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Cooke G.M.,Macquarie University | Cooke G.M.,The Australian Museum Research Institute | Landguth E.L.,University of Montana | Beheregaray L.B.,Macquarie University | Beheregaray L.B.,Flinders University
Evolution | Year: 2014

Ecological speciation involves the evolution of reproductive isolation and niche divergence in the absence of a physical barrier to gene flow. The process is one of the most controversial topics of the speciation debate, particularly in tropical regions. Here, we investigate ecologically based divergence across an Amazonian ecotone in the electric fish, Steatogenys elegans. We combine phylogenetics, genome scans, and population genetics with a recently developed individual-based evolutionary landscape genetics approach that incorporates selection. This framework is used to assess the relative contributions of geography and divergent natural selection between environments as biodiversity drivers. We report on two closely related and sympatric lineages that exemplify how divergent selection across a major Amazonian aquatic ecotone (i.e., between rivers with markedly different hydrochemical properties) may result in replicated ecologically mediated speciation. The results link selection across an ecological gradient with reproductive isolation and we propose that assortative mating based on water color may be driving the divergence. Divergence resulting from ecologically driven selection highlights the importance of considering environmental heterogeneity in studies of speciation in tropical regions. Furthermore, we show that framing ecological speciation in a spatially explicit evolutionary landscape genetics framework provides an important first step in exploring a wide range of the potential effects of spatial dependence in natural selection. © 2014 The Society for the Study of Evolution.


Beheregaray L.B.,Flinders University | Cooke G.M.,The Australian Museum Research Institute | Chao N.L.,Federal University of Amazonas | Landguth E.L.,University of Montana
Frontiers in Genetics | Year: 2015

Evolution creates and sustains biodiversity via adaptive changes in ecologically relevant traits. Ecologically mediated selection contributes to genetic divergence both in the presence or absence of geographic isolation between populations, and is considered an important driver of speciation. Indeed, the genetics of ecological speciation is becoming increasingly studied across a variety of taxa and environments. In this paper we review the literature of ecological speciation in the tropics. We report on low research productivity in tropical ecosystems and discuss reasons accounting for the rarity of studies. We argue for research programs that simultaneously address biogeographical and taxonomic questions in the tropics, while effectively assessing relationships between reproductive isolation and ecological divergence. To contribute toward this goal, we propose a new framework for ecological speciation that integrates information from phylogenetics, phylogeography, population genomics, and simulations in evolutionary landscape genetics (ELG). We introduce components of the framework, describe ELG simulations (a largely unexplored approach in ecological speciation), and discuss design and experimental feasibility within the context of tropical research. We then use published genetic datasets from populations of five codistributed Amazonian fish species to assess the performance of the framework in studies of tropical speciation. We suggest that these approaches can assist in distinguishing the relative contribution of natural selection from biogeographic history in the origin of biodiversity, even in complex ecosystems such as Amazonia. We also discuss on how to assess ecological speciation using ELG simulations that include selection. These integrative frameworks have considerable potential to enhance conservation management in biodiversity rich ecosystems and to complement historical biogeographic and evolutionary studies of tropical biotas. © 2015 Beheregaray, Cooke, Chao and Landguth.


Laity T.,Khan Research Laboratories | Laffan S.W.,University of New South Wales | Gonzalez-Orozco C.E.,University of Canberra | Faith D.P.,The Australian Museum Research Institute | And 9 more authors.
Science of the Total Environment | Year: 2015

Phylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g., species), phylodiversity measures provide important additional information about biodiversity that can improve conservation policy and outcomes. As a biodiverse nation with a strong legislative and policy framework, Australia provides an opportunity to use phylogenetic information to inform conservation decision-making.We explored the application of phylodiversity measures across Australia with a focus on two highly biodiverse regions, the south west of Western Australia (SWWA) and the South East Queensland bioregion (SEQ). We analysed seven diverse groups of organisms spanning five separate phyla on the evolutionary tree of life, the plant genera Acacia and Daviesia, mammals, hylid frogs, myobatrachid frogs, passerine birds, and camaenid land snails. We measured species richness, weighted species endemism (WE) and two phylodiversity measures, phylogenetic diversity (PD) and phylogenetic endemism (PE), as well as their respective complementarity scores (a measure of gains and losses) at 20. km resolution.Higher PD was identified within SEQ for all fauna groups, whereas more PD was found in SWWA for both plant groups. PD and PD complementarity were strongly correlated with species richness and species complementarity for most groups but less so for plants. PD and PE were found to complement traditional species-based measures for all groups studied: PD and PE follow similar spatial patterns to richness and WE, but highlighted different areas that would not be identified by conventional species-based biodiversity analyses alone.The application of phylodiversity measures, particularly the novel weighted complementary measures considered here, in conservation can enhance protection of the evolutionary history that contributes to present day biodiversity values of areas. Phylogenetic measures in conservation can include important elements of biodiversity in conservation planning, such as evolutionary potential and feature diversity that will improve decision-making and lead to better biodiversity conservation outcomes. © 2015.


