MULTILOCUS COALESCENCE ANALYSES SUPPORT A mtDNA-BASED PHYLOGEOGRAPHIC HISTORY FOR A WIDESPREAD PALEARCTIC PASSERINE BIRD, SITTA EUROPAEA

Abstract

Our understanding of species phylogeography in much of the Palearctic is incomplete. In addition, many existing studies based solely on mitochondrial DNA (mtDNA) can provide a biased view of phylogeographic history because of the effects of lineage sorting, natural selection, or hybridization. We analyzed 13 introns to assess a mtDNA study of the Eurasian nuthatch (Sitta europaea) that suggested a seemingly contemporaneous origin of distinct taxa in the Caucasus, Europe, and Asia. Neutrality tests showed no evidence of selection on either the mtDNA or nuclear sequences. Most nuclear gene trees, except for Z‐linked ones, did not recover the three lineages, which we attribute to recent splitting. Analyses of the 13 introns combined revealed the same three groups as did the mtDNA and suggested that nuthatches experienced a trichotomous (or two indistinguishable) split(s) 1–2 million years ago (Mya) and have remained isolated with trifling if not zero gene flow since then, and the Asian group increased in population size. This result demonstrates the usefulness of mtDNA in discovering phylogeographic patterns. The use of multiple nuclear loci facilitated detection of an introgressed individual and improved estimates of process parameters such as divergence time and population expansion. We recommend that phylogeographic studies should be based on both mtDNA and nuclear genes.

Matching loci surveyed to questions asked in phylogeography

“…However, our goal here is to provide a retrospective analysis on the mtDNA era of phylogeography and estimate the credibility of nearly three decades of mtDNA studies. Many studies have found that the results based on multiple nuclear genes or genome-wide data are often consistent with those based on one single mtDNA gene data in phylogeographic patterns or species delimitation ( [8,11,[44][45][46]56]; but see [5,41,42]). Here, we provide empirical data confirming the assertion that mtDNA is a useful marker for detecting recent population differentiation because of its fast coalescent time at least in avian taxa (figure 3).…”

Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial–nuclear comparison

“…The factors by which the estimated recombination rates exceed the background rate were calculated, and the upper and lower bounds of 95% credible intervals of these values were recorded. If one or more estimated values were significantly larger than one, it meant that there was significant recombination occurring between the corresponding sites (Hung et al, 2012). Otherwise, we assumed no intra-locus recombination.…”

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

“…A number of coalescent based methods have been developed to esti mate the species tree from multigene sequence data, including Bayesian (e.g., BUCKy, Ane et al, 2007; BEAST, Drummond et al, 2012) and likelihood approaches (e.g., STEM, Kubatko et al, 2009;STELLS, Wu, 2012). Coalescent based methods have been successfully implemented to disentangle the complex evolutionary history of several closely related bird species (Carling et al, 2010;Hung et al, 2012;Lavretsky et al, 2014).…”