:00:00ZLaplanche, C.Marques, T.A.Thomas, L.1. Information about at-depth behaviour of marine mammals is fundamental yet very hard to obtain from direct visual observation. Animal-borne multisensor electronic tags provide a unique window of observation into such behaviours. 2. Electronic tag sensors allow the estimation of the animal's 3-dimensional (3D) orientation, depth and speed. Using tag flow noise level to provide an estimate of animal speed, we extend existing approaches of 3D track reconstruction by allowing the direction of movement to differ from that of the animal's longitudinal axis. 3. Data are processed by a hierarchical Bayesian model that allows processing of multisource data, accounting for measurement errors and testing hypotheses about animal movement by comparing models. 4. We illustrate the approach by reconstructing the 3D track of a 52-min deep dive of a Blainville's beaked whale Mesoplodon densirostris adult male fit with a digital tag (DTAG) in the Bahamas. At depth, the whale alternated regular movements at large speed (>1·5 m s-1) and more complex movements at lower speed (<1·5 m s-1) with diﬀerences between movement and longitudinal axis directions of up to 28°. The reconstructed 3D track agrees closely with independent acoustic-based localizations. 5. The approach is potentially applicable to study the underwater behaviour (e.g. response to anthropogenic disturbances) of a wide variety of species of marine mammals ﬁtted with triaxial magnetometer and accelerometer tags.Constructing flag-transitive, point-imprimitive designsCameron, Peter JephsonPraeger, Cheryl E.http://hdl.handle.net/10023/85462017-04-25T08:28:02Z2016-05-04T00:00:00ZWe give a construction of a family of designs with a specified point-partition and determine the subgroup of automorphisms leaving invariant the point-partition. We give necessary and sufficient conditions for a design in the family to possess a flag-transitive group of automorphisms preserving the specified point-partition. We give examples of flag-transitive designs in the family, including a new symmetric 2-(1408,336,80) design with automorphism group 2^12:((3⋅M22):2) and a construction of one of the families of the symplectic designs (the designs S^−(n) ) exhibiting a flag-transitive, point-imprimitive automorphism group.
2016-05-04T00:00:00ZCameron, Peter JephsonPraeger, Cheryl E.We give a construction of a family of designs with a specified point-partition and determine the subgroup of automorphisms leaving invariant the point-partition. We give necessary and sufficient conditions for a design in the family to possess a flag-transitive group of automorphisms preserving the specified point-partition. We give examples of flag-transitive designs in the family, including a new symmetric 2-(1408,336,80) design with automorphism group 2^12:((3⋅M22):2) and a construction of one of the families of the symplectic designs (the designs S^−(n) ) exhibiting a flag-transitive, point-imprimitive automorphism group.Permutation groups and transformation semigroups : results and problemsAraujo, JoaoCameron, Peter Jephsonhttp://hdl.handle.net/10023/85322017-03-22T12:31:41Z2015-10-01T00:00:00ZJ.M. Howie, the influential St Andrews semigroupist, claimed that we value an area of pure mathematics to the extent that (a) it gives rise to arguments that are deep and elegant, and (b) it has interesting interconnections with other parts of pure mathematics. This paper surveys some recent results on the transformation semigroup generated by a permutation group G and a single non-permutation a. Our particular concern is the influence that properties of G (related to homogeneity, transitivity and primitivity) have on the structure of the semigroup. In the first part of the paper, we consider properties of S=<G,a> such as regularity and generation. The second is a brief report on the synchronization project, which aims to decide in what circumstances S contains an element of rank 1. The paper closes with a list of open problems on permutation groups and linear groups, and some comments about the impact on semigroups are provided. These two research directions outlined above lead to very interesting and challenging problems on primitive permutation groups whose solutions require combining results from several different areas of mathematics, certainly fulfilling both of Howie's elegance and value tests in a new and fascinating way.
2015-10-01T00:00:00ZAraujo, JoaoCameron, Peter JephsonJ.M. Howie, the influential St Andrews semigroupist, claimed that we value an area of pure mathematics to the extent that (a) it gives rise to arguments that are deep and elegant, and (b) it has interesting interconnections with other parts of pure mathematics. This paper surveys some recent results on the transformation semigroup generated by a permutation group G and a single non-permutation a. Our particular concern is the influence that properties of G (related to homogeneity, transitivity and primitivity) have on the structure of the semigroup. In the first part of the paper, we consider properties of S=<G,a> such as regularity and generation. The second is a brief report on the synchronization project, which aims to decide in what circumstances S contains an element of rank 1. The paper closes with a list of open problems on permutation groups and linear groups, and some comments about the impact on semigroups are provided. These two research directions outlined above lead to very interesting and challenging problems on primitive permutation groups whose solutions require combining results from several different areas of mathematics, certainly fulfilling both of Howie's elegance and value tests in a new and fascinating way.Guessing games on triangle-free graphsCameron, Peter JephsonDang, AnhRiis, Sorenhttp://hdl.handle.net/10023/85182017-03-05T02:33:16Z2016-01-01T00:00:00ZThe guessing game introduced by Riis is a variant of the "guessing your own hats" game and can be played on any simple directed graph G on n vertices. For each digraph G, it is proved that there exists a unique guessing number gn(G) associated to the guessing game played on G. When we consider the directed edge to be bidirected, in other words, the graph G is undirected, Christofides and Markström introduced a method to bound the value of the guessing number from below using the fractional clique cover number kappa_f(G). In particular they showed gn(G) >= |V(G)| - kappa_f(G). Moreover, it is pointed out that equality holds in this bound if the underlying undirected graph G falls into one of the following categories: perfect graphs, cycle graphs or their complement. In this paper, we show that there are triangle-free graphs that have guessing numbers which do not meet the fractional clique cover bound. In particular, the famous triangle-free Higman-Sims graph has guessing number at least 77 and at most 78, while the bound given by fractional clique cover is 50.
2016-01-01T00:00:00ZCameron, Peter JephsonDang, AnhRiis, SorenThe guessing game introduced by Riis is a variant of the "guessing your own hats" game and can be played on any simple directed graph G on n vertices. For each digraph G, it is proved that there exists a unique guessing number gn(G) associated to the guessing game played on G. When we consider the directed edge to be bidirected, in other words, the graph G is undirected, Christofides and Markström introduced a method to bound the value of the guessing number from below using the fractional clique cover number kappa_f(G). In particular they showed gn(G) >= |V(G)| - kappa_f(G). Moreover, it is pointed out that equality holds in this bound if the underlying undirected graph G falls into one of the following categories: perfect graphs, cycle graphs or their complement. In this paper, we show that there are triangle-free graphs that have guessing numbers which do not meet the fractional clique cover bound. In particular, the famous triangle-free Higman-Sims graph has guessing number at least 77 and at most 78, while the bound given by fractional clique cover is 50.Exploring dependence between categorical variables : benefits and limitations of using variable selection within Bayesian clustering in relation to log-linear modelling with interaction termsPapathomas, MichailRichardson, Sylviahttp://hdl.handle.net/10023/83562017-04-25T08:48:17Z2016-06-01T00:00:00ZThis manuscript is concerned with relating two approaches that can be used to explore complex dependence structures between categorical variables, namely Bayesian partitioning of the covariate space incorporating a variable selection procedure that highlights the covariates that drive the clustering, and log-linear modelling with interaction terms. We derive theoretical results on this relation and discuss if they can be employed to assist log-linear model determination, demonstrating advantages and limitations with simulated and real data sets. The main advantage concerns sparse contingency tables. Inferences from clustering can potentially reduce the number of covariates considered and, subsequently, the number of competing log-linear models, making the exploration of the model space feasible. Variable selection within clustering can inform on marginal independence in general, thus allowing for a more efficient exploration of the log-linear model space. However, we show that the clustering structure is not informative on the existence of interactions in a consistent manner. This work is of interest to those who utilize log-linear models, as well as practitioners such as epidemiologists that use clustering models to reduce the dimensionality in the data and to reveal interesting patterns on how covariates combine.
This work was supported by MRC grant G1002319.
2016-06-01T00:00:00ZPapathomas, MichailRichardson, SylviaThis manuscript is concerned with relating two approaches that can be used to explore complex dependence structures between categorical variables, namely Bayesian partitioning of the covariate space incorporating a variable selection procedure that highlights the covariates that drive the clustering, and log-linear modelling with interaction terms. We derive theoretical results on this relation and discuss if they can be employed to assist log-linear model determination, demonstrating advantages and limitations with simulated and real data sets. The main advantage concerns sparse contingency tables. Inferences from clustering can potentially reduce the number of covariates considered and, subsequently, the number of competing log-linear models, making the exploration of the model space feasible. Variable selection within clustering can inform on marginal independence in general, thus allowing for a more efficient exploration of the log-linear model space. However, we show that the clustering structure is not informative on the existence of interactions in a consistent manner. This work is of interest to those who utilize log-linear models, as well as practitioners such as epidemiologists that use clustering models to reduce the dimensionality in the data and to reveal interesting patterns on how covariates combine.Bayesian sequential tests of the initial size of a linear pure death processGoudie, I.B.J.http://hdl.handle.net/10023/82862017-04-25T08:27:30Z2015-05-01T00:00:00ZWe provide a recursive algorithm for determining the sampling plans of invariant Bayesian sequential tests of the initial size of a linear pure death process of unknown rate. These tests compare favourably with the corresponding truncated sequential probability ratio tests.
2015-05-01T00:00:00ZGoudie, I.B.J.We provide a recursive algorithm for determining the sampling plans of invariant Bayesian sequential tests of the initial size of a linear pure death process of unknown rate. These tests compare favourably with the corresponding truncated sequential probability ratio tests.Using species proportions to quantify turnover in biodiversityYuan, YuanBuckland, Stephen TerrenceHarrison, PhilFoss, SergeyJohnston, Alisonhttp://hdl.handle.net/10023/80332017-04-25T08:48:04Z2016-06-01T00:00:00ZQuantifying species turnover is an important aspect of biodiversity monitoring. Turnover measures are usually based on species presence/absence data, reflecting the rate at which species are replaced. However, measures that reflect the rate at which individuals of a species are replaced by individuals of another species are far more sensitive to change. In this paper, we propose families of turnover measures that reflect changes in species proportions. We study the properties of our measures, and use simulation to assess their success in detecting turnover. Using data on the British farmland bird community from the breeding bird survey, we evaluate our measures to quantify temporal turnover and how it varies across the British mainland.
We are very grateful to all the volunteers who have contributed to the BBS. Yuan was funded by EPSRC/NERC grant EP/1000917/1. Harrison was funded by the Scottish Government’s Centre of Expertise ClimateXChange (www.climatexchange.org.uk).
2016-06-01T00:00:00ZYuan, YuanBuckland, Stephen TerrenceHarrison, PhilFoss, SergeyJohnston, AlisonQuantifying species turnover is an important aspect of biodiversity monitoring. Turnover measures are usually based on species presence/absence data, reflecting the rate at which species are replaced. However, measures that reflect the rate at which individuals of a species are replaced by individuals of another species are far more sensitive to change. In this paper, we propose families of turnover measures that reflect changes in species proportions. We study the properties of our measures, and use simulation to assess their success in detecting turnover. Using data on the British farmland bird community from the breeding bird survey, we evaluate our measures to quantify temporal turnover and how it varies across the British mainland.Efficient abstracting of dive profiles using a broken-stick modelPhotopoulou, T.Lovell, PhilipFedak, M.A.Thomas, L.Matthiopoulos, J.http://hdl.handle.net/10023/79722017-05-28T01:34:27Z2015-03-01T00:00:00ZFor diving animals, animal-borne sensors are used to collect time-depth information for studying behaviour, ranging patterns and foraging ecology. Often, this information needs to be compressed for storage or transmission. Widely used devices called conductivity-temperature-depth satellite relay data loggers (CTD-SRDLs) sample time and depth at high resolution during a dive and then abstract the time-depth trajectory using a broken-stick model (BSM). This approximation method can summarize efficiently the curvilinear shape of a dive, using a piecewise linear shape with a small, fixed number of vertices, or break points. We present the process of abstracting dives using the BSM and quantify its performance, by measuring the uncertainty associated with the profiles it produces. We develop a method for obtaining a confidence zone and an index for the goodness-of-fit (dive zone index, DZI) for abstracted dive profiles. We validate our results with a case study using dives from elephant seals (Mirounga spp.). We use generalized additive models (GAMs) to determine whether the DZI can be used as a proxy for an absolute measure of fit and investigate the relationship between the DZI and the dive shape. We found a strong correlation between the residual sum of squares (RSS) for the difference between the detailed and abstracted profiles, and the DZI and maximum residual (R4), for dives resulting from CTD-SRDLs (69% deviance explained). On its own, the DZI explained a lower percentage of deviance which was variable for abstracted dives with different numbers of break points. We also found evidence for systematic differences in the DZI for different dive shapes (65% deviance explained). Although the proportional loss of information in the abstraction of time-depth dive profiles by BSM is high, what remains is sufficient to infer goodness-of-fit of the abstracted profile by reversing the abstraction process. Our results suggest that together the DZI and R4 can be used as a proxy for the RSS, and we present the method for obtaining these metrics for BSM-abstracted profiles.
This work was supported by SMRU Ltd (now SMRU Marine) in the form of a PhD fellowship (T.P.). Completion of the manuscript was supported by a National Research Foundation Scarce Skills Postdoctoral Fellowship at the University of Cape Town, South Africa (T.P.). The CTD-SRDL data presented in this manuscript were collected as part of a project funded by the Natural Environment Research Council (NERC) grants NE/E018289/1 and NER/D/S/2002/00426.
2015-03-01T00:00:00ZPhotopoulou, T.Lovell, PhilipFedak, M.A.Thomas, L.Matthiopoulos, J.For diving animals, animal-borne sensors are used to collect time-depth information for studying behaviour, ranging patterns and foraging ecology. Often, this information needs to be compressed for storage or transmission. Widely used devices called conductivity-temperature-depth satellite relay data loggers (CTD-SRDLs) sample time and depth at high resolution during a dive and then abstract the time-depth trajectory using a broken-stick model (BSM). This approximation method can summarize efficiently the curvilinear shape of a dive, using a piecewise linear shape with a small, fixed number of vertices, or break points. We present the process of abstracting dives using the BSM and quantify its performance, by measuring the uncertainty associated with the profiles it produces. We develop a method for obtaining a confidence zone and an index for the goodness-of-fit (dive zone index, DZI) for abstracted dive profiles. We validate our results with a case study using dives from elephant seals (Mirounga spp.). We use generalized additive models (GAMs) to determine whether the DZI can be used as a proxy for an absolute measure of fit and investigate the relationship between the DZI and the dive shape. We found a strong correlation between the residual sum of squares (RSS) for the difference between the detailed and abstracted profiles, and the DZI and maximum residual (R4), for dives resulting from CTD-SRDLs (69% deviance explained). On its own, the DZI explained a lower percentage of deviance which was variable for abstracted dives with different numbers of break points. We also found evidence for systematic differences in the DZI for different dive shapes (65% deviance explained). Although the proportional loss of information in the abstraction of time-depth dive profiles by BSM is high, what remains is sufficient to infer goodness-of-fit of the abstracted profile by reversing the abstraction process. Our results suggest that together the DZI and R4 can be used as a proxy for the RSS, and we present the method for obtaining these metrics for BSM-abstracted profiles.Dose response severity functions for acoustic disturbance in cetaceans using recurrent event survival analysisHarris, Catriona MSadykova, DinaraDe Ruiter, Stacy LynnTyack, Peter LloydMiller, PatrickKvadsheim, PetterLam, Frans-PeterThomas, Lenhttp://hdl.handle.net/10023/78452017-04-25T08:14:05Z2015-11-20T00:00:00ZBehavioral response studies (BRSs) aim to enhance our understanding of the behavior changes made by animals in response to specific exposure levels of different stimuli, often presented in an increasing dosage. Here, we focus on BRSs that aim to understand behavioral responses of free-ranging whales and dolphins to manmade acoustic signals (although the methods are applicable more generally). One desired outcome of these studies is dose-response functions relevant to different species, signals and contexts. We adapted and applied recurrent event survival analysis (Cox proportional hazard models) to data from the 3S BRS project, where multiple behavioral responses of different severities had been observed per experimental exposure and per individual based upon expert scoring. We included species, signal type, exposure number and behavioral state prior to exposure as potential covariates. The best model included all main effect terms, with the exception of exposure number, as well as two interaction terms. The interactions between signal and behavioral state, and between species and behavioral state highlighted that the sensitivity of animals to different signal types (a 6–7 kHz upsweep sonar signal [MFAS] or a 1–2 kHz upsweep sonar signal [LFAS]) depended on their behavioral state (feeding or nonfeeding), and this differed across species. Of the three species included in this analysis (sperm whale [Physeter macrocephalus], killer whale [Orcinus orca] and long-finned pilot whale [Globicephala melas]), killer whales were consistently the most likely to exhibit behavioral responses to naval sonar exposure. We conclude that recurrent event survival analysis provides an effective framework for fitting dose-response severity functions to data from behavioral response studies. It can provide outputs that can help government and industry to evaluate the potential impacts of anthropogenic sound production in the ocean.