Laity T.,Khan Research Laboratories | Laffan S.W.,University of New South Wales | Gonzalez-Orozco C.E.,University of Canberra | Faith D.P.,The Australian Museum Research Institute | And 9 more authors.
Science of the Total Environment | Year: 2015

Phylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g., species), phylodiversity measures provide important additional information about biodiversity that can improve conservation policy and outcomes. As a biodiverse nation with a strong legislative and policy framework, Australia provides an opportunity to use phylogenetic information to inform conservation decision-making.We explored the application of phylodiversity measures across Australia with a focus on two highly biodiverse regions, the south west of Western Australia (SWWA) and the South East Queensland bioregion (SEQ). We analysed seven diverse groups of organisms spanning five separate phyla on the evolutionary tree of life, the plant genera Acacia and Daviesia, mammals, hylid frogs, myobatrachid frogs, passerine birds, and camaenid land snails. We measured species richness, weighted species endemism (WE) and two phylodiversity measures, phylogenetic diversity (PD) and phylogenetic endemism (PE), as well as their respective complementarity scores (a measure of gains and losses) at 20. km resolution.Higher PD was identified within SEQ for all fauna groups, whereas more PD was found in SWWA for both plant groups. PD and PD complementarity were strongly correlated with species richness and species complementarity for most groups but less so for plants. PD and PE were found to complement traditional species-based measures for all groups studied: PD and PE follow similar spatial patterns to richness and WE, but highlighted different areas that would not be identified by conventional species-based biodiversity analyses alone.The application of phylodiversity measures, particularly the novel weighted complementary measures considered here, in conservation can enhance protection of the evolutionary history that contributes to present day biodiversity values of areas. Phylogenetic measures in conservation can include important elements of biodiversity in conservation planning, such as evolutionary potential and feature diversity that will improve decision-making and lead to better biodiversity conservation outcomes. © 2015 Published by Elsevier B.V.


Fitzhugh K.,Natural History Museum of Los Angeles County | de Matos Nogueira J.M.,University of Sao Paulo | Carrerette O.,University of Sao Paulo | Hutchings P.,The Australian Museum Research Institute
Zoological Journal of the Linnean Society | Year: 2015

A phylogenetic analysis was performed to determine the monophyly of non-monotypic genera of the terebelliform family Polycirridae, i.e. Polycirrus, Amaeana, Lysilla, and Hauchiella, and the evolution of characters among members of this clade. The monotypic genera, Enoplobranchus and Biremis, were also included, together with members of both known species in Hauchiella. Representative species were included for remaining genera: 14 species of Polycirrus, six species of Amaeana, and six species of Lysilla. Out-groups consisted of representatives of Spionidae, Cirratulidae, and Sabellariidae, as well as several species of Telothelepodidae. A total of 40 in- and out-group species were coded for 50 subjects ('characters') and 117 subject-predicate relationships ('states'). Although results are consistent with recent phylogenetic studies within Terebelliformia that suggest Polycirridae monophyly, only Hauchiella was found to be monophyletic, albeit part of the more inclusive clade comprising remaining polycirrid genera. Evolutionary transformation series are discussed for selected characters in relation to the non-monophyly of Polycirrus, Lysilla, and Amaeana. Implications for the use of supraspecific taxa as 'taxonomic surrogates' are highlighted. The definition of Polycirridae is emended. © 2015 The Linnean Society of London.


Functional diversity indices typically focus on a small number of recognised important traits. The phylogenetic diversity measure (PD) has provided one way to make inferences about a broader array of traits. However, PD’s assumption that shared ancestry explains shared features cannot account for all shared traits. An alternative functional diversity index, EDf, shifts the focus from shared ancestry to shared habitat as the explanation of shared traits among species. EDf calculations use a functional trait space with dimensions reflecting environmental or habitat gradients, contrasting with conventional traits spaces in which dimensions are defined by nominated traits. The EDf method assumes a unimodal relationship between traits and habitat gradients, reflecting its assumption that shared habitat explains shared traits among species. This model allows inference of the relative trait diversity of different subsets of species. EDf adapts the environmental diversity (ED) method, which was designed to evaluate the diversity of subsets of sites under a model of unimodal response of species to gradients. The re-casting of the model as unimodal response of traits to gradients means that EDf makes inferences about the relative number of traits represented by different subsets of species. This “counting-up” of traits means that EDf not only can evaluate the functional trait diversity of subsets of species but also provide other calculations supporting biodiversity conservation planning. For priority setting among species, weighted EDf distinctiveness indicates the extent to which a species has traits shared by few others. Probabilistic EDf integrates estimated species’ extinction probabilities. EDf can support conservation planning for functional diversity that effectively balances conservation of traits of known importance with conservation of more general functional trait diversity. © 2015, Springer Science+Business Media Dordrecht.

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