Centre for Biological Diversity (CBD)
https://hdl.handle.net/10023/2323
2024-03-28T08:38:09ZThe role of individual behaviour in the collective cultural evolution of humpback whale songs
https://hdl.handle.net/10023/18621
For more than forty years, the complex songs emitted by humpback whales have
fascinated the scientific community as well as the general public. These songs are
produced by males during the breeding season, and are hierarchically structured and
population specific. Within a population, males tend to conform to the same song type,
but songs undergo gradual unidirectional change. Instances of more rapid song changes
have also been recorded, where the song sung by a population has been replaced by the
song of an adjacent population. The learning mechanisms that concurrently drive song
conformity, and simultaneously allow gradual (evolution) and rapid (revolution) song
change are not currently understood. This thesis aims to address this gap by using
innovative theoretical models as well as more established empirical methods.
Chapter 1 provides a general introduction to the thesis topics. In chapter 2 I
introduce a spatially explicit agent-based modelling approach to investigate humpback
whale song evolution and transmission. I found that shared feeding grounds promote
inter-population song transmission, song conformity emerges as a function of breeding
ground geographical segregation, and production errors facilitate gradual evolution of
songs. In chapter 3, the same modelling approach is extended to simulate song
revolutions using a new learning bias in combination with different movement
scenarios. I found that the consistent emergence of song revolutions is dependent on
cognitive (song memory), behavioural (singing probability) and spatial (agent density)
factors. Finally, in chapter 4, I analyse intra- and inter- individual song variability at
different hierarchical levels of organisation in songs recorded off eastern Australia. I
found that variability is not homogeneously distributed across the different song levels.
Furthermore, I identified consistent and distinctive individual patterns of song
production consistent with the theory that songs could represent mate quality
advertisements for females.
2018-12-06T00:00:00ZLamoni, Luca UbaldoFor more than forty years, the complex songs emitted by humpback whales have
fascinated the scientific community as well as the general public. These songs are
produced by males during the breeding season, and are hierarchically structured and
population specific. Within a population, males tend to conform to the same song type,
but songs undergo gradual unidirectional change. Instances of more rapid song changes
have also been recorded, where the song sung by a population has been replaced by the
song of an adjacent population. The learning mechanisms that concurrently drive song
conformity, and simultaneously allow gradual (evolution) and rapid (revolution) song
change are not currently understood. This thesis aims to address this gap by using
innovative theoretical models as well as more established empirical methods.
Chapter 1 provides a general introduction to the thesis topics. In chapter 2 I
introduce a spatially explicit agent-based modelling approach to investigate humpback
whale song evolution and transmission. I found that shared feeding grounds promote
inter-population song transmission, song conformity emerges as a function of breeding
ground geographical segregation, and production errors facilitate gradual evolution of
songs. In chapter 3, the same modelling approach is extended to simulate song
revolutions using a new learning bias in combination with different movement
scenarios. I found that the consistent emergence of song revolutions is dependent on
cognitive (song memory), behavioural (singing probability) and spatial (agent density)
factors. Finally, in chapter 4, I analyse intra- and inter- individual song variability at
different hierarchical levels of organisation in songs recorded off eastern Australia. I
found that variability is not homogeneously distributed across the different song levels.
Furthermore, I identified consistent and distinctive individual patterns of song
production consistent with the theory that songs could represent mate quality
advertisements for females.Title redacted
https://hdl.handle.net/10023/16958
2016-06-01T00:00:00ZSugasawa, ShokoBayesPiles : visualisation support for Bayesian network structure learning
https://hdl.handle.net/10023/16636
We address the problem of exploring, combining, and comparing large collections of scored, directed networks for understanding inferred Bayesian networks used in biology. In this field, heuristic algorithms explore the space of possible network solutions, sampling this space based on algorithm parameters and a network score that encodes the statistical fit to the data. The goal of the analyst is to guide the heuristic search and decide how to determine a final consensus network structure, usually by selecting the top-scoring network or constructing the consensus network from a collection of high-scoring networks. BayesPiles, our visualisation tool, helps with understanding the structure of the solution space and supporting the construction of a final consensus network that is representative of the underlying dataset. BayesPiles builds upon and extends MultiPiles to meet our domain requirements. We developed BayesPiles in conjunction with computational biologists who have used this tool on datasets used in their research. The biologists found our solution provides them with new insights and helps them achieve results that are representative of the underlying data.