2015-11-20T00:00:00ZHarris, Catriona MSadykova, DinaraDe Ruiter, Stacy LynnTyack, Peter LloydMiller, PatrickKvadsheim, PetterLam, Frans-PeterThomas, LenBehavioral response studies (BRSs) aim to enhance our understanding of the behavior changes made by animals in response to specific exposure levels of different stimuli, often presented in an increasing dosage. Here, we focus on BRSs that aim to understand behavioral responses of free-ranging whales and dolphins to manmade acoustic signals (although the methods are applicable more generally). One desired outcome of these studies is dose-response functions relevant to different species, signals and contexts. We adapted and applied recurrent event survival analysis (Cox proportional hazard models) to data from the 3S BRS project, where multiple behavioral responses of different severities had been observed per experimental exposure and per individual based upon expert scoring. We included species, signal type, exposure number and behavioral state prior to exposure as potential covariates. The best model included all main effect terms, with the exception of exposure number, as well as two interaction terms. The interactions between signal and behavioral state, and between species and behavioral state highlighted that the sensitivity of animals to different signal types (a 6–7 kHz upsweep sonar signal [MFAS] or a 1–2 kHz upsweep sonar signal [LFAS]) depended on their behavioral state (feeding or nonfeeding), and this differed across species. Of the three species included in this analysis (sperm whale [Physeter macrocephalus], killer whale [Orcinus orca] and long-finned pilot whale [Globicephala melas]), killer whales were consistently the most likely to exhibit behavioral responses to naval sonar exposure. We conclude that recurrent event survival analysis provides an effective framework for fitting dose-response severity functions to data from behavioral response studies. It can provide outputs that can help government and industry to evaluate the potential impacts of anthropogenic sound production in the ocean.Passive acoustic monitoring of beaked whale densities in the Gulf of MexicoHildebrand, JohnBaumann-Pickering, SimoneFrasier, KaitlinTrickey, JenniferMerkens, KarlinaWiggins, SeanMcDonald, MarkGarrison, LanceHarris, DanielleMarques, Tiago A.Thomas, Lenhttp://hdl.handle.net/10023/77792017-04-25T08:45:33Z2015-11-12T00:00:00ZBeaked whales are deep diving elusive animals, difficult to census with conventional visual surveys. Methods are presented for the density estimation of beaked whales, using passive acoustic monitoring data collected at sites in the Gulf of Mexico (GOM) from the period during and following the Deepwater Horizon oil spill (2010–2013). Beaked whale species detected include: Gervais’ (Mesoplodon europaeus), Cuvier’s (Ziphius cavirostris), Blainville’s (Mesoplodon densirostris) and an unknown species of Mesoplodon sp. (designated as Beaked Whale Gulf — BWG). For Gervais’ and Cuvier’s beaked whales, we estimated weekly animal density using two methods, one based on the number of echolocation clicks, and another based on the detection of animal groups during 5 min time-bins. Density estimates derived from these two methods were in good general agreement. At two sites in the western GOM, Gervais’ beaked whales were present throughout the monitoring period, but Cuvier’s beaked whales were present only seasonally, with periods of low density during the summer and higher density in the winter. At an eastern GOM site, both Gervais’ and Cuvier’s beaked whales had a high density throughout the monitoring period.
Funding to support the tag data was also received from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.
2015-11-12T00:00:00ZHildebrand, JohnBaumann-Pickering, SimoneFrasier, KaitlinTrickey, JenniferMerkens, KarlinaWiggins, SeanMcDonald, MarkGarrison, LanceHarris, DanielleMarques, Tiago A.Thomas, LenBeaked whales are deep diving elusive animals, difficult to census with conventional visual surveys. Methods are presented for the density estimation of beaked whales, using passive acoustic monitoring data collected at sites in the Gulf of Mexico (GOM) from the period during and following the Deepwater Horizon oil spill (2010–2013). Beaked whale species detected include: Gervais’ (Mesoplodon europaeus), Cuvier’s (Ziphius cavirostris), Blainville’s (Mesoplodon densirostris) and an unknown species of Mesoplodon sp. (designated as Beaked Whale Gulf — BWG). For Gervais’ and Cuvier’s beaked whales, we estimated weekly animal density using two methods, one based on the number of echolocation clicks, and another based on the detection of animal groups during 5 min time-bins. Density estimates derived from these two methods were in good general agreement. At two sites in the western GOM, Gervais’ beaked whales were present throughout the monitoring period, but Cuvier’s beaked whales were present only seasonally, with periods of low density during the summer and higher density in the winter. At an eastern GOM site, both Gervais’ and Cuvier’s beaked whales had a high density throughout the monitoring period.Status and future of research on the behavioural responses of marine mammals to U.S. Navy sonarHarris, Catriona MThomas, Lenhttp://hdl.handle.net/10023/77412017-04-01T23:44:41Z2015-01-01T00:00:00ZA review of the status and future of research into behavioral responses of marine mammals to naval sonar exposure was undertaken to evaluate the return on investment of current US Navy funded programs, identify the data needs and the contributions of current research programs to meeting data needs, and determine the ability to meet outstanding data needs given the current state of technology. As part of this review, a workshop was held from 21-22 April 2015 in Monterey, California. Workshop attendees were key representatives of Navy-funded behavioral response studies, as well as three external reviewers who were selected because of their expertise in animal behavior and behavioral responses to anthropogenic stimuli in the aquatic and terrestrial environments. Prior to the workshop, a questionnaire was circulated to canvass the opinions of members of the scientific community (primarily workshop attendees exclusive of external reviewers) on each of the research approaches taken to address this topic. The workshop was then structured around the questionnaire and responses received, via a series of discussion sessions. Afterwards, each research approach was evaluated independently by the external reviewers. This report presents a synthesis of the evaluations and recommendations of the external reviewers on current and future behavioral response research relevant to naval sonar. All reviewers agreed that excellent progress has been made on this topic and that each of the research approaches has contributed to our understanding of cetacean responses to naval sonar. The report includes specific comments and recommendations of the reviewers relevant to each approach, but also includes suggestions for priority species and a comprehensive list of recommendations for the future of BRS research in general (Tables 1 and 2). In summary it was recommended that BRS research be continued and extended to increase sample sizes and experimental replication, and temporal duration and spatial scale including more research in areas where the animals are presumably more naïve than on the naval ranges. It was noted that future investigations would benefit from combining experimentation and observation to enable linkage of short-term behavioral response to long-term fitness consequences of repeated exposure. Beaked whales were the species group ranked highest in terms of research priority. The importance of baseline studies and longer-term monitoring of animals before and after exposure is emphasized throughout.
2015-01-01T00:00:00ZHarris, Catriona MThomas, LenA review of the status and future of research into behavioral responses of marine mammals to naval sonar exposure was undertaken to evaluate the return on investment of current US Navy funded programs, identify the data needs and the contributions of current research programs to meeting data needs, and determine the ability to meet outstanding data needs given the current state of technology. As part of this review, a workshop was held from 21-22 April 2015 in Monterey, California. Workshop attendees were key representatives of Navy-funded behavioral response studies, as well as three external reviewers who were selected because of their expertise in animal behavior and behavioral responses to anthropogenic stimuli in the aquatic and terrestrial environments. Prior to the workshop, a questionnaire was circulated to canvass the opinions of members of the scientific community (primarily workshop attendees exclusive of external reviewers) on each of the research approaches taken to address this topic. The workshop was then structured around the questionnaire and responses received, via a series of discussion sessions. Afterwards, each research approach was evaluated independently by the external reviewers. This report presents a synthesis of the evaluations and recommendations of the external reviewers on current and future behavioral response research relevant to naval sonar. All reviewers agreed that excellent progress has been made on this topic and that each of the research approaches has contributed to our understanding of cetacean responses to naval sonar. The report includes specific comments and recommendations of the reviewers relevant to each approach, but also includes suggestions for priority species and a comprehensive list of recommendations for the future of BRS research in general (Tables 1 and 2). In summary it was recommended that BRS research be continued and extended to increase sample sizes and experimental replication, and temporal duration and spatial scale including more research in areas where the animals are presumably more naïve than on the naval ranges. It was noted that future investigations would benefit from combining experimentation and observation to enable linkage of short-term behavioral response to long-term fitness consequences of repeated exposure. Beaked whales were the species group ranked highest in terms of research priority. The importance of baseline studies and longer-term monitoring of animals before and after exposure is emphasized throughout.A description of LATTE outputsMarques, Tiago A.Thomas, Lenhttp://hdl.handle.net/10023/77202017-04-01T23:44:39Z2015-10-30T00:00:00Z2015-10-30T00:00:00ZMarques, Tiago A.Thomas, LenImpacts of anthropogenic noise on marine life : publication patterns, new discoveries, and future directions in research and managementWilliams, RobertWright, Andrew JAshe, ErinBlight, LKBruintjes, RCanessa, RClark, CWCullis-Suzuki, SDakin, DTErbe, CHammond, Philip StevenMerchant, MDO'Hara, PDPurser, JRadford, ANSimpson, SDThomas, LenWale, MAhttp://hdl.handle.net/10023/76402017-06-18T01:30:48Z2015-10-01T00:00:00ZAnthropogenic underwater noise is now recognized as a world-wide problem, and recent studies have shown a broad range of negative effects in a variety of taxa. Underwater noise from shipping is increasingly recognized as a significant and pervasive pollutant with the potential to impact marine ecosystems on a global scale. We reviewed six regional case studies as examples of recent research and management activities relating to ocean noise in a variety of taxonomic groups, locations, and approaches. However, as no six projects could ever cover all taxa, sites and noise sources, a brief bibliometric analysis places these case studies into the broader historical and topical context of the peer-reviewed ocean noise literature as a whole. The case studies highlighted emerging knowledge of impacts, including the ways that non-injurious effects can still accumulate at the population level, and detailed approaches to guide ocean noise management. They build a compelling case that a number of anthropogenic noise types can affect a variety of marine taxa. Meanwhile, the bibliometric analyses revealed an increasing diversity of ocean noise topics covered and journal outlets since the 1940s. This could be seen in terms of both the expansion of the literature from more physical interests to ecological impacts of noise, management and policy, and consideration of a widening range of taxa. However, if our scientific knowledge base is ever to get ahead of the curve of rapid industrialization of the ocean, we are going to have to identify naïve populations and relatively pristine seas, and construct mechanistic models, so that we can predict impacts before they occur, and guide effective mitigation for the most vulnerable populations.
Funding for R. Bruintjes, J. Purser, A. N. Radford, S. D, Simpson and M. A. Wale was provided by the UK Department for Environment Food and Rural Affairs (Defra). N.D. Merchant received travel funding from Ocean Networks Canada. RW was supported by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme (Project CONCEAL, FP7, PIIF-GA-2009-253407), and received travel funding to attend IMCC3 from the Society for Conservation Biology (SCB) Marine Section and the International Whaling Commission’s Climate Change steering group (with thanks to Mark Simmonds). A.J. Wright also received travel funding to attend IMCC3 from the SCB Marine Section. Date of Acceptance: 28/05/2015
2015-10-01T00:00:00ZWilliams, RobertWright, Andrew JAshe, ErinBlight, LKBruintjes, RCanessa, RClark, CWCullis-Suzuki, SDakin, DTErbe, CHammond, Philip StevenMerchant, MDO'Hara, PDPurser, JRadford, ANSimpson, SDThomas, LenWale, MAAnthropogenic underwater noise is now recognized as a world-wide problem, and recent studies have shown a broad range of negative effects in a variety of taxa. Underwater noise from shipping is increasingly recognized as a significant and pervasive pollutant with the potential to impact marine ecosystems on a global scale. We reviewed six regional case studies as examples of recent research and management activities relating to ocean noise in a variety of taxonomic groups, locations, and approaches. However, as no six projects could ever cover all taxa, sites and noise sources, a brief bibliometric analysis places these case studies into the broader historical and topical context of the peer-reviewed ocean noise literature as a whole. The case studies highlighted emerging knowledge of impacts, including the ways that non-injurious effects can still accumulate at the population level, and detailed approaches to guide ocean noise management. They build a compelling case that a number of anthropogenic noise types can affect a variety of marine taxa. Meanwhile, the bibliometric analyses revealed an increasing diversity of ocean noise topics covered and journal outlets since the 1940s. This could be seen in terms of both the expansion of the literature from more physical interests to ecological impacts of noise, management and policy, and consideration of a widening range of taxa. However, if our scientific knowledge base is ever to get ahead of the curve of rapid industrialization of the ocean, we are going to have to identify naïve populations and relatively pristine seas, and construct mechanistic models, so that we can predict impacts before they occur, and guide effective mitigation for the most vulnerable populations.Procedure description : using AUTEC’s hydrophones surrounding a DTAGed whale to obtain localizationsMarques, Tiago A.Shaeffer, JessicaMoretti, DavidThomas, Lenhttp://hdl.handle.net/10023/75232017-04-01T23:44:35Z2015-01-01T00:00:00Z2015-01-01T00:00:00ZMarques, Tiago A.Shaeffer, JessicaMoretti, DavidThomas, LenCircular designs balanced for neighbours at distances one and twoAldred, R. E. L.Bailey, R. A.Mckay, Brendan D.Wanless, Ian M.http://hdl.handle.net/10023/74542017-04-25T08:19:21Z2014-12-01T00:00:00ZWe define three types of neighbour-balanced designs for experiments where the units are arranged in a circle or single line in space or time. The designs are balanced with respect to neighbours at distance one and at distance two. The variants come from allowing or forbidding self-neighbours, and from considering neighbours to be directed or undirected. For two of the variants, we give a method of constructing a design for all values of the number of treatments, except for some small values where it is impossible. In the third case, we give a partial solution that covers all sizes likely to be used in practice.
2014-12-01T00:00:00ZAldred, R. E. L.Bailey, R. A.Mckay, Brendan D.Wanless, Ian M.We define three types of neighbour-balanced designs for experiments where the units are arranged in a circle or single line in space or time. The designs are balanced with respect to neighbours at distance one and at distance two. The variants come from allowing or forbidding self-neighbours, and from considering neighbours to be directed or undirected. For two of the variants, we give a method of constructing a design for all values of the number of treatments, except for some small values where it is impossible. In the third case, we give a partial solution that covers all sizes likely to be used in practice.Evaluating the utility of B/Ca ratios in planktic foraminifera as a proxy for the carbonate system : a case study of Globigerinoides ruberHenehan, M.J.Foster, G.L.Rae, J.W.B.Prentice, K.C.Erez, J.Bostock, H.C.Marshall, B.J.Wilson, P.A.http://hdl.handle.net/10023/71332017-04-25T08:37:03Z2015-04-01T00:00:00ZB/Ca ratios in foraminifera have attracted considerable scientific attention as a proxy for past ocean carbonate system. However, the carbonate system controls on B/Ca ratios are not straightforward, with Δ[ CO32-] ([ CO32-]in situ - [ CO32-]at saturation) correlating best with B/Ca ratios in benthic foraminifera, rather than pH, B(OH)4-/HCO3-, or B(OH)4-/DIC (as a simple model of boron speciation in seawater and incorporation into CaCO3 would predict). Furthermore, culture experiments have shown that in planktic foraminifera properties such as salinity and [B]SW can have profound effects on B/Ca ratios beyond those predicted by simple partition coefficients. Here, we investigate the controls on B/Ca ratios in G. ruber via a combination of culture experiments and core-top measurements, and add to a growing body of evidence that suggests B/Ca ratios in symbiont-bearing foraminiferal carbonate are not a straightforward proxy for past seawater carbonate system conditions. We find that while B/Ca ratios in culture experiments covary with pH, in open ocean sediments this relationship is not seen. In fact, our B/Ca data correlate best with [ PO43-] (a previously undocumented association) and in most regions, salinity. These findings might suggest a precipitation rate or crystallographic control on boron incorporation into foraminiferal calcite. Regardless, our results underscore the need for caution when attempting to interpret B/Ca records in terms of the ocean carbonate system, at the very least in the case of mixed-layer planktic foraminifera.
This research was funded by NERC, Grant Number: NE/D00876X/2.
