Comparative phylogeography as an integrative approach to historical biogeography

Arbogast, Brian S.; Kenagy, G. J.

doi:10.1046/j.1365-2699.2001.00594.x

Cited by 347 publications

(240 citation statements)

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“…Comparative biogeographic studies have usually assumed that differences in coalescence times signal differences in divergence times, thus rejecting simultaneous diversification (Avise 1992;Arbogast & Kenagy 2001). However, coalescent theory predicts a large variation in the depths of gene trees even when multiple codistributed taxa have responded to the same barrier (Hudson 1990).…”

Section: Discussionmentioning

confidence: 99%

“…A common yet elusive goal in historical biogeography and comparative phylogeography is determining whether codistributed taxa have experienced simultaneous diversification owing to a common barrier (Nelson & Platnick 1981;Avise et al 1998;Bermingham & Moritz 1998;Avise 2000;Edwards & Beerli 2000;Arbogast & Kenagy 2001;Zink 2002). Estimates of the timing of vicariant events can be obtained by applying a molecular clock to species phylogenies.…”

Section: Introductionmentioning

confidence: 99%

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Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna

2010

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Understanding the evolutionary history of the species in a particular region provides insights into how that fauna was formed. Of particular interest to biogeographers is examining the impact a geographical barrier had in generating temporal genetic diversity among codistributed species. We examined the impact a major New World barrier, the Isthmus of Tehuantepec (IT) in southern Mexico, had on a regional bird fauna. Specifically, genetic data from 10 montane-forest bird taxa were analysed using approximate Bayesian computation (ABC) to test the hypothesis of simultaneous intraspecific diversification at the IT. Because effective population size (N e ) has the greatest impact on coalescent times, thereby affecting tests of divergence among codistributed taxa, we chose priors for both current and ancestral N e using empirical estimates of theta. The ABC method detected two discrete diversification events. Subsequent analysis with the number of diversification events constrained to two suggests that four taxa diverged in an older event, with the remaining six diverging more recently. Application of a range of mutation rates from 2.0 to 5.0% Myr 21 places both events within the Pleistocene or Late Pliocene, suggesting that fluctuations in montane habitat induced by climate cycles and a late Pliocene seaway may have fractured this montane bird fauna. The results presented here suggest this avian fauna responded in a relatively concerted fashion over the last several million years.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna

2010

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“…Comparative phylogeography emerged three decades ago as an integrative approach to historical biogeography (1,2), and has since offered invaluable insights into the factors that shape spatial and temporal patterns of genetic variation. An inherent emphasis on concordance in patterns of genetic variation as a criterion for evaluating hypotheses has accompanied the development of the field since its infancy.…”

Section: Historical Emphasis On Concordancementioning

confidence: 99%

“…Methodological advances of the last decade, especially coalescent-based tools for hypothesis testing and parameter estimation (16,17) that include statistical assessment of concordance across taxa, such as the widely used hierarchical approximate Bayesian computation (hABC) This article is a PNAS Direct Submission. 1 To whom correspondence should be addressed. Email: knowlesl@umich.edu.…”

Section: Historical Emphasis On Concordancementioning

confidence: 99%

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

Papadopoulou

Knowles

2016

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

187

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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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“…The observed genetic patterns of species may reveal historical processes at the landscape scale, but they may also be the result of the current balance between gene flow and genetic drift. The comparison of phylogeographic patterns of co-distributed taxa is able to reveal more general biogeographic patterns (Arbogast and Kenagy, 2001). In the present study, all species display a clear geographic clustering of haplotype clades, and several recurrent patterns are apparent:…”

Section: Comparative Phylogeographymentioning

confidence: 99%

Geographical patterns of deep mitochondrial differentiation in widespread Malagasy reptiles

Boumans

Vieites

Glaw

et al. 2007

Molecular Phylogenetics and Evolution

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This article was published in an Elsevier journal. The attached copy is furnished to the author for non-commercial research and education use, including for instruction at the author's institution, sharing with colleagues and providing to institution administration.Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. AbstractUsing sequences of the mitochondrial 16S rRNA gene, we reconstructed the phylogeography of six widely distributed Malagasy reptiles: two gekkonid lizard species, Phelsuma lineata and Hemidactylus mercatorius; two chameleons, the Calumma brevicorne complex, and Furcifer lateralis; and two skinks, Trachylepis gravenhorstii and Trachylepis elegans. Genetic differentiation among major haplotype lineages was high and in some cases indicates or confirms species status of the divergent populations. Maximum uncorrected sequence divergences were between 2.2% and 8.3% within the various species or species complexes. Haplotype lineages were exclusive to geographic regions, except in the commensal H. mercatorius where in three anthropogenic habitats coexistence of haplotype lineages was observed, possibly due to human translocation. The eastward flowing rivers Mangoro and Mananara may represent barriers to gene flow in the case of three species each. Some species sampled from humid eastern and arid western Madagascar showed no differentiation between populations from these two regions; instead the pattern observed was in several cases more concordant with a differentiation along a north-south axis.

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Comparative phylogeography as an integrative approach to historical biogeography

Cited by 347 publications

References 49 publications

Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna

Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna

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

Geographical patterns of deep mitochondrial differentiation in widespread Malagasy reptiles

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