2018-11-01T00:00:00ZVogogias, AthanasiosKennedy, JessieArchambault, DanielBach, BenjaminSmith, V AnneCurrant, HannahWe address the problem of exploring, combining, and comparing large collections of scored, directed networks for understanding inferred Bayesian networks used in biology. In this field, heuristic algorithms explore the space of possible network solutions, sampling this space based on algorithm parameters and a network score that encodes the statistical fit to the data. The goal of the analyst is to guide the heuristic search and decide how to determine a final consensus network structure, usually by selecting the top-scoring network or constructing the consensus network from a collection of high-scoring networks. BayesPiles, our visualisation tool, helps with understanding the structure of the solution space and supporting the construction of a final consensus network that is representative of the underlying dataset. BayesPiles builds upon and extends MultiPiles to meet our domain requirements. We developed BayesPiles in conjunction with computational biologists who have used this tool on datasets used in their research. The biologists found our solution provides them with new insights and helps them achieve results that are representative of the underlying data.Professional medical writing support and the reporting quality of randomized controlled trial abstracts among high-impact general medical journals
https://hdl.handle.net/10023/12994
Background : In articles reporting randomized controlled trials, professional medical writing support is associated with increased adherence to Consolidated Standards of Reporting Trials (CONSORT). We set out to determine whether professional medical writing support was also associated with improved adherence to CONSORT for Abstracts. Methods : Using data from a previously published cross-sectional study of 463 articles reporting randomized controlled trials published between 2011 and 2014 in five top medical journals, we determined the association between professional medical writing support and CONSORT for Abstracts items using a Wilcoxon rank-sum test. Results : The mean proportion of adherence to CONSORT for Abstracts items reported was similar with and without professional medical writing support (64.3% vs 66.5%, respectively; p=0.30). Professional medical writing support was associated with lower adherence to reporting study setting (relative risk [RR]; 0.40; 95% confidence interval [CI], 0.23–0.70), and higher adherence to disclosing harms/side effects (RR 2.04; 95% CI, 1.37–3.03) and funding source (RR 1.75; 95% CI, 1.18–2.60). Conclusions : Although professional medical writing support was not associated with increased overall adherence to CONSORT for Abstracts, important aspects were improved with professional medical writing support, including reporting of adverse events and funding source. This study identifies areas to consider for improvement.
2017-09-23T00:00:00ZMills, IraSheard, CatherineHays, MeredithDouglas, KevinWinchester, Christopher C.Gattrell, William T.Background : In articles reporting randomized controlled trials, professional medical writing support is associated with increased adherence to Consolidated Standards of Reporting Trials (CONSORT). We set out to determine whether professional medical writing support was also associated with improved adherence to CONSORT for Abstracts. Methods : Using data from a previously published cross-sectional study of 463 articles reporting randomized controlled trials published between 2011 and 2014 in five top medical journals, we determined the association between professional medical writing support and CONSORT for Abstracts items using a Wilcoxon rank-sum test. Results : The mean proportion of adherence to CONSORT for Abstracts items reported was similar with and without professional medical writing support (64.3% vs 66.5%, respectively; p=0.30). Professional medical writing support was associated with lower adherence to reporting study setting (relative risk [RR]; 0.40; 95% confidence interval [CI], 0.23–0.70), and higher adherence to disclosing harms/side effects (RR 2.04; 95% CI, 1.37–3.03) and funding source (RR 1.75; 95% CI, 1.18–2.60). Conclusions : Although professional medical writing support was not associated with increased overall adherence to CONSORT for Abstracts, important aspects were improved with professional medical writing support, including reporting of adverse events and funding source. This study identifies areas to consider for improvement.Biodiversity change in the Cerrado following invasive pine tree establishment
https://hdl.handle.net/10023/12220
How do newly established species interact with existing assemblage members to alter local biodiversity? This question is especially topical given growing concerns about increased temporal turnover levels relative to background rates. My PhD thesis concerns young, isolated pines Pinus elliottii invading the Cerrado (Brazilian savanna) as a study system to test the hypothesis that the impact of newly established individuals varies across habitat layers. I sampled both vegetation layers (shrub and grass) of two distinct habitats, the shrub-dominated campo sujo and the grass-dominated campo úmido. My results show that the pine is changing α diversity in the dominant vegetation layer of each habitat: the shrub layer of campo sujo and the grass layer of campo úmido. The shape of the diversity v. establishment time relationship is habitat dependent; there is a hump shaped relationship between diversity and pine size in the grass layer but a linear one in the shrub layer. β diversity metrics – which take species composition into account - reveal marked differences in species composition between the habitats in the shrub layer, whereas the corresponding pair of invaded and control sites of the same habitat and layer is more similar than expected (in both vegetation layers). The degree of similarity between sites also changes as the invasion proceeds. In the campo sujo habitat, sites become more compositionally distinct, whereas in the grass layer of campo úmido sites get more similar. This suggests that the timing of changes in species composition is habitat-dependent and reinforces the need to remove the invader individuals from the area. My results show that, though complex, the consequences for local biodiversity of non-native species establishment are not haphazard. As such they contribute to the understanding of species coexistence and help explain why species invasion can lead to very different biodiversity outcomes.
