Effects of Asymmetric Nuclear Introgression, Introgressive Mitochondrial Sweep, and Purifying Selection on Phylogenetic Reconstruction and Divergence Estimates in the Pacific Clade of Locustella Warblers

Abstract

When isolated but reproductively compatible populations expand geographically and meet, simulations predict asymmetric introgression of neutral loci from a local to invading taxon. Genetic introgression may affect phylogenetic reconstruction by obscuring topology and divergence estimates. We combined phylogenetic analysis of sequences from one mtDNA and 12 nuDNA loci with analysis of gene flow among 5 species of Pacific Locustella warblers to test for presence of genetic introgression and its effects on tree topology and divergence estimates. Our data showed that nuDNA introgression was substantial and asymmetrical among all members of superspecies groups whereas mtDNA showed no introgression except a single species pair where the invader's mtDNA was swept by mtDNA of the local species. This introgressive sweep of mtDNA had the opposite direction of the nuDNA introgression and resulted in the paraphyly of the local species' mtDNA haplotypes with respect to those of the invader. Тhe multilocus nuDNA species tree resolved all inter- and intraspecific relationships despite substantial introgression. However, the node ages on the species tree may be underestimated as suggested by the differences in node age estimates based on non-introgressing mtDNA and introgressing nuDNA. In turn, the introgressive sweep and strong purifying selection appear to elongate internal branches in the mtDNA gene tree.

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).…”

“…The high mutation rate, fast coalescence time owing to a small effective size and matrilineal inheritance make mtDNA more likely to track lineage divergence than any single nuclear gene, and is thus a relatively leading molecular indicator of population differentiation [2]. Nevertheless, analyses of mtDNA generate a single-gene tree and any single-locus tree could present a biased view of species history owing to the stochastic nature of the coalescence process or effects of selection [3][4][5]. In effect, the inferences from the first three decades of mtDNA phylogeography have been called into question [4,6].…”

“…If so, mtDNA divergence between populations should be a good predictor of actual divergence time. Alternatively, some studies suggest that the relationship between mtDNA and actual divergence are influenced by population size or selection [5,[12][13][14]. If so, mtDNA distance might provide a biased view of population divergence.…”

Recent results of molecularphylogenetic studies of endemic invertebrates inhabiting Lake Baikal

“…Однако следует отдавать себе отчет в том, что сравнение последовательностей разных генов может приводить к различным результатам (Roos et al, 2011;Oliver, 2013). Чем моложе сравниваемые виды, тем выше риск появления резко различающихся оценок возраста одних и тех же видов, главным образом, из-за неполного расхождения предковых линий и митохондри-альной либо ядерной трансгрессии (Bossu, Near, 2009;Roos et al, 2011;Oliver, 2013;Drovetski et al, 2015).…”

“…Такие несоответствия объяснимы митохондриальными и ядерными интрогрес-сиями, и, как правило, их связывают со временными на-рушениями репродуктивного барьера в обстоятельствах, когда один из видов гораздо более многочисленнее, чем другой (Bossu, Near, 2009;Thompson et al, 2010;Nevado et al, 2011;Roos et al, 2011;Drovetski et al, 2015).…”