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Decadal-interdecadal climate variability over Antarctica and linkages to the tropics : analysis of ice core, instrumental, and tropical proxy data

Okumura, Yuko — Thu, 01 Nov 2012 00:00:00 GMT

Abstract: The Antarctic continent contains the majority of the global ice volume and plays an important role in a changing climate. The nature and causes of Antarctic climate variability are, however, poorly understood beyond interannual time scales due to the paucity of long, reliable meteorological observations. This study analyzes decadal-interdecadal climate variability over Antarctica using a network of annually resolved ice core records and various instrumental and tropical proxy data for the 19th and 20th centuries. During the 20th century, Antarctic ice core records indicate strong linkages to sea surface temperature (SST) variations in the tropical Pacific and Atlantic on decadal-interdecadal time scales. Antarctic surface temperature anomalies inferred from the ice cores are consistent with the associated changes in atmospheric circulation and thermal advection. A set of atmospheric general circulation model experiments supports the idea that decadal SST variations in the tropics force atmospheric teleconnections that affect Antarctic surface temperatures. When coral and other proxies for tropical climate are used to extend the analysis back to 1799, a similar Antarctic-tropical Pacific linkage is found, with evidence for a weaker connection during the first half of the 19th century. Over the past 50 years, a change in the phase of Pacific and Atlantic interdecadal variability may have contributed to the rapid warming of the Antarctic Peninsula and West Antarctica.

Estimating animal population density using passive acoustics

Marques, Tiago A. — Wed, 01 May 2013 00:00:00 GMT

Abstract: Reliable 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

Estimating prevalence of injecting drug users and associated heroin-related death rates in England by using regional data and incorporating prior information

King, Ruth — Tue, 01 Jan 2013 00:00:00 GMT

Abstract: Injecting drug users (IDUs) have a direct social and economic effect yet can typically be regarded as a hidden population within a community. We estimate the size of the IDU population across the nine different Government Office regions of England in 2005–2006 by using capture–recapture methods with age (ranging from 15 to 64 years) and gender as covariate information. We consider a Bayesian model averaging approach using log-linear models, where we can include explicit prior information within the analysis in relation to the total IDU population (elicited from the number of drug-related deaths and injectors’ drug-related death rates). Estimation at the regional level allows for regional heterogeneity with these regional estimates aggregated to obtain a posterior mean estimate for the number of England's IDUs of 195840 with 95% credible interval (181700, 210480). There is significant variation in the estimated regional prevalence of current IDUs per million of population aged 15–64 years, and in injecting drug-related death rates across the gender × age cross-classifications. The propensity of an IDU to be seen by at least one source also exhibits strong regional variability with London having the lowest propensity of being observed (posterior mean probability 0.21) and the South West the highest propensity (posterior mean 0.46).

Estimating whale abundance using sparse hydrophone arrays

Harris, Danielle V. — Wed, 20 Jun 2012 00:00:00 GMT

Abstract: Passive acoustic monitoring has been used to investigate many aspects of marine mammal ecology, although methods to estimate absolute abundance and density using acoustic data have only been developed in recent years. The instrument configuration in an acoustic survey determines which abundance estimation methods can be used. Sparsely distributed arrays of instruments are useful because wide geographic areas can be covered. However, instrument spacing in sparse arrays is such that the same vocalisation will not be detected on multiple instruments, excluding the use of some abundance estimation methods. The aim of this thesis was to explore cetacean abundance and density estimation using novel sparse array datasets, applying existing methods where possible, or developing new approaches. The wealth of data collected by sparse arrays was demonstrated by analysing a 10-year dataset collected by the U.S. Navy’s Sound Surveillance System in the north-east Atlantic. Spatial and temporal patterns of blue (Balaenoptera musculus) and fin whale (Balaenoptera physalus) vocal activity were investigated using generalised additive models. Distance sampling-based methods were applied to fin whale calls recorded by an array of Ocean Bottom Seismometers in the north-east Atlantic. Estimated call density was 993 calls/1000 km².hr⁻¹ (CV: 0.39). Animal density could not be estimated because the call rate was unknown. Further development of the call localisation method is required so the current density estimate may be biased. Furthermore, analysing a single day of data resulted in a high variance estimate. Finally, a new simulation-based method developed to estimate density from single hydrophones was applied to blue whale calls recorded in the northern Indian Ocean. Estimated call density was 3 calls/1000 km².hr⁻¹ (CV: 0.17). Again, density of whales could not be estimated as the vocalisation rate was unknown. Lack of biological knowledge poses the greatest limitation to abundance and density estimation using acoustic data.

Competing conservation objectives for predators and prey : estimating killer whale prey requirements for Chinook salmon

Williams, Robert — Wed, 09 Nov 2011 00:00:00 GMT

Abstract: Ecosystem-based management (EBM) of marine resources attempts to conserve interacting species. In contrast to single-species fisheries management, EBM aims to identify and resolve conflicting objectives for different species. Such a conflict may be emerging in the northeastern Pacific for southern resident killer whales (Orcinus orca) and their primary prey, Chinook salmon (Oncorhynchus tshawytscha). Both species have at-risk conservation status and transboundary (Canada–US) ranges. We modeled individual killer whale prey requirements from feeding and growth records of captive killer whales and morphometric data from historic live-capture fishery and whaling records worldwide. The models, combined with caloric value of salmon, and demographic and diet data for wild killer whales, allow us to predict salmon quantities needed to maintain and recover this killer whale population, which numbered 87 individuals in 2009. Our analyses provide new information on cost of lactation and new parameter estimates for other killer whale populations globally. Prey requirements of southern resident killer whales are difficult to reconcile with fisheries and conservation objectives for Chinook salmon, because the number of fish required is large relative to annual returns and fishery catches. For instance, a U.S. recovery goal (2.3% annual population growth of killer whales over 28 years) implies a 75% increase in energetic requirements. Reducing salmon fisheries may serve as a temporary mitigation measure to allow time for management actions to improve salmon productivity to take effect. As ecosystem-based fishery management becomes more prevalent, trade-offs between conservation objectives for predators and prey will become increasingly necessary. Our approach offers scenarios to compare relative influence of various sources of uncertainty on the resulting consumption estimates to prioritise future research efforts, and a general approach for assessing the extent of conflict between conservation objectives for threatened or protected wildlife where the interaction between affected species can be quantified.

Estimating seasonal abundance of a central place forager using counts and telemetry data

Sharples, RJ — Thu, 01 Jan 2009 00:00:00 GMT

Abstract: Obtaining population estimates of species that are not easily observed directly can be problematic. However, central place foragers can often be observed some of the time, e.g. when seals are hauled out. In these instances, population estimates can be derived from counts, combined with information on the proportion of time that animals can be observed. We present a modelling framework to estimate seasonal absolute abundance using counts and information from satellite telemetry data. The method was tested on a harbour seal population in an area of southeast Scotland. Counts were made monthly, between November 2001 and June 2003, when seals were hauled out on land and were corrected for the proportion of time the seals were at sea using satellite telemetry. Harbour seals (n=25) were tagged with satellite relay data loggers between November 2001 and March 2003. To estimate the proportion of time spent hauled out, time at sea on foraging trips was modelled separately from haul-out behaviour close to haul-out sites because of the different factors affecting these processes. A generalised linear mixed model framework was developed to capture the longitudinal nature of the data and the repeated measures across individuals. Despite seasonal variability in the number of seals counted at haul-out sites, the model generated estimates of abundance, with an overall mean of 846 (95% CI: 767 to 979). The methodology shows the value of using count and telemetry data collected concurrently for estimating absolute abundance, information that is essential to assess interactions between predators, fish stocks and fisheries. Description: R.J.S. was supported by a Natural Environment Research Council studentship.

Male mating tactics in the rose bitterling (Rhodeus ocellatus) and European bitterling (Rhodeus amarus)

Casalini, Mara — Wed, 26 Jun 2013 00:00:00 GMT

Abstract: The aim of this study was to investigate the basis to male mating decisions in two related species of bitterling: Rhodeus ocellatus and R. amarus. Bitterling have a resource-based mating system; females lay eggs in the gills of live freshwater mussels and males fertilize the eggs by releasing sperm into the inhalant syphon of the mussel. Male bitterling perform courtship behaviour and aggressively defend mussels in a territory from which they exclude other males. Using laboratory and field experiments it was shown that male aggressive behaviour is inherited through additive maternal genes. Male aggression is also influenced by the number of conspecific males encountered in competition for a mussel, and by the degree of clustering of mussels. Limited availability of mussels results in stronger selection on traits males use in mating context: hence they are more aggressive, larger and more colourful. The differences in mating behaviours in different environments may indicate a conflict between male dominance and female choice, but have not led to reproductive isolation. Resource availability during ontogenesis and male density during embryogenesis, however, do not exert an effect on male aggressive behaviour. Red carotenoid-based nuptial coloration functions as an inter- and intra-sexual signal and undergoes rapid variation in response to changes in mating context. Male bitterling do not modulate their courtship and aggressive behaviour in response to variation in female size, and their choice of mussel species is influenced by, and consistent with, female oviposition choice.

Photo-grammetric measurements of swimming speed and body length of basking sharks observed around the Hebrides, Scotland

Lacey, Claire — Mon, 01 Mar 2010 00:00:00 GMT

Abstract: Photo-grammetric techniques developed for measuring body length and small scale movement patterns of cetaceans were applied to surface swimming basking sharks off the west coast of Scotland. These methods removed the need for close approaches, reducing the likelihood of disturbing the focal animal. Average swimming speed was calculated from the total path length between shark locations measured at approximately one minute intervals. These average speeds varied from 0.49 to 0.73 ms−1 for tracks of between 30 and 170 minutes' duration. Body length measurements ranged between 2.35 and 6.43 m. For ten sharks where body length and swimming speed were measured there was a significant correlation between body length (L) and swimming speed (V) expressed as V = 0.36L033.

Sharp global nonlinear stability for a fluid overlying a highly porous material

Hill, Antony A. — Fri, 08 Jan 2010 00:00:00 GMT

Abstract: The stability of convection in a two-layer system in which a layer of fluid with a temperature-dependent viscosity overlies and saturates a highly porous material is studied. Owing to the difficulties associated with incorporating the nonlinear advection term in the Navier-Stokes equations into a stability analysis, previous literature on fluid/porous thermal convection has modelled the fluid using the linear Stokes equations. This paper derives global stability for the full nonlinear system, by utilizing a model proposed by Ladyzhenskaya. The nonlinear stability boundaries are shown to be sharp when compared with the linear instability thresholds.

Nonlinear stability of the one-domain approach to modelling convection in superposed fluid and porous layers

Hill, A A — Wed, 01 Sep 2010 00:00:00 GMT

Abstract: Studies of the nonlinear stability of fluid/porous systems have been developed very recently. A two-domain modelling approach has been adopted in previous works, but was restricted to specific configurations. The extension to the more general case of a Navier–Stokes modelled fluid over a porous material was not achieved for the two-domain approach owing to the difficulties associated with handling the interfacial boundary conditions. This paper addresses this issue by adopting a one-domain approach, where the governing equations for both regions are combined into a unique set of equations that are valid for the entire domain. It is shown that the nonlinear stability bound, in the one-domain approach, is very sharp and hence excludes the possibility of subcritical instabilities. Moreover, the one-domain approach is compared with an equivalent two-domain approach, and excellent agreement is found between the two.

Instability in internal solitary waves with trapped cores

Carr, Magda — Sun, 01 Jan 2012 00:00:00 GMT

Abstract: A numerical method that employs a combination of contour advection and pseudo-spectral techniques is used to investigate instability in internal solitary waves with trapped cores. A three-layer configuration for the background stratification in which the top two layers are linearly stratified and the lower layer is homogeneous is considered throughout. The strength of the stratification in the very top layer is chosen to be sufficient so that waves of depression with trapped cores can be generated. The flow is assumed to satisfy the Dubriel-Jacotin-Long equation both inside and outside of the core region. The Brunt-Vaisala frequency is modelled such that it varies from a constant value outside of the core to zero inside the core over a sharp but continuous transition length. This results in a stagnant core in which the vorticity is zero and the density is homogeneous and approximately equal to that at the core boundary. The time dependent simulations show that instability occurs on the boundary of the core. The instability takes the form of Kelvin-Helmholtz billows. If the instability in the vorticity field is energetic enough, disturbance in the buoyancy field is also seen and fluid exchange takes place across the core boundary. Occurrence of the Kelvin-Helmholtz billows is attributed to the sharp change in the vorticity field at the boundary between the core and the pycnocline. The numerical scheme is not limited by small Richardson number unlike the other alternatives currently available in the literature which appear to be.

Shear induced breaking of large amplitude internal solitary waves

Fructus, D — Sun, 01 Feb 2009 00:00:00 GMT

Convectively induced shear instability in large amplitude internal solitary waves

Carr, Magda — Mon, 01 Dec 2008 00:00:00 GMT

Abstract: Laboratory study has been carried out to investigate the instability of an internal solitary wave of depression in a shallow stratified fluid system. The experimental campaign has been supported by theoretical computations and has focused on a two layered stratification consisting of a homogeneous dense layer below a linearly stratified top layer. The initial background stratification has been varied and it is found that the onset and intensity of breaking are affected dramatically by changes in the background stratification. Manifestations of a combination of shear and convective instability are seen on the leading face of the wave. It is shown that there is an interplay between the two instability types and convective instability induces shear by enhancing isopycnal compression. Variation in the upper boundary condition is also found to have an effect on stability. In particular, the implications for convective instability are shown to be profound and a dramatic increase in wave amplitude is seen for a fixed (as opposed to free) upper boundary condition.

To ping or not to ping : the use of active acoustic devices in mitigating interactions between small cetaceans and gillnet fisheries

Dawson, Steve — Tue, 01 Jan 2013 00:00:00 GMT

Abstract: Active sound emitters (‘pingers’) are used in several gillnet fisheries to reduce bycatch of small cetaceans, and/or to reduce depredation by dolphins. Here, we review studies conducted to determine how effective these devices may be as management tools. Significant reductions in bycatch of harbour porpoise Phocoena phocoena, franciscana Pontoporia blainvillei, common Delphinus delphis and striped dolphin Stenella coeruleoalba, and beaked whales as a group have been demonstrated. For harbour porpoise this result has been replicated in 14 controlled experiments in North America and Europe, and appears to be due to porpoises avoiding the area ensonified by pingers. Two gillnet fisheries (California-Oregon driftnet fishery for swordfish; New England groundfish fishery) with mandatory pinger use have been studied for over a decade. Bycatch rates of dolphins/porpoises have fallen by 50 to 60%, and there is no evidence of bycatch increasing over time due to habituation. In both fisheries, bycatch rates were significantly higher in nets sparsely equipped with pingers or in which pingers had failed, than in nets without any pingers at all. Studies of pinger use to reduce depredation by bottlenose dolphins Tursiops truncatus generally show small and inconsistent improvements in fish catches and somewhat reduced net damage. Dolphin bycatch in these fisheries is rare, but still occurs in nets with pingers. Taken together, these studies suggest that the most promising candidates for bycatch reduction via pinger use will be gillnet fisheries in developed countries in which the bycaught cetaceans are generally neophobic species with large home ranges. We offer a set of lessons learned from the last decade of bycatch management.

Tissue-specific transcriptomics in the field cricket Teleogryllus oceanicus

Bailey, Nathan William — Fri, 01 Feb 2013 00:00:00 GMT

Abstract: Field crickets (family Gryllidae) frequently are used in studies of behavioral genetics, sexual selection, and sexual conflict, but there have been no studies of transcriptomic differences among different tissue types. We evaluated transcriptome variation among testis, accessory gland, and the remaining whole-body preparations from males of the field cricket, Teleogryllus oceanicus. Non-normalized cDNA libraries from each tissue were sequenced on the Roche 454 platform, and a master assembly was constructed using testis, accessory gland, and whole-body preparations. A total of 940,200 reads were assembled into 41,962 contigs, to which 36,856 singletons (reads not assembled into a contig) were added to provide a total of 78,818 sequences used in annotation analysis. A total of 59,072 sequences (75%) were unique to one of the three tissues. Testis tissue had the greatest proportion of tissue-specific sequences (62.6%), followed by general body (56.43%) and accessory gland tissue (44.16%). We tested the hypothesis that tissues expressing gene products expected to evolve rapidly as a result of sexual selection—testis and accessory gland—would yield a smaller proportion of BLASTx matches to homologous genes in the model organism Drosophila melanogaster compared with whole-body tissue. Uniquely expressed sequences in both testis and accessory gland showed a significantly lower rate of matching to annotated D. melanogaster genes compared with those from general body tissue. These results correspond with empirical evidence that genes expressed in testis and accessory gland tissue are rapidly evolving targets of selection. Description: This work was supported by a Natural Environment Research Council Junior Postdoctoral Fellowship (NE/G014906/1) and Pacific Rim Foundation funding (08-T-PRRP-05-0029) to N.W.B.

Mg structural state in coral aragonite and implications for the paleoenvironmental proxy

Finch, Adrian A. — Sat, 19 Apr 2008 00:00:00 GMT

Abstract: Thermodynamic calculations and inorganic precipitation experiments indicate a relationship between aragonite Mg/Ca and water temperature. This offers a route to reconstruct seawater temperatures from fossil corals. Fundamental to this is the assumption that Mg2+ exchanges for Ca2+ within carbonate. We present X-ray Absorption Fine Structure (XAFS) data to indicate the structural state of Mg in modern Porites coral skeletons. We show Mg is not in aragonite, but hosted by a disordered Mg-bearing material. Mg may be predominantly hosted in organic materials or as a highly disordered inorganic phase, e. g., a nanoparticulate form of Mg carbonate or hydroxide. Reported correlations between seawater temperature and coral Mg/Ca are unlikely to be consistent between corals and hence analysis of Mg/Ca in fossils is unlikely to produce accurate climate reconstructions. We anticipate XAFS will be applied widely to environmental proxies and become an important tool in identifying those that reconstruct accurate climates.

Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba

Jelinska, Clare — Thu, 01 Apr 2010 00:00:00 GMT

Abstract: Archaea use a variety of small basic proteins to package their DNA. One of the most widespread and highly conserved is the Alba (Sso10b) protein. Alba interacts with both DNA and RNA in vitro, and we show in the present study that it binds more tightly to dsDNA (double-stranded DNA) than to either ssDNA (single-stranded DNA) or RNA. The Alba protein is dimeric in solution, and forms distinct ordered complexes with DNA that have been visualized by electron microscopy studies; these studies suggest that, on binding dsDNA, the protein forms extended helical protein fibres. An end-to-end association of consecutive Alba dimers is suggested by the presence of a dimer-dimer interface in crystal structures of Alba from several species, and by the strong conservation of the interface residues, centred on Are and Phe(60). In the present study we map perturbation of the polypeptide backbone of Alba upon binding to DNA and RNA by NMR, and demonstrate the central role of Phe(60) in forming the dimer dimer interface. Site-directed spin labelling and pulsed ESR are used to confirm that an end-to-end, dimer dimer interaction forms in the presence of dsDNA.

Seasonal inflow of warm water onto the southern Weddell Sea continental shelf, Antarctica

Arthun, Marius — Sat, 01 Sep 2012 00:00:00 GMT

Abstract: To capture the austral summer to winter transition in water mass properties over the southern Weddell Sea continental shelf and slope region Weddell seals were tagged with miniaturized conductivity–temperature–depth sensors in February 2011. During the following 8 months the instruments yielded about 9000 temperature–salinity profiles from a previously undersampled area. This allows, for the first time, a description of the seasonality of warm water intrusions onto the shelf. A temperature section across the Filchner Depression and eastern shelf shows a pronounced decrease in warm water inflow from summer to winter, further supported by an almost 3–year long time series from a shelf–break mooring. The seasonal variability is related to the surface wind stress and an associated deepening of the off–shore core of Warm Deep Water.

Fitting complex ecological point process models with integrated nested Laplace approximation

Illian, Janine Baerbel — Tue, 01 Jan 2013 00:00:00 GMT

Abstract: Summary 1. We highlight an emerging statistical method, integrated nested Laplace approximation (INLA), which is ideally suited for fitting complex models to many of the rich spatial data sets that ecologists wish to analyse. 2. INLA is an approximation method that nevertheless provides very exact estimates. In this article, we describe the INLA methodology highlighting where it offers opportunities for drawing inference from (spatial) ecological data that would previously have been too complex to make practical model fitting feasible. 3. We use INLA to fit a complex joint model to the spatial pattern formed by a plant species, Thymus carnosus, as well as to the health status of each individual. 4. The key ecological result revealed by our spatial analysis of these data, relates to the distance-to-water covariate. We find that T. carnosus plants are generally healthier when they are further away from the water. 5. We suggest that this may be the result of a combination of (1) plants having alternative rooting strategies depending on how close to water they grow and (2) the rooting strategy determining how well the plants were able to tolerate an unusually dry summer. 6. We anticipate INLA becoming widely used within spatial ecological analysis over the next decade and suggest that both ecologists and statisticians will benefit greatly from working collaboratively to further develop and apply these emerging statistical methods.

Vocal copying of individually distinctive signature whistles in bottlenose dolphins

King, Stephanie Laura — Mon, 22 Apr 2013 00:00:00 GMT

Abstract: Vocal learning is relatively common in birds but less so in mammals. Sexual selection and individual or group recognition have been identified as major forces in its evolution. While important in the development of vocal displays, vocal learning also allows signal copying in social interactions. Such copying can function in addressing or labelling selected conspecifics. Most examples of addressing in non-humans come from bird song, where matching occurs in an aggressive context. However, in other animals, addressing with learned signals is very much an affiliative signal. We studied the function of vocal copying in a mammal that shows vocal learning as well as complex cognitive and social behaviour, the bottlenose dolphin (Tursiops truncatus). Copying occurred almost exclusively between close associates such as mother–calf pairs and male alliances during separation and was not followed by aggression. All copies were clearly recognizable as such because copiers consistently modified some acoustic parameters of a signal when copying it. We found no evidence for the use of copying in aggression or deception. This use of vocal copying is similar to its use in human language, where the maintenance of social bonds appears to be more important than the immediate defence of resources.

The role of endosymbionts in the evolution of haploid-male genetic systems in scale insects (Coccoidea)

Ross, Laura — Tue, 01 May 2012 00:00:00 GMT

Abstract: There is an extraordinary diversity in genetic systems across species, but this variation remains poorly understood. In part, this is because the mechanisms responsible for transitions between systems are often unknown. A recent hypothesis has suggested that conflict between hosts and endosymbiotic microorganisms over transmission could drive the transition from diplodiploidy to systems with male haploidy (haplodiploidy, including arrhenotoky and paternal genome elimination [PGE]). Here, we present the first formal test of this idea with a comparative analysis across scale insects (Hemiptera: Coccoidea). Scale insects are renowned for their large variation in genetic systems, and multiple transitions between diplodiploidy and haplodiploidy have taken place within this group. Additionally, most species rely on endosymbiotic microorganisms to provide them with essential nutrients lacking in their diet. We show that species harboring endosymbionts are indeed more likely to have a genetic system with male haploidy, which supports the hypothesis that endosymbionts might have played a role in the transition to haplodiploidy. We also extend our analysis to consider the relationship between endosymbiont presence and transitions to parthenogenesis. Although in scale insects there is no such overall association, species harboring eukaryote endosymbionts were more likely to be parthenogenetic than those with bacterial symbionts. These results support the idea that intergenomic conflict can drive the evolution of novel genetic systems and affect host reproduction.

A family of spatial biodiversity measures based on graphs

Rajala, T — Sat, 01 Dec 2012 00:00:00 GMT

Abstract: While much research in ecology has focused on spatially explicit modelling as well as on measures of biodiversity, the concept of spatial (or local) biodiversity has been discussed very little. This paper generalises existing measures of spatial biodiversity and introduces a family of spatial biodiversity measures by flexibly defining the notion of the individuals’ neighbourhood within the framework of graphs associated to a spatial point pattern. We consider two non-independent aspects of spatial biodiversity, scattering, i.e. the spatial arrangement of the individuals in the study area and exposure, the local diversity in an individual’s neighbourhood. A simulation study reveals that measures based on the most commonly used neigh-bourhood defined by the geometric graph do not distinguish well between scattering and exposure. This problem is much less pronounced when other graphs are used. In an analysis of the spatial diversity in a rainforest, the results based on the geometric graph have been shown to spuriously indicate a decrease in spatial biodiversity when no such trend was detected by the other types of neighbourhoods. We also show that the choice neighbourhood markedly impacts on the classification of species according to how strongly and in what way different species spatially structure species diversity. Clearly, in an analysis of spatial or local diversity an appropriate choice of local neighbourhood is crucial in particular in terms of the biological interpretation of the results. Due to its general definition, the approach discussed here offers the necessary flexibility that allows suitable and varying neighbourhood structures to be chosen.

Multispecies functional response of the minke whale Balaenoptera acutorostrata based on small-scale foraging studies

Smout, Sophie Caroline — Sun, 01 Jul 2007 00:00:00 GMT

Abstract: Atlantic minke whales are important predators in the Barents Sea ecosystem; capelin Mallotus villosus, krill Thysanoessa sp. and Meganyctephanes norvegica and herring Clupea harengus are their major prey. Their consumption of commercial species may present an economic problem for the local fishery. In order to estimate this consumption and understand the potential consequences for prey dynamics, it is essential to determine the multispecies functional response of the whales. The parameterisation of a functional response requires measurements of consumption rates and prey availability. In this localised study, undigested stomach contents were used to assess the amount of each prey that had been consumed immediately prior to capture. To determine the availability of prey to the whales, standard acoustic surveys were run in the same area within 2 d of the capture of the whales. The spatial distribution of prey was modelled using generalised additive models (GAMs). In order to generate a measure of prey availability and the uncertainty in this value, a simple model was assumed for whale movement, and prey abundance was sampled over space according to a Gaussian kernel. A multispecies functional response (MSFR) model was then fitted to the consumption and prey availability data using Bayesian methods. Simple simulations, based on the fitted MSFR, indicate that minke whales may deplete local capelin aggregations at small spatial scales. This is the first time that a multispecies functional response has been fitted for a cetacean predator, and the methods outlined here may prove useful for modelling marine mammal-fish interactions in other systems.

Estimating demographic parameters for capture-recapture data in the presence of multiple mark types

Smout, Sophie Caroline — Wed, 01 Jun 2011 00:00:00 GMT

Abstract: In mark-recapture studies, various techniques can be used to uniquely identify individual animals, such as ringing, tagging or photo-identification using natural markings. In some long-term studies more than one type of marking procedure may be implemented during the study period. In these circumstances, ignoring the different mark types can produce biased survival estimates since the assumption that the different mark types are equally catchable (homogeneous capture probability across mark types) may be incorrect.We implement an integrated approach where we simultaneously analyse data obtained using three different marking techniques, assuming that animals can be cross-classified across the different mark types. We discriminate between competing models using the AIC statistic. This technique also allows us to estimate both relative mark-loss probabilities and relative recapture efficiency rates for the different marking methods.We initially perform a simulation study to explore the different biases that can be introduced if we assume a homogeneous recapture probability over mark type, before applying the method to a real dataset. We make use of data obtained from an intensive long-term observational study of UK female grey seals (Halichoerus grypus) at a single breeding colony, where three different methods are used to identify individuals within a single study: branding, tagging and photo-identification based on seal coat pattern or pelage.

Evolution of ancient functions in the vertebrate insulin-like growth factor system uncovered by study of duplicated salmonid fish genomes

MacQueen, Daniel John — Tue, 01 Jan 2013 00:00:00 GMT

Abstract: Whole genome duplication (WGD) was experienced twice by the vertebrate ancestor (2 rounds; 2R), again by the teleost fish ancestor (3R) and most recently in certain teleost lineages (4R). Consequently, vertebrate gene families are often expanded in 3R and 4R genomes. Arguably, many types of ‘functional divergence’ present across 2R gene families will exceed that between 3R/4R paralogues of genes comprising 2R families. Accordingly, 4R offers a form of replication of 2R. Examining if this concept has implications for molecular evolutionary research, we studied insulin-like growth factor (IGF) binding proteins (IGFBPs), whose six 2R family members carry IGF hormones and regulate interactions between IGFs and IGF1-receptors (IGF1Rs). Using phylogenomic approaches, we resolved the complete IGFBP repertoire of 4R-derived salmonid fishes (nineteen genes; thirteen more than human) and established evolutionary relationships/nomenclature with respect to WGDs. Traits central to IGFBP action were determined for all genes, including atomic interactions in IGFBP-IGF1/IGF2 complexes regulating IGF-IGF1R binding. Using statistical methods, we demonstrate that attributes of these protein interfaces are overwhelming a product of 2R IGFBP family membership, explain 49-68% of variation in IGFBP mRNA concentration in several different tissues and strongly predict the strength and direction of IGFBP transcriptional regulation under differing nutritional-states. The results support a model where vertebrate IGFBP family members evolved divergent structural attributes to provide distinct competition for IGFs with IGF1Rs, pre-disposing different functions in the regulation of IGF-signaling. Evolution of gene expression acted to ensure the appropriate physiological production of IGFBPs according to their structural specializations, leading to optimal IGF-signaling according to nutritional-status and the endocrine/local mode of action. This study demonstrates that relatively recent gene family expansion can facilitate inference of functional evolution within ancient genetic systems. Description: This work was supported by the Marine Alliance for Science and Technology for Scotland pooling initiative, funded by the Scottish Funding Council (grant number HR09011) and contributing institutions.

The influence of a fluid-porous interface on solar pond stability

Hill, A. A — Fri, 01 Feb 2013 00:00:00 GMT

Abstract: The linear instability of the gradient zone of a solar pond containing a fluidporous interface is investigated. It is found that the gradient zone can retain the same stability for lower values of the solute Rayleigh number with the introduction of a porous material compared with a purely fluid layer, whilst maintaining the same lower convective zone temperature. Interestingly, it is also shown that for certain parameter values the penetration of a porous medium into the gradient zone can cause the temperature of the lower convective zone to rise. However, for certain parameter ranges, when the fluid-porous interface is towards the top of the gradient zone, the solar pond can become highly unstable.

Development temperature has persistent effects on muscle growth responses in gilthead sea bream

Garcia de la Serrana Castillo, Daniel — Mon, 17 Dec 2012 00:00:00 GMT

Abstract: Initially we characterised growth responses to altered nutritional input at the transcriptional and tissue levels in the fast skeletal muscle of juvenile gilthead sea bream. Fish reared at 21–22°C (range) were fed a commercial diet at 3% body mass d−1 (non-satiation feeding, NSF) for 4 weeks, fasted for 4d (F) and then fed to satiation (SF) for 21d. 13 out of 34 genes investigated showed consistent patterns of regulation between nutritional states. Fasting was associated with a 20-fold increase in MAFbx, and a 5-fold increase in Six1 and WASp expression, which returned to NSF levels within 16h of SF. Refeeding to satiation was associated with a rapid (<24 h) 12 to 17-fold increase in UNC45, Hsp70 and Hsp90α transcripts coding for molecular chaperones associated with unfolded protein response pathways. The growth factors FGF6 and IGF1 increased 6.0 and 4.5-fold within 16 h and 24 h of refeeding respectively. The average growth in diameter of fast muscle fibres was checked with fasting and significant fibre hypertrophy was only observed after 13d and 21d SF. To investigate developmental plasticity in growth responses we used the same experimental protocol with fish reared at either 17.5–18.5°C (range) (LT) or 21–22°C (range) (HT) to metamorphosis and then transferred to 21–22°C. There were persistent effects of development temperature on muscle growth patterns with 20% more fibres of lower average diameter in LT than HT group of similar body size. Altering the nutritional input to the muscle to stimulate growth revealed cryptic changes in the expression of UNC45 and Hsp90α with higher transcript abundance in the LT than HT groups, whereas there were no differences in the expression of MAFbx and Six1. It was concluded that myogenesis and gene expression patterns during growth are not fixed, but can be modified by temperature during the early stages of the life cycle.

Phasing of muscle gene expression with fasting-induced recovery growth in Atlantic salmon

Bower, Neil I. — Mon, 24 Aug 2009 00:00:00 GMT

Abstract: Background: Many fish species experience long periods of fasting in nature often associated with seasonal reductions in water temperature and prey availability or spawning migrations. During periods of nutrient restriction, changes in metabolism occur to provide cellular energy via catabolic processes. Muscle is particularly affected by prolonged fasting as myofibrillar proteins act as a major energy source. To investigate the mechanisms of metabolic reorganisation with fasting and refeeding in a saltwater stage of Atlantic salmon (Salmo salar L.) we analysed the expression of genes involved in myogenesis, growth signalling, lipid biosynthesis and myofibrillar protein degradation and synthesis pathways using qPCR. Results: Hierarchical clustering of gene expression data revealed three clusters. The first cluster comprised genes involved in lipid metabolism and triacylglycerol synthesis (ALDOB, DGAT1 and LPL) which had peak expression 3-14d after refeeding. The second cluster comprised ADIPOQ, MLC2, IGF-I and TALDO1, with peak expression 14-32d after refeeding. Cluster III contained genes strongly down regulated as an initial response to feeding and included the ubiquitin ligases MuRF1 and MAFbx, myogenic regulatory factors and some metabolic genes. Conclusion: Early responses to refeeding in fasted salmon included the synthesis of triacylglycerols and activation of the adipogenic differentiation program. Inhibition of MuRF1 and MAFbx respectively may result in decreased degradation and concomitant increased production of myofibrillar proteins. Both of these processes preceded any increase in expression of myogenic regulatory factors and IGF-I. These responses could be a necessary strategy for an animal adapted to long periods of food deprivation whereby energy reserves are replenished prior to the resumption of myogenesis.

Mechanisms of gene duplication and translocation and progress towards understanding their relative contributions to animal genome evolution

Mendivil Ramos, Olivia — Sun, 01 Jan 2012 00:00:00 GMT

Abstract: Duplication of genetic material is clearly a major route to genetic change, with consequences for both evolution and disease. A variety of forms and mechanisms of duplication are recognised, operating across the scales of a few base pairs upto entire genomes. With the ever-increasing amounts of gene and genome sequence data that are becoming available, our understanding of the extent of duplication is greatly improving, both in terms of the scales of duplication events as well as their rates of occurrence. An accurate understanding of these processes is vital if we are to properly understand important events in evolution as well as mechanisms operating at the level of genome organisation. Here we will focus on duplication in animal genomes and how the duplicated sequences are distributed, with the aim of maintaining a focus on principles of evolution and organisation that are most directly applicable to the shaping of our own genome.

How many seals were there? The global shelf loss during the Last Glacial Maximum and its effect on the size and distribution of grey seal populations

Boehme, Lars — Wed, 26 Dec 2012 00:00:00 GMT

Abstract: Predicting how marine mammal populations act to habitat changes will be essential for developing conservation management strategies by marine mammal ecologists in the 21st century. Responses to previous environmental change may be informative in the development of predictive models. Here we describe the likely effects of the last ice age on grey seal population size and distribution. We use satellite telemetry data to define grey seal foraging habitat in terms of the temperature and depth ranges exploited by the contemporary populations. We estimate the available extent of such habitat in the North Atlantic at present and at the last glacial maximum (LGM); taking account of glacial and seasonal sea-ice coverage, estimated reductions of sea-level (123m) and seawater temperature hind-casts from GLAMAP-2000. Most of the extensive continental shelf waters (North Sea, Baltic Sea and Scotian Shelf), currently supporting >95% of grey seals, were unavailable at the LGM. A combination of lower sea-level and extensive ice-sheets, massively increased seasonal sea-ice coverage and southerly extent of cold water would have pushed grey seals into areas with no significant shelf waters. The habitat during the LGM might have been as small as 4%, when compared to today’s extent and grey seal populations may have fallen to similarly. An alternative scenario involving a major change to a pelagic/bathy-pelagic foraging niche cannot be discounted. However, hooded seals that appear to out-compete and effectively exclude grey seals from such habitat currently dominate that niche. If as seems likely, the grey seal population fell to very low levels it would have remained low for several thousand years before expanding into current habitats over the last 12000 years or so.

