Inference of Population History by Coupling Exploratory and Model-Driven Phylogeographic Analyses

Abstract

Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions.

The uncertainty of Late Pleistocene range expansions in the western Mediterranean: a case study of the colonization of south‐eastern Spain by the spur‐thighed tortoise, Testudo graeca

“…Whereas the study of genealogies can elucidate population processes, phylogeographical events or even speciation, allele frequencies can yield information on demographic trends (Sunnucks, 2000). The combination of these data types provides a more complete understanding of how an organism has responded to changes in the biogeographical landscape in a broad temporal spectrum, and the use of complementary analyses allows the study of different components of a species' evolutionary history (Garrick et al, 2010). In this sense, the scale of resolution achieved by previous studies which employed mitochondrial DNA (mtDNA) only allowed rejection of the hypothesis that T. graeca arrived in the Iberian Peninsula before the Strait of Gibraltar opened (Á lvarez et al, 2000;Fritz et al, 2009;Salinas et al, 2011).…”

Twenty Years of Molecular Biogeography in the West Mediterranean Islands of Corsica and Sardinia: Lessons Learnt and Future Prospects

“…The flourishing of new methods to harness large numbers of tailored-to-the-scope molecular markers has proceeded in parallel with (and partially stimulated) the development of sophisticated phylogeographic analytical tools [62]. At the same time, the rise of the coalescence theory is causing a shift in the treatment of phylogeographic data from exploratory to modeldriven [62,63].…”

“…At the same time, the rise of the coalescence theory is causing a shift in the treatment of phylogeographic data from exploratory to modeldriven [62,63]. In an exploratory framework, phylogeographic inferences are based on qualitative interpretations of (often) single-locus gene genealogies.…”

“…In the fortunate circumstance that such a priori hypotheses exist, alternative scenarios could be discriminated statistically and the one that fits the data best be chosen [64]. In doing that we obviously restrict ourselves to a subset of the whole possible scenarios but with the advantage to accurately estimate key components of the species demography and history of divergence ( [62] and references therein). Under a model-driven approach, gene genealogies are not anymore central to the phylogeographic analysis but they rather represent variables for connecting data to demographic parameters under an explicit statistical coalescent model [63].…”

True syntopy between chromosomal races of the Cryptocercus punctulatus wood-roach species complex

“…Second, it identifies the location of a ''testing ground'' for assessing the Biological Species Concept. This information, when coupled with the development of versatile co-dominant nuclear genetic markers (e.g., Garrick et al 2010), should facilitate future studies aimed at resolving taxonomic uncertainty surrounding this group.…”