2015-04-01T00:00:00ZHenehan, M.J.Foster, G.L.Rae, J.W.B.Prentice, K.C.Erez, J.Bostock, H.C.Marshall, B.J.Wilson, P.A.B/Ca ratios in foraminifera have attracted considerable scientific attention as a proxy for past ocean carbonate system. However, the carbonate system controls on B/Ca ratios are not straightforward, with Δ[ CO32-] ([ CO32-]in situ - [ CO32-]at saturation) correlating best with B/Ca ratios in benthic foraminifera, rather than pH, B(OH)4-/HCO3-, or B(OH)4-/DIC (as a simple model of boron speciation in seawater and incorporation into CaCO3 would predict). Furthermore, culture experiments have shown that in planktic foraminifera properties such as salinity and [B]SW can have profound effects on B/Ca ratios beyond those predicted by simple partition coefficients. Here, we investigate the controls on B/Ca ratios in G. ruber via a combination of culture experiments and core-top measurements, and add to a growing body of evidence that suggests B/Ca ratios in symbiont-bearing foraminiferal carbonate are not a straightforward proxy for past seawater carbonate system conditions. We find that while B/Ca ratios in culture experiments covary with pH, in open ocean sediments this relationship is not seen. In fact, our B/Ca data correlate best with [ PO43-] (a previously undocumented association) and in most regions, salinity. These findings might suggest a precipitation rate or crystallographic control on boron incorporation into foraminiferal calcite. Regardless, our results underscore the need for caution when attempting to interpret B/Ca records in terms of the ocean carbonate system, at the very least in the case of mixed-layer planktic foraminifera.Spatial variation in maximum dive depth in gray seals in relation to foraging.Photopoulou, TheoniFedak, MikeThomas, LenMatthiopoulos, Jasonhttp://hdl.handle.net/10023/68862017-04-25T08:04:34Z2014-07-01T00:00:00ZHabitat preference maps are a way of representing animals’ space use in two dimensions. For marine animals, the third dimension is an important aspect of spatial ecology. We used dive data from seven gray seals Halichoerus grypus (a primarily benthic forager) collected with GPS phone tags (Sea Mammal Research Unit) to investigate the distribution of the maximum depth visited in each dive. We modeled maximum dive depth as a function of spatiotemporal covariates using a generalized additive mixed model (GAMM) with individual as a random effect. Bathymetry, horizontal displacement, latitude and longitude, Julian day, sediment type, and light conditions accounted for 37% of the variability in the data. Persistent patterns of autocorrelation in the raw data suggest that individual intrinsic rhythm might be an important factor, not captured by external covariates. The strength of using this statistical method to generate spatial predictions of the distribution of maximum dive depth is its applicability to other plunge and pursuit divers. Despite being predictions of a point estimate, these maps provide some insight into the third dimension of habitat use in marine animals. The capacity to predict this aspect of vertical habitat use may help avoid conflict between animal habitat and coastal or offshore developments
Theoni Photopoulou was funded by SMRU Ltd in the form of a Ph.D. studentship, 2008–2012.
2014-07-01T00:00:00ZPhotopoulou, TheoniFedak, MikeThomas, LenMatthiopoulos, JasonHabitat preference maps are a way of representing animals’ space use in two dimensions. For marine animals, the third dimension is an important aspect of spatial ecology. We used dive data from seven gray seals Halichoerus grypus (a primarily benthic forager) collected with GPS phone tags (Sea Mammal Research Unit) to investigate the distribution of the maximum depth visited in each dive. We modeled maximum dive depth as a function of spatiotemporal covariates using a generalized additive mixed model (GAMM) with individual as a random effect. Bathymetry, horizontal displacement, latitude and longitude, Julian day, sediment type, and light conditions accounted for 37% of the variability in the data. Persistent patterns of autocorrelation in the raw data suggest that individual intrinsic rhythm might be an important factor, not captured by external covariates. The strength of using this statistical method to generate spatial predictions of the distribution of maximum dive depth is its applicability to other plunge and pursuit divers. Despite being predictions of a point estimate, these maps provide some insight into the third dimension of habitat use in marine animals. The capacity to predict this aspect of vertical habitat use may help avoid conflict between animal habitat and coastal or offshore developmentsAnnual report on the implementation of Council Regulation (EC) No 812/2004 during 2014Northridge, SimonKingston, AlThomas, Lenhttp://hdl.handle.net/10023/68552017-04-01T23:44:28Z2015-06-01T00:00:00Z2015-06-01T00:00:00ZNorthridge, SimonKingston, AlThomas, LenUsing accelerometers to determine the calling behavior of tagged baleen whalesGoldbogen, JeremyDe Ruiter, Stacy LynnStimpert, AlisonCalambokidis, JohnFriedlaender, AriSchorr, GregMoretti, DavidTyack, Peter LloydSouthall, Brandonhttp://hdl.handle.net/10023/66232017-05-21T01:33:11Z2014-07-15T00:00:00ZLow-frequency acoustic signals generated by baleen whales can propagate over vast distances, making the assignment of calls to specific individuals problematic. Here, we report the novel use of acoustic recording tags equipped with high-resolution accelerometers to detect vibrations from the surface of two tagged fin whales that directly match the timing of recorded acoustic signals. A tag deployed on a buoy in the vicinity of calling fin whales and a recording from a tag that had just fallen off a whale were able to detect calls acoustically but did not record corresponding accelerometer signals that were measured on calling individuals. Across the hundreds of calls measured on two tagged fin whales, the accelerometer response was generally anisotropic across all three axes, appeared to depend on tag placement and increased with the level of received sound. These data demonstrate that high-sample rate accelerometry can provide important insights into the acoustic behavior of baleen whales that communicate at low frequencies. This method helps identify vocalizing whales, which in turn enables the quantification of call rates, a fundamental component of models used to estimate baleen whale abundance and distribution from passive acoustic monitoring.
2014-07-15T00:00:00ZGoldbogen, JeremyDe Ruiter, Stacy LynnStimpert, AlisonCalambokidis, JohnFriedlaender, AriSchorr, GregMoretti, DavidTyack, Peter LloydSouthall, BrandonLow-frequency acoustic signals generated by baleen whales can propagate over vast distances, making the assignment of calls to specific individuals problematic. Here, we report the novel use of acoustic recording tags equipped with high-resolution accelerometers to detect vibrations from the surface of two tagged fin whales that directly match the timing of recorded acoustic signals. A tag deployed on a buoy in the vicinity of calling fin whales and a recording from a tag that had just fallen off a whale were able to detect calls acoustically but did not record corresponding accelerometer signals that were measured on calling individuals. Across the hundreds of calls measured on two tagged fin whales, the accelerometer response was generally anisotropic across all three axes, appeared to depend on tag placement and increased with the level of received sound. These data demonstrate that high-sample rate accelerometry can provide important insights into the acoustic behavior of baleen whales that communicate at low frequencies. This method helps identify vocalizing whales, which in turn enables the quantification of call rates, a fundamental component of models used to estimate baleen whale abundance and distribution from passive acoustic monitoring.Nested row-column designs for near-factorial experiments with two treatment factors and one control treatmentBailey, Rosemary AnneLacka, Agnieszkahttp://hdl.handle.net/10023/65562017-04-25T08:28:13Z2015-10-01T00:00:00ZThis paper presents some methods of designing experiments in a block design with nested rows and columns. The treatments consist of all combinations of levels of two treatment factors, with an additional control treatment.
The authors also thank Queen Mary, University of London, the University of St Andrews and the Poznan University of Life Sciences for financial support. The second author was also supported by the British-Polish Young Scientists Programme, grant WAR/342/116.
2015-10-01T00:00:00ZBailey, Rosemary AnneLacka, AgnieszkaThis paper presents some methods of designing experiments in a block design with nested rows and columns. The treatments consist of all combinations of levels of two treatment factors, with an additional control treatment.The effect of animal movement on line transect estimates of abundanceGlennie, R.Buckland, S.T.Thomas, L.http://hdl.handle.net/10023/64662017-04-30T05:31:16Z2015-03-23T00:00:00ZLine transect sampling is a distance sampling method for estimating the abundance of wild animal populations. One key assumption of this method is that all animals are detected at their initial location. Animal movement independent of the transect and observer can thus cause substantial bias. We present an analytic expression for this bias when detection within the transect is certain (strip transect sampling) and use simulation to quantify bias when detection falls off with distance from the line (line transect sampling). We also explore the non-linear relationship between bias, detection, and animal movement by varying detectability and movement type. We consider animals that move in randomly orientated straight lines, which provides an upper bound on bias, and animals that are constrained to a home range of random radius. We find that bias is reduced when animal movement is constrained, and bias is considerably smaller in line transect sampling than strip transect sampling provided that mean animal speed is less than observer speed. By contrast, when mean animal speed exceeds observer speed the bias in line transect sampling becomes comparable with, and may exceed, that of strip transect sampling. Bias from independent animal movement is reduced by the observer searching further perpendicular to the transect, searching a shorter distance ahead and by ignoring animals that may overtake the observer from behind. However, when animals move in response to the observer, the standard practice of searching further ahead should continue as the bias from responsive movement is often greater than that from independent movement.
This work was supported by the University of St Andrews (http://www.st-andrews.ac.uk/; RG, STB, LT) and by a summer scholarship and PhD grant from The Carnegie Trust for the Universities of Scotland (http://www.carnegie-trust.org/) to RG.
2015-03-23T00:00:00ZGlennie, R.Buckland, S.T.Thomas, L.Line transect sampling is a distance sampling method for estimating the abundance of wild animal populations. One key assumption of this method is that all animals are detected at their initial location. Animal movement independent of the transect and observer can thus cause substantial bias. We present an analytic expression for this bias when detection within the transect is certain (strip transect sampling) and use simulation to quantify bias when detection falls off with distance from the line (line transect sampling). We also explore the non-linear relationship between bias, detection, and animal movement by varying detectability and movement type. We consider animals that move in randomly orientated straight lines, which provides an upper bound on bias, and animals that are constrained to a home range of random radius. We find that bias is reduced when animal movement is constrained, and bias is considerably smaller in line transect sampling than strip transect sampling provided that mean animal speed is less than observer speed. By contrast, when mean animal speed exceeds observer speed the bias in line transect sampling becomes comparable with, and may exceed, that of strip transect sampling. Bias from independent animal movement is reduced by the observer searching further perpendicular to the transect, searching a shorter distance ahead and by ignoring animals that may overtake the observer from behind. However, when animals move in response to the observer, the standard practice of searching further ahead should continue as the bias from responsive movement is often greater than that from independent movement.Mixture models for distance sampling detection functionsMiller, David LawrenceThomas, Lenhttp://hdl.handle.net/10023/64632017-04-25T07:47:44Z2015-03-20T00:00:00ZWe present a new class of models for the detection function in distance sampling surveys of wildlife populations, based on finite mixtures of simple parametric key functions such as the half-normal. The models share many of the features of the widely-used “key function plus series adjustment” (K+A) formulation: they are flexible, produce plausible shapes with a small number of parameters, allow incorporation of covariates in addition to distance and can be fitted using maximum likelihood. One important advantage over the K+A approach is that the mixtures are automatically monotonic non-increasing and non-negative, so constrained optimization is not required to ensure distance sampling assumptions are honoured. We compare the mixture formulation to the K+A approach using simulations to evaluate its applicability in a wide set of challenging situations. We also re-analyze four previously problematic real-world case studies. We find mixtures outperform K+A methods in many cases, particularly spiked line transect data (i.e., where detectability drops rapidly at small distances) and larger sample sizes. We recommend that current standard model selection methods for distance sampling detection functions are extended to include mixture models in the candidate set.
Funding: EPSRC DTG
2015-03-20T00:00:00ZMiller, David LawrenceThomas, LenWe present a new class of models for the detection function in distance sampling surveys of wildlife populations, based on finite mixtures of simple parametric key functions such as the half-normal. The models share many of the features of the widely-used “key function plus series adjustment” (K+A) formulation: they are flexible, produce plausible shapes with a small number of parameters, allow incorporation of covariates in addition to distance and can be fitted using maximum likelihood. One important advantage over the K+A approach is that the mixtures are automatically monotonic non-increasing and non-negative, so constrained optimization is not required to ensure distance sampling assumptions are honoured. We compare the mixture formulation to the K+A approach using simulations to evaluate its applicability in a wide set of challenging situations. We also re-analyze four previously problematic real-world case studies. We find mixtures outperform K+A methods in many cases, particularly spiked line transect data (i.e., where detectability drops rapidly at small distances) and larger sample sizes. We recommend that current standard model selection methods for distance sampling detection functions are extended to include mixture models in the candidate set.Most switching classes with primitive automorphism groups contain graphs with trivial groupsCameron, Peter JephsonSpiga, Pablohttp://hdl.handle.net/10023/64292017-01-01T04:09:06Z2015-06-01T00:00:00ZThe operation of switching a graph Gamma with respect to a subset X of the vertex set interchanges edges and non-edges between X and its complement, leaving the rest of the graph unchanged. This is an equivalence relation on the set of graphs on a given vertex set, so we can talk about the automorphism group of a switching class of graphs. It might be thought that switching classes with many automorphisms would have the property that all their graphs also have many automorphisms. But the main theorem of this paper shows a different picture: with finitely many exceptions, if a non-trivial switching class S has primitive automorphism group, then it contains a graph whose automorphism group is trivial. We also find all the exceptional switching classes; up to complementation, there are just six.
2015-06-01T00:00:00ZCameron, Peter JephsonSpiga, PabloThe operation of switching a graph Gamma with respect to a subset X of the vertex set interchanges edges and non-edges between X and its complement, leaving the rest of the graph unchanged. This is an equivalence relation on the set of graphs on a given vertex set, so we can talk about the automorphism group of a switching class of graphs. It might be thought that switching classes with many automorphisms would have the property that all their graphs also have many automorphisms. But the main theorem of this paper shows a different picture: with finitely many exceptions, if a non-trivial switching class S has primitive automorphism group, then it contains a graph whose automorphism group is trivial. We also find all the exceptional switching classes; up to complementation, there are just six.Statistical ecology comes of ageGimenez, OlivierBuckland, Stephen TerrenceMorgan, Byron J. T.Bez, NicolasBertrand, SophieChoquet, RemiDray, StephaneEtienne, Marie-PierreFewster, RachelGosselin, FredericMerigot, BastienMonestiez, PascalMorales, Juan M.Mortier, FredericMunoz, FrancoisOvaskainen, OtsoPavoine, SandrinePradel, RogerSchurr, Frank M.Thomas, LenThuiller, WilfriedTrenkel, Verenade Valpine, PerryRexstad, Erichttp://hdl.handle.net/10023/61282017-04-30T05:31:01Z2014-12-24T00:00:00ZThe desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1 –4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.
2014-12-24T00:00:00ZGimenez, OlivierBuckland, Stephen TerrenceMorgan, Byron J. T.Bez, NicolasBertrand, SophieChoquet, RemiDray, StephaneEtienne, Marie-PierreFewster, RachelGosselin, FredericMerigot, BastienMonestiez, PascalMorales, Juan M.Mortier, FredericMunoz, FrancoisOvaskainen, OtsoPavoine, SandrinePradel, RogerSchurr, Frank M.Thomas, LenThuiller, WilfriedTrenkel, Verenade Valpine, PerryRexstad, EricThe desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1 –4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.Inter-annual and seasonal trends in cetacean distribution, density and abundance off southern CaliforniaCampbell, G.S.Thomas, L.Whitaker, K.Douglas, A.B.Calambokidis, J.Hildebrand, J.A.http://hdl.handle.net/10023/60882017-04-25T08:23:12Z2015-02-01T00:00:00ZTrends in cetacean density and distribution off southern California were assessed through visual line-transect surveys during thirty-seven California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises from July 2004–November 2013. From sightings of the six most commonly encountered cetacean species, seasonal, annual and overall density estimates were calculated. Blue whales (Balaenoptera musculus), fin whales (Balaenoptera physalus) and humpback whales (Megaptera novaeangliae) were the most frequently sighted baleen whales with overall densities of 0.91/1000 km2 (CV=0.27), 2.73/1000 km2 (CV=0.19), and 1.17/1000 km2 (CV=0.21) respectively. Species specific density estimates, stratified by cruise, were analyzed using a generalized additive model to estimate long-term trends and correct for seasonal imbalances. Variances were estimated using a non-parametric bootstrap with one day of effort as the sampling unit. Blue whales were primarily observed during summer and fall while fin and humpback whales were observed year-round with peaks in density during summer and spring respectively. Short-beaked common dolphins (Delphinus delphis), Pacific white-sided dolphins (Lagenorhynchus obliquidens) and Dall’s porpoise (Phocoenoidesdalli) were the most frequently encountered small cetaceans with overall densities of 705.83/1000 km2 (CV=0.22), 51.98/1000 km2 (CV=0.27), and 21.37/1000 km2 (CV=0.19) respectively. Seasonally, short-beaked common dolphins were most abundant in winter whereas Pacific white-sided dolphins and Dall’s porpoise were most abundant during spring. There were no significant long-term changes in blue whale, fin whale, humpback whale, short-beaked common dolphin or Dall’s porpoise densities while Pacific white-sided dolphins exhibited a significant decrease in density across the ten-year study. The results from this study were fundamentally consistent with earlier studies, but provide greater temporal and seasonal resolution
Funding was provided by the Chief of Naval Operations Environmental Readiness Division, the United States Navy’s Pacific Fleet, the Naval Postgraduate School Grant #N00244-11-1-027, and the Naval Facilities Engineering Command Living Marine Resources Program.