Variation in female grey seal (Halichoerus grypus) reproductive performance correlates to proactive-reactive behavioural types

Twiss, Sean D — Fri, 16 Nov 2012 00:00:00 GMT

Abstract: Consistent individual differences (CIDs) in behaviour, indicative of behavioural types or personalities, have been shown in taxa ranging from Cnidaria to Mammalia. However, despite numerous theoretical explanations there remains limited empirical evidence for selective mechanisms that maintain such variation within natural populations. We examined behavioural types and fitness proxies in wild female grey seals at the North Rona breeding colony. Experiments in 2009 and 2010 employed a remotely-controlled vehicle to deliver a novel auditory stimulus to females to elicit changes in pup-checking behaviour. Mothers tested twice during lactation exhibited highly repeatable individual pup-checking rates within and across breeding seasons. Observations of undisturbed mothers (i.e. experiencing no disturbance from conspecifics or experimental test) also revealed CIDs in pup-checking behaviour. However, there was no correlation between an individuals’ pup-checking rate during undisturbed observations with the rate in response to the auditory test, indicating plasticity across situations. The extent to which individuals changed rates of pup-checking from undisturbed to disturbed conditions revealed a continuum of behavioural types from proactive females, who maintained a similar rate throughout, to reactive females, who increased pup-checking markedly in response to the test. Variation in maternal expenditure (daily mass loss rate) was greater among more reactive mothers than proactive mothers. Consequently pups of more reactive mothers had more varied growth rates centred around the long-term population mean. These patterns could not be accounted for by other measured covariates as behavioural type was unrelated to a mother’s prior experience, degree of inter-annual site fidelity, physical characteristics of their pupping habitat, pup sex or pup activity. These findings are consistent with the hypothesis that variation in behavioural types is maintained by spatial and temporal environmental variation combined with limits to phenotype-environment matching.

What is biodiversity?

Magurran, Anne E. — Wed, 15 Dec 2010 00:00:00 GMT

The geometric mean of relative abundance indices : a biodiversity measure with a difference

Buckland, Stephen Terrence — Fri, 02 Sep 2011 00:00:00 GMT

Abstract: The 2010 Biodiversity Target of the Convention on Biological Diversity (CBD), set in 2002, which stated that there should be ‘a significant reduction of the current rate of biodiversity loss' by 2010, highlighted the need for informative and tractable metrics that can be used to evaluate change in biological diversity. While the subsequent Aichi 2020 targets are more wide-ranging, they also seek to reduce the rate of biodiversity loss. The geometric mean of relative abundance indices, G, is increasingly being used to examine trends in biological diversity and to assess whether biodiversity targets are being met. Here, we explore the mathematical and statistical properties of G that make it useful for judging temporal change in biological diversity, and we discuss its advantages and limitations relative to other measures. We demonstrate that the index reflects trends in both abundance and evenness, and that it is not prone to bias when detectability of individuals varies by species. We note that it allows data from different surveys to be combined to generate a composite index. However, the index exhibits high variance and unstable behaviour when rarely-recorded species are included in the analyses. Read More: http://www.esajournals.org/doi/abs/10.1890/ES11-00186.1

Local and regional rarity in a diverse tropical fish assemblage

Hercos, A — Tue, 01 Jan 2013 00:00:00 GMT

Abstract: Because most species in an ecological assemblage are rare, much of the species richness we value is due to taxa with few individuals or a restricted distribution. It has been apparent since the time of ecological pioneers such as Bates and Darwin that tropical systems have disproportionately large numbers of rare species, yet the distribution and abundance patterns of these species remain largely unknown. Here, we examine the diversity of freshwater fish in a series of lakes in the Amazonian várzea, and relate relative abundance, both as numbers of individuals and as biomass, to the occurrence of species in space and time. We find a bimodal relationship of occurrence that distinguishes temporally and spatially persistent species from those that are infrequent in both space and time. Logistic regression reveals that information on occurrence helps distinguish those species that are rare in this locality but abundant elsewhere, from those that are rare throughout the region. These results form a link between different approaches used to evaluate commonness and rarity. In doing so, they provide a tool for identifying species of high conservation priority in poorly documented but species rich localities.

Using INLA to fit a complex point process model with temporally varying effects – a case study

Illian, Janine Baerbel — Sun, 01 Jul 2012 00:00:00 GMT

Abstract: Integrated nested Laplace approximation (INLA) provides a fast and yet quite exact approach to fitting complex latent Gaussian models which comprise many statistical models in a Bayesian context, including log Gaussian Cox processes. This paper discusses how a joint log Gaussian Cox process model may be fitted to independent replicated point patterns. We illustrate the approach by fitting a model to data on the locations of muskoxen (Ovibos moschatus) herds in Zackenberg valley, Northeast Greenland and by detailing how this model is specified within the R-interface R-INLA. The paper strongly focuses on practical problems involved in the modelling process, including issues of spatial scale, edge effects and prior choices, and finishes with a discussion on models with varying boundary conditions.

A Bayesian approach to fitting Gibbs processes with temporal random effects

King, Ruth — Sat, 01 Dec 2012 00:00:00 GMT

Abstract: We consider spatial point pattern data that have been observed repeatedly over a period of time in an inhomogeneous environment. Each spatial point pattern can be regarded as a “snapshot” of the underlying point process at a series of times. Thus, the number of points and corresponding locations of points differ for each snapshot. Each snapshot can be analyzed independently, but in many cases there may be little information in the data relating to model parameters, particularly parameters relating to the interaction between points. Thus, we develop an integrated approach, simultaneously analyzing all snapshots within a single robust and consistent analysis. We assume that sufficient time has passed between observation dates so that the spatial point patterns can be regarded as independent replicates, given spatial covariates. We develop a joint mixed effects Gibbs point process model for the replicates of spatial point patterns by considering environmental covariates in the analysis as fixed effects, to model the heterogeneous environment, with a random effects (or hierarchical) component to account for the different observation days for the intensity function. We demonstrate how the model can be fitted within a Bayesian framework using an auxiliary variable approach to deal with the issue of the random effects component. We apply the methods to a data set of musk oxen herds and demonstrate the increased precision of the parameter estimates when considering all available data within a single integrated analysis.

Estimated tissue and blood N2 levels and risk of in vivo bubble formation in deep-, intermediate- and shallow diving toothed whales during exposure to naval sonar.

Kvadsheim, Petter H — Thu, 10 May 2012 00:00:00 GMT

Abstract: Naval sonar has been accused of causing whale stranding by a mechanism which increases formation of tissue N2 gas bubbles. Increased tissue and blood N2 levels, and thereby increased risk of decompression sickness (DCS), is thought to result from changes in behavior or physiological responses during diving. Previous theoretical studies have used hypothetical sonar-induced changes in both behavior and physiology to model blood and tissue N2 tension PN2, but this is the first attempt to estimate the changes during actual behavioral responses to sonar. We used an existing mathematical model to estimate blood and tissue N2 tension PN2 from dive data recorded from sperm, killer, long-finned pilot, Blainville’s beaked, and Cuvier’s beaked whales before and during exposure to Low- (1–2 kHz) and Mid- (2–7 kHz) frequency active sonar. Our objectives were: (1) to determine if differences in dive behavior affects risk of bubble formation, and if (2) behavioral- or (3) physiological responses to sonar are plausible risk factors. Our results suggest that all species have natural high N2 levels, with deep diving generally resulting in higher end-dive PN2 as compared with shallow diving. Sonar exposure caused some changes in dive behavior in both killer whales, pilot whales and beaked whales, but this did not lead to any increased risk of DCS. However, in three of eight exposure session with sperm whales, the animal changed to shallower diving, and in all these cases this seem to result in an increased risk of DCS, although risk was still within the normal risk range of this species. When a hypothetical removal of the normal dive response (bradycardia and peripheral vasoconstriction), was added to the behavioral response during model simulations, this led to an increased variance in the estimated end-dive N2 levels, but no consistent change of risk. In conclusion, we cannot rule out the possibility that a combination of behavioral and physiological responses to sonar have the potential to alter the blood and tissue end-dive N2 tension to levels which could cause DCS and formation of in vivo bubbles, but the actually observed behavioral responses of cetaceans to sonar in our study, do not imply any significantly increased risk of DCS.

Conventional and unconventional antimicrobials from fish, marine invertebrates and micro-algae

Smith, Valerie Jane — Wed, 14 Apr 2010 00:00:00 GMT

Abstract: All eukaryotic organisms, single-celled or multi-cellular, produce a diverse array of natural anti-infective agents that, in addition to conventional antimicrobial peptides, also include proteins and other molecules often not regarded as part of the innate defences. Examples range from histones, fatty acids, and other structural components of cells to pigments and regulatory proteins. These probably represent very ancient defence factors that have been re-used in new ways during evolution. This review discusses the nature, biological role in host protection and potential biotechnological uses of some of these compounds, focusing on those from fish, marine invertebrates and marine micro-algae.

Quantifying temporal change in biodiversity : challenges and opportunities

Dornelas, Maria — Tue, 01 Jan 2013 00:00:00 GMT

Abstract: Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series—lack of physical boundaries, uni-dimensionality, autocorrelation and directionality—that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.

Reasons for the invasive success of a guppy (Poecilia reticulata) population in Trinidad

Sievers, Caya — Thu, 31 May 2012 00:00:00 GMT

Abstract: The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype.

Photoacclimation, growth and distribution of massive coral species in clear and turbid waters

Hennige, S.J. — Mon, 13 Oct 2008 00:00:00 GMT

Abstract: ABSTRACT: Massive coral species play a key role in coral reef ecosystems, adding significantly to physical integrity, long term stability and reef biodiversity. This study coupled the assessment of the distribution and abundance of 4 dominant massive coral species, Diploastrea heliopora, Favia speciosa, F. matthaii and Porites lutea, with investigations into species-specific photoacclimatory responses within the Wakatobi Marine National Park of southeast Sulawesi, Indonesia, to determine the potential of photoacclimation to be a driver of biological success. For this, rapid light curves using pulse amplitude modulated (PAM) chlorophyll a fluorescence techniques were employed with additional manipulations to circumvent differences of light quality and absorption between species and across environmental gradients. P. lutea was examined over a range of depths and sites to determine patterns of photoacclimation, and all 4 species were assessed at a single depth between sites for which long-term data for coral community structure and growth existed. Light availability was more highly constrained with depth than between sites; consequently, photoacclimation patterns for P. lutea appeared greater with depth than across environmental gradients. All 4 species were found to differentially modify the extent of non-photochemical quenching to maintain a constant photochemical operating efficiency (qP). Therefore, our results suggest that these massive corals photoacclimate to ensure a constant light-dependent rate of reduction of the plastoquinone pool across growth environments.

Evolution of the multifaceted eukaryotic akirin gene family

Macqueen, Daniel J. — Fri, 06 Feb 2009 00:00:00 GMT

Abstract: Background: Akirins are nuclear proteins that form part of an innate immune response pathway conserved in Drosophila and mice. This studies aim was to characterise the evolution of akirin gene structure and protein function in the eukaryotes. Results: akirin genes are present throughout the metazoa and arose before the separation of animal, plant and fungi lineages. Using comprehensive phylogenetic analysis, coupled with comparisons of conserved synteny and genomic organisation, we show that the intron-exon structure of metazoan akirin genes was established prior to the bilateria and that a single proto-orthologue duplicated in the vertebrates, before the gnathostome-agnathan separation, producing akirin1 and akirin2. Phylogenetic analyses of seven vertebrate gene families with members in chromosomal proximity to both akirin1 and akirin2 were compatible with a common duplication event affecting the genomic neighbourhood of the akirin proto-orthologue. A further duplication of akirins occurred in the teleost lineage and was followed by lineage-specific patterns of paralogue loss. Remarkably, akirins have been independently characterised by five research groups under different aliases and a comparison of the available literature revealed diverse functions, generally in regulating gene expression. For example, akirin was characterised in arthropods as subolesin, an important growth factor and in Drosophila as bhringi, which has an essential myogenic role. In vertebrates, akirin1 was named mighty in mice and was shown to regulate myogenesis, whereas akirin2 was characterised as FB11 in rats and promoted carcinogenesis, acting as a transcriptional repressor when bound to a 14-3-3 protein. Both vertebrate Akirins have evolved under comparably strict constraints of purifying selection, although a likelihood ratio test predicted that functional divergence has occurred between paralogues. Bayesian and maximum likelihood tests identified amino-acid positions where the rate of evolution had shifted significantly between paralogues. Interestingly, the highest scoring position was within a conserved, validated binding-site for 14-3-3 proteins. Conclusion: This work offers an evolutionary framework to facilitate future studies of eukaryotic akirins and provides insight into their multifaceted and conserved biochemical functions.

Evolution of a complex locus : exon gain, loss and divergence at the Gr39a locus in Drosophila

Gardiner, Anastasia — Wed, 30 Jan 2008 00:00:00 GMT

Abstract: Background. Gene families typically evolve by gene duplication followed by the adoption of new or altered gene functions. A different way to evolve new but related functions is alternative splicing of existing exons of a complex gene. The chemosensory gene families of animals are characterised by numerous loci of related function. Alternative splicing has only rarely been reported in chemosensory loci, for example in 5 out of around 120 loci in Drosophila melanogaster. The gustatory receptor gene Gr39a has four large exons that are alternatively spliced with three small conserved exons. Recently the genome sequences of eleven additional species of Drosophila have become available allowing us to examine variation in the structure of the Gr39a locus across a wide phylogenetic range of fly species. Methodology/Principal Findings. We describe a fifth exon and show that the locus has a complex evolutionary history with several duplications, pseudogenisations and losses of exons. PAML analyses suggested that the whole gene has a history of purifying selection, although this was less strong in exons which underwent duplication. Conclusions/Significance. Estimates of functional divergence between exons were similar in magnitude to functional divergence between duplicated genes, suggesting that exon divergence is broadly equivalent to gene duplication.

An update on MyoD evolution in teleosts and a proposed consensus nomenclature to accommodate the tetraploidization of different vertebrate genomes

Macqueen, Daniel J. — Wed, 06 Feb 2008 00:00:00 GMT

Abstract: Background: MyoD is a muscle specific transcription factor that is essential for vertebrate myogenesis. In several teleost species, including representatives of the Salmonidae and Acanthopterygii, but not zebrafish, two or more MyoD paralogues are conserved that are thought to have arisen from distinct, possibly lineage-specific duplication events. Additionally, two MyoD paralogues have been characterised in the allotetraploid frog, Xenopus laevis. This has lead to a confusing nomenclature since MyoD paralogues have been named outside of an appropriate phylogenetic framework. Methods and Principal Findings: Here we initially show that directly depicting the evolutionary relationships of teleost MyoD orthologues and paralogues is hindered by the asymmetric evolutionary rate of Acanthopterygian MyoD2 relative to other MyoD proteins. Thus our aim was to confidently position the event from which teleost paralogues arose in different lineages by a comparative investigation of genes neighbouring myod across the vertebrates. To this end, we show that genes on the single myod-containing chromosome of mammals and birds are retained in both zebrafish and Acanthopterygian teleosts in a striking pattern of double conserved synteny. Further, phylogenetic reconstruction of these neighbouring genes using Bayesian and maximum likelihood methods supported a common origin for teleost paralogues following the split of the Actinopterygii and Sarcopterygii. Conclusion: Our results strongly suggest that myod was duplicated during the basal teleost whole genome duplication event, but was subsequently lost in the Ostariophysi ( zebrafish) and Protacanthopterygii lineages. We propose a sensible consensus nomenclature for vertebrate myod genes that accommodates polyploidization events in teleost and tetrapod lineages and is justified from a phylogenetic perspective. Description: DJM was supported by a Natural Environment Research Council studentship (NERC/S/A/2004/12435).

The functional response of a generalist predator

Smout, Sophie Caroline — Thu, 27 May 2010 00:00:00 GMT

Abstract: Background: Predators can have profound impacts on the dynamics of their prey that depend on how predator consumption is affected by prey density (the predator's functional response). Consumption by a generalist predator is expected to depend on the densities of all its major prey species (its multispecies functional response, or MSFR), but most studies of generalists have focussed on their functional response to only one prey species. Methodology and principal findings: Using Bayesian methods, we fit an MSFR to field data from an avian predator (the hen harrier Circus cyaneus) feeding on three different prey species. We use a simple graphical approach to show that ignoring the effects of alternative prey can give a misleading impression of the predator's effect on the prey of interest. For example, in our system, a “predator pit” for one prey species only occurs when the availability of other prey species is low. Conclusions and significance: The Bayesian approach is effective in fitting the MSFR model to field data. It allows flexibility in modelling over-dispersion, incorporates additional biological information into the parameter priors, and generates estimates of uncertainty in the model's predictions. These features of robustness and data efficiency make our approach ideal for the study of long-lived predators, for which data may be sparse and management/conservation priorities pressing.

Repeated elicitation of the acoustic startle reflex leads to sensitisation in subsequent avoidance behaviour and induces fear conditioning

Gotz, Thomas — Sat, 01 Jan 2011 00:00:00 GMT

Abstract: Background: Autonomous reflexes enable animals to respond quickly to potential threats, prevent injury and mediate fight or flight responses. Intense acoustic stimuli with sudden onsets elicit a startle reflex while stimuli of similar intensity but with longer rise times only cause a cardiac defence response. In laboratory settings, habituation appears to affect all of these reflexes so that the response amplitude generally decreases with repeated exposure to the stimulus. The startle reflex has become a model system for the study of the neural basis of simple learning processes and emotional processing and is often used as a diagnostic tool in medical applications. However, previous studies did not allow animals to avoid the stimulus and the evolutionary function and long-term behavioural consequences of repeated startling remain speculative. In this study we investigate the follow-up behaviour associated with the startle reflex in wild-captured animals using an experimental setup that allows individuals to exhibit avoidance behaviour. Results: We present evidence that repeated elicitation of the acoustic startle reflex leads to rapid and pronounced sensitisation of sustained spatial avoidance behaviour in grey seals (Halichoerus grypus). Animals developed rapid flight responses, left the exposure pool and showed clear signs of fear conditioning. Once sensitised, seals even avoided a known food source that was close to the sound source. In contrast, animals exposed to non-startling (long rise time) stimuli of the same maximum sound pressure habituated and flight responses waned or were absent from the beginning. The startle threshold of grey seals expressed in units of sensation levels was comparable to thresholds reported for other mammals (93 dB). Conclusions: Our results demonstrate that the acoustic startle reflex plays a crucial role in mediating flight responses and strongly influences the motivational state of an animal beyond a short-term muscular response by mediating long-term avoidance. The reflex is therefore not only a measure of emotional state but also influences emotional processing. The biological function of the startle reflex is most likely associated with mediating rapid flight responses. The data indicate that repeated startling by anthropogenic noise sources might have severe effects on long-term behaviour. Future, studies are needed to investigate whether such effects can be associated with reduced individual fitness or even longevity of individuals.

