Evidence for Climate-Driven Diversification? A Caution for Interpreting Abc Inferences of Simultaneous Historical Events

Oaks, Jamie R.; Sukumaran, Jeet; Esselstyn, Jacob A.; Linkem, Charles W.; Siler, Cameron D.; Holder, Mark T.; Brown, Rafe M.

doi:10.1111/j.1558-5646.2012.01840.x

Cited by 68 publications

(208 citation statements)

References 76 publications

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“…Null expectations of concordance among taxa with disparate traits are prevalent in the comparative phylogeographic literature (9,10,(33)(34)(35), even though it is well documented that certain ecological or life history traits can influence greatly genetic structure (36,37), especially with respect to species' responses to biogeographic barriers and climatic change (27,38). A main concern with such generic hypotheses of global phylogeographic concordance is their reduced predictive power (39), i.e., rejection of concordance leads to rather inconclusive statements that do not offer particularly meaningful insights (23).…”

Section: Reduced Predictive Power Of Generic Expectations Of Concordamentioning

confidence: 99%

“…In other words, without knowing Box 1: Refined vs. Generic Hypotheses in hABC to Evaluate Climate-Driven Diversification hABC analyses are widely used in comparative phylogeography to evaluate scenarios of climate-driven diversification by testing for simultaneous divergence among population pairs of codistributed taxa (12,66,67). Here we highlight two case studies that applied hABC to island taxa to assess the hypothesized "species-pump" action of rising and falling sea levels under the Pleistocene Aggregate Island Complex (PAIC) (68) model of diversification, which is expected to produce a pattern of temporally clustered divergence times coinciding with high sea level periods (35) (Fig. 1A).…”

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

confidence: 99%

“…1A). 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.…”

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

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

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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Section: Reduced Predictive Power Of Generic Expectations Of Concordamentioning

confidence: 99%

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

confidence: 99%

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

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

220

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“…Several iterations of divergence time (t) prior were examined to explore the parameter space adequately (details in electronic supplementary material, S2). As MsBayes is considered to show a bias towards inferring a concordant divergence largely owing to broad uninformative prior distributions used [31], we also analysed the data with DPPmsBayes [32], which allows for more flexible priors and uses a non-parametric approach-Drichlet-process priors on divergence models [32].…”

Section: (B) Temporal Concordance In Divergencesmentioning

confidence: 99%

Deep and wide valleys drive nested phylogeographic patterns across a montane bird community

et al. 2015

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Montane species distributions interrupted by valleys can lead to range fragmentation, differentiation and ultimately speciation. Paleoclimatic fluctuations may accentuate or reduce such diversification by temporally altering the extent of montane habitat and may affect species differentially. We examined how an entire montane bird community of the Western Ghats-a linear, coastal tropical mountain range-responds to topographic valleys that host different habitats. Using genetic data from 23 species (356 individuals) collected across nine locations, we examined if different species in the community reveal spatial concordance in population differentiation, and whether the timing of these divergences correlate with climatic events. Our results reveal a nested effect of valleys, with several species (10 of 23) demonstrating the oldest divergences associated with the widest and deepest valley in the mountain range, the Palghat Gap. Further, a subset of these 10 species revealed younger divergences across shallower, narrower valleys. We recovered discordant divergence times for all valley-affected montane birds, mostly in the Pleistocene, supporting the Pliestocene-pump hypotheses and highlighting the role of climatic fluctuations during this period in driving species evolution. A majority of species remain unaffected by valleys, perhaps owing to geneflow or extinction-recolonization dynamics. Studying almost the entire community allowed us to uncover a range of species' responses, including some generalizable and other unpredicted patterns.

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“…These include methods that identify the optimal species delimitation using likelihood ratio tests (70), reversible-jump Markov chain Monte Carlo (71,72), information theory (73), ABC (74), and marginalized likelihoods (75). Methods for analyzing comparative phylogeographic data are also under active development, including the use of hierarchical Bayesian models to test simultaneous divergence (76,77) or simultaneous population expansion (78,79).…”

Section: Resultsmentioning

confidence: 99%

Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs

Thomé

Carstens

2016

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

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Phylogeographic research investigates biodiversity at the interface between populations and species, in a temporal and geographic context. Phylogeography has benefited from analytical approaches that allow empiricists to estimate parameters of interest from the genetic data (e.g., θ = 4Neμ, population divergence, gene flow), and the widespread availability of genomic data allow such parameters to be estimated with greater precision. However, the actual inferences made by phylogeographers remain dependent on qualitative interpretations derived from these parameters' values and as such may be subject to overinterpretation and confirmation bias. Here we argue in favor of using an objective approach to phylogeographic inference that proceeds by calculating the probability of multiple demographic models given the data and the subsequent ranking of these models using information theory. We illustrate this approach by investigating the diversification of two sister species of four-eyed frogs of northeastern Brazil using single nucleotide polymorphisms obtained via restriction-associated digest sequencing. We estimate the composite likelihood of the observed data given nine demographic models and then rank these models using Akaike information criterion. We demonstrate that estimating parameters under a model that is a poor fit to the data is likely to produce values that lead to spurious phylogeographic inferences. Our results strongly imply that identifying which parameters to estimate from a given system is a key step in the process of phylogeographic inference and is at least as important as being able to generate precise estimates of these parameters. They also illustrate that the incorporation of model uncertainty should be a component of phylogeographic hypothesis tests. information theory | model selection | Pleurodema | site frequency spectrum | Caatinga I n biological populations with interbreeding individuals, allele frequencies will inevitably change with time, both in stochastic and systematic manners, through neutral and adaptive processes. These processes-genetic drift, gene flow, mutation, recombination, and natural selection -constitute observable phenomena that lead directly to population structure, population divergence, and eventually speciation. Phylogeography is ideally situated to investigate systems where the microevolutionary processes that act within gene pools begin to form macroevolutionary patterns and has been described as the bridge between population genetics and phylogenetics (1). The power of the discipline comes from the consideration of geographic origin of individuals and populations along the continuum between populations and species (2, 3).Phylogeographic research has progressed through several stages since Avise et al.(1) introduced the term. Initial studies were based on information that can be gathered from the genetic data under few assumptions, for example by calculating summary statistics or estimating gene trees. Inferences were then derived from qualitative interpretations ...

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Evidence for Climate-Driven Diversification? A Caution for Interpreting Abc Inferences of Simultaneous Historical Events

Cited by 68 publications

References 76 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

Deep and wide valleys drive nested phylogeographic patterns across a montane bird community

Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs

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