Past hybridization between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus)

Abstract

IntroductionIncomplete lineage sorting and hybridization are two major nonexclusive causes of haplotype sharing between species. Distinguishing between these two processes is notoriously difficult as they can generate similar genetic signatures. Previous studies revealed that the mitochondrial DNA (mtDNA) differentiation between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus) was extremely low, even lower than intraspecific differentiation in some other long-tailed tits. Using a combination of multilocus and coalescent analyses, we explored the causes of the anomalous lack of mtDNA differentiation between the two species.ResultsThe mtDNA divergence between the two species was shallow, while the nuclear DNA (nuDNA) divergence was considerably deeper. The IMa analyses based on the mtDNA dataset suggested relatively high gene flow from A. fuliginosus to A. bonvaloti, while negligible gene flow in the opposite direction. In contrast to mtDNA, the migration rates at autosomal and Z-linked nuDNA loci were negligible or much lower. The NEWHYBRIDS analysis assigned all individuals except one to pure parental species with high posterior probability. The Bayesian skyline plot showed that both species underwent population expansions during the Last Glacial Maximum (LGM), and the ecological niche modelling suggested that their ranges overlapped more during the LGM than at present.ConclusionsWe suggest that historical hybridization, in combination with selective sweep and/or genetic drift might be the main causes of the extremely low mtDNA differentiation between the two species. The hybridization probably occurred mainly between A. fuliginosus females and A. bonvaloti males. The LGM distribution expansion might have facilitated hybridization, while the post-LGM distribution contraction could have facilitated some mtDNA sorting. Ongoing hybridization between the two species might be very limited, but further studies with more samples from the contact zone are needed to test this conclusion.

At the passing gate: past introgression in the process of species formation betweenAmazilia violicepsandA. viridifronshummingbirds along the Mexican Transition Zone

“…Thus, an introgression zone could have arisen as a result of geological change and volcanism during the last episode of formation of the TMVB (3.5–0.3 Ma; Gómez‐Tuena et al ., ) and during Pleistocene climatic fluctuations or because of subsequent range expansion or gene flow due to unknown movements of A. violiceps (Howell, ) tracking phenological changes of floral resources, allowing contact between southern populations of A. violiceps and A. viridifrons populations. However, putatively introgressed haplotypes are not geographically structured, which should be the case if the incongruence has arisen due to incomplete lineage sorting (Sullivan et al ., ; Wang et al ., ). Our data suggest that the genetic exchange between A. violiceps populations is limited across the volcanic belt, consistent with it being a well‐known barrier to highland taxa (Halffter, ).…”

“…,206,998 177,836 5,192,642 Values are average of three runs of mean parameter estimates and the 90% highest posterior density (HPD) intervals of each parameter; T, average generation time. 2014; Wang et al, 2014). Our data suggest that the genetic exchange between A. violiceps populations is limited across the volcanic belt, consistent with it being a well-known barrier to highland taxa (Halffter, 1987).…”

“…Incomplete lineage sorting and hybridization are two major causes of haplotype sharing between species (Rheindt & Edwards, ), and distinguishing between these two processes is very difficult during species formation because they can produce similar genetic signatures (e.g. Wang et al ., ). Despite the high variability of the coalescent process, our current sampling of two loci (one nuclear and four regions of mtDNA) suggests that the true species diversity in the A. violiceps / viridifrons group is currently underestimated.…”

“…For glaciated regions such as North America and Europe, the Pleistocene climate cycles shaped the distribution and genetic attributes of species (reviewed in Avise, ), and phylogeographical studies have shown that bird populations expanded from southern refugia after the LGM (23–18 ka; Qu et al ., ; Malpica & Ornelas, ). In contrast, at lower northern latitudes, glaciations developed only around high mountains, not on the plateau surface, or occurred asynchronously (highest volcanoes along the TMVB, Caballero et al ., ; Qinghai‐Tibetan Plateau, Qu et al ., ), where the effects were mild and bird populations mostly distributed on the plateau experienced population expansion following the LIG or retreat of a previous glaciation (500–175 ka; Qu et al ., ; but see Wang et al ., ). The larger size of the ancestral population suggest that a large amount of ancestral variation should still exist in descendant populations, and evidence of migration would be preserved as observed from south to north of the TMVB.…”

Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

“…Whether discordance in genetic patterns in mtDNA and microsatellites is explained by selection that may favour some mitochondrial variants over others due to selection to maintain ancestral mtDNA or selection for environmental gradients (Cheviron & Brumfield, 2009), allowing populations to remain as a different mitochondrial group is unlikely according to the neutrality test results. We must be careful, however, about over-interpreting these results until additional genome-wide markers become available because incomplete lineage sorting and introgressive hybridization can produce similar genetic signatures (i.e., haplotype sharing between species; Rheindt & Edwards, 2011), particularly during species formation (Qu et al, 2012;Wang et al, 2014;Rodríguez-Gómez & Ornelas, 2015).…”