A non-technical overview of spatially explicit capture-recapture models

Borchers, David — Wed, 01 Feb 2012 00:00:00 GMT

Abstract: Most capture-recapture studies are inherently spatial in nature, with capture probabilities depending on the location of traps relative to animals. The spatial component of the studies has until recently, however, not been incorporated in statistical capture-recapture models. This paper reviews capture-recapture models that do include an explicit spatial component. This is done in a non-technical way, omitting much of the algebraic detail and focussing on the model formulation rather than on the estimation methods (which include inverse prediction, maximum likelihood and Bayesian methods). One can view spatially explicit capture-recapture (SECR) models as an endpoint of a series of spatial sampling models, starting with circular plot survey models and moving through conventional distance sampling models, with and without measurement errors, through mark-recapture distance sampling (MRDS) models. This paper attempts a synthesis of these models in what I hope is a style accessible to non-specialists, placing SECR models in the context of other spatial sampling models.

Tunicates push the limits of animal evo-devo

Ferrier, David Ellard Keith — Thu, 20 Jan 2011 00:00:00 GMT

Abstract: The phylum to which humans belong, Chordata, takes its name from one of the major shared derived features of the group, the notochord. All chordates have a notochord, at least during embryogenesis, and there is little doubt about notochord homology at the morphological level. A study in BMC Evolutionary Biology now shows that there is greater variability in the molecular genetics underlying notochord development than previously appreciated.

Sexual and postmating reproductive isolation between allopatric Drosophila montana populations suggest speciation potential

Jennings, Jackson H. — Mon, 14 Mar 2011 00:00:00 GMT

Abstract: Background: Widely distributed species with populations adapted to different environmental conditions can provide valuable opportunities for tracing the onset of reproductive incompatibilities and their role in the speciation process. Drosophila montana, a D. virilis group species found in high latitude boreal forests in Nearctic and Palearctic regions around the globe, could be an excellent model system for studying the early stages of speciation, as a wealth of information concerning this species' ecology, mating system, life history, genetics and phylogeography is available. However, reproductive barriers between populations have hereto not been investigated. Results: We report both pre- and postmating barriers to reproduction between flies from European (Finnish) and North American (Canadian) populations of Drosophila montana. Using a series of mate-choice designs, we show that flies from these two populations mate assortatively (i.e., exhibit significant sexual isolation) while emphasizing the importance of experimental design in these kinds of studies. We also assessed potential postmating isolation by quantifying egg and progeny production in intra-and interpopulation crosses and show a significant one-way reduction in progeny production, affecting both male and female offspring equally. Conclusion: We provide evidence that allopatric D. montana populations exhibit reproductive isolation and we discuss the potential mechanisms involved. Our data emphasize the importance of experimental design in studies on premating isolation between recently diverged taxa and suggest that postmating barriers may be due to postcopulatory-prezygotic mechanisms. D. montana populations seem to be evolving multiple barriers to gene flow in allopatry and our study lays the groundwork for future investigations of the genetic and phenotypic mechanisms underlying these barriers.

Fitness consequences of female multiple mating : A direct test of indirect benefits

Barbosa, Miguel — Sat, 15 Sep 2012 00:00:00 GMT

Abstract: Background The observation that females mate multiply when males provide nothing but sperm - which sexual selection theory suggests is unlikely to be limiting - continues to puzzle evolutionary biologists. Here we test the hypothesis that multiple mating is prevalent under such circumstances because it enhances female fitness. We do this by allowing female Trinidadian guppies to mate with either a single male or with multiple males, and then tracking the consequences of these matings across two generations. Results Overall, multiply mated females produced 67% more F2 grand-offspring than singly mated females. These offspring, however, did not grow or mature faster, nor were they larger at birth, than F2 grand-offspring of singly mated females. Our results, however, show that multiple mating yields benefits to females in the form of an increase in the production of F1. The higher fecundity among multiply mated mothers was driven by greater production of sons but not daughters. However, contrary to expectation, individually, the offspring of multiply mated females do not grow at different rates than offspring of singly mated females, nor do any indirect fitness benefits or costs accrue to second-generation offspring. Conclusions The study provides strong evidence that multiple mating is advantageous to females, even when males contribute only sperm. This benefit is achieved through an increase in fecundity in the first generation, rather than through other fitness correlates such as size at birth, growth rate, time to sexual maturation and survival. Considered alongside previous work that female guppies can choose to mate with multiple partners, our results provide compelling evidence that direct fitness benefits underpin these mating decisions.

Why do adaptive immune responses cross-react?

Fairlie-Clarke, KJ — Sun, 01 Feb 2009 00:00:00 GMT

Abstract: Antigen specificity of adaptive immune responses is often in the host's best interests, but with important and as yet unpredictable exceptions. For example, antibodies that bind to multiple flaviviral or malarial species can provide hosts with simultaneous protection against many parasite genotypes. Vaccinology often aims to harness such imprecision, because cross-reactive antibodies might provide broad-spectrum protection in the face of antigenic variation by parasites. However, the causes of cross-reactivity among immune responses are not always known, and here, we explore potential proximate and evolutionary explanations for cross-reactivity. We particularly consider whether cross-reactivity is the result of constraints on the ability of the immune system to process information about the world of antigens, or whether an intermediate level of cross-reactivity may instead represent an evolutionary optimum. We conclude with a series of open questions for future interdisciplinary research, including the suggestion that the evolutionary ecology of information processing might benefit from close examination of immunological data.

The influence of mid-ocean ridges on euphausiid and pelagic ecology

Letessier, Tom Bech — Tue, 19 Jun 2012 00:00:00 GMT

Abstract: 1 & 2. Euphausiids comprise a major component of ecosystems in the pelagic realm, the world’s largest habitat, but basin scale drivers of euphausiids diversity and abundance are poorly understood. Mid-Ocean Ridges are the largest topographical feature in the pelagic realm and their benthic and pelagic fauna have only just recently become the focus of research. This thesis present new analyses on the drivers of euphausiids species richness in the Atlantic and the Pacific, giving specific attention to the influence of Mid- Ocean Ridges. New information is given on the biogeography of euphausiids and pelagic food-web trophology of the Mid-Atlantic Ridge, and on the biogeography of pelagic decapods on the South-West Indian Ocean ridge. 3. A Generalized Additive Model framework was used to explore spatial patterns of variability in euphausiid species richness (from recognized areas of occurrence) and in numerical abundance (from the Continuous Plankton Recorder survey) in conjunction with variability in a suite of biological, physical and environmental parameters on, and at either side of, the Mid-Atlantic Ridge. Euphausiid species richness peaked in midlatitudes and was significantly higher on the ridge than in adjacent waters, but the ridge did not influence numerical abundance in the top 10 m significantly. Sea surface temperature (SST) was the most important single factor influencing both euphausiid numerical abundance (-76.7%) and species richness (34.44%). Dissolved silicate concentration, a proxy for diatom abundance, significantly increased species richness (29.46%). Increases in sea surface height variance, a proxy for mixing, increased the numerical abundance of euphausiids. GAM predictions of variability in species richness as a function of SST and depth of the mixed layer were consistent with present theories, which suggest that pelagic niche-availability is related to the thermal structure of the near surface water. 4. Using a Generalized Additive Model in the Pacific, the main drivers of species richness, in order of decreasing importance, were found to be sea surface temperature (explaining 29.53% in species variability), salinity (20.29%), longitude (-15.01%, species richness decreased from West to East), distance to coast (10.99%), and dissolved silicate concentration (9.03%). An additional linear model poorly predicted numerical abundance. The practical differences in drivers of species richness in the Atlantic and Pacific Ocean were compared. Predictions of future species richness changes in the Pacific and Atlantic were made using projected environmental change from the IPCC A1B climate scenario, suggesting an increase in species richness in temperature latitudes (30° to 60° N and S) and little to no change in low latitudes (20° N to 20° S). 5. New baseline information is presented on biogeography, abundance and vertical distribution of euphausiids along the Mid-Atlantic Ridge (40° to 62° N). 18 species were recorded, with Euphausia krohni and Thysanoessa longicaudata being most abundant. Eight species had not been recorded in the area previously. The Subpolar Front is a northern boundary to some southern species, but not a southern boundary to northern ubiquitous species that show submergence. Four major species assemblages were identified and characterised in terms of spatial distribution and species composition. Numerical abundance was highly variable but decreased by orders of magnitude with depth. The Mid-Atlantic Ridge showed only a marginal effect on euphausiid distribution and abundance patterns. 6. Zooplankton and micronektic invertebrate epi- and mesopelagic (0-200 and 200- 800m) vertical distribution (e.g. Euphausiacea, Decapoda, Amphipoda, Thecosomata, Lophogastrida) on either side of the Subpolar Front of the Mid-Atlantic Ridge is described. Dietary relationships are explored, using stable isotope ratios and fatty acid trophic marker (FATM) composition. An increase in trophic level with size was observed. Individuals from southern stations were higher in dinoflagellate Fatty Acid Trophic Markers (FATM) (22:6(n-3)) and individuals from northern stations were higher in Calanus spp and storage FATMs (20:1(n-9) and 22:1(n-9)) reflecting primary production patterns in the two survey sectors. Observations on the geographical and vertical variability in trophodynamics are discussed. 7. New baseline information is presented on the biogeography, abundance, and vertical distribution of mesopelagic (200-1000 m), crustacean micronekton on- and offseamounts of the South-West Indian Ocean Ridge (26° to 42° S). Species richness and numerical abundance were typically higher near seamounts and lower over the abyssal plains, with several species being caught uniquely on seamounts. Observations suggest that the ‘oasis effect’ of seamounts conventionally associated with higher trophic levels is also applicable to pelagic micronektic crustaceans at lower trophic levels. Biophysical coupling of micronekton to seamounts may be an important factor controlling benthopelagic coupling in seamount food-webs. 8. Euphausiid and pelagic diversity is driven primarily by geographical variability in temperature, by longitudinal patterns in upwellings, and by variability in nutrient concentration. Mid-Ocean Ridges modify pelagic ecology, by raising the seafloor and by bringing in proximity true pelagic and bathypelagic predators associated with the seabed. The increase in specialized fauna and biomass associated with ridges and seamounts serves to deplete zooplankton in the near bottom layer (0-200 m) and affect systems in and above the benthic boundary layer (<200 m from the seafloor), and the benthopelagic faunal layer. Mid-Ocean Ridges may serve to structure pelagic faunal distribution, and increase the overall diversity of the world ocean. The influence of ridges in the ocean basin may be comparable to that of hedges in a farmland; whilst delimiting the extent of crops (or zooplankton assemblages), hedges serve as local hotspots of mammal and avian diversity.

Examining the response of top marine predators to ecological change using stable isotope proxies

Hanson, Nora N. — Fri, 30 Nov 2012 00:00:00 GMT

Abstract: Monitoring the response of upper trophic level animals to ecological change is important to understanding the state and stability of ecosystems. Marine predators integrate information over large geographical scales and are relatively long-lived; furthermore, many of these organisms are restricted to terrestrial or freshwater habitats at certain times during their life history and are accessible to researchers. This thesis investigated the response of marine predators to ecological change at a variety of spatial and temporal scales using stable isotope ratio methods with the aims of developing meaningful proxies, or indices, of variability in marine ecosystems. The first study explored the intrinsic (i.e. ontogenetic) and extrinsic (i.e. environmental) factors important to modulating variation in the stable isotope ratios of C and N in tooth dentin of male Antarctic fur seals (Arctocephalus gazella) in the Southern Ocean. In the second study, long-term records of variation in δ15N δ13C values of Atlantic salmon (Salmo salar) scales and grey seal (Halichoerus grypus) tooth dentin provided evidence for large-scale climate forcing across the eastern North Atlantic. In the following study, a more detailed examination of intra- and inter-individual stable isotope variation in Atlantic salmon within a single year was undertaken in an attempt to better understand recent declines in somatic condition of these fish. The last two studies were concerned with the development of high resolution sampling of fish otoliths using secondary mass spectrometry (SIMS) and the application of this technique to reconstructing the thermal and metabolic histories of individual Atlantic salmon from intra-otolith δ13C and δ18O values. Stable isotope proxies can be used to document shifts in trophic dynamics and animal movement that may be associated with ecological change. Using multiple tissues, elements and species, such studies provide unique monitoring tools at a range of spatial and temporal scales.

Workshop on new developments in cetacean survey methods

Borchers, David Louis — Sat, 01 Jan 2011 00:00:00 GMT

Abstract: This 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.

Impact of environmental change on primary production in model marine coastal ecosystems

Hicks, Natalie — Sat, 01 Jan 2011 00:00:00 GMT

Abstract: Coastal ecosystems, including estuaries, provide a range of services to humans, mediated by the species within these ecosystems. Microphytobenthos (MPB) play a vital role in many key processes within estuarine ecosystems, and provide a food source for higher trophic levels. Anthropogenic activity is already causing changes to ecosystems, through pollution, overexploitation and, more recently, climate change. Increasing temperature and carbon dioxide levels, and altered biodiversity, are likely to affect species, and their interactions, within these ecosystems. Much ecological research has focused on the effects of a single stressor on specific species or ecosystems, with relatively little work examining the effects of multiple stressors. The research in this thesis investigates the effects of altered environmental variables (light, tidal regime, temperature and carbon dioxide) and different macrofaunal diversity on primary production (MPB biomass) through a series of manipulative lab-based mesocosm experiments. This work also examines the temporal variability of environmental stressors on species across two trophic levels. Results demonstrate how multiple environmental stressors interact in a complex and non-additive way to determine an ecosystem response (MPB biomass, nutrient concentration), and the effects of altered biodiversity were underpinned by strong species effects. Temporal variation of stressors had a strong effect on ecosystem response. In marine coastal ecosystems, environmental changes through ocean acidification will have economic and social repercussions, directly impacting the human services and livelihoods that these systems provide. As such, future research should be focused on identifying and mitigating the inevitable multiple effects that future global change may have on coastal ecosystems.

Identification of learning mechanisms in a wild meerkat population

Hoppitt, William John Edward — Wed, 08 Aug 2012 00:00:00 GMT

Abstract: Vigorous debates as to the evolutionary origins of culture remain unresolved due to an absence of methods for identifying learning mechanisms in natural populations. While laboratory experiments on captive animals have revealed evidence for a number of mechanisms, these may not necessarily reflect the processes typically operating in nature. We developed a novel method that allows social and asocial learning mechanisms to be determined in animal groups from the patterns of interaction with, and solving of, a task. We deployed it to analyse learning in groups of wild meerkats (Suricata suricatta) presented with a novel foraging apparatus. We identify nine separate learning processes underlying the meerkats' foraging behaviour, in each case precisely quantifying their strength and duration, including local enhancement, emulation, and a hitherto unrecognized form of social learning, which we term `observational perseverance'. Our analysis suggests a key factor underlying the stability of behavioural traditions is a high ratio of specific to generalized social learning effects. The approach has widespread potential as an ecologically valid tool to investigate learning mechanisms in natural groups of animals, including humans.

Vessel noise affects beaked whale behavior : Results of a dedicated acoustic response study

Pirotta, Enrico — Fri, 03 Aug 2012 00:00:00 GMT

Abstract: Some 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.

Spatial variation in foraging behaviour of a marine top predator (Phoca vitulina) determined by a large-scale satellite tagging program

Sharples, Ruth Jemma — Mon, 21 May 2012 00:00:00 GMT

Abstract: The harbour seal (Phoca vitulina) is a widespread marine predator in Northern Hemisphere waters. British populations have been subject to rapid declines in recent years. Food supply or inter-specific competition may be implicated but basic ecological data are lacking and there are few studies of harbour seal foraging distribution and habits. In this study, satellite tagging conducted at the major seal haul outs around the British Isles showed both that seal movements were highly variable among individuals and that foraging strategy appears to be specialized within particular regions. We investigated whether these apparent differences could be explained by individual level factors: by modelling measures of trip duration and distance travelled as a function of size, sex and body condition. However, these were not found to be good predictors of foraging trip duration or distance, which instead was best predicted by tagging region, time of year and inter-trip duration. Therefore, we propose that local habitat conditions and the constraints they impose are the major determinants of foraging movements. Specifically the distance to profitable feeding grounds from suitable haul-out locations may dictate foraging strategy and behaviour. Accounting for proximity to productive foraging resources is likely to be an important component of understanding population processes. Despite more extensive offshore movements than expected, there was also marked fidelity to the local haul-out region with limited connectivity between study regions. These empirical observations of regional exchange at short time scales demonstrates the value of large scale electronic tagging programs for robust characterization of at-sea foraging behaviour at a wide spatial scale.

Global coverage of cetacean line-transect surveys : status quo, data gaps and future challenges

Kaschner, Kristin — Wed, 12 Sep 2012 00:00:00 GMT

Abstract: Knowledge of abundance, trends and distribution of cetacean populations is needed to inform marine conservation efforts, ecosystem models and spatial planning. We compiled a geo-spatial database of published data on cetacean abundance from dedicated visual line-transect surveys and encoded >1100 abundance estimates for 47 species from 430 surveys conducted worldwide from 1975-2005. Our subsequent analyses revealed large spatial, temporal and taxonomic variability and gaps in survey coverage. With the exception of Antarctic waters, survey coverage was biased toward the northern hemisphere, especially US and northern European waters. Overall, <25% of the world’s ocean surface was surveyed and only 6% had been covered frequently enough (≥ 5 times) to allow trend estimation. Almost half the global survey effort, defined as total area (km2) covered by all survey study areas across time, was concentrated in the Eastern Tropical Pacific (ETP). Neither the number of surveys conducted nor the survey effort had increased in recent years. Across species, an average of 10% of a species’ predicted range had been covered by at least one survey, but there was considerable variation among species. With the exception of three delphinid species, <1% of all species’ ranges had been covered frequently enough for trend analysis. We use a data-rich species, sperm whale, as an example to illustrate the challenges of using available data from line-transect surveys for the detection of trends or for spatial planning. Finally, we propose and contrast several field and analytical methods to fill in data gaps to improve future cetacean conservation management efforts.

