Recommendations for Using Msbayes to Incorporate Uncertainty in Selecting an Abc Model Prior: A Response to Oaks Et Al.

Hickerson, Michael J.; Stone, Graham N.; Lohse, Konrad; Demos, Terrence C.; Xie, Xiaoou; Landerer, Cedric; Takebayashi, Naoki

doi:10.1111/evo.12241

Cited by 32 publications

(161 citation statements)

References 51 publications

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“…; Hickerson et al . ). Thirty species were analysed in the comparison between El Copé and Brewster, and fifteen species were compared between Cana and Brewster (Fig.…”

Section: Methodsmentioning

confidence: 97%

Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait‐based phylogeographic approach

et al. 2015

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Hypotheses to explain phylogeographic structure traditionally invoke geographic features, but often fail to provide a general explanation for spatial patterns of genetic variation. Organisms' intrinsic characteristics might play more important roles than landscape features in determining phylogeographic structure. We developed a novel comparative approach to explore the role of ecological and life-history variables in determining spatial genetic variation and tested it on frog communities in Panama. We quantified spatial genetic variation within 31 anuran species based on mitochondrial DNA sequences, for which hierarchical approximate Bayesian computation analyses rejected simultaneous divergence over a common landscape. Regressing ecological variables, on genetic divergence allowed us to test the importance of individual variables revealing that body size, current landscape resistance, geographic range, biogeographic origin and reproductive mode were significant predictors of spatial genetic variation. Our results support the idea that phylogeographic structure represents the outcome of an interaction between organisms and their environment, and suggest a conceptual integration we refer to as trait-based phylogeography.

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“…; Hickerson et al . ). Thirty species were analysed in the comparison between El Copé and Brewster, and fifteen species were compared between Cana and Brewster (Fig.…”

Section: Methodsmentioning

confidence: 97%

Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait‐based phylogeographic approach

et al. 2015

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“…As a goodness-of-fit check to ascertain whether the model and our chosen priors can produce the main features of the observed data and to check for prior sampling efficiency (Hickerson et al 2014), we deployed a PCA on prior and posterior samples of the 16 summary statistics. Initially, we used the first two principal components of the summary statistics calculated from 1,000 random draws from the simulated prior distribution and 1,000 samples from the hABC posterior to compare with these first two components from the 32 avian population samples ( D* ).…”

Section: Methodsmentioning

confidence: 99%

Detecting Concerted Demographic Response across Community Assemblages Using Hierarchical Approximate Bayesian Computation

Chan

Schanzenbach

Hickerson

2014

Molecular Biology and Evolution

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112

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Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate.

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“…Consider the case in which initial hABC analyses of 22 taxon pairs spanning five orders of terrestrial vertebrates sampled from six island pairs across the Philippine archipelago fit a model of simultaneous divergence, seemingly providing support for the "species-pump" diversification hypothesis (35). However, when the authors performed a suite of simulation-based power analyses and discovered inherent bias in inferences because of improper priors on demographic and divergence-time parameters in the msBayes program (69,70), reanalysis showed divergence times were not clustered. The merit of identifying methodological biases not withstanding, equivalent scrutiny should be given to the metric used to evaluate support for the species-pump diversification hypothesis, that is, the concordance criterion.…”

Section: Insights Gained From Discordance Highlight the Promise Of A mentioning

confidence: 99%

Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses

Papadopoulou

Knowles

2016

Proc. Natl. Acad. Sci. U.S.A.

189

220

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For three decades, comparative phylogeography has conceptually and methodologically relied on the concordance criterion for providing insights into the historical/biogeographic processes driving population genetic structure and divergence. Here we discuss how this emphasis, and the corresponding lack of methods for extracting information about biotic/intrinsic contributions to patterns of genetic variation, may bias our general understanding of the factors driving genetic structure. Specifically, this emphasis has promoted a tendency to attribute discordant phylogeographic patterns to the idiosyncracies of history, as well as an adherence to generic null expectations of concordance with reduced predictive power. We advocate that it is time for a paradigm shift in comparative phylogeography, especially given the limited utility of the concordance criterion as genomic data provide ever-increasing levels of resolution. Instead of adhering to the concordance-discordance dichotomy, comparative phylogeography needs to emphasize the contribution of taxon-specific traits that will determine whether concordance is a meaningful criterion for evaluating hypotheses or may predict discordant phylogeographic structure. Through reference to some case studies we illustrate how refined hypotheses based on taxon-specific traits can provide improved predictive frameworks to forecast species responses to climatic change or biogeographic barriers while gaining unique insights about the taxa themselves and their interactions with their environment. We outline a potential avenue toward a synthetic comparative phylogeographic paradigm that includes addressing some important conceptual and methodological challenges related to study design and application of model-based approaches for evaluating support of trait-based hypotheses under the proposed paradigm.biogeography | ecological traits | coalescent modeling | Pleistocene | statistical phylogeography P aralleling its critical role in identifying biogeographic phenomena by common structuring of genetic variation across taxa, comparative phylogeography has the potential to offer unprecedented insights about the taxa themselves. We here make an argument that such a paradigm shift, in which the contribution of biotic attributes are a focal point, as opposed to an emphasis on abiotic factors, is not only a valuable endeavor in itself, but it is also critical to (i) understanding the relative contributions of abiotic/extrinsic (e.g., geography, geological, or climatic history) vs. biotic/intrinsic (e.g., ecological or life history traits; hereafter referred to as biotic) factors in structuring genetic variation and divergence across taxa, as well as (ii) determining the relative prevalence of deterministic processes versus stochasticity in the evolutionary history of taxa, and we argue that (iii) the key to meaningful insights is not just a function of the statistical support we might have for a model, but it also depends on the creativity of biologists to identify hypotheses that are releva...

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Recommendations for Using Msbayes to Incorporate Uncertainty in Selecting an Abc Model Prior: A Response to Oaks Et Al.

Cited by 32 publications

References 51 publications

Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait‐based phylogeographic approach

Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait‐based phylogeographic approach

Detecting Concerted Demographic Response across Community Assemblages Using Hierarchical Approximate Bayesian Computation

Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses

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