2015-02-01T00:00:00ZCampbell, G.S.Thomas, L.Whitaker, K.Douglas, A.B.Calambokidis, J.Hildebrand, J.A.Trends in cetacean density and distribution off southern California were assessed through visual line-transect surveys during thirty-seven California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises from July 2004–November 2013. From sightings of the six most commonly encountered cetacean species, seasonal, annual and overall density estimates were calculated. Blue whales (Balaenoptera musculus), fin whales (Balaenoptera physalus) and humpback whales (Megaptera novaeangliae) were the most frequently sighted baleen whales with overall densities of 0.91/1000 km2 (CV=0.27), 2.73/1000 km2 (CV=0.19), and 1.17/1000 km2 (CV=0.21) respectively. Species specific density estimates, stratified by cruise, were analyzed using a generalized additive model to estimate long-term trends and correct for seasonal imbalances. Variances were estimated using a non-parametric bootstrap with one day of effort as the sampling unit. Blue whales were primarily observed during summer and fall while fin and humpback whales were observed year-round with peaks in density during summer and spring respectively. Short-beaked common dolphins (Delphinus delphis), Pacific white-sided dolphins (Lagenorhynchus obliquidens) and Dall’s porpoise (Phocoenoidesdalli) were the most frequently encountered small cetaceans with overall densities of 705.83/1000 km2 (CV=0.22), 51.98/1000 km2 (CV=0.27), and 21.37/1000 km2 (CV=0.19) respectively. Seasonally, short-beaked common dolphins were most abundant in winter whereas Pacific white-sided dolphins and Dall’s porpoise were most abundant during spring. There were no significant long-term changes in blue whale, fin whale, humpback whale, short-beaked common dolphin or Dall’s porpoise densities while Pacific white-sided dolphins exhibited a significant decrease in density across the ten-year study. The results from this study were fundamentally consistent with earlier studies, but provide greater temporal and seasonal resolutionHigher biodiversity is required to sustain multiple ecosystem processes across temperature regimesPerkins, D.M.Bailey, R.A.Dossena, M.Gamfeldt, L.Reiss, J.Trimmer, M.Woodward, G.http://hdl.handle.net/10023/59752017-05-28T01:33:11Z2015-01-01T00:00:00ZBiodiversity loss is occurring rapidly worldwide, yet it is uncertain whether few or many species are required to sustain ecosystem functioning in the face of environmental change. The importance of biodiversity might be enhanced when multiple ecosystem processes (termed multifunctionality) and environmental contexts are considered, yet no studies have quantified this explicitly to date. We measured five key processes and their combined multifunctionality at three temperatures (5, 10 and 15 °C) in freshwater aquaria containing different animal assemblages (1-4 benthic macroinvertebrate species). For single processes, biodiversity effects were weak and were best predicted by additive-based models, i.e. polyculture performances represented the sum of their monoculture parts. There were, however, significant effects of biodiversity on multifunctionality at the low and the high (but not the intermediate) temperature. Variation in the contribution of species to processes across temperatures meant that greater biodiversity was required to sustain multifunctionality across different temperatures than was the case for single processes. This suggests that previous studies might have underestimated the importance of biodiversity in sustaining ecosystem functioning in a changing environment.
The authors thank the Natural Environment Research Council for financial support awarded to G. W. (Grant reference: NE/D013305/1) that funded D. M. P.'s research. Accepted 11 July 2014.
2015-01-01T00:00:00ZPerkins, D.M.Bailey, R.A.Dossena, M.Gamfeldt, L.Reiss, J.Trimmer, M.Woodward, G.Biodiversity loss is occurring rapidly worldwide, yet it is uncertain whether few or many species are required to sustain ecosystem functioning in the face of environmental change. The importance of biodiversity might be enhanced when multiple ecosystem processes (termed multifunctionality) and environmental contexts are considered, yet no studies have quantified this explicitly to date. We measured five key processes and their combined multifunctionality at three temperatures (5, 10 and 15 °C) in freshwater aquaria containing different animal assemblages (1-4 benthic macroinvertebrate species). For single processes, biodiversity effects were weak and were best predicted by additive-based models, i.e. polyculture performances represented the sum of their monoculture parts. There were, however, significant effects of biodiversity on multifunctionality at the low and the high (but not the intermediate) temperature. Variation in the contribution of species to processes across temperatures meant that greater biodiversity was required to sustain multifunctionality across different temperatures than was the case for single processes. This suggests that previous studies might have underestimated the importance of biodiversity in sustaining ecosystem functioning in a changing environment.A unifying model for capture-recapture and distance sampling surveys of wildlife populationsBorchers, D. L.Stevenson, B.C.Kidney, D.Thomas, L.Marques, T.A.http://hdl.handle.net/10023/57972017-06-04T00:30:42Z2015-01-01T00:00:00ZSpatially explicit capture-recapture (SECR) methods extend traditional capture-recapture methods for estimating population density by using information contained in the location of traps. The The central feature of the improvement is estimation from the locations of traps at which animals were and were not captured to estimate of the distance over which animals are susceptible to capture. We show that standard SECR models are a special case of a more general class of model in which animal detection is not certain, but some information is available about the location of detected animals. The model class accommodates a range of spatial data types and includes as a special case mark-recapture distance sampling, where distances to detected animals are recorded by multiple observers. Other examples of additional information that can be included are bearing to detected animals, strength of acoustic signals received from detected animals, and time of arrival of acoustic signals at detectors. Errors in variables are easily incorporated. We illustrate the versatility of the model and method through a number of applications, in each case using real and simulated data, and comparing our results with those from previous studies where these are available.
Funding: Part-funded by Fundacao Nacional para a Cienca e Technologia, Portugal (FCT) under the project PEst OE/MAT/UI0006/2011 (Marques) and the UK Engineering and Physical Sciences Research Council EP/I000917/1
2015-01-01T00:00:00ZBorchers, D. L.Stevenson, B.C.Kidney, D.Thomas, L.Marques, T.A.Spatially explicit capture-recapture (SECR) methods extend traditional capture-recapture methods for estimating population density by using information contained in the location of traps. The The central feature of the improvement is estimation from the locations of traps at which animals were and were not captured to estimate of the distance over which animals are susceptible to capture. We show that standard SECR models are a special case of a more general class of model in which animal detection is not certain, but some information is available about the location of detected animals. The model class accommodates a range of spatial data types and includes as a special case mark-recapture distance sampling, where distances to detected animals are recorded by multiple observers. Other examples of additional information that can be included are bearing to detected animals, strength of acoustic signals received from detected animals, and time of arrival of acoustic signals at detectors. Errors in variables are easily incorporated. We illustrate the versatility of the model and method through a number of applications, in each case using real and simulated data, and comparing our results with those from previous studies where these are available.Acoustic and foraging behavior of a Baird’s beaked whale, Berardius bairdii, exposed to simulated sonarStimpert, AlisonDe Ruiter, Stacy LynnSouthall, BrandonMoretti, DavidFalcone, ErinGoldbogen, JeremyFriedlaender, AriSchorr, GregCalambokidis, Johnhttp://hdl.handle.net/10023/57872017-05-21T01:33:08Z2014-11-13T00:00:00ZBeaked whales are hypothesized to be particularly sensitive to anthropogenic noise, based on previous strandings and limited experimental and observational data. However, few species have been studied in detail. We describe the underwater behavior of a Baird's beaked whale (Berardius bairdii) from the first deployment of a multi-sensor acoustic tag on this species. The animal exhibited shallow (23 ± 15 m max depth), intermediate (324 ± 49 m), and deep (1138 ± 243 m) dives. Echolocation clicks were produced with a mean inter-click interval of approximately 300 ms and peak frequency of 25 kHz. Two deep dives included presumed foraging behavior, with echolocation pulsed sounds (presumed prey capture attempts) associated with increased maneuvering, and sustained inverted swimming during the bottom phase of the dive. A controlled exposure to simulated mid-frequency active sonar (3.5–4 kHz) was conducted 4 hours after tag deployment, and within 3 minutes of exposure onset, the tagged whale increased swim speed and body movement, and continued to show unusual dive behavior for each of its next three dives, one of each type. These are the first data on the acoustic foraging behavior in this largest beaked whale species, and the first experimental demonstration of a response to simulated sonar.
Research was supported by the US Navy Chief of Naval Operations, Environmental Readiness Program, the Office of Naval Research, the Naval Postgraduate School, and the National Research Council.
2014-11-13T00:00:00ZStimpert, AlisonDe Ruiter, Stacy LynnSouthall, BrandonMoretti, DavidFalcone, ErinGoldbogen, JeremyFriedlaender, AriSchorr, GregCalambokidis, JohnBeaked whales are hypothesized to be particularly sensitive to anthropogenic noise, based on previous strandings and limited experimental and observational data. However, few species have been studied in detail. We describe the underwater behavior of a Baird's beaked whale (Berardius bairdii) from the first deployment of a multi-sensor acoustic tag on this species. The animal exhibited shallow (23 ± 15 m max depth), intermediate (324 ± 49 m), and deep (1138 ± 243 m) dives. Echolocation clicks were produced with a mean inter-click interval of approximately 300 ms and peak frequency of 25 kHz. Two deep dives included presumed foraging behavior, with echolocation pulsed sounds (presumed prey capture attempts) associated with increased maneuvering, and sustained inverted swimming during the bottom phase of the dive. A controlled exposure to simulated mid-frequency active sonar (3.5–4 kHz) was conducted 4 hours after tag deployment, and within 3 minutes of exposure onset, the tagged whale increased swim speed and body movement, and continued to show unusual dive behavior for each of its next three dives, one of each type. These are the first data on the acoustic foraging behavior in this largest beaked whale species, and the first experimental demonstration of a response to simulated sonar.Optimal cross-over designs for full interaction modelsBailey, Rosemary AnneDruilhet, Pierrehttp://hdl.handle.net/10023/57682017-04-25T08:14:58Z2014-11-01T00:00:00ZWe consider repeated measurement designs when a residual or carry-over effect may be present in at most one later period. Since assuming an additive model may be unrealistic for some applications and leads to biased estimation of treatment effects, we consider a model with interactions between carry-over and direct treatment effects. When the aim of the experiment is to study the effects of a treatment used alone, we obtain universally optimal approximate designs. We also propose some efficient designs with a reduced number of subjects.
July 2014
2014-11-01T00:00:00ZBailey, Rosemary AnneDruilhet, PierreWe consider repeated measurement designs when a residual or carry-over effect may be present in at most one later period. Since assuming an additive model may be unrealistic for some applications and leads to biased estimation of treatment effects, we consider a model with interactions between carry-over and direct treatment effects. When the aim of the experiment is to study the effects of a treatment used alone, we obtain universally optimal approximate designs. We also propose some efficient designs with a reduced number of subjects.Computing in permutation groups without memoryCameron, Peter JephsonFairbairn, BenGadouleau, Maximilienhttp://hdl.handle.net/10023/57272017-04-25T08:14:17Z2014-11-02T00:00:00ZMemoryless computation is a new technique to compute any function of a set of registers by updating one register at a time while using no memory. Its aim is to emulate how computations are performed in modern cores, since they typically involve updates of single registers. The memoryless computation model can be fully expressed in terms of transformation semigroups, or in the case of bijective functions, permutation groups. In this paper, we consider how efficiently permutations can be computed without memory. We determine the minimum number of basic updates required to compute any permutation, or any even permutation. The small number of required instructions shows that very small instruction sets could be encoded on cores to perform memoryless computation. We then start looking at a possible compromise between the size of the instruction set and the length of the resulting programs. We consider updates only involving a limited number of registers. In particular, we show that binary instructions are not enough to compute all permutations without memory when the alphabet size is even. These results, though expressed as properties of special generating sets of the symmetric or alternating groups, provide guidelines on the implementation of memoryless computation.
Funding: UK Engineering and Physical Sciences Research Council (EP/K033956/1)
2014-11-02T00:00:00ZCameron, Peter JephsonFairbairn, BenGadouleau, MaximilienMemoryless computation is a new technique to compute any function of a set of registers by updating one register at a time while using no memory. Its aim is to emulate how computations are performed in modern cores, since they typically involve updates of single registers. The memoryless computation model can be fully expressed in terms of transformation semigroups, or in the case of bijective functions, permutation groups. In this paper, we consider how efficiently permutations can be computed without memory. We determine the minimum number of basic updates required to compute any permutation, or any even permutation. The small number of required instructions shows that very small instruction sets could be encoded on cores to perform memoryless computation. We then start looking at a possible compromise between the size of the instruction set and the length of the resulting programs. We consider updates only involving a limited number of registers. In particular, we show that binary instructions are not enough to compute all permutations without memory when the alphabet size is even. These results, though expressed as properties of special generating sets of the symmetric or alternating groups, provide guidelines on the implementation of memoryless computation.Computing in matrix groups without memoryCameron, Peter JephsonFairbairn, BenGadouleau, Maximilienhttp://hdl.handle.net/10023/57152017-04-25T08:14:18Z2014-11-02T00:00:00ZMemoryless computation is a novel means of computing any function of a set of registers by updating one register at a time while using no memory. We aim to emulate how computations are performed on modern cores, since they typically involve updates of single registers. The computation model of memoryless computation can be fully expressed in terms of transformation semigroups, or in the case of bijective functions, permutation groups. In this paper, we view registers as elements of a finite field and we compute linear permutations without memory. We first determine the maximum complexity of a linear function when only linear instructions are allowed. We also determine which linear functions are hardest to compute when the field in question is the binary field and the number of registers is even. Secondly, we investigate some matrix groups, thus showing that the special linear group is internally computable but not fast. Thirdly, we determine the smallest set of instructions required to generate the special and general linear groups. These results are important for memoryless computation, for they show that linear functions can be computed very fast or that very few instructions are needed to compute any linear function. They thus indicate new advantages of using memoryless computation.
Funding: UK Engineering and Physical Sciences Research Council award EP/K033956/1
2014-11-02T00:00:00ZCameron, Peter JephsonFairbairn, BenGadouleau, MaximilienMemoryless computation is a novel means of computing any function of a set of registers by updating one register at a time while using no memory. We aim to emulate how computations are performed on modern cores, since they typically involve updates of single registers. The computation model of memoryless computation can be fully expressed in terms of transformation semigroups, or in the case of bijective functions, permutation groups. In this paper, we view registers as elements of a finite field and we compute linear permutations without memory. We first determine the maximum complexity of a linear function when only linear instructions are allowed. We also determine which linear functions are hardest to compute when the field in question is the binary field and the number of registers is even. Secondly, we investigate some matrix groups, thus showing that the special linear group is internally computable but not fast. Thirdly, we determine the smallest set of instructions required to generate the special and general linear groups. These results are important for memoryless computation, for they show that linear functions can be computed very fast or that very few instructions are needed to compute any linear function. They thus indicate new advantages of using memoryless computation.Most primitive groups are full automorphism groups of edge-transitive hypergraphsBabai, LaszloCameron, Peter Jephsonhttp://hdl.handle.net/10023/55802017-04-25T08:14:01Z2015-01-01T00:00:00ZWe prove that, for a primitive permutation group G acting on a set of size n, other than the alternating group, the probability that Aut(X,YG) = G for a random subset Y of X, tends to 1 as n tends to infinity. So the property of the title holds for all primitive groups except the alternating groups and finitely many others. This answers a question of M. Klin. Moreover, we give an upper bound n1/2+ε for the minimum size of the edges in such a hypergraph. This is essentially best possible.
2015-01-01T00:00:00ZBabai, LaszloCameron, Peter JephsonWe prove that, for a primitive permutation group G acting on a set of size n, other than the alternating group, the probability that Aut(X,YG) = G for a random subset Y of X, tends to 1 as n tends to infinity. So the property of the title holds for all primitive groups except the alternating groups and finitely many others. This answers a question of M. Klin. Moreover, we give an upper bound n1/2+ε for the minimum size of the edges in such a hypergraph. This is essentially best possible.The effects of acoustic misclassification on cetacean species abundance estimationCaillat, Marjolaine AnnieThomas, LenGillespie, Douglas Michaelhttp://hdl.handle.net/10023/51632017-04-25T07:51:20Z2013-12-25T00:00:00ZTo estimate the density or abundance of a cetacean species using acoustic detection data, it is necessary to correctly identify the species that are detected. Developing an automated species classifier with 100% correct classification rate for any species is likely to stay out of reach. It is therefore necessary to consider the effect of misidentified detections on the number of observed data and consequently on abundance or density estimation, and develop methods to cope with these misidentifications. If misclassification rates are known, it is possible to estimate the true numbers of detected calls without bias. However, misclassification and uncertainties in the level of misclassification increase the variance of the estimates. If the true numbers of calls from different species are similar, then a small amount of misclassification between species and a small amount of uncertainty around the classification probabilities does not have an overly detrimental effect on the overall variance. However, if there is a difference in the encounter rate between species calls and/or a large amount of uncertainty in misclassification rates, then the variance of the estimates becomes very large and this dramatically increases the variance of the final abundance estimate.
