In the Light of Evolution Volume X: Comparative Phylogeography (2017) / Chapter Skim
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8 Toward a Paradigm Shift in Comparative Phylogeography Driven by Trait-Based Hypotheses - Anna Papadopoulou and L. Lacey Knowles
8 Toward a Paradigm Shift in Comparative Phylogeography Driven by Trait-Based Hypotheses - Anna Papadopoulou and L. Lacey Knowles
Pages 155-170
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From page 155... ...
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 l evels of resolution. Instead of adhering to the concordance-discordance dichotomy, comparative phylogeography needs to emphasize the contri bution of taxon-specific traits that will determine whether concordance is a meaningful criterion for evaluating hypotheses or may predict dis cordant phylogeographic structure.
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From page 156... ...
We g present a variety of examples to highlight some of the interesting ecological and evolutionary questions that can be addressed using refined hypotheses based on species-specific traits, but also to emphasize the broader significance of this proposed paradigm shift to ecology and evolution. HISTORICAL EMPHASIS ON CONCORDANCE Comparative phylogeography emerged three decades ago as an integrative approach to historical biogeography (Arbogast and Kenagy, 2001;
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From page 157... ...
. Such highly influential studies clearly demonstrated the strength of the concordance criterion, and their legacy is evident in that tests of concordance became the central paradigm in comparative phylogeographic analyses.
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From page 158... ...
Invoking the idiosyncratic nature of history makes discordant phylogeographic structure uninteresting in a comparative framework (i.e., it implies there are no conclusions to be drawn about deterministic processes from discordant patterns of genetic variation) , limiting the generalizations comparative phylogeography might provide about the influence of biotic factors on genetic structure.
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From page 159... ...
For example, comparative phylogeography of two alpine butterfly species in the Rocky Mountains (DeChaine and Martin, 2005) or two saproxylic springtail species in southeastern Australia (Garrick et al., 2008)
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For example, when applying coalescent-based hypothesis testing using hABC to assess simultaneous population divergence across a set of disparate codistributed taxa ( ickerson et al., 2006b; Huang et al., 2011) , the rejection of a global model H 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 (Papadopoulou and Knowles, 2015b)
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However, these tests do not provide explicit links with the underlying microevolutionary divergence processes themselves. Comparative phylogeography has the potential to bridge this gap, providing insights about the role of ecological and life
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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 simulta neous divergence among population pairs of codistributed taxa (Carnaval et al., 2009; Bell et al., 2012; Hope et al., 2013)
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From page 163... ...
This example illustrates the reduced predictive power of generic hypotheses of concordance in hABC analyses in comparison with a refined hypothesis based on taxon-specific traits. Moreover, together the examples highlight how a bias in our understanding of the factors driving divergence may not be limited to algorithmic issues associated with comparative phylogeographic analyses, but may also be introduced by how we apply the concordance criterion to make inferences about the factors driving divergence.
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From page 164... ...
We fully acknowledge that this is not the only approach that might be applied. In fact, the full potential of this paradigm shift will not be realized without additional conceptual and methodological development from a diversity of researchers, in much the same way that comparative phylogeography evolved gradually to provide a robust framework for understanding the role of abiotic factors in structuring genetic variation.
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. A Model-Based Framework for Generating Species-Specific Predictions The proposed paradigm shift in comparative phylogeography will require an appropriate statistical framework to accommodate and interpret phylogeographic discordance.
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generates species specific expectations for patterns of genetic variation under a broad range of biologically informed hypotheses, which can then be tested against the empirical genetic data using ABC (Beaumont et al., 2002)
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, making it an especially useful tool in comparative phylogeography. FIGURE 8.2 The iDDC procedure generates species-specific predictions for patterns of genetic variation, which when coupled with approximate Bayesian computation (ABC)
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From page 168... ...
, and the power to distinguish among alternative models with genomic data, biologically informed hypotheses are poised to provide insights into questions that could not be addressed before. Methodological Challenges for Trait-Based Comparative Phylogeography As with any model-based approach for phylogeographic inference, there are important methodological and conceptual challenges with such tests of taxon-specific traits.
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From page 169... ...
. CONCLUSIONS After three decades of comparative phylogeography providing invaluable insights into the biogeographic factors structuring genetic variation, now is the time for the field to consider a shift that has the potential to offer equivalent insights about the biotic component: the taxa themselves and the lessons they can provide on ecological and evolutionary thought.
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From page 170... ...
We outlined a proposal of refined hypotheses based on species-specific traits to improve the predictive power of comparative phylogeography, as well as aspects in need of methodological development for this paradigm shift to realize its full potential. Building on the foundations of phylogeography that underlie the field's prominence in ecology and evolution, its integrative approach of drawing on input from multiple disciplines, the biologically informed hypotheses that are central to trait-based comparative phylogeography will continue to be an integral part of the field's continued success in the future.
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