2017-12-07T00:00:00ZRocha Kortz, AlessandraHow do newly established species interact with existing assemblage members to alter local biodiversity? This question is especially topical given growing concerns about increased temporal turnover levels relative to background rates. My PhD thesis concerns young, isolated pines Pinus elliottii invading the Cerrado (Brazilian savanna) as a study system to test the hypothesis that the impact of newly established individuals varies across habitat layers. I sampled both vegetation layers (shrub and grass) of two distinct habitats, the shrub-dominated campo sujo and the grass-dominated campo úmido. My results show that the pine is changing α diversity in the dominant vegetation layer of each habitat: the shrub layer of campo sujo and the grass layer of campo úmido. The shape of the diversity v. establishment time relationship is habitat dependent; there is a hump shaped relationship between diversity and pine size in the grass layer but a linear one in the shrub layer. β diversity metrics – which take species composition into account - reveal marked differences in species composition between the habitats in the shrub layer, whereas the corresponding pair of invaded and control sites of the same habitat and layer is more similar than expected (in both vegetation layers). The degree of similarity between sites also changes as the invasion proceeds. In the campo sujo habitat, sites become more compositionally distinct, whereas in the grass layer of campo úmido sites get more similar. This suggests that the timing of changes in species composition is habitat-dependent and reinforces the need to remove the invader individuals from the area. My results show that, though complex, the consequences for local biodiversity of non-native species establishment are not haphazard. As such they contribute to the understanding of species coexistence and help explain why species invasion can lead to very different biodiversity outcomes.A behavioural and genomic approach to studying the evolution of reproductive isolation : a contact zone between closely related field crickets in the genus Teleogryllus
https://hdl.handle.net/10023/10260
What processes contribute to the evolution of reproductive isolation and the coexistence of interfertile species in the same habitat? This thesis investigates the relative roles of species interactions and intraspecific processes in contributing to reproductive isolation. I combine behavioural and genomic approaches to test hypotheses about what mechanisms maintain the general species boundary between two closely related field cricket species: Teleogryllus oceanicus and T. commodus. These species are a classic study system for sexual communication and readily hybridize in the laboratory, however little is known about species interactions in sympatric populations. I examine patterns of geographic variation in two key sexual traits: calling song and cuticular hydrocarbons (CHCs), and the geographic distribution of genetic variation across a broad sample of allopatric and sympatric populations. I test whether X chromosomes play a pronounced role in population divergence and reproductive isolation. Using close range mating trials and hybridization experiments I identify numerous pre-mating and post-mating barriers between the species. The results indicate that the species are currently reproductively isolated and the pattern of population differentiation does not strongly support contemporary species interactions contributing to phenotypic diversity. Numerous barriers exist between the species, in particular hybrid females are sterile in both cross directions, while hybrid males are relatively fertile. This provides a rare exception to Haldane’s rule which is central to many genetic theories of speciation. Established theory predicts that X chromosomes should play a pronounced role in the evolution of both pre- and postzygotic barriers. Contrary to this, I found no evidence that X chromosomes contribute to hybrid female sterility. Moreover, X-linked loci exhibited an unexpected pattern of reduced population differentiation within species, but increased species divergence compared to autosomal loci, which may indicate selective sweeps or sex-biased processes. Taken together, the results suggest that the causes and consequences of X chromosome evolution, in particular among XO taxa, may contradict some of the established theories.