Defining and evaluating the impact of cross-disciplinary conservation research

Evely, Anna C. — Wed, 01 Dec 2010 00:00:00 GMT

Abstract: Cross-disciplinary research is advocated as a way of improving understanding of the complexity of environmental problems; cross-disciplinary projects, centres and academic institutes have increased. However, there is confusion over the nature of cross-disciplinary research. Through review of papers defining themselves as cross-disciplinary that aim to address conservation problems, and by standardizing the definition of cross-disciplinary research, it is possible to evaluate the potential research impact on peers and practitioners. When papers were reclassified by authors, those reclassified as transdisciplinary were perceived to have a greater impact on practitioners, and those reclassified as non cross-disciplinary had the greatest impact on colleagues. Having clear definitions for types of cross-disciplinary research would help establish a firm foundation, not only for improving research quality, but also for evaluating research impact. While the number of cross-disciplinary studies is increasing, cross-disciplinary research falls short of integrating disciplinary methods in much depth and does not have much impact on participants outside of academia.

Numerical simulation of shear-induced instabilities in internal solitary waves

Carr, Magda — Sun, 25 Sep 2011 00:00:00 GMT

Abstract: A numerical method that employs a combination of contour advection and pseudo-spectral techniques is used to simulate shear-induced instabilities in an internal solitary wave (ISW). A three-layer configuration for the background stratification, in which a linearly stratified intermediate layer is sandwiched between two homogeneous ones, is considered throughout. The flow is assumed to satisfy the inviscid, incompressible, Oberbeck–Boussinesq equations in two dimensions. Simulations are initialized by fully nonlinear, steady-state, ISWs. The results of the simulations show that the instability takes place in the pycnocline and manifests itself as Kelvin–Helmholtz billows. The billows form near the trough of the wave, subsequently grow and disturb the tail. Both the critical Richardson number (Ric) and the critical amplitude required for instability are found to be functions of the ratio of the undisturbed layer thicknesses. It is shown, therefore, that the constant, critical bound for instability in ISWs given in Barad & Fringer (J. Fluid Mech., vol. 644, 2010, pp. 61–95), namely Ric = 0.1 ± 0.01 , is not a sufficient condition for instability. It is also shown that the critical value of Lx/λ required for instability, where Lx is the length of the region in a wave in which Ri < 1/4 and λ is the half-width of the wave, is sensitive to the ratio of the layer thicknesses. Similarly, a linear stability analysis reveals that δiTw (where δi is the growth rate of the instability averaged over Tw, the period in which parcels of fluid are subjected to Ri < 1/4) is very sensitive to the transition between the undisturbed pycnocline and the homogeneous layers, and the amplitude of the wave. Therefore, the alternative tests for instability presented in Fructus et al. (J. Fluid Mech., vol. 620, 2009, pp. 1–29) and Barad & Fringer (J. Fluid Mech., vol. 644, 2010, pp. 61–95), respectively, namely Lx/λ ≥ 0.86 and δiTw > 5 , are shown to be valid only for a limited parameter range. Description: This work was supported by the UK Engineering and Physical Sciences Research Council [grant number EP/F030622/1]

Fast skeletal muscle transcriptome of the Gilthead sea bream (Sparus aurata) determined by next generation sequencing

Garcia de la Serrana Castillo, Daniel — Fri, 11 May 2012 00:00:00 GMT

Abstract: Background: The gilthead sea bream (Sparus aurata L.) occurs around the Mediterranean and along Eastern Atlantic coasts from Great Britain to Senegal. It is tolerant of a wide range of temperatures and salinities and is often found in brackish coastal lagoons and estuarine areas, particularly early in its life cycle. Gilthead sea bream are extensively cultivated in the Mediterranean with an annual production of 125,000 metric tonnes. Here we present a de novo assembly of the fast skeletal muscle transcriptome of gilthead sea bream using 454 reads and identify gene paralogues, splice variants and microsatellite repeats. An annotated transcriptome of the skeletal muscle will facilitate understanding of the genetic and molecular basis of traits linked to production in this economically important species. Results: Around 2.7 million reads of mRNA sequence data were generated from the fast myotomal of adult fish (~2 kg) and juvenile fish (~0.09 kg) that had been either fed to satiation, fasted for 3-5d or transferred to low (11°C) or high (33°C) temperatures for 3-5d. Newbler v2.5 assembly resulted in 43,461 isotigs >100 bp. The number of sequences annotated by searching protein and gene ontology databases was 10,465. The average coverage of the annotated isotigs was x40 containing 5655 unique gene IDs and 785 full-length cDNAs coding for proteins containing 58–1536 amino acids. The v2.5 assembly was found to be of good quality based on validation using 200 full-length cDNAs from GenBank. Annotated isotigs from the reference transcriptome were attributable to 344 KEGG pathway maps. We identified 26 gene paralogues (20 of them teleost-specific) and 43 splice variants, of which 12 had functional domains missing that were likely to affect their biological function. Many key transcription factors, signaling molecules and structural proteins necessary for myogenesis and muscle growth have been identified. Physiological status affected the number of reads that mapped to isotigs, reflecting changes in gene expression between treatments. Conclusions: We have produced a comprehensive fast skeletal muscle transcriptome for the gilthead sea bream, which will provide a resource for SNP discovery in genes with a large effect on production traits of commercial interest and for expression studies of growth and adaptation.

In and out of Madagascar : dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae)

Strijk, Joeri S — Fri, 10 Aug 2012 00:00:00 GMT

Abstract: Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.

How selection structures species abundance distributions

Magurran, Anne E. — Sat, 22 Sep 2012 00:00:00 GMT

Abstract: How do species divide resources to produce the characteristic species abundance distributions seen in nature? One way to resolve this problem is to examine how the biomass (or capacity) of the spatial guilds that combine to produce an abundance distribution is allocated among species. Here we argue that selection on body size varies across guilds occupying spatially distinct habitats. Using an exceptionally well-characterized estuarine fish community, we show that biomass is concentrated in large bodied species in guilds where habitat structure provides protection from predators, but not in those guilds associated with open habitats and where safety in numbers is a mechanism for reducing predation risk. We further demonstrate that while there is temporal turnover in the abundances and identities of species that comprise these guilds, guild rank order is conserved across our 30-year time series. These results demonstrate that ecological communities are not randomly assembled but can be decomposed into guilds where capacity is predictably allocated among species.

Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates

Tinti, Michele — Sun, 01 Jul 2012 00:00:00 GMT

Abstract: 14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders.

Incipient speciation in Drosophila melanogaster involves chemical signals

Grillet, Micheline — Thu, 19 Jan 2012 00:00:00 GMT

Abstract: The sensory and genetic bases of incipient speciation between strains of Drosophila melanogaster from Zimbabwe and those from elsewhere are unknown. We studied mating behaviour between eight strains - six from Zimbabwe, together with two cosmopolitan strains. The Zimbabwe strains showed significant sexual isolation when paired with cosmopolitan males, due to Zimbabwe females discriminating against these males. Our results show that flies' cuticular hydrocarbons (CHs) were involved in this sexual isolation, but that visual and acoustic signals were not. The mating frequency of Zimbabwe females was highly significantly negatively correlated with the male's relative amount of 7-tricosene (%7-T), while the mating of cosmopolitan females was positively correlated with %7-T. Variation in transcription levels of two hydrocarbon-determining genes, desat1 and desat2, did not correlate with the observed mating patterns. Our study represents a step forward in our understanding of the sensory processes involved in this classic case of incipient speciation.

Temperature, age of mating and starvation determine the role of maternal effects on sex allocation in the mealybug Planococcus citri

Ross, Laura — Sun, 01 May 2011 00:00:00 GMT

Abstract: Environmental effects on sex allocation are common, yet the evolutionary significance of these effects remains poorly understood. Environmental effects might influence parents, such that their condition directly influences sex allocation by altering the relative benefits of producing sons versus daughters. Alternatively, the environment might influence the offspring themselves, such that the conditions they find themselves in influence their contribution to parental fitness. In both cases, parents might be selected to bias their sex ratio according to the prevailing environmental conditions. Here, we consider sex allocation in the citrus mealybug Planococcus citri, a species with an unusual genetic system in which paternal genes are lost from the germline in males. We test environmental factors that may influence either female condition directly (rearing temperature and food restriction) or that may be used as cues of the future environment (age at mating). Using cytological techniques to obtain primary sex ratios, we show that high temperature, older age at mating and starvation all affect sex allocation, resulting in female-biased sex ratios. However, the effect of temperature is rather weak, and food restriction appears to be strongly associated with reduced longevity and a truncation of the usual schedule of male and offspring production across a female's reproductive lifetime. Instead, facultative sex allocation seems most convincingly affected by age at mating, supporting previous work that suggests that social interactions experienced by adult P. citri females are used when allocating sex. Our results highlight that, even within one species, different aspects of the environment may have conflicting effects on sex allocation.

How reproductive ecology contributes to the spread of a globally invasive fish

Deacon, Amy E. — Mon, 19 Sep 2011 00:00:00 GMT

Abstract: Invasive freshwater fish represent a major threat to biodiversity. Here, we first demonstrate the dramatic, human-mediated range expansion of the Trinidadian guppy (Poecilia reticulata), an invasive fish with a reputation for negatively impacting native freshwater communities. Next, we explore possible mechanisms that might explain successful global establishment of this species. Guppies, along with some other notable invasive fish species such as mosquitofish (Gambusia spp.), have reproductive adaptations to ephemeral habitats that may enable introductions of very small numbers of founders to succeed. The remarkable ability of single pregnant guppies to routinely establish viable populations is demonstrated using a replicated mesocosm set up. In 86% of cases, these populations persisted for two years (the duration of the experiment). Establishment success was independent of founder origin (high and low predation habitats), and there was no loss of behavioural performance amongst mesocosm juveniles. Behavioural "signatures" of the founding locality were, however, evident in mesocosm fish. Our results demonstrate that introductions consisting of a single individual can lead to thriving populations of this invasive fish and suggest that particular caution should be exercised when introducing this species, or other livebearers, to natural water bodies. Description: The work was funded by Natural Environment Research Council (NERC) (UK) and the European Research Council.

The quantitative genetic basis of sex ratio variation in Nasonia vitripennis : a QTL study

Pannebakker, B. A. — Sat, 01 Jan 2011 00:00:00 GMT

Abstract: Our understanding of how natural selection should shape sex allocation is perhaps more developed than for any other trait. However, this understanding is not matched by our knowledge of the genetic basis of sex allocation. Here, we examine the genetic basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, a species well known for its response to local mate competition (LMC). We identified a quantitative trait locus (QTL) for sex ratio on chromosome 2 and three weaker QTL on chromosomes 3 and 5. We tested predictions that genes associated with sex ratio should be pleiotropic for other traits by seeing if sex ratio QTL co-occurred with clutch size QTL. We found one clutch size QTL on chromosome 1, and six weaker QTL across chromosomes 2, 3 and 5, with some overlap to regions associated with sex ratio. The results suggest rather limited scope for pleiotropy between these traits.

Phocid seal leptin : tertiary structure and hydrophobic receptor binding site preservation during distinct leptin gene evolution

Hammond, John Anthony — Thu, 19 Apr 2012 00:00:00 GMT

Abstract: The cytokine hormone leptin is a key signalling molecule in many pathways that control physiological functions. Although leptin demonstrates structural conservation in mammals, there is evidence of positive selection in primates, lagomorphs and chiropterans. We previously reported that the leptin genes of the grey and harbour seals (phocids) have significantly diverged from other mammals. Therefore we further investigated the diversification of leptin in phocids, other marine mammals and terrestrial taxa by sequencing the leptin genes of representative species. Phylogenetic reconstruction revealed that leptin diversification was pronounced within the phocid seals with a high dN/dS ratio of 2.8, indicating positive selection. We found significant evidence of positive selection along the branch leading to the phocids, within the phocid clade, but not over the dataset as a whole. Structural predictions indicate that the individual residues under selection are away from the leptin receptor (LEPR) binding site. Predictions of the surface electrostatic potential indicate that phocid seal leptin is notably different to other mammalian leptins, including the otariids. Cloning the grey seal leptin binding domain of LEPR confirmed that this was structurally conserved. These data, viewed in toto, support a hypothesis that phocid leptin divergence is unlikely to have arisen by random mutation. Based upon these phylogenetic and structural assessments, and considering the comparative physiology and varying life histories among species, we postulate that the unique phocid diving behaviour has produced this selection pressure. The Phocidae includes some of the deepest diving species, yet have the least modified lung structure to cope with pressure and volume changes experienced at depth. Therefore, greater surfactant production is required to facilitate rapid lung re-inflation upon surfacing, while maintaining patent airways. We suggest that this additional surfactant requirement is met by the leptin pulmonary surfactant production pathway which normally appears only to function in the mammalian foetus.

Modeling distribution and abundance of Antarctic baleen whales using ships of opportunity

Williams, Robert — Thu, 01 Jun 2006 00:00:00 GMT

Abstract: Information on animal abundance and distribution is at the cornerstone of many wildlife and conservation strategies. However, these data can be difficult and costly to obtain for cetacean species. The expense of sufficient ship time to conduct design-unbiased line transect surveys may be simply out of reach for researchers in many countries, which nonetheless grapple with problems of conservation of endangered species, by-catch of small cetaceans in commercial fisheries, and progression toward ecosystem-based fisheries management. Recently developed spatial modeling techniques show promise for estimating wildlife abundance using non-randomized surveys, but have yet to receive much field-testing in areas where designed surveys have also been conducted. Effort and sightings data were collected along 9 650 km of transects aboard ships of opportunity in the Southern Ocean during the austral summers of 2000 - 2001 and 2001 - 2002. Generalized additive models with generalized cross-validation were used to express heterogeneity of cetacean sightings as functions of spatial covariates. Models were used to map predicted densities and to estimate abundance of humpback, minke, and fin whales in the Drake Passage and along the Antarctic Peninsula. All species' distribution maps showed strong density gradients, which were robust to jackknife resampling when each of 14 trips was removed sequentially with replacement. Looped animations of model predictions of whale density illustrate uncertainty in distribution estimates in a way that is informative to non-scientists. The best abundance estimate for humpback whales was 1 829 (95% CI: 978- 3 422). Abundance of fin whales was 4 487 ( 95% CI: 1 326 - 15 179) and minke whales was 1,544 ( 95% CI: 1,221 - 1,953). These estimates agreed roughly with those reported from a designed survey conducted in the region during the previous austral summer. These estimates assumed that all animals on the trackline were detected, but preliminary results suggest that any negative bias due to violation of this assumption was likely small. Similarly, current methodological limitations prohibit inclusion of all known sources of uncertainty in the favored variance estimator. Meanwhile, our approach can be seen generally as an inexpensive pilot study to identify areas of predicted high density that could be targeted to: inform stratified designs for future line transect surveys, making them less expensive and more precise; increase efficiency of future photo-identification or biopsy studies; identify candidate time-area fisheries closures to minimize by-catch; or direct ecotourism activities. The techniques are likely to apply to areas where funding is limiting, where cetacean studies or wilderness-based tourism are just beginning, or in regions where even a very rough estimate of animal abundance is needed for conservation or management purposes.

Methods for investigating measurement error in cetacean line-transect surveys

Williams, Robert — Mon, 26 Feb 2007 00:00:00 GMT

Abstract: Line-transect estimates of abundance generally assume that distances and angles to animals are measured without error. Biased distance measurements will lead to corresponding bias in abundance estimates. Efforts to address this have been made, but measuring distance to cetaceans at sea remains problematic. Four distance-estimation experiments were conducted to explore relationships between estimated and measured distance, Heteroscedasticity was found in all four cases. Preliminary evidence suggested that an observer differed in the ability to judge distance to fixed, continuously-visible cues and ephemeral, cetacean cues, which calls into the question the common practice of using marker buoys as cetacean proxies in distance-estimation experiments. Two studies found visual estimates to be positively biased, and two studies found reticule measurements to be negatively biased. Suitable correction factors were developed to address systematic bias from visual estimates, but these varied widely among observers and were sometimes non-linear. Errors in three studies showed positive skew, suggesting that ranges were overestimated to a larger degree than they were underestimated. if reticule and photogrammetric measurements yield log-normally distributed errors generally, then a least-squares regression will always overstimate the correction factor, underestimate range, and overestimate abundance. Photogrammetric methods to measure range to cetaceans performed well, and their use is encouraged. When measurements cannot be made to all sightings, however, it is recommended that experiements be conducted that generate sufficient sample size (of the target species, across typical survey conditions, and beyond the maximum range that most estimates will be made during the survey) to assess error distributions, examine evidence for non-linearity, and to consider inter-observer differences. Distance experiments, and training on survey protocols, and be conducted using ships of opportunity prior to the beginning of a dedicated survey, which would improve observer efficiency while reducing the costs of dedicated vessel time.

Global analysis of cetacean line-transect surveys : detecting trends in cetacean density

Jewell, Rebecca Lucy — Mon, 07 May 2012 00:00:00 GMT

Abstract: Measuring 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.

Inbreeding and selection on sex ratio in the bark beetle Xylosandrus germanus

Keller, Laurent — Tue, 13 Dec 2011 00:00:00 GMT

Abstract: Background: Local Mate Competition (LMC) theory predicts a female should produce a more female-biased sex ratio if her sons compete with each other for mates. Because it provides quantitative predictions that can be experimentally tested, LMC is a textbook example of the predictive power of evolutionary theory. A limitation of many earlier studies in the field is that the population structure and mating system of the studied species are often estimated only indirectly. Here we use microsatellites to characterize the levels of inbreeding of the bark beetle Xylosandrus germanus, a species where the level of LMC is expected to be high. Results: For three populations studied, genetic variation for our genetic markers was very low, indicative of an extremely high level of inbreeding (F-IS = 0.88). There was also strong linkage disequilibrium between microsatellite loci and a very strong genetic differentiation between populations. The data suggest that matings among non-siblings are very rare (3%), although sex ratios from X. germanus in both the field and the laboratory have suggested more matings between non-sibs, and so less intense LMC. Conclusions: Our results confirm that caution is needed when inferring mating systems from sex ratio data, especially when a lack of biological detail means the use of overly simple forms of the model of interest.