This work was funded through the Natural Environment Research Council and SMRU Ltd.
2013-12-25T00:00:00ZCaillat, Marjolaine AnnieThomas, LenGillespie, Douglas MichaelTo estimate the density or abundance of a cetacean species using acoustic detection data, it is necessary to correctly identify the species that are detected. Developing an automated species classifier with 100% correct classification rate for any species is likely to stay out of reach. It is therefore necessary to consider the effect of misidentified detections on the number of observed data and consequently on abundance or density estimation, and develop methods to cope with these misidentifications. If misclassification rates are known, it is possible to estimate the true numbers of detected calls without bias. However, misclassification and uncertainties in the level of misclassification increase the variance of the estimates. If the true numbers of calls from different species are similar, then a small amount of misclassification between species and a small amount of uncertainty around the classification probabilities does not have an overly detrimental effect on the overall variance. However, if there is a difference in the encounter rate between species calls and/or a large amount of uncertainty in misclassification rates, then the variance of the estimates becomes very large and this dramatically increases the variance of the final abundance estimate.Dose-response relationships for the onset of avoidance of sonar by free-ranging killer whalesMiller, PatrickAntunes, Ricardo NunoWensveen, Paulus JacobusSamarra, Filipa Isabel PereiraAlves, Ana Catarina De CarvalhoTyack, Peter LloydKvadsheim, Petter H.Kleivane, LarsLam, Frans-Peter A.Ainslie, Michael A.Thomas, Lenhttp://hdl.handle.net/10023/50922017-05-28T01:30:18Z2014-02-01T00:00:00ZEight experimentally controlled exposures to 1−2 kHz or 6−7 kHz sonar signals were conducted with four killer whale groups. The source level and proximity of the source were increased during each exposure in order to reveal response thresholds. Detailed inspection of movements during each exposure session revealed sustained changes in speed and travel direction judged to be avoidance responses during six of eight sessions. Following methods developed for Phase-I clinical trials in human medicine, response thresholds ranging from 94 to 164 dB re 1 μPa received sound pressure level (SPL) were fitted to Bayesian dose-response functions. Thresholds did not consistently differ by sonar frequency or whether a group had previously been exposed, with a mean SPL response threshold of 142 ± 15 dB (mean ± s.d.). High levels of between- and within-individual variability were identified, indicating that thresholds depended upon other undefined contextual variables. The dose-response functions indicate that some killer whales started to avoid sonar at received SPL below thresholds assumed by the U.S. Navy. The predicted extent of habitat over which avoidance reactions occur depends upon whether whales responded to proximity or received SPL of the sonar or both, but was large enough to raise concerns about biological consequences to the whales.
The authors acknowledge the support of the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) in the completion of this study. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.
2014-02-01T00:00:00ZMiller, PatrickAntunes, Ricardo NunoWensveen, Paulus JacobusSamarra, Filipa Isabel PereiraAlves, Ana Catarina De CarvalhoTyack, Peter LloydKvadsheim, Petter H.Kleivane, LarsLam, Frans-Peter A.Ainslie, Michael A.Thomas, LenEight experimentally controlled exposures to 1−2 kHz or 6−7 kHz sonar signals were conducted with four killer whale groups. The source level and proximity of the source were increased during each exposure in order to reveal response thresholds. Detailed inspection of movements during each exposure session revealed sustained changes in speed and travel direction judged to be avoidance responses during six of eight sessions. Following methods developed for Phase-I clinical trials in human medicine, response thresholds ranging from 94 to 164 dB re 1 μPa received sound pressure level (SPL) were fitted to Bayesian dose-response functions. Thresholds did not consistently differ by sonar frequency or whether a group had previously been exposed, with a mean SPL response threshold of 142 ± 15 dB (mean ± s.d.). High levels of between- and within-individual variability were identified, indicating that thresholds depended upon other undefined contextual variables. The dose-response functions indicate that some killer whales started to avoid sonar at received SPL below thresholds assumed by the U.S. Navy. The predicted extent of habitat over which avoidance reactions occur depends upon whether whales responded to proximity or received SPL of the sonar or both, but was large enough to raise concerns about biological consequences to the whales.Using hidden Markov models to deal with availability bias on line transect surveysBorchers, David LouisZucchini, WalterHeide-Jørgensen, M.P.Cañadas, A.Langrock, Rolandhttp://hdl.handle.net/10023/50172017-04-25T07:47:41Z2013-01-01T00:00:00ZWe develop estimators for line transect surveys of animals that are stochastically unavailable for detection while within detection range. The detection process is formulated as a hidden Markov model with a binary state-dependent observation model that depends on both perpendicular and forward distances. This provides a parametric method of dealing with availability bias when estimates of availability process parameters are available even if series of availability events themselves are not. We apply the estimators to an aerial and a shipboard survey of whales, and investigate their properties by simulation. They are shown to be more general and more flexible than existing estimators based on parametric models of the availability process. We also find that methods using availability correction factors can be very biased when surveys are not close to being instantaneous, as can estimators that assume temporal independence in availability when there is temporal dependence.
This work was supported by EPSRC grant EP/I000917/1
2013-01-01T00:00:00ZBorchers, David LouisZucchini, WalterHeide-Jørgensen, M.P.Cañadas, A.Langrock, RolandWe develop estimators for line transect surveys of animals that are stochastically unavailable for detection while within detection range. The detection process is formulated as a hidden Markov model with a binary state-dependent observation model that depends on both perpendicular and forward distances. This provides a parametric method of dealing with availability bias when estimates of availability process parameters are available even if series of availability events themselves are not. We apply the estimators to an aerial and a shipboard survey of whales, and investigate their properties by simulation. They are shown to be more general and more flexible than existing estimators based on parametric models of the availability process. We also find that methods using availability correction factors can be very biased when surveys are not close to being instantaneous, as can estimators that assume temporal independence in availability when there is temporal dependence.An approximate Bayesian method applied to estimating the trajectories of four British grey seal (Halichoerus grypus) populations from pup counts.Lonergan, Michael EdwardThompson, DavidThomas, Leonard JosephDuck, Callan Davidhttp://hdl.handle.net/10023/46882017-04-25T07:37:13Z2011-01-01T00:00:00Z1. For British grey seals, as with many pinniped species, population monitoring is implemented by aerial surveys of pups at breeding colonies. Scaling pup counts up to population estimates requires assumptions about population structure; this is straightforward when populations are growing exponentially, but not when growth slows, since it is unclear whether density dependence affects pup survival or fecundity. 2. We present an approximate Bayesian method for fitting pup trajectories, estimating adult population size and investigating alternative biological models. The method is equivalent to fitting a density dependent Leslie matrix model, within a Bayesian framework, but with the forms of the density dependent effects as outputs rather than assumptions. 3. This approach requires fewer assumptions than the state space models currently used, and produces similar estimates. The simplifications made the models easier to fit, reducing their computational intensity and allowing regional differences in demographic parameters to be considered. 4. The approach is not restricted to situations where only a single component of the population is observable, but, particularly in those cases, provides a practical method for extracting information from limited datasets. 5. We discuss the potential and limitations of the method and suggest that this approach provides a useful tool for at least the preliminary analysis of similar datasets.
2011-01-01T00:00:00ZLonergan, Michael EdwardThompson, DavidThomas, Leonard JosephDuck, Callan David1. For British grey seals, as with many pinniped species, population monitoring is implemented by aerial surveys of pups at breeding colonies. Scaling pup counts up to population estimates requires assumptions about population structure; this is straightforward when populations are growing exponentially, but not when growth slows, since it is unclear whether density dependence affects pup survival or fecundity. 2. We present an approximate Bayesian method for fitting pup trajectories, estimating adult population size and investigating alternative biological models. The method is equivalent to fitting a density dependent Leslie matrix model, within a Bayesian framework, but with the forms of the density dependent effects as outputs rather than assumptions. 3. This approach requires fewer assumptions than the state space models currently used, and produces similar estimates. The simplifications made the models easier to fit, reducing their computational intensity and allowing regional differences in demographic parameters to be considered. 4. The approach is not restricted to situations where only a single component of the population is observable, but, particularly in those cases, provides a practical method for extracting information from limited datasets. 5. We discuss the potential and limitations of the method and suggest that this approach provides a useful tool for at least the preliminary analysis of similar datasets.Modelling group dynamic animal movementLangrock, RolandHopcraft, GrantBlackwell, PaulGoodall, VictoriaKing, RuthNiu, MuPatterson, TobyPedersen, MartinSkarin, AnnaSchick, Robert Schillinghttp://hdl.handle.net/10023/45552017-04-09T00:32:24Z2014-02-01T00:00:00Z1). Group dynamics are a fundamental aspect of many species' movements. The need to adequately model individuals' interactions with other group members has been recognized, particularly in order to differentiate the role of social forces in individual movement from environmental factors. However, to date, practical statistical methods, which can include group dynamics in animal movement models, have been lacking. 2). We consider a flexible modelling framework that distinguishes a group-level model, describing the movement of the group's centre, and an individual-level model, such that each individual makes its movement decisions relative to the group centroid. The basic idea is framed within the flexible class of hidden Markov models, extending previous work on modelling animal movement by means of multistate random walks. 3). While in simulation experiments parameter estimators exhibit some bias in non-ideal scenarios, we show that generally the estimation of models of this type is both feasible and ecologically informative. 4). We illustrate the approach using real movement data from 11 reindeer (Rangifer tarandus). Results indicate a directional bias towards a group centroid for reindeer in an encamped state. Though the attraction to the group centroid is relatively weak, our model successfully captures group-influenced movement dynamics. Specifically, as compared to a regular mixture of correlated random walks, the group dynamic model more accurately predicts the non-diffusive behaviour of a cohesive mobile group. 5). As technology continues to develop, it will become easier and less expensive to tag multiple individuals within a group in order to follow their movements. Our work provides a first inferential framework for understanding the relative influences of individual versus group-level movement decisions. This framework can be extended to include covariates corresponding to environmental influences or body condition. As such, this framework allows for a broader understanding of the many internal and external factors that can influence an individual's movement.
2014-02-01T00:00:00ZLangrock, RolandHopcraft, GrantBlackwell, PaulGoodall, VictoriaKing, RuthNiu, MuPatterson, TobyPedersen, MartinSkarin, AnnaSchick, Robert Schilling1). Group dynamics are a fundamental aspect of many species' movements. The need to adequately model individuals' interactions with other group members has been recognized, particularly in order to differentiate the role of social forces in individual movement from environmental factors. However, to date, practical statistical methods, which can include group dynamics in animal movement models, have been lacking. 2). We consider a flexible modelling framework that distinguishes a group-level model, describing the movement of the group's centre, and an individual-level model, such that each individual makes its movement decisions relative to the group centroid. The basic idea is framed within the flexible class of hidden Markov models, extending previous work on modelling animal movement by means of multistate random walks. 3). While in simulation experiments parameter estimators exhibit some bias in non-ideal scenarios, we show that generally the estimation of models of this type is both feasible and ecologically informative. 4). We illustrate the approach using real movement data from 11 reindeer (Rangifer tarandus). Results indicate a directional bias towards a group centroid for reindeer in an encamped state. Though the attraction to the group centroid is relatively weak, our model successfully captures group-influenced movement dynamics. Specifically, as compared to a regular mixture of correlated random walks, the group dynamic model more accurately predicts the non-diffusive behaviour of a cohesive mobile group. 5). As technology continues to develop, it will become easier and less expensive to tag multiple individuals within a group in order to follow their movements. Our work provides a first inferential framework for understanding the relative influences of individual versus group-level movement decisions. This framework can be extended to include covariates corresponding to environmental influences or body condition. As such, this framework allows for a broader understanding of the many internal and external factors that can influence an individual's movement.A risk function for behavioral disruption of Blainville’s beaked whales (Mesoplodon densirostris) from mid-frequency active sonarMoretti, DavidThomas, LenMarques, Tiago A.Harwood, JohnDilley, AshleyNeales, BertShaffer, JessicaMccarthy, ENew, Leslie FrancesJarvis, SMorrissey, Ronhttp://hdl.handle.net/10023/45222017-04-25T07:58:53Z2014-01-01T00:00:00ZThere is increasing concern about the potential effects of noise pollution on marine life in the world’s oceans. For marine mammals, anthropogenic sounds may cause behavioral disruption, and this can be quantified using a risk function that relates sound exposure to a measured behavioral response. Beaked whales are a taxon of deep diving whales that may be particularly susceptible to naval sonar as the species has been associated with sonar-related mass stranding events. Here we derive the first empirical risk function for Blainville’s beaked whales (Mesoplodon densirostris) by combining in situ data from passive acoustic monitoring of animal vocalizations and navy sonar operations with precise ship tracks and sound field modeling. The hydrophone array at the Atlantic Undersea Test and Evaluation Center, Bahamas, was used to locate vocalizing groups of Blainville’s beaked whales and identify sonar transmissions before, during, and after Mid-Frequency Active (MFA) sonar operations. Sonar transmission times and source levels were combined with ship tracks using a sound propagation model to estimate the received level (RL) at each hydrophone. A generalized additive model was fitted to data to model the presence or absence of the start of foraging dives in 30-minute periods as a function of the corresponding sonar RL at the hydrophone closest to the center of each group. This model was then used to construct a risk function that can be used to estimate the probability of a behavioral change (cessation of foraging) the individual members of a Blainville’s beaked whale population might experience as a function of sonar RL. The function predicts a 0.5 probability of disturbance at a RL of 150dBrms re µPa (CI: 144 to 155) This is 15dB lower than the level used historically by the US Navy in their risk assessments but 10 dB higher than the current 140 dB step-function
2014-01-01T00:00:00ZMoretti, DavidThomas, LenMarques, Tiago A.Harwood, JohnDilley, AshleyNeales, BertShaffer, JessicaMccarthy, ENew, Leslie FrancesJarvis, SMorrissey, RonThere is increasing concern about the potential effects of noise pollution on marine life in the world’s oceans. For marine mammals, anthropogenic sounds may cause behavioral disruption, and this can be quantified using a risk function that relates sound exposure to a measured behavioral response. Beaked whales are a taxon of deep diving whales that may be particularly susceptible to naval sonar as the species has been associated with sonar-related mass stranding events. Here we derive the first empirical risk function for Blainville’s beaked whales (Mesoplodon densirostris) by combining in situ data from passive acoustic monitoring of animal vocalizations and navy sonar operations with precise ship tracks and sound field modeling. The hydrophone array at the Atlantic Undersea Test and Evaluation Center, Bahamas, was used to locate vocalizing groups of Blainville’s beaked whales and identify sonar transmissions before, during, and after Mid-Frequency Active (MFA) sonar operations. Sonar transmission times and source levels were combined with ship tracks using a sound propagation model to estimate the received level (RL) at each hydrophone. A generalized additive model was fitted to data to model the presence or absence of the start of foraging dives in 30-minute periods as a function of the corresponding sonar RL at the hydrophone closest to the center of each group. This model was then used to construct a risk function that can be used to estimate the probability of a behavioral change (cessation of foraging) the individual members of a Blainville’s beaked whale population might experience as a function of sonar RL. The function predicts a 0.5 probability of disturbance at a RL of 150dBrms re µPa (CI: 144 to 155) This is 15dB lower than the level used historically by the US Navy in their risk assessments but 10 dB higher than the current 140 dB step-functionUsing energetic models to investigate the survival and reproduction of beaked whales (family Ziphiidae)New, Leslie FrancesMoretti, DavidHooker, Sascha KateCosta, Daniel P.Simmons, Samantha E.http://hdl.handle.net/10023/40532017-06-11T00:31:29Z2013-07-17T00:00:00ZMass stranding of several species of beaked whales (family Ziphiidae) associated with exposure to anthropogenic sounds has raised concern for the conservation of these species. However, little is known about the species’ life histories, prey or habitat requirements. Without this knowledge, it becomes difficult to assess the effects of anthropogenic sound, since there is no way to determine whether the disturbance is impacting the species’ physical or environmental requirements. Here we take a bioenergetics approach to address this gap in our knowledge, as the elusive, deep-diving nature of beaked whales has made it hard to study these effects directly. We develop a model for Ziphiidae linking feeding energetics to the species’ requirements for survival and reproduction, since these life history traits would be the most likely to be impacted by non-lethal disturbances. Our models suggest that beaked whale reproduction requires energy dense prey, and that poor resource availability would lead to an extension of the inter-calving interval. Further, given current information, it seems that some beaked whale species require relatively high quality habitat in order to meet their requirements for survival and reproduction. As a result, even a small non-lethal disturbance that results in displacement of whales from preferred habitats could potentially impact a population if a significant proportion of that population was affected. We explored the impact of varying ecological parameters and model assumptions on survival and reproduction, and find that calf and fetus survival appear more readily affected than the survival of adult females.