2017-06-21T00:00:00ZMoran, PeterWhat processes contribute to the evolution of reproductive isolation and the coexistence of interfertile species in the same habitat? This thesis investigates the relative roles of species interactions and intraspecific processes in contributing to reproductive isolation. I combine behavioural and genomic approaches to test hypotheses about what mechanisms maintain the general species boundary between two closely related field cricket species: Teleogryllus oceanicus and T. commodus. These species are a classic study system for sexual communication and readily hybridize in the laboratory, however little is known about species interactions in sympatric populations. I examine patterns of geographic variation in two key sexual traits: calling song and cuticular hydrocarbons (CHCs), and the geographic distribution of genetic variation across a broad sample of allopatric and sympatric populations. I test whether X chromosomes play a pronounced role in population divergence and reproductive isolation. Using close range mating trials and hybridization experiments I identify numerous pre-mating and post-mating barriers between the species. The results indicate that the species are currently reproductively isolated and the pattern of population differentiation does not strongly support contemporary species interactions contributing to phenotypic diversity. Numerous barriers exist between the species, in particular hybrid females are sterile in both cross directions, while hybrid males are relatively fertile. This provides a rare exception to Haldane’s rule which is central to many genetic theories of speciation. Established theory predicts that X chromosomes should play a pronounced role in the evolution of both pre- and postzygotic barriers. Contrary to this, I found no evidence that X chromosomes contribute to hybrid female sterility. Moreover, X-linked loci exhibited an unexpected pattern of reduced population differentiation within species, but increased species divergence compared to autosomal loci, which may indicate selective sweeps or sex-biased processes. Taken together, the results suggest that the causes and consequences of X chromosome evolution, in particular among XO taxa, may contradict some of the established theories.Distribution ecology of Palearctic migrants in the humid Guinea savannah in West Africa
https://hdl.handle.net/10023/7446
Declines in breeding populations of most migrants across much of the Palearctic have been linked to environmental conditions in their African non-breeding grounds. Studying winter distribution dynamics for these species is necessary to understand how factors in these areas may influence their overall population dynamics. This thesis explored in detail the distribution ecology of migrants in the Guinea savannah, the region from where wintering migrants currently show the greatest breeding population declines. In particular, I investigated some prevailing but hitherto little tested ecological hypothesis concerning impacts of geographical, vegetation and anthropogenic characteristics on the densities and winter distribution of migrants in Africa. Migrant distribution seemed to fit a pattern where decisions leading to winter habitat choice and association were hierarchical and jointly influenced by factors extrinsic and intrinsic to the habitats at large and finer scales respectively. Migrants were distributed in reasonable densities across a wide range of habitats. There was also evidence for an independent effect of latitude on densities and distribution, even after controlling for habitat characteristics. There was no evidence of large changes in latitudinal density patterns within a given winter season and site density patterns were generally consistent over the study duration. Migrants and taxonomically-related/ecologically similar Afrotropical residents showed similarities in habitat requirements and utilization, although migrants utilized habitats over a wider latitudinal range. Some migrants tended to show correspondence in site occurrence between consecutive winters but less so within a given winter season and there was an overall low transferability of habitat models for Palearctic migrants between sites in Nigeria. Collectively, the results describe distribution mechanisms typical for ecologically flexible species that can best be described as habitat generalists. As generalists, migrants are expected to show some resilience, especially in dealing with local and small scale changes on their wintering grounds such that these are unlikely to be the primary limiting factor in their population dynamics. However, the scale of ongoing habitat change across much of Africa is perhaps contributing to overcome the resilience engendered by their generalism. Conservation efforts for these mainly generalists species may therefore aim to preserve habitat on a large scale, perhaps through the promotion of sustainable land use practices.
2015-11-30T00:00:00ZIvande, Samuel T.Declines in breeding populations of most migrants across much of the Palearctic have been linked to environmental conditions in their African non-breeding grounds. Studying winter distribution dynamics for these species is necessary to understand how factors in these areas may influence their overall population dynamics. This thesis explored in detail the distribution ecology of migrants in the Guinea savannah, the region from where wintering migrants currently show the greatest breeding population declines. In particular, I investigated some prevailing but hitherto little tested ecological hypothesis concerning impacts of geographical, vegetation and anthropogenic characteristics on the densities and winter distribution of migrants in Africa. Migrant distribution seemed to fit a pattern where decisions leading to winter habitat choice and association were hierarchical and jointly influenced by factors extrinsic and intrinsic to the habitats at large and finer scales respectively. Migrants were distributed in reasonable densities across a wide range of habitats. There was also evidence for an independent effect of latitude on densities and distribution, even after controlling for habitat characteristics. There was no evidence of large changes in latitudinal density patterns within a given winter season and site density patterns were generally consistent over the study duration. Migrants and taxonomically-related/ecologically similar Afrotropical residents showed similarities in habitat requirements and utilization, although migrants utilized habitats over a wider latitudinal range. Some migrants tended to show correspondence in site occurrence between consecutive winters but less so within a given winter season and there was an overall low transferability of habitat models for Palearctic migrants between sites in Nigeria. Collectively, the results describe distribution mechanisms typical for ecologically flexible species that can best be described as habitat generalists. As generalists, migrants are expected to show some resilience, especially in dealing with local and small scale changes on their wintering grounds such that these are unlikely to be the primary limiting factor in their population dynamics. However, the scale of ongoing habitat change across much of Africa is perhaps contributing to overcome the resilience engendered by their generalism. Conservation efforts for these mainly generalists species may therefore aim to preserve habitat on a large scale, perhaps through the promotion of sustainable land use practices.Genetic analysis of life-history constraint and evolution in a wild ungulate population
https://hdl.handle.net/10023/3363
Trade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.
2012-04-01T00:00:00ZMorrissey, Michael BlairWalling, CraigWilson, AlastairPemberton, JosephineClutton-Brock, TimKruuk, LoeskeTrade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.