A general discrete-time modeling framework for animal movement using multi-state random walks

McClintock, Brett Thomas — Sun, 01 Jan 2012 00:00:00 GMT

Abstract: Recent developments in animal tracking technology have permitted the collection of detailed data on the movement paths of individuals from many species. However, analysis methods for these data have not developed at a similar pace, largely due to a lack of suitable candidate models, coupled with the technical difficulties of fitting such models to data. To facilitate a general modeling framework, we propose that complex movement paths can be conceived as a series of movement strategies among which animals transition as they are affected by changes in their internal and external environment. We synthesize previously existing and novel methodologies to develop a general suite of mechanistic models based on biased and correlated random walks that allow different behavioral states for directed (e.g., migration), exploratory (e.g., dispersal), area-restricted (e.g., foraging), and other types of movement. Using this “tool-box” of nested model components, multi-state movement models may be custom-built for a wide variety of species and applications. As a unified state-space modeling framework, it allows the simultaneous investigation of numerous hypotheses about animal movement from imperfectly observed data, including time allocations to different movement behavior states, transitions between states, the use of memory or navigation, and strengths of attraction (or repulsion) to specific locations. The inclusion of covariate information permits further investigation of specific hypotheses related to factors driving different types of movement behavior. Using reversible jump Markov chain Monte Carlo methods to facilitate Bayesian model selection and multi-model inference, we apply the proposed methodology to real data by adapting it to the natural history of the grey seal (Halichoerus grypus) in the North Sea. Although previous grey seal studies tended to focus on correlated movements, we found overwhelming evidence that bias towards haul-out or foraging locations better explained seal movement than simple or correlated random walks. Posterior model probabilities also provided evidence that seals transition among directed, area-restricted, and exploratory movements associated with haul-out, foraging, and other behaviors. With this intuitive framework for modeling and interpreting animal movement, we believe the development and application of bespoke movement models will become more accessible to ecologists and non-statisticians.

The influence of the freshwater environment and the biological characteristics of Atlantic salmon smolts on their subsequent marine survival

Russell, Ian — Sun, 01 Jan 2012 00:00:00 GMT

Abstract: Atlantic salmon have declined markedly in the past 20-30 years throughout their range. Much of the focus for this decline has been on increased mortality during the marine phase of the life cycle. However, marine mortality does not operate independently of factors acting in freshwater and the biological characteristics of smolts migrating to sea. Over recent decades, juvenile salmon in many rivers have grown faster and migrated to sea at a younger age, and thus typically smaller. This has shortened the generation time for many individuals, and may dampen the impact of increased marine mortality, assuming expected higher in-river survival prior to smolting is not outweighed by increased mortality of smaller smolts at sea. Over the same period, smolt run-timing across the geographic range has been occurring earlier, at a rate of almost three days per decade, on average. This has given rise to growing concerns about smolts potentially missing the optimum environmental migration “window”, the timing of which may also be changing. Contaminants and other factors operating in freshwater also impact on smolt quality with adverse consequences for their physiological readiness for life at sea. Given that managers have very limited ability to influence the broad scale factors limiting salmon survival at sea, it is vital that freshwater habitats are managed to both maximise smolt output and to minimise the impact of factors acting in freshwater which may compromise salmon once they migrate to sea.

The use of active sonar to study cetaceans

Bernasconi, Matteo — Fri, 01 Jun 2012 00:00:00 GMT

Abstract: Cetacean species face serious challenges worldwide due to the increasing noise pollution brought to their environment by human activities such as seismic exploration. Regulation of these activities is vaguely defined and uncoordinated. Visual observations and passive listening devices, aimed at preventing conflicts between human wealth and cetaceans’ health have some fundamental limitations and may consequently fail their mitigation purposes. Active sonar technology could be the optimal solution to implement mitigation of such human activities. In my thesis, the proper sonar unit was used to test the feasibility to detect cetaceans in situ. Omnidirectional sonars could be the optimal solution to monitor the presence of cetaceans in the proximity of potential danger areas. To use this class of sonar in a quantitative manner, the first step was to develop a calibration method. This thesis links in situ measurements of target strength (TS) with variation trends linked to the behavior, morphology and physiology of cetacean. The butterfly effect of a cetacean’s body was described for a fin whale insonified from different angles. A relationship between whale respiration and TS energy peaks was tested through a simple prediction model which seems very promising for further implementation. The effect of lung compression on cetacean TS due to increasing depth was tested through a basic mathematical model. The model fit the in situ TS measurements. TS measurements at depth of a humpback whale, when post-processed, correspond to TS measurements recorded at the surface. Sonar technology is clearly capable of detecting whale foot prints around an operating vessel. Sonar frequency response shows that frequencies between 18 and 38 kHz should be employed. This work has established a baseline and raised new questions so that active sonar can be developed and employed in the best interest for the whales involved in potentially harmful conflicts with man.

Status assessment of the Critically Endangered Azores Bullfinch Pyrrhula murina

Ceia, Ricardo S. — Sat, 01 Jan 2011 00:00:00 GMT

Abstract: The Azores Bullfinch is endemic to the island of São Miguel (Azores, Portugal). Its status was uplisted to Critically Endangered in 2005 on the basis of an extremely small and declining population that was considered to be restricted to a very small mountain range (43 km2), in a single location, within which the spread of invasive plants constituted a threat to habitat quality. Nevertheless, information was mostly inferred, or the product of, non-systematic studies. In order to carry out a complete assessment of the conservation status we analysed: (i) population trend, calculated from annual monitoring 1991–2008, (ii) population size, and (iii) range size, obtaining estimates in a single morning study in 2008 involving the simultaneous participation of 48 observers. Contrary to previous inferences, the population is no longer decreasing, although quality of laurel forest habitat continues to decline due to the persistent threat of invasive species. Population size (mean ± SE) was estimated at 1,064 ± 304 individuals using distance sampling methods, although the estimate was very sensitive to the survey method used. Range size estimates (extent of occurrence and area of occupancy) were 144 km2 and 83 km2 respectively. Given the present information, we propose the downlisting of Azores Bullfinch to Endangered on the IUCN Red List.

Deadly diving? Physiological and behavioural management of decompression stress in diving mammals

Hooker, S. K. — Thu, 22 Mar 2012 00:00:00 GMT

Abstract: Decompression sickness (DCS; 'the bends') is a disease associated with gas uptake at pressure. The basic pathology and cause are relatively well known to human divers. Breath-hold diving marine mammals were thought to be relatively immune to DCS owing to multiple anatomical, physiological and behavioural adaptations that reduce nitrogen gas (N-2) loading during dives. However, recent observations have shown that gas bubbles may form and tissue injury may occur in marine mammals under certain circumstances. Gas kinetic models based on measured time-depth profiles further suggest the potential occurrence of high blood and tissue N-2 tensions. We review evidence for gas-bubble incidence in marine mammal tissues and discuss the theory behind gas loading and bubble formation. We suggest that diving mammals vary their physiological responses according to multiple stressors, and that the perspective on marine mammal diving physiology should change from simply minimizing N-2 loading to management of the N-2 load. This suggests several avenues for further study, ranging from the effects of gas bubbles at molecular, cellular and organ function levels, to comparative studies relating the presence/absence of gas bubbles to diving behaviour. Technological advances in imaging and remote instrumentation are likely to advance this field in coming years.

Temporal turnover and the maintenance of diversity in ecological assemblages

Magurran, Anne E. — Sat, 27 Nov 2010 00:00:00 GMT

Abstract: Temporal variation in species abundances occurs in all ecological communities. Here, we explore the role that this temporal turnover plays in maintaining assemblage diversity. We investigate a three-decade time series of estuarine fishes and show that the abundances of the individual species fluctuate asynchronously around their mean levels. We then use a time-series modelling approach to examine the consequences of different patterns of turnover, by asking how the correlation between the abundance of a species in a given year and its abundance in the previous year influences the structure of the overall assemblage. Classical diversity measures that ignore species identities reveal that the observed assemblage structure will persist under all but the most extreme conditions. However, metrics that track species identities indicate a narrower set of turnover scenarios under which the predicted assemblage resembles the natural one. Our study suggests that species diversity metrics are insensitive to change and that measures that track species ranks may provide better early warning that an assemblage is being perturbed. It also highlights the need to incorporate temporal turnover in investigations of assemblage structure and function.

Ancient homeobox gene loss and the evolution of chordate brain and pharynx development : deductions from amphioxus gene expression

Butts, Thomas — Mon, 22 Nov 2010 00:00:00 GMT

Abstract: Homeobox genes encode a large superclass of transcription factors with widespread roles in animal development. Within chordates there are over 100 homeobox genes in the invertebrate cephalochordate amphioxus and over 200 in humans. Set against this general trend of increasing gene number in vertebrate evolution, some ancient homeobox genes that were present in the last common ancestor of chordates have been lost from vertebrates. Here, we describe the embryonic expression of four amphioxus descendants of these genes—AmphiNedxa, AmphiNedxb, AmphiMsxlx and AmphiNKx7. All four genes are expressed with a striking asymmetry about the left–right axis in the pharyngeal region of neurula embryos, mirroring the pronounced asymmetry of amphioxus embryogenesis. AmphiMsxlx and AmphiNKx7 are also transiently expressed in an anterior neural tube region destined to become the cerebral vesicle. These findings suggest significant rewiring of developmental gene regulatory networks occurred during chordate evolution, coincident with homeobox gene loss. We propose that loss of otherwise widely conserved genes is possible when these genes function in a confined role in development that is subsequently lost or significantly modified during evolution. In the case of these homeobox genes, we propose that this has occurred in relation to the evolution of the chordate pharynx and brain.

Sexual selection on song and cuticular hydrocarbons in two distinct populations of Drosophila montana

Veltsos, Paris — Sun, 01 Jan 2012 00:00:00 GMT

Abstract: Sexual selection has the potential to contribute to population divergence and speciation. Most studies of sexual selection in Drosophila have concentrated on a single signaling modality, usually either courtship song or cuticular hydrocarbons (CHCs), which can act as contact pheromones. We have examined the relationship between both signal types and reproductive success using F1–3 offspring of wild- collected flies, raised in the lab. We used two populations of the Holarctic species Drosophila montana that represent different phylogeographic clades that have been separate for ca. 0.5 million years (MY), and differ to some extent in both traits. Here, we characterize the nature and identify the targets of sexual selection on song, CHCs, and both traits combined within the populations. Three measures of courtship outcome were used as fitness proxies. They were the probability of mating, mating latency, and the production of rejection song by females, and showed patterns of association with different traits that included both linear and quadratic selection. Courtship song predicted courtship outcome better than CHCs and the signal modalities acted in an additive rather than synergistic manner. Selection was generally consistent in direction and strength between the two populations and favored males that sang more vigorously. Sexual selection differed in the extent, strength, and nature on some of the traits between populations. However, the differences in the directionality of selection detected were not a good predictor of population differences. In addition, a character previously shown to be important for species recognition, interpulse interval, was found to be under sexual selection. Our results highlight the complexity of understanding the relationship between within-population sexual selection and population differences. Sexual selection alone cannot predict differences between populations.

Beaked whales respond to simulated and actual navy sonar

Tyack, Peter L. — Mon, 14 Mar 2011 00:00:00 GMT

Abstract: Beaked whales have mass stranded during some naval sonar exercises, but the cause is unknown. They are difficult to sight but can reliably be detected by listening for echolocation clicks produced during deep foraging dives. Listening for these clicks, we documented Blainville's beaked whales, Mesoplodon densirostris, in a naval underwater range where sonars are in regular use near Andros Island, Bahamas. An array of bottom-mounted hydrophones can detect beaked whales when they click anywhere within the range. We used two complementary methods to investigate behavioral responses of beaked whales to sonar: an opportunistic approach that monitored whale responses to multi-day naval exercises involving tactical mid-frequency sonars, and an experimental approach using playbacks of simulated sonar and control sounds to whales tagged with a device that records sound, movement, and orientation. Here we show that in both exposure conditions beaked whales stopped echolocating during deep foraging dives and moved away. During actual sonar exercises, beaked whales were primarily detected near the periphery of the range, on average 16 km away from the sonar transmissions. Once the exercise stopped, beaked whales gradually filled in the center of the range over 2-3 days. A satellite tagged whale moved outside the range during an exercise, returning over 2-3 days post-exercise. The experimental approach used tags to measure acoustic exposure and behavioral reactions of beaked whales to one controlled exposure each of simulated military sonar, killer whale calls, and band-limited noise. The beaked whales reacted to these three sound playbacks at sound pressure levels below 142 dB re 1 mu Pa by stopping echolocation followed by unusually long and slow ascents from their foraging dives. The combined results indicate similar disruption of foraging behavior and avoidance by beaked whales in the two different contexts, at exposures well below those used by regulators to define disturbance.

The first animals : ca. 760-million-year-old sponge-like fossils from Namibia

Brain, C. K. 'Bob' — Sun, 01 Jan 2012 00:00:00 GMT

Abstract: One of the most profound events in biospheric evolution was the emergence of animals, which is thought to have occurred some 600-650 Ma. Here we report on the discovery of phosphatised body fossils that we interpret as ancient sponge-like fossils and term them Otavia antiqua gen. et sp. nov. The fossils are found in Namibia in rocks that range in age between about 760 Ma and 550 Ma. This age places the advent of animals some 100 to 150 million years earlier than proposed, and prior to the extreme climatic changes and postulated stepwise increases in oxygen levels of Ediacaran time. These findings support the predictions based on genetic sequencing and inferences drawn from biomarkers that the first animals were sponges. Further, the deposition and burial of Otavia as sedimentary particles may have driven the large positive C-isotopic excursions and increases in oxygen levels that have been inferred for Neoproterozoic time.

A critical review of the literature on population modelling

Cabrelli, Abigail — Thu, 01 Jan 2009 00:00:00 GMT

Abstract: The 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. Description: Final Report to the Joint Industry Project of the International Association of Oil & Gas Producers on contract JIP22 07_20

Universal scaling rules predict evolutionary patterns of myogenesis in species with indeterminate growth

Johnston, Ian Alistair — Thu, 07 Jun 2012 00:00:00 GMT

Abstract: Intraspecific phenotypic variation is ubiquitous and often associated with resource exploitation in emerging habitats. For example, reduced body size has evolved repeatedly in Arctic charr (Salvelinus alpinus L.) and threespine stickleback (Gasterosteus aculeatus L.) across post-glacial habitats of the Northern Hemisphere. Exploiting these models, we examined how body size and myogenesis evolve with respect to the 'optimum fibre size hypothesis', which predicts that selection acts to minimize energetic costs associated with ionic homeostasis by optimizing muscle fibre production during development. In eight dwarf Icelandic Arctic charr populations, the ultimate production of fast-twitch muscle fibres (FN(max)) was only 39.5 and 15.5 per cent of that in large-bodied natural and aquaculture populations, respectively. Consequently, average fibre diameter (FD) scaled with a mass exponent of 0.19, paralleling the relaxation of diffusional constraints associated with mass-specific metabolic rate scaling. Similar reductions in FN(max) were observed for stickleback, including a small-bodied Alaskan population derived from a larger-bodied oceanic stock over a decadal timescale. The results suggest that in species showing indeterminate growth, body size evolution is accompanied by strong selection for fibre size optimization, theoretically allowing resources saved from ionic homeostasis to be allocated to other traits affecting fitness, including reproduction. Gene flow between small- and large-bodied populations residing in sympatry may counteract the evolution of this trait.

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. — Sun, 01 Jan 2012 00:00:00 GMT

A toolbox for fitting complex spatial point process models using integrated nested Laplace approximation (INLA)

Illian, Janine Baerbel — Sat, 01 Dec 2012 00:00:00 GMT

Abstract: This paper develops methodology that provides a toolbox for routinely fitting complex models to realistic spatial point pattern data. We consider models that are based on log-Gaussian Cox processes and include local interaction in these by considering constructed covariates. This enables us to use integrated nested Laplace approximation and to considerably speed up the inferential task. In addition, methods for model comparison and model assessment facilitate the modelling process. The performance of the approach is assessed in a simulation study. To demonstrate the versatility of the approach, models are tted to two rather dierent examples, a large rainforest data set with covariates and a point pattern with multiple marks.

Selection of reference genes for expression studies with fish myogenic cell cultures

Bower, Neil I. — Mon, 10 Aug 2009 00:00:00 GMT

Abstract: Background: Relatively few studies have used cell culture systems to investigate gene expression and the regulation of myogenesis in fish. To produce robust data from quantitative real-time PCR mRNA levels need to be normalised using internal reference genes which have stable expression across all experimental samples. We have investigated the expression of eight candidate genes to identify suitable reference genes for use in primary myogenic cell cultures from Atlantic salmon (Salmo salar L.). The software analysis packages geNorm, Normfinder and Best keeper were used to rank genes according to their stability across 42 samples during the course of myogenic differentiation. Results: Initial results showed several of the candidate genes exhibited stable expression throughout myogenic culture while Sdha was identified as the least stable gene. Further analysis with geNorm, Normfinder and Bestkeeper identified Ef1 alpha, Hprt1, Ppia and RNApolII as stably expressed. Comparison of data normalised with the geometric average obtained from combinations of any three of these genes showed no significant differences, indicating that any combination of these genes is valid. Conclusion: The geometric average of any three of Hprt1, Ef1 a, Ppia and RNApolII is suitable for normalisation of gene expression data in primary myogenic cultures from Atlantic salmon.

Transcriptional regulation of the IGF signaling pathway by amino acids and insulin-like growth factors during myogenesis in Atlantic salmon

Bower, Neil I. — Mon, 14 Jun 2010 00:00:00 GMT

Abstract: The insulin-like growth factor signalling pathway is an important regulator of skeletal muscle growth. We examined the mRNA expression of components of the insulin-like growth factor (IGF) signalling pathway as well as Fibroblast Growth Factor 2 (FGF2) during maturation of myotubes in primary cell cultures isolated from fast myotomal muscle of Atlantic salmon (Salmo salar). The transcriptional regulation of IGFs and IGFBP expression by amino acids and insulin-like growth factors was also investigated. Proliferation of cells was 15% d(-1) at days 2 and 3 of the culture, increasing to 66% d(-1) at day 6. Three clusters of elevated gene expression were observed during the maturation of the culture associated with mono-nucleic cells (IGFBP5.1 and 5.2, IGFBP-6, IGFBP-rP1, IGFBP-2.2 and IGF-II), the initial proliferation phase (IGF-I, IGFBP-4, FGF2 and IGF-IRb) and terminal differentiation and myotube production (IGF2R, IGF-IRa). In cells starved of amino acids and serum for 72 h, IGF-I mRNA decreased 10-fold which was reversed by amino acid replacement. Addition of IGF-I and amino acids to starved cells resulted in an 18-fold increase in IGF-I mRNA indicating synergistic effects and the activation of additional pathway(s) leading to IGF-I production via a positive feedback mechanism. IGF-II, IGFBP-5.1 and IGFBP-5.2 expression was unchanged in starved cells, but increased with amino acid replacement. Synergistic increases in expression of IGFBP5.2 and IGFBP-4, but not IGFBP5.1 were observed with addition of IGF-I, IGF-II or insulin and amino acids to the medium. IGF-I and IGF-II directly stimulated IGFBP-6 expression, but not when amino acids were present. These findings indicate that amino acids alone are sufficient to stimulate myogenesis in myoblasts and that IGF-I production is controlled by both endocrine and paracrine pathways. A model depicting the transcriptional regulation of the IGF pathway in Atlantic salmon muscle following feeding is proposed.