2013-07-17T00:00:00ZNew, Leslie FrancesMoretti, DavidHooker, Sascha KateCosta, Daniel P.Simmons, Samantha E.Mass stranding of several species of beaked whales (family Ziphiidae) associated with exposure to anthropogenic sounds has raised concern for the conservation of these species. However, little is known about the species’ life histories, prey or habitat requirements. Without this knowledge, it becomes difficult to assess the effects of anthropogenic sound, since there is no way to determine whether the disturbance is impacting the species’ physical or environmental requirements. Here we take a bioenergetics approach to address this gap in our knowledge, as the elusive, deep-diving nature of beaked whales has made it hard to study these effects directly. We develop a model for Ziphiidae linking feeding energetics to the species’ requirements for survival and reproduction, since these life history traits would be the most likely to be impacted by non-lethal disturbances. Our models suggest that beaked whale reproduction requires energy dense prey, and that poor resource availability would lead to an extension of the inter-calving interval. Further, given current information, it seems that some beaked whale species require relatively high quality habitat in order to meet their requirements for survival and reproduction. As a result, even a small non-lethal disturbance that results in displacement of whales from preferred habitats could potentially impact a population if a significant proportion of that population was affected. We explored the impact of varying ecological parameters and model assumptions on survival and reproduction, and find that calf and fetus survival appear more readily affected than the survival of adult females.Spatial models for distance sampling data : recent developments and future directionsMiller, David LawrenceBurt, M LouiseRexstad, EricThomas, Lenhttp://hdl.handle.net/10023/40462017-06-04T00:30:47Z2013-11-01T00:00:00ZOur understanding of a biological population can be greatly enhanced by modelling their distribution in space and as a function of environmental covariates. Density surface models consist of a spatial model of the abundance of a biological population which has been corrected for uncertain detection via distance sampling methods. We offer a comparison of recent advances in the field and consider the likely directions of future research. In particular we consider spatial modelling techniques that may be advantageous to applied ecologists such as quantification of uncertainty in a two-stage model and smoothing in areas with complex boundaries. The methods discussed are available in an \textsf{R} package developed by the authors and are largely implemented in the popular Windows package Distance (or are soon to be incorporated). Density surface modelling enables applied ecologists to reliably estimate abundances and create maps of animal/plant distribution. Such models can also be used to investigate the relationships between distribution and environmental covariates.
2013-11-01T00:00:00ZMiller, David LawrenceBurt, M LouiseRexstad, EricThomas, LenOur understanding of a biological population can be greatly enhanced by modelling their distribution in space and as a function of environmental covariates. Density surface models consist of a spatial model of the abundance of a biological population which has been corrected for uncertain detection via distance sampling methods. We offer a comparison of recent advances in the field and consider the likely directions of future research. In particular we consider spatial modelling techniques that may be advantageous to applied ecologists such as quantification of uncertainty in a two-stage model and smoothing in areas with complex boundaries. The methods discussed are available in an \textsf{R} package developed by the authors and are largely implemented in the popular Windows package Distance (or are soon to be incorporated). Density surface modelling enables applied ecologists to reliably estimate abundances and create maps of animal/plant distribution. Such models can also be used to investigate the relationships between distribution and environmental covariates.Estimating resource acquisition and at-sea body condition of a marine predatorSchick, Robert SchillingNew, LeslieThomas, LenCosta, DanielHindell, MarkMcMahon, CliveRobinson, PatrickSimmons, SamanthaThums, MicheleHarwood, JohnClark, Jameshttp://hdl.handle.net/10023/38672017-04-25T07:51:21Z2013-01-01T00:00:00Z(1) Body condition plays a fundamental role in many ecological and evolutionary processes at a variety of scales and across a broad range of animal taxa. An understanding of how body condition changes at fine spatial and temporal scales as a result of interaction with the environment provides necessary information about how animals acquire resources. (2) However, comparatively little is known about intra- and interindividual variation of condition in marine systems. Where condition has been studied, changes typically are recorded at relatively coarse time-scales. By quantifying how fine-scale interaction with the environment influences condition, we can broaden our understanding of how animals acquire resources and allocate them to body stores. (3) Here we used a hierarchical Bayesian state-space model to estimate the body condition as measured by the size of an animal's lipid store in two closely related species of marine predator that occupy different hemispheres: northern elephant seals (Mirounga angustirostris) and southern elephant seals (Mirounga leonina). The observation model linked drift dives to lipid stores. The process model quantified daily changes in lipid stores as a function of the physiological condition of the seal (lipid:lean tissue ratio, departure lipid and departure mass), its foraging location, two measures of behaviour and environmental covariates. (4) We found that physiological condition significantly impacted lipid gain at two time-scales – daily and at departure from the colony – that foraging location was significantly associated with lipid gain in both species of elephant seals and that long-term behavioural phase was associated with positive lipid gain in northern and southern elephant seals. In northern elephant seals, the occurrence of short-term behavioural states assumed to represent foraging were correlated with lipid gain. Lipid gain was a function of covariates in both species. Southern elephant seals performed fewer drift dives than northern elephant seals and gained lipids at a lower rate. (5) We have demonstrated a new way to obtain time series of body condition estimates for a marine predator at fine spatial and temporal scales. This modelling approach accounts for uncertainty at many levels and has the potential to integrate physiological and movement ecology of top predators. The observation model we used was specific to elephant seals, but the process model can readily be applied to other species, providing an opportunity to understand how animals respond to their environment at a fine spatial scale.
This article was made open access through BIS OA funding.
2013-01-01T00:00:00ZSchick, Robert SchillingNew, LeslieThomas, LenCosta, DanielHindell, MarkMcMahon, CliveRobinson, PatrickSimmons, SamanthaThums, MicheleHarwood, JohnClark, James(1) Body condition plays a fundamental role in many ecological and evolutionary processes at a variety of scales and across a broad range of animal taxa. An understanding of how body condition changes at fine spatial and temporal scales as a result of interaction with the environment provides necessary information about how animals acquire resources. (2) However, comparatively little is known about intra- and interindividual variation of condition in marine systems. Where condition has been studied, changes typically are recorded at relatively coarse time-scales. By quantifying how fine-scale interaction with the environment influences condition, we can broaden our understanding of how animals acquire resources and allocate them to body stores. (3) Here we used a hierarchical Bayesian state-space model to estimate the body condition as measured by the size of an animal's lipid store in two closely related species of marine predator that occupy different hemispheres: northern elephant seals (Mirounga angustirostris) and southern elephant seals (Mirounga leonina). The observation model linked drift dives to lipid stores. The process model quantified daily changes in lipid stores as a function of the physiological condition of the seal (lipid:lean tissue ratio, departure lipid and departure mass), its foraging location, two measures of behaviour and environmental covariates. (4) We found that physiological condition significantly impacted lipid gain at two time-scales – daily and at departure from the colony – that foraging location was significantly associated with lipid gain in both species of elephant seals and that long-term behavioural phase was associated with positive lipid gain in northern and southern elephant seals. In northern elephant seals, the occurrence of short-term behavioural states assumed to represent foraging were correlated with lipid gain. Lipid gain was a function of covariates in both species. Southern elephant seals performed fewer drift dives than northern elephant seals and gained lipids at a lower rate. (5) We have demonstrated a new way to obtain time series of body condition estimates for a marine predator at fine spatial and temporal scales. This modelling approach accounts for uncertainty at many levels and has the potential to integrate physiological and movement ecology of top predators. The observation model we used was specific to elephant seals, but the process model can readily be applied to other species, providing an opportunity to understand how animals respond to their environment at a fine spatial scale.Evidence for density-dependent changes in body condition and pregnancy rate of North Atlantic fin whales over four decades of varying environmental conditionsWilliams, RobertVikingsson, Gisli A.Gislason, AstthorLockyer, ChristinaNew, LeslieThomas, LenHammond, Philip Stevenhttp://hdl.handle.net/10023/38542017-06-11T00:31:23Z2013-03-01T00:00:00ZA central theme in ecology is the search for pattern in the response of a species to changing environmental conditions. Natural resource management and endangered species conservation require an understanding of density-dependent and density-independent factors that regulate populations. Marine mammal populations are expected to express density dependence in the same way as terrestrial mammals, but logistical difficulties in data acquisition for many large whale species have hindered attempts to identify population-regulation mechanisms. We explored relationships between body condition (inferred from patterns in blubber thickness) and per capita prey abundance, and between pregnancy rate and body condition in North Atlantic fin whales as environmental conditions and population size varied between 1967 and 2010. Blubber thickness in both males and females declined at low per capita prey availability, and in breeding-age females, pregnancy rate declined at low blubber thickness, demonstrating a density-dependent response of pregnancy to prey limitation mediated through body condition. To the best of our knowledge, this is the first time a quantitative relationship among per capita prey abundance, body condition, and pregnancy rate has been documented for whales. As long-lived predators, marine mammals can act as indicators of the state of marine ecosystems. Improving our understanding of the relationships that link prey, body condition, and population parameters such as pregnancy rate and survival will become increasingly useful as these systems are affected by natural and anthropogenic change. Quantifying linkages among prey, fitness and vital rates will improve our ability to predict population consequences of subtle, sublethal impacts of ocean noise and other anthropogenic stressors.
2013-03-01T00:00:00ZWilliams, RobertVikingsson, Gisli A.Gislason, AstthorLockyer, ChristinaNew, LeslieThomas, LenHammond, Philip StevenA central theme in ecology is the search for pattern in the response of a species to changing environmental conditions. Natural resource management and endangered species conservation require an understanding of density-dependent and density-independent factors that regulate populations. Marine mammal populations are expected to express density dependence in the same way as terrestrial mammals, but logistical difficulties in data acquisition for many large whale species have hindered attempts to identify population-regulation mechanisms. We explored relationships between body condition (inferred from patterns in blubber thickness) and per capita prey abundance, and between pregnancy rate and body condition in North Atlantic fin whales as environmental conditions and population size varied between 1967 and 2010. Blubber thickness in both males and females declined at low per capita prey availability, and in breeding-age females, pregnancy rate declined at low blubber thickness, demonstrating a density-dependent response of pregnancy to prey limitation mediated through body condition. To the best of our knowledge, this is the first time a quantitative relationship among per capita prey abundance, body condition, and pregnancy rate has been documented for whales. As long-lived predators, marine mammals can act as indicators of the state of marine ecosystems. Improving our understanding of the relationships that link prey, body condition, and population parameters such as pregnancy rate and survival will become increasingly useful as these systems are affected by natural and anthropogenic change. Quantifying linkages among prey, fitness and vital rates will improve our ability to predict population consequences of subtle, sublethal impacts of ocean noise and other anthropogenic stressors.First direct measurements of behavioural responses by Cuvier's beaked whales to mid-frequency active sonarDe Ruiter, Stacy LynnSouthall, Brandon L.Calambokidis, JohnZimmer, Walter M. X.Sadykova, DinaraFalcone, Erin A.Friedlaender, Ari S.Joseph, John E.Moretti, DavidSchorr, Gregory S.Thomas, LenTyack, Peter Lloydhttp://hdl.handle.net/10023/38362017-06-18T00:31:42Z2013-01-01T00:00:00ZMost marine mammal strandings coincident with naval sonar exercises have involved Cuvier's beaked whales (Ziphius cavirostris). We recorded animal movement and acoustic data on two tagged Ziphius and obtained the first direct measurements of behavioural responses of this species to mid-frequency active (MFA) sonar signals. Each recording included a 30-min playback (one 1.6-s simulated MFA sonar signal repeated every 25 s); one whale was also incidentally exposed to MFA sonar from distant naval exercises. Whales responded strongly to playbacks at low received levels (RLs; 89–127 dB re 1 µPa): after ceasing normal fluking and echolocation, they swam rapidly, silently away, extending both dive duration and subsequent non-foraging interval. Distant sonar exercises (78–106 dB re 1 µPa) did not elicit such responses, suggesting that context may moderate reactions. The observed responses to playback occurred at RLs well below current regulatory thresholds; equivalent responses to operational sonars could elevate stranding risk and reduce foraging efficiency.
2013-01-01T00:00:00ZDe Ruiter, Stacy LynnSouthall, Brandon L.Calambokidis, JohnZimmer, Walter M. X.Sadykova, DinaraFalcone, Erin A.Friedlaender, Ari S.Joseph, John E.Moretti, DavidSchorr, Gregory S.Thomas, LenTyack, Peter LloydMost marine mammal strandings coincident with naval sonar exercises have involved Cuvier's beaked whales (Ziphius cavirostris). We recorded animal movement and acoustic data on two tagged Ziphius and obtained the first direct measurements of behavioural responses of this species to mid-frequency active (MFA) sonar signals. Each recording included a 30-min playback (one 1.6-s simulated MFA sonar signal repeated every 25 s); one whale was also incidentally exposed to MFA sonar from distant naval exercises. Whales responded strongly to playbacks at low received levels (RLs; 89–127 dB re 1 µPa): after ceasing normal fluking and echolocation, they swam rapidly, silently away, extending both dive duration and subsequent non-foraging interval. Distant sonar exercises (78–106 dB re 1 µPa) did not elicit such responses, suggesting that context may moderate reactions. The observed responses to playback occurred at RLs well below current regulatory thresholds; equivalent responses to operational sonars could elevate stranding risk and reduce foraging efficiency.Estimating animal population density using passive acousticsMarques, Tiago A.Thomas, LenMartin, StephenMellinger, DavidWard, JessicaMoretti, DavidHarris, Danielle VeronicaTyack, Peter Lloydhttp://hdl.handle.net/10023/34962017-06-18T00:31:19Z2013-05-01T00:00:00ZReliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture-recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast-developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics-based density estimation, illustrated with examples from real-world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic-based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture-recapture. The methods are also applicable to other aquatic and terrestrial sound-producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented here
2013-05-01T00:00:00ZMarques, Tiago A.Thomas, LenMartin, StephenMellinger, DavidWard, JessicaMoretti, DavidHarris, Danielle VeronicaTyack, Peter LloydReliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture-recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast-developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics-based density estimation, illustrated with examples from real-world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic-based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture-recapture. The methods are also applicable to other aquatic and terrestrial sound-producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented hereDecomposition tables for experiments : II. Two–one randomizationsBrien, C. J.Bailey, Rosemary Annehttp://hdl.handle.net/10023/34792017-04-25T07:51:10Z2010-10-01T00:00:00ZWe investigate structure for pairs of randomizations that do not follow each other in a chain. These are unrandomized-inclusive, independent, coincident or double randomizations. This involves taking several structures that satisfy particular relations and combining them to form the appropriate orthogonal decomposition of the data space for the experiment. We show how to establish the decomposition table giving the sources of variation, their relationships and their degrees of freedom, so that competing designs can be evaluated. This leads to recommendations for when the different types of multiple randomization should be used.
2010-10-01T00:00:00ZBrien, C. J.Bailey, Rosemary AnneWe investigate structure for pairs of randomizations that do not follow each other in a chain. These are unrandomized-inclusive, independent, coincident or double randomizations. This involves taking several structures that satisfy particular relations and combining them to form the appropriate orthogonal decomposition of the data space for the experiment. We show how to establish the decomposition table giving the sources of variation, their relationships and their degrees of freedom, so that competing designs can be evaluated. This leads to recommendations for when the different types of multiple randomization should be used.Decomposition tables for experiments : I. A chain of randomizationsBrien, C. J.Bailey, Rosemary Annehttp://hdl.handle.net/10023/34782017-04-25T07:51:09Z2009-12-01T00:00:00ZOne aspect of evaluating the design for an experiment is the discovery of the relationships between subspaces of the data space. Initially we establish the notation and methods for evaluating an experiment with a single randomization. Starting with two structures, or orthogonal decompositions of the data space, we describe how to combine them to form the overall decomposition for a single-randomization experiment that is "structure balanced." The relationships between the two structures are characterized using efficiency factors. The decomposition is encapsulated in a decomposition table. Then, for experiments that involve multiple randomizations forming a chain, we take several structures that pairwise are structure balanced and combine them to establish the form of the orthogonal decomposition for the experiment. In particular, it is proven that the properties of the design for Such an experiment are derived in a straightforward manner from those of the individual designs. We show how to formulate an extended decomposition table giving the sources of variation, their relationships and their degrees of freedom, so that competing designs can be evaluated.
