The burgeoning field of statistical phylogeography

Abstract

In the newly emerging field of statistical phylogeography, consideration of the stochastic nature of genetic processes and explicit reference to theoretical expectations under various models has dramatically transformed how historical processes are studied. Rather than being restricted to ad hoc explanations for observed patterns of genetic variation, assessments about the underlying evolutionary processes are now based on statistical tests of various hypotheses, as well as estimates of the parameters specified by the models. A wide range of demographical and biogeographical processes can be accommodated by these new analytical approaches, providing biologically more realistic models. Because of these advances, statistical phylogeography can provide unprecedented insights about a species' history, including decisive information about the factors that shape patterns of genetic variation, species distributions, and speciation. However, to improve our understanding of such processes, a critical examination and appreciation of the inherent difficulties of historical inference and challenges specific to testing phylogeographical hypotheses are essential. As the field of statistical phylogeography continues to take shape many difficulties have been resolved. Nonetheless, careful attention to the complexities of testing historical hypotheses and further theoretical developments are essential to improving the accuracy of our conclusions about a species' history.

Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds

“…) Phylogeography can help define where in the landscape or between which populations of a species one might usefully look for incipient reproductive isolation. It offers patterns for further investigation, not a mechanism of speciation (Edwards 2008a(Edwards , 2008b and issues of tension between phylogeography and speciation research can be tested with phylogeographic methods (Knowles 2004). Examples are whether founder events are involved in speciation or whether reproductive isolation is a by-product of the gradual accumulation of species differences by genetic drift.…”

Amphibian phylogeography: a model for understanding historical aspects of species distributions

“…These and other issues have led to the development of methods that should permit a more rigorous, statistical appraisal of phylogeographic hypotheses (Knowles and Maddison, 2002;Knowles, 2004). Until recently, most conclusions have been based on post hoc interpretations of gene trees and/or the results of NCA and mismatch distribution analysis.…”

“…In particular, it will be increasingly important to use multiple loci and include model parameters of migration rates, admixture and effective population sizes. Fortunately, ever more sophisticated analytical methods are becoming available for this task using coalescent-based, Bayesian and likelihood approaches (Knowles, 2004). Recent studies with Ascaphus species in North America, combining genetic and ecological models, is a good example of how phylogeographic inferences can be tested and refined (Carstens and Richards, 2007).…”

Population genetic structure of sexual and parthenogenetic damselflies inferred from mitochondrial and nuclear markers

“…However, because of the severe limitations of the nested clade phylogeographic analysis to infer the multiple historical processes that may characterize a species' history (see Knowles and Maddison, 2002;Petit and Grivet, 2002;Knowles, 2004;Panchal and Beaumont, 2007;Petit, 2008a, b;Beaumont et al, 2010) we did not use this analysis to make any inferences about the demographical or historical processes that could have shaped the genetic variation observed in I. hastata.…”