Targeted rapid amplification of cDNA ends (T-RACE)-an improved RACE reaction through degradation of non-target sequences

Bower, Neil I. — Mon, 01 Nov 2010 00:00:00 GMT

Abstract: Amplification of the 5' ends of cDNA, although simple in theory, can often be difficult to achieve. We describe a novel method for the specific amplification of cDNA ends. An oligo-dT adapter incorporating a dUTP-containing PCR primer primes first-strand cDNA synthesis incorporating dUTP. Using the Cap finder approach, another distinct dUTP containing adapter is added to the 3' end of the newly synthesized cDNA. Second-strand synthesis incorporating dUTP is achieved by PCR, using dUTP-containing primers complimentary to the adapter sequences incorporated in the cDNA ends. The double-stranded cDNA-containing dUTP serves as a universal template for the specific amplification of the 3' or 5' end of any gene. To amplify the ends of cDNA, asymmetric PCR is performed using a single gene-specific primer and standard dNTPs. The asymmetric PCR product is purified and non-target transcripts containing dUTP degraded by Uracil DNA glycosylase, leaving only those transcripts produced during the asymmetric PCR. Subsequent PCR using a nested gene-specific primer and the 3' or 5' T-RACE primer results in specific amplification of cDNA ends. This method can be used to specifically amplify the 3' and 5' ends of numerous cDNAs from a single cDNA synthesis reaction.

Identifying social learning in animal populations : A new ‘option-bias’ method

Kendal, R L — Sat, 01 Aug 2009 00:00:00 GMT

Abstract: Studies of natural animal populations reveal widespread evidence for the diffusion of novel behaviour patterns, and for intra- and inter-population variation in behaviour. However, claims that these are manifestations of animal ‘culture’ remain controversial because alternative explanations to social learning remain difficult to refute. This inability to identify social learning in social settings has also contributed to the failure to test evolutionary hypotheses concerning the social learning strategies that animals deploy. We present a solution to this problem, in the form of a new means of identifying social learning in animal populations. The method is based on the assumption that social learning will generate greater homogeneity in behaviour between animals than expected in its absence. Our procedure compares the observed level of homogeneity to a bootstrapped sampling distribution utilizing randomization and other procedures. We illustrate the method on data from groups of monkeys provided with novel two-option extractive foraging tasks, demonstrating that social learning can indeed be distinguished from unlearned processes and asocial learning, and revealing that the monkeys only employed social learning for the more difficult tasks. The method is further validated against published datasets and through simulation, and exhibits higher statistical power than conventional inferential statistics.

The steady-state form of large-amplitude internal solitary waves

King, Stuart Edward — Mon, 10 Jan 2011 00:00:00 GMT

Abstract: A new numerical scheme for obtaining the steady-state form of an internal solitary wave of large amplitude is presented. A stratified inviscid two-dimensional fluid under the Boussinesq approximation flowing between horizontal rigid boundaries is considered. The stratification is stable, and buoyancy is continuously differentiable throughout the domain of the flow. Solutions are obtained by tracing the buoyancy frequency along streamlines from the undisturbed far field. From this the vorticity field can be constructed and the streamfunction may then be obtained by inversion of Laplace's operator. The scheme is presented as an iterative solver, where the inversion of Laplace's operator is performed spectrally. The solutions agree well with previous results for stratification in which the buoyancy frequency is a discontinuous function. The new numerical scheme allows significantly larger amplitude waves to be computed than have been presented before and it is shown that waves with Richardson numbers as low as 0.062 can be computed straightforwardly. The method is also extended to deal in a novel way with closed streamlines when they occur in the domain. The new solutions are tested in independent fully nonlinear time-dependent simulations and are verified to be steady. Waves with regions of recirculation are also discussed.

Complex Region Spatial Smoother (CReSS)

Scott Hayward, Lindesay Alexandra Sarah — Sat, 01 Jan 2011 00:00:00 GMT

Abstract: Conventional 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.

Technical Note: Animal-borne CTD-Satellite Relay Data Loggers for real-time oceanographic data collection

Boehme, L. — Tue, 15 Dec 2009 00:00:00 GMT

Abstract: The increasing need for continuous monitoring of the world oceans has stimulated the development of a range of autonomous sampling platforms. One novel addition to these approaches is a small, relatively inexpensive data-relaying device that can be deployed on marine mammals to provide vertical oceanographic profiles throughout the upper 2000 m of the water column. When an animal dives, the CTD-Satellite Relay Data Logger (CTD-SRDL) records vertical profiles of temperature, conductivity and pressure. Data are compressed once the animal returns to the surface where it is located by, and relays data to, the Argos satellite system. The technical challenges met in the design of the CTD-SRDL are the maximising of energy efficiency and minimising size, whilst simultaneously maintaining the reliability of an instrument that cannot be recovered and is required to survive its lifetime attached to a marine mammal. The CTD-SRDLs record temperature and salinity with an accuracy of better than 0.005 degrees C and 0.02 respectively. However, due to the limited availability of reference data, real-time data from remote places are often associated with slightly higher errors. The potential to collect large numbers of profiles cost-effectively makes data collection using CTD-SRDL technology particularly beneficial in regions where traditional oceanographic measurements are scarce or even absent. Depending on the CTD-SRDL configuration, it is possible to sample and transmit hydrographic profiles on a daily basis, providing valuable and often unique information for a real-time ocean observing system. Description: Funded by NERC grants NE/E018289/1 and NER/D/S/2002/00426

Integrated holographic system for all-optical manipulation of developing embryos

Torres, Maria Leilani — Wed, 01 Jun 2011 00:00:00 GMT

Abstract: We demonstrate a system for the combined optical injection and trapping of developing embryos. A Ti:sapphire femtosecond laser in tandem with a spatial light modulator, is used to perform fast and accurate beam-steering and multiplexing. We show successful intracellular delivery of a range of impermeable molecules into individual blastomeres of the annelid Pomatoceros lamarckii embryo by optoinjection, even when the embryo is still enclosed in a chorion. We also demonstrate the ability of the femtosecond laser optoinjection to deliver materials into inner layers of cells in a well-developed embryo. By switching to the continuous wave mode of the Ti:sapphire laser, the same system can be employed to optically trap and orient the 60 μm sized P. lamarckii embryo whilst maintaining its viability. Hence, a complete all-optical manipulation platform is demonstrated paving the way towards single-cell genetic modification and cell lineage mapping in emerging developmental biology model species.

Darwin in mind : new opportunities for evolutionary psychology

Bolhuis, Johan — Tue, 19 Jul 2011 00:00:00 GMT

Abstract: Evolutionary Psychology (EP) views the human mind as organized into many modules, each underpinned by psychological adaptations designed to solve problems faced by our Pleistocene ancestors. We argue that the key tenets of the established EP paradigm require modification in the light of recent findings from a number of disciplines, including human genetics, evolutionary biology, cognitive neuroscience, developmental psychology, and paleoecology. For instance, many human genes have been subject to recent selective sweeps; humans play an active, constructive role in co-directing their own development and evolution; and experimental evidence often favours a general process, rather than a modular account, of cognition. A redefined EP could use the theoretical insights of modern evolutionary biology as a rich source of hypotheses concerning the human mind, and could exploit novel methods from a variety of adjacent research fields.

Annelid Distal-less/Dlx duplications reveal varied post-duplication fates

McDougall, Carmel — Tue, 16 Aug 2011 00:00:00 GMT

Abstract: Background: Dlx (Distal-less) genes have various developmental roles and are widespread throughout the animal kingdom, usually occurring as single copy genes in non-chordates and as multiple copies in most chordate genomes. While the genomic arrangement and function of these genes is well known in vertebrates and arthropods, information about Dlx genes in other organisms is scarce. We investigate the presence of Dlx genes in several annelid species and examine Dlx gene expression in the polychaete Pomatoceros lamarckii. Results: Two Dlx genes are present in P. lamarckii, Capitella teleta and Helobdella robusta. The C. teleta Dlx genes are closely linked in an inverted tail-to-tail orientation, reminiscent of the arrangement of vertebrate Dlx pairs, and gene conversion appears to have had a role in their evolution. The H. robusta Dlx genes, however, are not on the same genomic scaffold and display divergent sequences, while, if the P. lamarckii genes are linked in a tail-to-tail orientation they are a minimum of 41 kilobases apart and show no sign of gene conversion. No expression in P. lamarckii appendage development has been observed, which conflicts with the supposed conserved role of these genes in animal appendage development. These Dlx duplications do not appear to be annelid-wide, as the polychaete Platynereis dumerilii likely possesses only one Dlx gene. Conclusions: On the basis of the currently accepted annelid phylogeny, we hypothesise that one Dlx duplication occurred in the annelid lineage after the divergence of P. dumerilii from the other lineages and these duplicates then had varied evolutionary fates in different species. We also propose that the ancestral role of Dlx genes is not related to appendage development. Description: Additional files can be viewed at http://www.biomedcentral.com/1471-2148/11/241/additional/

A first survey of the global population size and distribution of the Scottish Crossbill Loxia scotica

Summers, Ron W — Wed, 01 Jun 2011 00:00:00 GMT

Abstract: A survey of Scottish Crossbills Loxia scotica was carried out in 3,506 km2 of conifer woodland in northern Scotland during January to April 2008 to provide the first estimate of the global population size for this endemic bird. Population estimates were also made for Common Crossbills L. curvirostra and Parrot Crossbills L. pytyopsittacus within this range. Crossbills were lured to systematically selected survey points for counting, sexing and recording their calls for later call-type (species) identification from sonograms. Crossbills were located at 451 of the 852 survey points, and adequate tape-recordings made at 387 of these. The Scottish Crossbill had a disjunct distribution, occurring largely within the eastern part of the study area, but also in the northwest. Common Crossbills had a mainly westerly distribution. The population size of postjuvenile Scottish Crossbills was estimated as 13,600 (95%C.I. 8,130–22,700), which will approximate to 6,800 (4,065–11,350) pairs. Common Crossbills were more abundant within this range (27,100, 95% C.I. 14,700–38,400) and Parrot Crossbills rare (about 100). The sex ratio was not significantly different from parity for Scottish Crossbills. The modal number at survey points was two but numbers were larger in January than later in the survey. The numbers and distribution of all crossbill species are likely to vary between years, depending upon the size of the cone crops of the different conifers: all were coning in 2008. Common Crossbill and Parrot Crossbill numbers will also be affected by irruptions from continental Europe. A monitoring scheme is required to detect any population trend, and further work on their habitat requirement (e.g. conifer selection at different seasons) is needed to inform habitat management of native and planted conifer forests to ensure a secure future for this endemic bird.

Detrital record of mountain building : Provenance of Jurassic foreland basin to the Dabie Mountains

Yang, Jianghai — Tue, 27 Jul 2010 00:00:00 GMT

Abstract: The Huangshi foreland basin developed on the southern margin of the Dabie Mountains as a result of tectonic loading during Triassic collisional suturing between the North China and South China cratons. Modal and detrital zircon data for Jurassic samples within the basin suggest a multicomponent source with input from both the South China Craton and Dabie Orogen. Samples are predominantly quartz arenites derived, on the basis of framework compositions, from a recycled orogen source. Detrital zircons range in age from Archean to Triassic with a dominant component in the late Paleoproterozoic between 1.9-1.7 Ga and subsidiary components at 2.6-2.2 Ga, 0.8-0.7 Ga, 0.5-0.4 Ga, and 0.33-0.2 Ga. Age data integrated with cathodoluminescence and trace element data for the zircons indicate that the Archean and Proterozoic detritus was derived from igneous and metamorphic sources that overlap with time-equivalent pulses of such activity within the South China Craton. Phanerozoic zircon ages overlap the times of the Ordovician, Carboniferous and Triassic high-pressure metamorphism in the Dabie Mountains. The provenance record, integrated with paleocurrent and regional relations, enables a paleogeographic reconstruction in which the Huangshi Basin was fed by a major axial flowing trunk river system carrying detritus from eastern and southern sources within the South China Craton and was also fed by short south flowing tributaries supplying some detritus from the evolving Dabie Orogen. The dominance of cratonic-derived detritus within the provenance record of the Huangshi Basin contrasts with that of the Hefei foreland basin that lies to the north of the Dabie Mountains, which is dominated by Neoproterozoic - Mesozoic detritus derived directly from the Dabie Mountains and lacks any significant older Paleoproterozoic or Archean components. Easterly extensions of the Dabie-Sulu collisional suture and of the resultant Huangshi Basin occur in Korea and Japan over an along strike length of some 2000 km. Citation: Yang, J., P. A. Cawood, and Y. Du (2010), Detrital record of mountain building: Provenance of Jurassic foreland basin to the Dabie Mountains, Tectonics, 29, TC4011, doi: 10.1029/2009TC002600.

Double-observer line transect methods : levels of independence

Buckland, Stephen T. — Mon, 01 Mar 2010 00:00:00 GMT

Abstract: Double-observer line transect methods are becoming increasingly widespread, especially for the estimation of marine mammal abundance from aerial and shipboard surveys when detection of animals on the line is uncertain. The resulting data supplement conventional distance sampling data with two-sample mark–recapture data. Like conventional mark–recapture data, these have inherent problems for estimating abundance in the presence of heterogeneity. Unlike conventional mark–recapture methods, line transect methods use knowledge of the distribution of a covariate, which affects detection probability (namely, distance from the transect line) in inference. This knowledge can be used to diagnose unmodeled heterogeneity in the mark–recapture component of the data. By modeling the covariance in detection probabilities with distance, we show how the estimation problem can be formulated in terms of different levels of independence. At one extreme, full independence is assumed, as in the Petersen estimator (which does not use distance data); at the other extreme, independence only occurs in the limit as detection probability tends to one. Between the two extremes, there is a range of models, including those currently in common use, which have intermediate levels of independence. We show how this framework can be used to provide more reliable analysis of double-observer line transect data. We test the methods by simulation, and by analysis of a dataset for which true abundance is known. We illustrate the approach through analysis of minke whale sightings data from the North Sea and adjacent waters.

An International Quiet Ocean Experiment

Boyd, Ian L. — Wed, 01 Jun 2011 00:00:00 GMT

Abstract: The effect of noise on marine life is one of the big unknowns of current marine science. Considerable evidence exists that the human contribution to ocean noise has increased during the past few decades: human noise has become the dominant component of marine noise in some regions, and noise is directly correlated with the increasing industrialization of the ocean. Sound is an important factor in the lives of many marine organisms, and theory and increasing observations suggest that human noise could be approaching levels at which negative effects on marine life may be occurring. Certain species already show symptoms of the effects of sound. Although some of these effects are acute and rare, chronic sublethal effects may be more prevalent, but are difficult to measure. We need to identify the thresholds of such effects for different species and be in a position to predict how increasing anthropogenic sound will add to the effects. To achieve such predictive capabilities, the Scientific Committee on Oceanic Research (SCOR) and the Partnership for Observation of the Global Oceans (POGO) are developing an International Quiet Ocean Experiment (IQOE), with the objective of coordinating the international research community to both quantify the ocean soundscape and examine the functional relationship between sound and the viability of key marine organisms. SCOR and POGO will convene an open science meeting to gather community input on the important research, observations, and modeling activities that should be included in IQOE.

Impact of biodiversity-climate futures on primary production and metabolism in a model benthic estuarine system

Hicks, Natalie — Sat, 01 Jan 2011 00:00:00 GMT

Abstract: Understanding the effects of anthropogenically-driven changes in global temperature, atmospheric carbon dioxide and biodiversity on the functionality of marine ecosystems is crucial for predicting and managing the associated impacts. Coastal ecosystems are important sources of carbon (primary production) to shelf waters and play a vital role in global nutrient cycling. These systems are especially vulnerable to the effects of human activities and will be the first areas impacted by rising sea levels. Within these coastal ecosystems, microalgal assemblages (microphytobenthos: MPB) are vital for autochthonous carbon fixation. The level of in situ production by MPB mediates the net carbon cycling of transitional ecosystems between net heterotrophic or autotrophic metabolism. In this study, we examine the interactive effects of elevated atmospheric CO2 concentrations (370, 600, and 1000 ppmv), temperature (6°C, 12°C, and 18°C) and invertebrate biodiversity on MPB biomass in experimental systems. We assembled communities of three common grazing invertebrates (Hydrobia ulvae, Corophium volutator and Hediste diversicolor) in monoculture and in all possible multispecies combinations. This experimental design specifically addresses interactions between the selected climate change variables and any ecological consequences caused by changes in species composition or richness. Description: All work was supported by NERC grant NE/E006795/1

Variation in habitat preference and distribution of harbour porpoises west of Scotland

Booth, Cormac G — Tue, 30 Nov 2010 00:00:00 GMT

Abstract: The waters off the west coast of Scotland have one of the highest densities of harbour porpoise (Phocoena phocoena) in Europe. Harbour porpoise are listed under Annex II of the EU Habitats Directive, requiring the designation of Special Areas of Conservation (SACs) for the species’ protection and conservation. The main aim of this thesis is to identify habitat preferences for harbour porpoise, and key regions that embody these preferences, which could therefore be suitable as SACs; and to determine how harbour porpoise use these regions over time and space. Designed visual and acoustic line-transect surveys were conducted between 2003 and 2008. Generalised Estimating Equations (GEEs) were used to determine relationships between the relative density of harbour porpoise and temporally and spatially variable oceanographic covariates. Predictive models showed that depth, slope, distance to land and spring tidal range were all important in explaining porpoise distribution. There were also significant temporal variations in habitat use. However, whilst some variation was observed among years and months, consistent preferences for water depths between 50 and 150 m and highly sloped regions were observed across the temporal models. Predicted surfaces revealed a consistent inshore distribution for the species throughout the west coast of Scotland. Regional models revealed similar habitat preferences to the full-extent models, and indicated that the Small Isles and Sound of Jura were the most consistently important regions for harbour porpoise, and that these regions could be suitable as SACs. The impacts of seal scarers on distribution and habitat use were also investigated, and there were indications that these devices have the potential to displace harbour porpoise. These results should be considered in the assessment of sites for SAC designation, and in implementing appropriate conservation measures for harbour porpoise.