2009-12-01T00:00:00ZBrien, C. J.Bailey, Rosemary AnneOne aspect of evaluating the design for an experiment is the discovery of the relationships between subspaces of the data space. Initially we establish the notation and methods for evaluating an experiment with a single randomization. Starting with two structures, or orthogonal decompositions of the data space, we describe how to combine them to form the overall decomposition for a single-randomization experiment that is "structure balanced." The relationships between the two structures are characterized using efficiency factors. The decomposition is encapsulated in a decomposition table. Then, for experiments that involve multiple randomizations forming a chain, we take several structures that pairwise are structure balanced and combine them to establish the form of the orthogonal decomposition for the experiment. In particular, it is proven that the properties of the design for Such an experiment are derived in a straightforward manner from those of the individual designs. We show how to formulate an extended decomposition table giving the sources of variation, their relationships and their degrees of freedom, so that competing designs can be evaluated.Workshop on new developments in cetacean survey methodsBorchers, David LouisThomas, LenBuckland, Stephen TerrenceSkaug, HansBarlow, Jayhttp://hdl.handle.net/10023/32162017-04-01T23:44:00Z2011-01-01T00:00:00ZThis report contains the slides from a workshop on New Developments in Cetacean Survey Methods held on 27th November 2011 at the 19th Biennial Conference on the Biology of Marine Mammals, Tampa, Florida. Review talks were given on Passive Acoustic Density Estimation (Len Thomas); Dealing with g(0)<1: Perception Bias (Stephen Buckland); Dealing with g(0)<1: Availability Bias (Hans Skaug); Dealing with Measurement Error (David Borchers); and Density Surface Modelling (Jay Barlow). The sessions were followed by a discussion, and this is summarized at the end of the report.
2011-01-01T00:00:00ZBorchers, David LouisThomas, LenBuckland, Stephen TerrenceSkaug, HansBarlow, JayThis report contains the slides from a workshop on New Developments in Cetacean Survey Methods held on 27th November 2011 at the 19th Biennial Conference on the Biology of Marine Mammals, Tampa, Florida. Review talks were given on Passive Acoustic Density Estimation (Len Thomas); Dealing with g(0)<1: Perception Bias (Stephen Buckland); Dealing with g(0)<1: Availability Bias (Hans Skaug); Dealing with Measurement Error (David Borchers); and Density Surface Modelling (Jay Barlow). The sessions were followed by a discussion, and this is summarized at the end of the report.Vessel noise affects beaked whale behavior : Results of a dedicated acoustic response studyPirotta, EnricoMilor, RachelQuick, Nicola JaneMoretti, DavidDimarzio, NancyTyack, Peter LloydBoyd, IanHastie, Gordon Drummondhttp://hdl.handle.net/10023/30782017-04-30T04:30:19Z2012-08-03T00:00:00ZSome beaked whale species are susceptible to the detrimental effects of anthropogenic noise. Most studies have concentrated on the effects of military sonar, but other forms of acoustic disturbance (e.g. shipping noise) may disrupt behavior. An experiment involving the exposure of target whale groups to intense vessel-generated noise tested how these exposures influenced the foraging behavior of Blainville’s beaked whales (Mesoplodon densirostris) in the Tongue of the Ocean (Bahamas). A military array of bottom-mounted hydrophones was used to measure the response based upon changes in the spatial and temporal pattern of vocalizations. The archived acoustic data were used to compute metrics the echolocation-based foraging behavior for 16 targeted groups, 10 groups further away on the range, and 26 nonexposed groups. The duration of foraging bouts was not significantly affected by the exposure. Changes in the hydrophone over which the group was most frequently detected occurred as the animals moved around within a foraging bout, and their number was significantly less the closer the whales were to the sound source. Non-exposed groups also had significantly more changes in the primary hydrophone than exposed groups irrespective of distance. Our results suggested that broadband ship noise caused a significant change in beaked whale behavior up to at least 5.2 kilometers away from the vessel. The observed change could potentially correspond to a restriction in the movement of groups, a period of more directional travel, a reduction in the number of individuals clicking within the group, or a response to changes in prey movement.
2012-08-03T00:00:00ZPirotta, EnricoMilor, RachelQuick, Nicola JaneMoretti, DavidDimarzio, NancyTyack, Peter LloydBoyd, IanHastie, Gordon DrummondSome beaked whale species are susceptible to the detrimental effects of anthropogenic noise. Most studies have concentrated on the effects of military sonar, but other forms of acoustic disturbance (e.g. shipping noise) may disrupt behavior. An experiment involving the exposure of target whale groups to intense vessel-generated noise tested how these exposures influenced the foraging behavior of Blainville’s beaked whales (Mesoplodon densirostris) in the Tongue of the Ocean (Bahamas). A military array of bottom-mounted hydrophones was used to measure the response based upon changes in the spatial and temporal pattern of vocalizations. The archived acoustic data were used to compute metrics the echolocation-based foraging behavior for 16 targeted groups, 10 groups further away on the range, and 26 nonexposed groups. The duration of foraging bouts was not significantly affected by the exposure. Changes in the hydrophone over which the group was most frequently detected occurred as the animals moved around within a foraging bout, and their number was significantly less the closer the whales were to the sound source. Non-exposed groups also had significantly more changes in the primary hydrophone than exposed groups irrespective of distance. Our results suggested that broadband ship noise caused a significant change in beaked whale behavior up to at least 5.2 kilometers away from the vessel. The observed change could potentially correspond to a restriction in the movement of groups, a period of more directional travel, a reduction in the number of individuals clicking within the group, or a response to changes in prey movement.Global analysis of cetacean line-transect surveys : detecting trends in cetacean densityJewell, Rebecca LucyThomas, LenHarris, Catriona MKaschner, KristinWiff, Rodrigo AlexisHammond, Philip StevenQuick, Nicola Janehttp://hdl.handle.net/10023/27472017-04-25T07:45:35Z2012-05-07T00:00:00ZMeasuring the effect of anthropogenic change on cetacean populations is hampered by our lack of understanding about population status and a lack of power in the available data to detect trends in abundance. Often long-term data from repeated surveys are lacking, and alternative approaches to trend detection must be considered. We utilised an existing database of line transect survey records to determine whether temporal trends could be detected when survey effort from around the world was combined. We extracted density estimates for 25 species and fitted generalised additive models (GAMs) to investigate whether taxonomic, spatial or methodological differences among systematic line-transect surveys affect estimates of density and whether we can identify temporal trends in the data once these factors are accounted for. The selected GAM consisted of 2 parts: an intercept term that was a complex interaction of taxonomic, spatial and methodological factors and a smooth temporal term with trends varying by family and ocean basin. We discuss the trends found and assess the suitability of published density estimates for detecting temporal trends using retrospective power analysis. In conclusion, increasing sample size through combining survey effort across a global scale does not necessarily result in sufficient power to detect trends because of the extent of variability across surveys, species and oceans. Instead, results from repeated dedicated surveys designed specifically for the species and geographical region of interest should be used to inform conservation and management.
2012-05-07T00:00:00ZJewell, Rebecca LucyThomas, LenHarris, Catriona MKaschner, KristinWiff, Rodrigo AlexisHammond, Philip StevenQuick, Nicola JaneMeasuring the effect of anthropogenic change on cetacean populations is hampered by our lack of understanding about population status and a lack of power in the available data to detect trends in abundance. Often long-term data from repeated surveys are lacking, and alternative approaches to trend detection must be considered. We utilised an existing database of line transect survey records to determine whether temporal trends could be detected when survey effort from around the world was combined. We extracted density estimates for 25 species and fitted generalised additive models (GAMs) to investigate whether taxonomic, spatial or methodological differences among systematic line-transect surveys affect estimates of density and whether we can identify temporal trends in the data once these factors are accounted for. The selected GAM consisted of 2 parts: an intercept term that was a complex interaction of taxonomic, spatial and methodological factors and a smooth temporal term with trends varying by family and ocean basin. We discuss the trends found and assess the suitability of published density estimates for detecting temporal trends using retrospective power analysis. In conclusion, increasing sample size through combining survey effort across a global scale does not necessarily result in sufficient power to detect trends because of the extent of variability across surveys, species and oceans. Instead, results from repeated dedicated surveys designed specifically for the species and geographical region of interest should be used to inform conservation and management.A critical review of the literature on population modellingCabrelli, AbigailHarwood, JohnMatthiopoulos, JasonNew, Leslie FrancesThomas, Lenhttp://hdl.handle.net/10023/22412017-04-01T23:43:51Z2009-01-01T00:00:00ZThe 2005 report of the National Research Council’s ‘Committee on Characterizing Biologically Significant Marine Mammal Behavior’ proposed a framework, which they called PCAD - Population Consequences of Acoustic Disturbance, that uses a series of transfer functions to link behavioural responses to sound with life functions, vital rates, and population change. The Committee suggested that the best understood transfer functions are those linking vital rates to population change. One of the main aims of this report is to document that understanding. However, we also show how the existing frameworks for modelling the dynamics of marine mammal populations can be extended to include the effects of behavioural responses on vital rates. In Chapter 1 we introduce the central concept of the rate of increase (lambda) of a population, which we believe is the most useful measure of the effects of behavioural responses on the dynamics of a population. If the value of lambda exceeds one, then thepopulation will increase over time; if it is less than one it will decrease. We show how changes in lambda provide a measure of the impact of human activities (such as exploitation, conservation, or disturbance) on a population. We also introduce structured population models, which take account of the fact that all individuals in a population are not identical, and show how the dynamics of different parts of a population can be modelled using a population projection matrix. The mathematical properties of this projection matrix can be used to determine the sensitivity of lambda to small changes in vital rates. Finally, we provide a very brief introduction to the concept of stochasticity, and the use of lambda to predict when (and if) a population might be driven to extinction. Chapter 2 describes how lambda also provides a measure of the Darwinian fitness of the individual members of a population. An individual’s fitness, the contribution it will make to future generations, depends to a large extent on its body condition and on the risks of mortality to which it is exposed. Both of these could be affected by behaviour responses to sound. We also explain current theories about the relationship between an individual’s feeding behaviour and the abundance and distribution of prey, and how this can affect body condition. Chapter 3 provides a more detailed description of how elasticity analysis can be used to investigate the impact of changes in vital rates on lambda . Elasticity analysis is a useful tool for detecting which vital rates are most important in determining the dynamics of a population. However, its value is limited because it does not take account of random variations (stochasticity) and, in theory, it can only predict the effect of small changes in vital rates. Chapter 4 describes the fundamental concept of density dependence: the way in which vital rates change with population size or the availability of resources, such as prey. Not only is density dependence an essential prerequisite for population stability and sustainable use, but the form it takes will also determine how a population responds to behavioural changes. This is because behaviour, and particularly the effect of behavioural change on body condition, plays a central role in many of the mechanistic models of density dependence. Chapters 5 and 6 explore the way in which additional complexities, such as social structure and the way in which populations are distributed in space, can affect the dynamics of populations. Models that account for these complexities behave in a much less predictable way than the relatively simple structured models that form the core of Chapters 1-4. So far, the models of population dynamics that we have reviewed have been deterministic. That is, they have assumed that the only way in which vital rates can vary is in response to a change in abundance, via density dependent mechanisms. In Chapters 7 and 8 we investigate the effect of random variation (stochasticity) on population dynamics. We distinguish the effects of demographic stochasticity, chance variations in the number of animals that die or give birth in a time interval that occur even if vital rates do not vary over time, and environmental stochasticity, which is the result of variations in vital rates across years. Variation in abundance may also occur as a result of environmental change and changes in the ecological community of which a population is a part. The effect of all these sources of variation is to reduce the realised growth rate of a population, and therefore its risk of extinction. In Chapter 9 we consider how the basic population modelling framework described in Chapters 1-8 might be extended to take account of the life functions identified by the NRC Committee. We suggest that these life functions are useful for defining the context in which behavioural responses might affect vital rates, but that they do not need to be modelled explicitly. Removing vital functions from the PCAD framework results in a much simpler structure, which is compatible with existing population modelling frameworks. However, these will have to be extended to allow population states, like body condition, that vary continuously to be modelled. Chapter 10 describes how changes in lambda can be detected. The simple analytical frameworks that are available for this are all vulnerable to the effects of variability that we introduced in Chapter 7. However, there is a framework (state-space and hidden Markov process modelling) that can account for the effects of this variability, and we recommend its use for detecting trends. The additional benefit of this approach is that its use results in a detailed model of the dynamics of the population that is under investigation. Chapter 11 reviews the different model structures that can be used to describe the dynamics of a population, and explains when different forms of population models (e.g. discrete vs. continuous time, deterministic vs. stochastic) are most appropriate. We also discuss how these different frameworks can be extended to account for continuous population states, as recommended in Chapter 8. The final focus is on how state-space models can be fitted to time series of abundance estimates and information on vital rates. Chapter 12 looks at the relevance of the different modelling approaches described in the previous chapters for analysing the potential effects of behavioural responses to sound on population dynamics, particularly the kinds of sounds that may be generated by the oil and gas industry. We conclude that lambda , the population rate of increase, and its variation provides a useful measure of these effects. We also believe that the models used for this purpose will certainly have to account for the effects of variability and density dependence. They will probably also have to account for the effects of social structure and the way in which populations use space. The state-space modelling framework outlined in Chapter 11 can, in principle, be extended to capture all of these features although work on this is still in its infancy.
Final Report to the Joint Industry Project of the International Association of Oil & Gas Producers on contract JIP22 07_20
2009-01-01T00:00:00ZCabrelli, AbigailHarwood, JohnMatthiopoulos, JasonNew, Leslie FrancesThomas, LenThe 2005 report of the National Research Council’s ‘Committee on Characterizing Biologically Significant Marine Mammal Behavior’ proposed a framework, which they called PCAD - Population Consequences of Acoustic Disturbance, that uses a series of transfer functions to link behavioural responses to sound with life functions, vital rates, and population change. The Committee suggested that the best understood transfer functions are those linking vital rates to population change. One of the main aims of this report is to document that understanding. However, we also show how the existing frameworks for modelling the dynamics of marine mammal populations can be extended to include the effects of behavioural responses on vital rates. In Chapter 1 we introduce the central concept of the rate of increase (lambda) of a population, which we believe is the most useful measure of the effects of behavioural responses on the dynamics of a population. If the value of lambda exceeds one, then thepopulation will increase over time; if it is less than one it will decrease. We show how changes in lambda provide a measure of the impact of human activities (such as exploitation, conservation, or disturbance) on a population. We also introduce structured population models, which take account of the fact that all individuals in a population are not identical, and show how the dynamics of different parts of a population can be modelled using a population projection matrix. The mathematical properties of this projection matrix can be used to determine the sensitivity of lambda to small changes in vital rates. Finally, we provide a very brief introduction to the concept of stochasticity, and the use of lambda to predict when (and if) a population might be driven to extinction. Chapter 2 describes how lambda also provides a measure of the Darwinian fitness of the individual members of a population. An individual’s fitness, the contribution it will make to future generations, depends to a large extent on its body condition and on the risks of mortality to which it is exposed. Both of these could be affected by behaviour responses to sound. We also explain current theories about the relationship between an individual’s feeding behaviour and the abundance and distribution of prey, and how this can affect body condition. Chapter 3 provides a more detailed description of how elasticity analysis can be used to investigate the impact of changes in vital rates on lambda . Elasticity analysis is a useful tool for detecting which vital rates are most important in determining the dynamics of a population. However, its value is limited because it does not take account of random variations (stochasticity) and, in theory, it can only predict the effect of small changes in vital rates. Chapter 4 describes the fundamental concept of density dependence: the way in which vital rates change with population size or the availability of resources, such as prey. Not only is density dependence an essential prerequisite for population stability and sustainable use, but the form it takes will also determine how a population responds to behavioural changes. This is because behaviour, and particularly the effect of behavioural change on body condition, plays a central role in many of the mechanistic models of density dependence. Chapters 5 and 6 explore the way in which additional complexities, such as social structure and the way in which populations are distributed in space, can affect the dynamics of populations. Models that account for these complexities behave in a much less predictable way than the relatively simple structured models that form the core of Chapters 1-4. So far, the models of population dynamics that we have reviewed have been deterministic. That is, they have assumed that the only way in which vital rates can vary is in response to a change in abundance, via density dependent mechanisms. In Chapters 7 and 8 we investigate the effect of random variation (stochasticity) on population dynamics. We distinguish the effects of demographic stochasticity, chance variations in the number of animals that die or give birth in a time interval that occur even if vital rates do not vary over time, and environmental stochasticity, which is the result of variations in vital rates across years. Variation in abundance may also occur as a result of environmental change and changes in the ecological community of which a population is a part. The effect of all these sources of variation is to reduce the realised growth rate of a population, and therefore its risk of extinction. In Chapter 9 we consider how the basic population modelling framework described in Chapters 1-8 might be extended to take account of the life functions identified by the NRC Committee. We suggest that these life functions are useful for defining the context in which behavioural responses might affect vital rates, but that they do not need to be modelled explicitly. Removing vital functions from the PCAD framework results in a much simpler structure, which is compatible with existing population modelling frameworks. However, these will have to be extended to allow population states, like body condition, that vary continuously to be modelled. Chapter 10 describes how changes in lambda can be detected. The simple analytical frameworks that are available for this are all vulnerable to the effects of variability that we introduced in Chapter 7. However, there is a framework (state-space and hidden Markov process modelling) that can account for the effects of this variability, and we recommend its use for detecting trends. The additional benefit of this approach is that its use results in a detailed model of the dynamics of the population that is under investigation. Chapter 11 reviews the different model structures that can be used to describe the dynamics of a population, and explains when different forms of population models (e.g. discrete vs. continuous time, deterministic vs. stochastic) are most appropriate. We also discuss how these different frameworks can be extended to account for continuous population states, as recommended in Chapter 8. The final focus is on how state-space models can be fitted to time series of abundance estimates and information on vital rates. Chapter 12 looks at the relevance of the different modelling approaches described in the previous chapters for analysing the potential effects of behavioural responses to sound on population dynamics, particularly the kinds of sounds that may be generated by the oil and gas industry. We conclude that lambda , the population rate of increase, and its variation provides a useful measure of these effects. We also believe that the models used for this purpose will certainly have to account for the effects of variability and density dependence. They will probably also have to account for the effects of social structure and the way in which populations use space. The state-space modelling framework outlined in Chapter 11 can, in principle, be extended to capture all of these features although work on this is still in its infancy.An update to the methods in Endangered Species Research 2011 paper "Estimating North Pacific right whale Eubalaena japonica density using passive acoustic cue counting"Marques, Tiago A.Munger, LisaThomas, LenWiggins, SeanHildebrand, Johnhttp://hdl.handle.net/10023/21582017-04-01T23:43:50Z2012-01-01T00:00:00Z2012-01-01T00:00:00ZMarques, Tiago A.Munger, LisaThomas, LenWiggins, SeanHildebrand, JohnComplex Region Spatial Smoother (CReSS)Scott Hayward, Lindesay Alexandra SarahMacKenzie, Monique LeaDonovan, Carl RobertWalker, CameronAshe, Erinhttp://hdl.handle.net/10023/20482017-04-01T23:43:34Z2011-01-01T00:00:00ZConventional smoothing over complicated coastal and island regions may result in errors across boundaries, due to the use of Euclidean distances to represent inter-point similarity. The new Complex Region Spatial Smoother (CReSS) method presented here, uses estimated geodesic distances, model averaging and a local radial basis function to provide improved smoothing over complex domains. CReSS is compared, via simulation, to recent related smoothing techniques, Thin Plate Splines (TPS, Harder and Desmarais, 1972), geodesic low rank TPS [Wang and Ranalli, 2007] and the Soap film smoother [Wood et al., 2008]. The GLTPS method cannot be used in areas with islands and SOAP can be hard to parameterize. CReSS is comparable with, if not better than, all considered methods on a range of simulations. Supplementary materials for this article are available online.
