MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity

Huang, Wen; Takebayashi, Naoki; Qi, Yuanming; Hickerson, Michael J.

doi:10.1186/1471-2105-12-1

Cited by 1,021 publications

(530 citation statements)

References 67 publications

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“…Similarly, some common practices in hABC implementations adopt computational shortcuts that also limit the interpretation of discordance. For example, the default option of resorting the summary statistics vector (e.g., in msBayes) (18,42) reduces the number of simulations required for hABC analyses but comes at the expense of losing information critical to interpretation (23,40). This lack of methodological attention for testing predictions of discordance therefore reinforces the current knowledge gap about biotic contributions to patterns of genetic variation.…”

Section: Methodsogical Developments Reinforce the Knowledge Gap Createdmentioning

confidence: 90%

“…As a consequence, the standard comparative phylogeographic toolbox indirectly encourages users to emphasize congruence and disregard discordance as uninteresting. For example, when applying coalescent-based hypothesis testing using hABC to assess simultaneous population divergence across a set of disparate codistributed taxa (18,42), the rejection of a global model of temporal congruence will unavoidably emphasize idiosyncratic aspects of history, if the test is not pursued under an appropriate study design allowing for an improved predictive framework based on taxon attributes (23). Similarly, some common practices in hABC implementations adopt computational shortcuts that also limit the interpretation of discordance.…”

Section: Methodsogical Developments Reinforce the Knowledge Gap Createdmentioning

confidence: 99%

“…Email: knowlesl@umich.edu. (18,19), also promoted the utility of the concordance criterion. At the same time, such statistical frameworks have been critical for overcoming past perceptions of phylogeography as primarily a descriptive field that lacked rigor (20).…”

Section: Historical Emphasis On Concordancementioning

confidence: 99%

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

Papadopoulou

Knowles

2016

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

189

228

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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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Section: Methodsogical Developments Reinforce the Knowledge Gap Createdmentioning

confidence: 90%

Section: Methodsogical Developments Reinforce the Knowledge Gap Createdmentioning

confidence: 99%

See 1 more Smart Citation

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

Papadopoulou

Knowles

2016

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

189

228

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“…(e) Test of simultaneous vicariance To explicitly test for simultaneous vicariance in the five taxa, we used MTML-msBayes, a hierarchical approximate Bayesian computation (ABC) method that allows for acrossspecies demographic variation, inter-gene variability in coalescent times and DNA mutation rate heterogeneity [48,49]. The analysis was conducted in three stages.…”

Section: Methods (A) Sampling Detailsmentioning

confidence: 99%

Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs

et al. 2011

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Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the Late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum. Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species' responses to past climate fluctuations. We apply this approach to multi-locus sequence data from five co-distributed frog species endemic to the Wet Tropics rainforests of northeast Australia. Our results demonstrate at least two episodes of vicariance owing to climate-driven forest contractions: one in the Early Pleistocene and the other considerably older. Understanding how repeated cycles of rainforest contraction and expansion differentially affected lineage divergence among co-distributed species provides a framework for identifying evolutionary processes that underlie population divergence and speciation.

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“…The other approach relies on estimating phylogeographic parameters from phylogenetic trees and coalescent modeling and then assesses the level of congruence in parameters among codistributed species. Both of these methodological frameworks have been used to evaluate the historical assembly of bird faunas from a range of systems, including the Neotropics (Burney and Brumfield 2009;, the Afrotropics (Voelker et al 2013), Australia (Huang et al 2011;Dolman and Joseph 2012), montane forests in Mexico (Barber and Klicka 2010), the Malay Archipelago (Lim et al 2011), North American deserts (Zink et al 2001), and the Caribbean (Sly et al 2011). An overall goal of both analytical approaches is to evaluate whether patterns inferred from neutral genetic variation are consistent with the predictions of geological changes or climatic fluctuations.…”

mentioning

confidence: 99%

Robust Estimates of Divergence Times and Selection with a Poisson Random Field Model: A Case Study of Comparative Phylogeographic Data

Amei

Smith

2014

Genetics

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Mutation frequencies can be modeled as a Poisson random field (PRF) to estimate speciation times and the degree of selection on newly arisen mutations. This approach provides a quantitative theory for comparing intraspecific polymorphism with interspecific divergence in the presence of selection and can be used to estimate population genetic parameters. Although the original PRF model has been extended to more general biological settings to make statistical inference about selection and divergence among model organisms, it has not been incorporated into phylogeographic studies that focus on estimating population genetic parameters for nonmodel organisms. Here, we modified a recently developed time-dependent PRF model to independently estimate genetic parameters from a nuclear and mitochondrial DNA data set of 22 sister pairs of birds that have diverged across a biogeographic barrier. We found that species that inhabit humid habitats had more recent divergence times and larger effective population sizes than those that inhabit drier habitats, and divergence time estimated from the PRF model were similar to estimates from a coalescent species-tree approach. Selection coefficients were higher in sister pairs that inhabited drier habitats than in those in humid habitats, but overall the mitochondrial DNA was under weak selection. Our study indicates that PRF models are useful for estimating various population genetic parameters and serve as a framework for incorporating estimates of selection into comparative phylogeographic studies.A range of analytical approaches have been developed to estimate divergence times and effective population sizes from DNA data (Takahata et al. 1995;Yang 1997Yang , 2002Hickerson et al. 2003;Rannala and Yang 2003;Hey and Nielsen 2004;Heled and Drummond 2010). These types of models have been applied to an array of empirical systems and used to reconstruct population history (e.g., Jennings and Edwards 2005;Won and Hey 2005;Lee and Edwards 2008;Hurt et al. 2009;Hailer et al. 2012), but the extension of these analyses to incorporate selection has been limited. A potential means of including selection estimates into studies examining population or phylogeographic history is the implementation of approaches that compare polymorphic and fixed nucleotide patterns within and between species (Hudson et al. 1987). Using this method, McDonald and Kreitman (1991) proposed a statistical test for homogeneity of synonymous and nonsynonymous DNA mutations among closely related species and demonstrated that an excess of nonsynonymous differences among fruit fly species was the result of the fixation of beneficial mutations.The McDonald-Kreitman test was extended and incorporated into a quantitative model used to compare intraspecific polymorphism with interspecific divergence by modeling mutation frequencies as a Poisson random field (PRF) (Sawyer and Hartl 1992). The PRF models the number of synonymous and nonsynonymous fixed differences and polymorphic sites as independent Poisson random varia...

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MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity

Cited by 1,021 publications

References 67 publications

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

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

Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs

Robust Estimates of Divergence Times and Selection with a Poisson Random Field Model: A Case Study of Comparative Phylogeographic Data

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