Density estimation implications of increasing ambient noise on beaked whale click detection and classification

Marques, Tiago Andre Lamas Oliveira — Fri, 01 Jan 2010 00:00:00 GMT

Abstract: Acoustic based density estimates are being increasingly used. Usually density estimation methods require one to evaluate the eﬀective survey area of the acoustic sensors, or equivalently estimate the mean detection probability of detecting the animals or cues of interest. This is often done based on an estimated detection function, the probability of detecting an object of interest as a function of covariates, usually distance and additional covariates. If the actual survey data and the data used to estimate a detection function are not collected simultaneously, as in Marques et al. (2009), the estimated detection function might not correspond to the detection process that generated the survey data. This would lead to biaseddensity estimates. Here we evaluate the inﬂuence of ambient noise in the detection and classiﬁcation of beaked whale clicks at the Atlantic Undersea Test and Evaluation Center (AUTEC) hydrophones, to assess if the density estimates reported in Marques et al. (2009) might have been biased. To do so we contaminated a data set with increasing levels of ambient noise, and then estimated the detection function accounting for the noise level as an additional covariate. The results obtained suggest that for the particular results obtained at AUTEC’s deep water hydrophones the inﬂuence of ambient noise on the beaked whale’s click detection probability might have been minor, and hence unlikely to have had an impact on density estimates. However, we do not exclude the possibility that the results could be diﬀerent under other scenarios.

Can methods applied in medicine be used to summarize and disseminate conservation research?

Fazey, Ioan Raymond Albert — Wed, 01 Sep 2004 00:00:00 GMT

Abstract: To ensure that the best scientific evidence is available to guide conservation action, effective mechanisms for communicating the results of research are necessary. In medicine, an evidence-based approach assists doctors in applying scientific evidence when treating patients. The approach has required the development of new methods for systematically reviewing research, and has led to the establishment of independent organizations to disseminate the conclusions of reviews. (1) Such methods could help bridge gaps between researchers and practitioners of environmental conservation. In medicine, systematic reviews place strong emphasis on reviewing experimental clinical trials that meet strict standards. Although experimental studies are much less common in conservation, many of the components of systematic reviews that reduce the biases when identifying, selecting and appraising relevant studies could still be applied effectively. Other methods already applied in medicine for the review of non-experimental studies will therefore be required in conservation. (2) Using systematic reviews and an evidence-based approach will only be one tool of many to reduce uncertainty when making conservation-related decisions. Nevertheless an evidence-based approach does complement other approaches (for example adaptive management), and could facilitate the use of the best available research in environmental management. (3) In medicine, the Cochrane Collaboration was established as an independent organization to guide the production and dissemination of systematic reviews. It has provided many benefits that could apply to conservation, including a forum for producing and disseminating reviews with emphasis on the requirements of practitioners, and a forum for feedback between researchers and practitioners and improved access to the primary research. Without the Cochrane Collaboration, many of the improvements in research communication that have occurred in medicine over the last decade would not have been possible.

The nature and role of experiential knowledge for environmental conservation

Fazey, Ioan Raymond Albert — Wed, 01 Mar 2006 00:00:00 GMT

Abstract: Understanding the nature and role of experiential knowledge for environmental conservation is a necessary step towards understanding if it should be used and how it might be applied with other types of knowledge in an evidence-based approach. This paper describes the nature of experiential and expert knowledge. It then discusses the role of experiential knowledge as a complement to scientific knowledge and explains the interplay between experiential knowledge with conservation research and practice using a simple conceptual model of how individuals learn. There are five main conclusions: (1) because experiential knowledge will always play a role in decision-making, enhancing ability to learn from experiences (including research) will have a significant influence on the effectiveness of conservation outcomes; (2) while experiential knowledge is qualitatively very different from quantitative information, both are important and complementary; (3) some experiential knowledge can be expressed quantitatively, but experiential knowledge can be difficult to isolate as single facts or propositions and qualitative methods will therefore often be required to elicit experiential knowledge; (4) because each person's expertise is unique, when using experiential knowledge the extent of a person's experience and its relevance to a particular problem need to be specified; and (5) as with any form of knowledge, there are limitations to that derived from personal experience. Synthesis and communication of research is therefore essential to help prevent erroneous thinking and, where possible, experiential knowledge should be used in conjunction with other types of information to guide conservation actions.

Rapid primary productivity changes in one of the last coastal rainforests : the case of Kahua, Solomon Islands

Garonna, Irene — Tue, 01 Sep 2009 00:00:00 GMT

Abstract: The growth of human populations has many direct and indirect impacts on tropical forest ecosystems both locally and globally. This is particularly true in the Solon-ion Islands, where coastal rainforest cover still remains, but where climate change and a growing human Population is putting increasing pressure on ecosystems. This study assessed recent primary productivity changes in the Kahua region (Makira, Solomon Islands) using remote sensing data (normalized difference vegetation index, NDVI). In this area, there has been no commercial logging and there is no existing information about the state of the forests. Results indicate that primary productivity has been decreasing in recent years, and that the recent changes arc more marked near vi I]ages. Multiple factors may explain the reported pattern in primary productivity. The study highlights the need to (1) assess how accurately remote sensing data-based results match field data on the ground; (2) identify, the relative contribution of the climatic, socioeconomic and political drivers of such changes; and (3) evaluate how primary productivity changes affect biodiversity level, ecosystem functioning and human livelihoods.

Learning more effectively from experience

Fazey, Ioan Raymond Albert — Thu, 01 Dec 2005 00:00:00 GMT

Abstract: Developing the capacity for individuals to learn effectively from their experiences is an important part of building the knowledge and skills in organizations to do good adaptive management. This paper reviews some of the research from cognitive psychology and phenomenography to present a way of thinking about learning to assist individuals to make better use of their personal experiences to develop understanding of environmental systems. We suggest that adaptive expertise (an individual's ability to deal flexibly with new situations) is particularly relevant for environmental researchers and practitioners. To develop adaptive expertise, individuals need to: (1) vary and reflect on their experiences and become adept at seeking out and taking different perspectives; and (2) become proficient at making balanced judgements about how or if an experience will change their current perspective or working representation of a social, economic, and biophysical system by applying principles of "good thinking." Such principles include those that assist individuals to be open to the possibility of changing their current way of thinking (e. g., the disposition to be adventurous) and those that reduce the likelihood of making erroneous interpretations (e. g., the disposition to be intellectually careful). An example of applying some of the principles to assist individuals develop their understanding of a dynamically complex wetland system (the Macquarie Marshes in Australia) is provided. The broader implications of individual learning are also discussed in relation to organizational learning, the role of experiential knowledge for conservation, and for achieving greater awareness of the need for ecologically sustainable activity.

Eliciting the implicit knowledge and perceptions of on-ground conservation managers of the Macquarie Marshes

Fazey, Ioan Raymond Albert — Thu, 01 Jun 2006 00:00:00 GMT

Abstract: Knowledge that has been developed through extensive experience of receiving and responding to ecological feedback is particularly valuable for informing and guiding environmental management. This paper captures the implicit understanding of seven experienced on-ground conservation managers about the conservation issues affecting the Ramsar listed Macquarie Marshes in New South Wales, Australia. Multiple interviews, a workshop, and meetings were used to elicit the manager's knowledge. The managers suggest that the Macquarie Marshes are seriously threatened by a lack of water, and immediate steps need to be taken to achieve more effective water delivery. Their knowledge and perceptions of the wider societal impediments to achieving more effective water delivery have also led the managers to suggest that there may be system feedbacks that are reinforcing the tendency for water agencies to favor the short-term interests of the irrigation industry. Although the managers clearly have certain personal interests that influence their understanding and perceptions, much of their knowledge also appears to have been heavily influenced by their ecological understanding of the wetland's dynamics. This paper highlights that although all stakeholders clearly need to be involved in making decisions about conservation and how resources should be used, such decisions should not be confused with the need for consulting people with the appropriate ecological expertise to help determine the degree to which an ecological system is threatened, the likely ecological causes of the threats, and actions that may be needed to restore and maintain a functional ecosystem.

The influence of philosophical perspectives in integrative research : a conservation case study in the Cairngorms National Park

Evely, Anna C. — Mon, 01 Dec 2008 00:00:00 GMT

Abstract: The benefits of increasing the contribution of the social sciences in the fields of environmental and conservation science disciplines are increasingly recognized. However, integration between the social and natural sciences has been limited, in part because of the barrier caused by major philosophical differences in the perspectives between these research areas. This paper aims to contribute to more effective interdisciplinary integration by explaining some of the philosophical views underpinning social research and how these views influence research methods and outcomes. We use a project investigating the motivation of volunteers working in an adaptive co-management project to eradicate American Mink from the Cairngorms National Park in Scotland as a case study to illustrate the impact of philosophical perspectives on research. Consideration of different perspectives promoted explicit reflection of the contributing researcher's assumptions, and the implications of his or her perspectives on the outcomes of the research. We suggest a framework to assist conservation research projects by: ( 1) assisting formulation of research questions; ( 2) focusing dialogue between managers and researchers, making underlying worldviews explicit; and ( 3) helping researchers and managers improve longer-term strategies by helping identify overall goals and objectives and by identifying immediate research needs.

What is social learning?

Reed, Mark — Fri, 01 Oct 2010 00:00:00 GMT

Abstract: Social learning is increasingly becoming a normative goal in natural resource management and policy. However, there remains little consensus over its meaning or theoretical basis. There are still considerable differences in understanding of the concept in the literature, including a number of articles published in Ecology & Society. Social learning is often conflated with other concepts such as participation and proenvironmental behavior, and there is often little distinction made between individual and wider social learning. Many unsubstantiated claims for social learning exist, and there is frequently confusion between the concept itself and its potential outcomes. This lack of conceptual clarity has limited our capacity to assess whether social learning has occurred, and if so, what kind of learning has taken place, to what extent, between whom, when, and how. This response attempts to provide greater clarity on the conceptual basis for social learning. We argue that to be considered social learning, a process must: (1) demonstrate that a change in understanding has taken place in the individuals involved; (2) demonstrate that this change goes beyond the individual and becomes situated within wider social units or communities of practice; and (3) occur through social interactions and processes between actors within a social network. A clearer picture of what we mean by social learning could enhance our ability to critically evaluate outcomes and better understand the processes through which social learning occurs. In this way, it may be possible to better facilitate the desired outcomes of social learning processes.

Resilience and higher order thinking

Fazey, Ioan Raymond Albert — Sun, 01 Aug 2010 00:00:00 GMT

Abstract: To appreciate, understand, and tackle chronic global social and environmental problems, greater appreciation of the importance of higher order thinking is required. Such thinking includes personal epistemological beliefs (PEBs), i.e., the beliefs people hold about the nature of knowledge and how something is known. These beliefs have profound implications for the way individuals relate to each other and the world, such as how people understand complex social-ecological systems. Resilience thinking is an approach to environmental stewardship that includes a number of interrelated concepts and has strong foundations in systemic ways of thinking. This paper (1) summarizes a review of educational psychology literature on PEBs, (2) explains why resilience thinking has potential to facilitate development of more sophisticated PEBs, (3) describes an example of a module designed to teach resilience thinking to undergraduate students in ways conducive to influencing PEBs, and (4) discusses a pilot study that evaluates the module's impact. Theoretical and preliminary evidence from the pilot evaluation suggests that resilience thinking which is underpinned by systems thinking has considerable potential to influence the development of more sophisticated PEBs. To be effective, however, careful consideration of how resilience thinking is taught is required. Finding ways to encourage students to take greater responsibility for their own learning and ensuring close alignment between assessment and desired learning outcomes are particularly important.

Antibacterial free fatty acids : activities, mechanisms of action and biotechnological potential

Desbois, Andrew Paul — Mon, 01 Feb 2010 00:00:00 GMT

Abstract: Amongst the diverse and potent biological activities of free fatty acids (FFAs) is the ability to kill or inhibit the growth of bacteria. The antibacterial properties of FFAs are used by many organisms to defend against parasitic or pathogenic bacteria. Whilst their antibacterial mode of action is still poorly understood, the prime target of FFA action is the cell membrane, where FFAs disrupt the electron transport chain and oxidative phosphorylation. Besides interfering with cellular energy production, FFA action may also result from the inhibition of enzyme activity, impairment of nutrient uptake, generation of peroxidation and auto-oxidation degradation products or direct lysis of bacterial cells. Their broad spectrum of activity, non-specific mode of action and safety makes them attractive as antibacterial agents for various applications in medicine, agriculture and food preservation, especially where the use of conventional antibiotics is undesirable or prohibited. Moreover, the evolution of inducible FFA-resistant phenotypes is less problematic than with conventional antibiotics. The potential for commercial or biomedical exploitation of antibacterial FFAs, especially for those from natural sources, is discussed.

Assessing the effectiveness of conservation measures : resolving the "wicked" problem of the Steller sea lion

Boyd, Ian Lamont — Thu, 01 Jul 2010 00:00:00 GMT

Abstract: “Wicked” problems are those that are complex and that change when solutions are applied. Many conflicts in conservation fall in to this category. The study approached the problem of how to constrain the apparent wickedness of a problem in the conservation management of a species by using simple empirical indicators to carry out iterative assessment of the risk to a population and to document how this risk evolves in relation to the addition of new data and the implementation of management actions. Effects of high levels of uncertainty within data and also concerning population structure were examined through stochastic simulation and by exploration of scenarios. Historical trends in the example used, the Steller sea lion, showed rapid declines in abundance in some regions during the 1980s. The current total population is 130,000-150,000 Steller sea lions through Alaska and British Columbia and this number has been stable since about 1990 in spite of regional differences in population dynamics. Regional differences in the sequence of changes in the number of pups and non-pups, suggested that an internal re-distribution of juveniles could have happened between 1980 and 1990. Current productivity also appears close to the long term mean. Stochastic population projection using various scenarios showed that, based upon this history, the risk of extinction for the population has declined and is below reasonable thresholds for considering the population to be endangered.

The problem of dating quartz 1 : Spectroscopic ionoluminescence of dose dependence

King, Georgina — Sat, 01 Jan 2011 00:00:00 GMT

Abstract: A suite of quartz samples of different provenances, irradiation, thermal and depositional histories were analysed using spectroscopic ionoluminescence (IL) to investigate variations in emission spectra as a function of cumulative radiation dosing. Protons were selected for implantation to mimic the effect of natural radiation over geological timescales. All samples exhibited depletion in the UV-violet emission (3.2-3.4 eV) with increasing cumulative dose, whilst the red emission (1.8-1.9 eV) increased. A power-law relationship exists between the two emissions. It is inferred that the luminescence emission of quartz is indicative of its radiation history, and spectral analyses could be used to determine the utility of different quartz samples for optically stimulated luminescence dating (OSL) where the detection range is limited to 3.4-4.6 eV.

Cellular and molecular studies of postembryonic muscle fibre recruitment in zebrafish (Danio rerio L.)

Lee, Hung-Tai — Wed, 23 Jun 2010 00:00:00 GMT

Abstract: Cellular and molecular mechanisms of postembryonic muscle fibre recruitment were investigated in zebrafish (Danio rerio L.), a standard animal model for developmental and genetic studies. Distinct cellular mechanisms of postembryonic muscle fibre recruitment in fast and slow myotomal muscles were found. In slow muscle, three overlapping waves of stratified hyperplasia (SH) from distinct germinal zones sequentially contributed to a slow and steady increase in fibre number (FN) through the life span. In fast muscle, SH only contributed to an initial increase of FN in early larvae. Strikingly, mosaic hyperplasia (MH) appeared in late larvae and early juveniles and remained active until early adult stages, accounting for >70% of the final fibre number (FFN). The molecular regulation of postembryonic muscle fibre recruitment was then studied by characterising myospryn and cee, two strong candidate genes previously identified from a large scale screen for genes differentially expressed during the transition from hyperplastic to hypertrophic muscle phenotypes. Zebrafish myospryn contained very similar functional domains to its mammalian orthologues, which function to bind to other proteins known to regulate muscle dystrophy. Zebrafish myospryn also shared a highly conserved syntenic genomic neighbourhood with other vertebrate orthologues. As in mammals, zebrafish myospryn were specifically expressed in striated muscles. Zebrafish cee was a single-copy gene, highly conserved among metazoans, ubiquitously expressed across tissues, and did not form part of any wider gene family. Its protein encompassed a single conserved domain (DUF410) of unknown function although knock-down of cee in C. elegans and yeast have suggested a role in regulating growth patterns. Both myospyrn and cee transcripts were up-regulated concomitant with the cessation of postembryonic muscle fibre recruitment in zebrafish, indicating a potential role in regulating muscle growth. Furthermore, a genome-wide screen of genes involved in the regulation of postembryonic muscle fibre recruitment was performed using microarray. 85 genes were found to be consistently and differentially expressed between growth stages where muscle hyperplasia was active or inactive, including genes associated with muscle contraction, metabolism, and immunity. Further bioinformatic annotation indicated these genes comprised a complex transcriptional network with molecular functions, including catalytic activity and protein binding as well as pathways associated with metabolism, tight junctions, and human diseases. Finally, developmental plasticity of postembryonic muscle fibre recruitment to embryonic temperature was characterised. It involved transient effects including the relative timing and contribution of SH and MH, plus the rate and duration of fibre production, as well as a persistent alteration to FFN. Further investigation of FFN of fish over a broader range of embryonic temperature treatments (22, 26, 28, 31, 35°C) indicated that 26°C produced the highest FFN that was approximately 17% greater than at other temperatures. This finding implies the existence of an optimal embryonic temperature range for maximising FFN across a reaction norm. Additionally, a small but significant effect of parental temperature on FFN (up to 6% greater at 24 and 26°C than at 31°C) was evident, suggesting some parental mechanisms can affect muscle fibre recruitment patterns of progeny. This work provides a comprehensive investigation of mechanisms underlying postembryonic muscle fibre recruitment and demonstrates the power of zebrafish as an ideal teleost model for addressing mechanistic and practical aspects of postembryonic muscle recruitment, especially the presence of all major phases of muscle fibre production in larger commercially important teleost species.