This work is supported with funding from NERC UK
2011-01-01T00:00:00ZScott Hayward, Lindesay Alexandra SarahMacKenzie, Monique LeaDonovan, Carl RobertWalker, CameronAshe, ErinConventional smoothing over complicated coastal and island regions may result in errors across boundaries, due to the use of Euclidean distances to represent inter-point similarity. The new Complex Region Spatial Smoother (CReSS) method presented here, uses estimated geodesic distances, model averaging and a local radial basis function to provide improved smoothing over complex domains. CReSS is compared, via simulation, to recent related smoothing techniques, Thin Plate Splines (TPS, Harder and Desmarais, 1972), geodesic low rank TPS [Wang and Ranalli, 2007] and the Soap film smoother [Wood et al., 2008]. The GLTPS method cannot be used in areas with islands and SOAP can be hard to parameterize. CReSS is comparable with, if not better than, all considered methods on a range of simulations. Supplementary materials for this article are available online.Distance software: design and analysis of distance sampling surveys for estimating population sizeThomas, LenBuckland, Stephen TerrenceRexstad, EricLaake, J LStrindberg, SHedley, S LBishop, J R BMarques, Tiago Andre Lamas Oliveirahttp://hdl.handle.net/10023/8172016-03-28T10:57:17Z2010-01-01T00:00:00Z1. Distance sampling is a widely used technique for estimating the size or density of biological populations. Many distance sampling designs and most analyses use the software Distance. 2. We briefly review distance sampling and its assumptions, outline the history, structure and capabilities of Distance, and provide hints on its use. 3. Good survey design is a crucial pre-requisite for obtaining reliable results. Distance has a survey design engine, with a built-in geographic information system, that allows properties of different proposed designs to be examined via simulation, and survey plans to be generated. 4. A first step in analysis of distance sampling data is modelling the probability of detection. Distance contains three increasingly sophisticated analysis engines for this: CDS (conventional distance sampling), which models detection probability as a function of distance from the transect and assumes all objects at zero distance are detected; MCDS (multiple covariate distance sampling), which allows covariates in addition to distance; and MRDS (mark-recapture distance sampling), which relaxes the assumption of certain detection at zero distance. 5. All three engines allow estimation of density or abundance, stratified if required, with associated measures of precision calculated either analytically or via the bootstrap. 6. Advanced analysis topics covered include the use of multipliers to allow analysis of indirect surveys (such as dung or nest surveys), the DSM (density surface modelling) analysis engine for spatial and habitat modelling, and information about accessing the analysis engines directly from other software. 7. Synthesis and applications. Distance sampling is a key method for producing abundance and density estimates in challenging field conditions. The theory underlying the methods continues to expand to cope with realistic estimation situations. In step with theoretical developments, state-of-the-art software that implements these methods is described that makes the methods accessible to practicing ecologists.
2010-01-01T00:00:00ZThomas, LenBuckland, Stephen TerrenceRexstad, EricLaake, J LStrindberg, SHedley, S LBishop, J R BMarques, Tiago Andre Lamas Oliveira1. Distance sampling is a widely used technique for estimating the size or density of biological populations. Many distance sampling designs and most analyses use the software Distance. 2. We briefly review distance sampling and its assumptions, outline the history, structure and capabilities of Distance, and provide hints on its use. 3. Good survey design is a crucial pre-requisite for obtaining reliable results. Distance has a survey design engine, with a built-in geographic information system, that allows properties of different proposed designs to be examined via simulation, and survey plans to be generated. 4. A first step in analysis of distance sampling data is modelling the probability of detection. Distance contains three increasingly sophisticated analysis engines for this: CDS (conventional distance sampling), which models detection probability as a function of distance from the transect and assumes all objects at zero distance are detected; MCDS (multiple covariate distance sampling), which allows covariates in addition to distance; and MRDS (mark-recapture distance sampling), which relaxes the assumption of certain detection at zero distance. 5. All three engines allow estimation of density or abundance, stratified if required, with associated measures of precision calculated either analytically or via the bootstrap. 6. Advanced analysis topics covered include the use of multipliers to allow analysis of indirect surveys (such as dung or nest surveys), the DSM (density surface modelling) analysis engine for spatial and habitat modelling, and information about accessing the analysis engines directly from other software. 7. Synthesis and applications. Distance sampling is a key method for producing abundance and density estimates in challenging field conditions. The theory underlying the methods continues to expand to cope with realistic estimation situations. In step with theoretical developments, state-of-the-art software that implements these methods is described that makes the methods accessible to practicing ecologists.The importance of analysis method for breeding bird survey population trend estimatesThomas, LenMartin, Kathyhttp://hdl.handle.net/10023/6852016-03-28T10:50:56Z1996-01-01T00:00:00ZPopulation trends from the Breeding Bird Survey are widely used to focus conservation efforts on species thought to be in decline and to test preliminary hypotheses regarding the causes of these declines. A number of statistical methods have been used to estimate population trends, but there is no consensus us to which is the most reliable. We quantified differences in trend estimates or different analysis methods applied to the same subset of Breeding Bird Survey data. We estimated trends for 115 species in British Columbia using three analysis methods: U.S. National Biological Service route regression, Canadian Wildlife Service route regression, and nonparametric rank-trends analysis. Overall, the number of species estimated to be declining was similar among the three methods, but the number of statistically significant declines was not similar (15, 8, and 29 respectively). In addition, many differences existed among methods in the trend estimates assigned to individual species. Comparing the two route regression methods, Canadian Wildlife Service estimates had a greater absolute magnitude on average than those of the U.S. National Biological Service method. U.S. National Biological Service estimates were on average more positive than the Canadian Wildlife Service estimates when the respective agency's data selection criteria were applied separately. These results imply that our ability to detect population declines and to prioritize species of conservation concern depend strongly upon the analysis method used. This highlights the need for further research to determine how best to accurately estimate trends from the data. We suggest a method for evaluating the performance of the analysis methods by using simulated Breeding Bird Survey data.
1996-01-01T00:00:00ZThomas, LenMartin, KathyPopulation trends from the Breeding Bird Survey are widely used to focus conservation efforts on species thought to be in decline and to test preliminary hypotheses regarding the causes of these declines. A number of statistical methods have been used to estimate population trends, but there is no consensus us to which is the most reliable. We quantified differences in trend estimates or different analysis methods applied to the same subset of Breeding Bird Survey data. We estimated trends for 115 species in British Columbia using three analysis methods: U.S. National Biological Service route regression, Canadian Wildlife Service route regression, and nonparametric rank-trends analysis. Overall, the number of species estimated to be declining was similar among the three methods, but the number of statistically significant declines was not similar (15, 8, and 29 respectively). In addition, many differences existed among methods in the trend estimates assigned to individual species. Comparing the two route regression methods, Canadian Wildlife Service estimates had a greater absolute magnitude on average than those of the U.S. National Biological Service method. U.S. National Biological Service estimates were on average more positive than the Canadian Wildlife Service estimates when the respective agency's data selection criteria were applied separately. These results imply that our ability to detect population declines and to prioritize species of conservation concern depend strongly upon the analysis method used. This highlights the need for further research to determine how best to accurately estimate trends from the data. We suggest a method for evaluating the performance of the analysis methods by using simulated Breeding Bird Survey data.Retrospective power analysisThomas, Lenhttp://hdl.handle.net/10023/6792016-03-28T10:56:07Z1997-01-01T00:00:00ZMany papers have appeared in the recent biological literature encouraging us to incorporate statistical power analysis into our hypothesis testing protocol (Peterman 1990; Fairweather 1991; Muller & Benignus 1992; Taylor & Gerrodette 1993; Searcy-Bernal 1994; Thomas & Juanes 1996). The importance of doing a power analysis before beginning a study (prospective power analysis) is universally accepted: such analyses help us to decide how many samples are required to have a good chance of getting unambiguous results. In contrast, the role of power analysis after the data are collected and analyzed (retrospective power analysis) is controversial, as is evidenced by the papers of Reed and Blaustein (1995) and Hayes and Steidl (1997). The controversy is over the use of information from the sample data in retrospective power calculations. As I will show, the type of information used has fundamental implications for the value of such analyses. I compare the approaches to calculating retrospective power, noting the strengths and weaknesses of each, and make general recommendations as to how and when retrospective power analyses should be conducted.
The pdf contains the article; the ASCII file contains SAS code to calculate power and confidence limits for simple linear regression, as detailed in the article appendix.
1997-01-01T00:00:00ZThomas, LenMany papers have appeared in the recent biological literature encouraging us to incorporate statistical power analysis into our hypothesis testing protocol (Peterman 1990; Fairweather 1991; Muller & Benignus 1992; Taylor & Gerrodette 1993; Searcy-Bernal 1994; Thomas & Juanes 1996). The importance of doing a power analysis before beginning a study (prospective power analysis) is universally accepted: such analyses help us to decide how many samples are required to have a good chance of getting unambiguous results. In contrast, the role of power analysis after the data are collected and analyzed (retrospective power analysis) is controversial, as is evidenced by the papers of Reed and Blaustein (1995) and Hayes and Steidl (1997). The controversy is over the use of information from the sample data in retrospective power calculations. As I will show, the type of information used has fundamental implications for the value of such analyses. I compare the approaches to calculating retrospective power, noting the strengths and weaknesses of each, and make general recommendations as to how and when retrospective power analyses should be conducted.A unified framework for modelling wildlife population dynamicsThomas, LenBuckland, Stephen T.Newman, KBHarwood, Johnhttp://hdl.handle.net/10023/6782016-03-28T10:49:58Z2005-01-01T00:00:00ZThis paper proposes a unified framework for defining and fitting stochastic, discrete-time, discrete-stage population dynamics models. The biological system is described by a state–space model, where the true but unknown state of the population is modelled by a state process, and this is linked to survey data by an observation process. All sources of uncertainty in the inputs, including uncertainty about model specification, are readily incorporated. The paper shows how the state process can be represented as a generalization of the standard Leslie or Lefkovitch matrix. By dividing the state process into subprocesses, complex models can be constructed from manageable building blocks. The paper illustrates the approach with a model of the British Grey Seal metapopulation, using sequential importance sampling with kernel smoothing to fit the model.
The pdf document contains the full article text; program code (in S-PLUS 6.1) for the example analysis is in the three text files; data is available from the Sea Mammal Research Unit (http://www.smru.st-and.ac.uk)
2005-01-01T00:00:00ZThomas, LenBuckland, Stephen T.Newman, KBHarwood, JohnThis paper proposes a unified framework for defining and fitting stochastic, discrete-time, discrete-stage population dynamics models. The biological system is described by a state–space model, where the true but unknown state of the population is modelled by a state process, and this is linked to survey data by an observation process. All sources of uncertainty in the inputs, including uncertainty about model specification, are readily incorporated. The paper shows how the state process can be represented as a generalization of the standard Leslie or Lefkovitch matrix. By dividing the state process into subprocesses, complex models can be constructed from manageable building blocks. The paper illustrates the approach with a model of the British Grey Seal metapopulation, using sequential importance sampling with kernel smoothing to fit the model.WinBUGS for population ecologists: Bayesian modeling using Markov Chain Monte Carlo methods.Giminez, OBonner, S JKing, RuthParker, R ABrooks, S PJamieson, L EGrosbois, VMorgan, B J TThomas, Lenhttp://hdl.handle.net/10023/6772016-04-27T16:25:51Z2008-01-01T00:00:00ZThe computer package WinBUGS is introduced. We first give a brief introduction to Bayesian theory and its implementation using Markov chain Monte Carlo (MCMC) algorithms. We then present three case studies showing how WinBUGS can be used when classical theory is difficult to implement. The first example uses data on white storks from Baden Württemberg, Germany, to demonstrate the use of mark-recapture models to estimate survival, and also how to cope with unexplained variance through random effects. Recent advances in methodology and also the WinBUGS software allow us to introduce (i) a flexible way of incorporating covariates using spline smoothing and (ii) a method to deal with missing values in covariates. The second example shows how to estimate population density while accounting for detectability, using distance sampling methods applied to a test dataset collected on a known population of wooden stakes. Finally, the third case study involves the use of state-space models of wildlife population dynamics to make inferences about density dependence in a North American duck species. Reversible Jump MCMC is used to calculate the probability of various candidate models. For all examples, data and WinBUGS code are provided.
This paper was presented at the EURING 2007 Technical Meeting, January 14-21, Dunedin, New Zealand. It has been submitted for publication in the conference proceedings, which will appear as a special issue of Environmental and Ecological Statistics.; The zip file contains accompanying code in WinBUGS
2008-01-01T00:00:00ZGiminez, OBonner, S JKing, RuthParker, R ABrooks, S PJamieson, L EGrosbois, VMorgan, B J TThomas, LenThe computer package WinBUGS is introduced. We first give a brief introduction to Bayesian theory and its implementation using Markov chain Monte Carlo (MCMC) algorithms. We then present three case studies showing how WinBUGS can be used when classical theory is difficult to implement. The first example uses data on white storks from Baden Württemberg, Germany, to demonstrate the use of mark-recapture models to estimate survival, and also how to cope with unexplained variance through random effects. Recent advances in methodology and also the WinBUGS software allow us to introduce (i) a flexible way of incorporating covariates using spline smoothing and (ii) a method to deal with missing values in covariates. The second example shows how to estimate population density while accounting for detectability, using distance sampling methods applied to a test dataset collected on a known population of wooden stakes. Finally, the third case study involves the use of state-space models of wildlife population dynamics to make inferences about density dependence in a North American duck species. Reversible Jump MCMC is used to calculate the probability of various candidate models. For all examples, data and WinBUGS code are provided.