We combined genetic sequence data and ecological niche modelling to resolve the impacts of past climatic fluctuations on the distribution, genetic diversification, and demographic dynamics of an East Asian montane bird, the green-backed tit (Parus monticolus).
Phylogenetic analyses were carried out using four mitochondrial fragments and seven nuclear loci from 161 birds sampled from 29 localities spanning the entire geographical range of the green-backed tit. We used *beast to estimate the species tree and calculate divergence times. Extended Bayesian skyline plots were used to infer potential historical shifts in population size. We used MaxEnt to predict potential distributions during three periods: the present day, the Last Glacial Maximum and the Last Interglacial.
The mitochondrial DNA (mtDNA) gene tree showed strong support for three reciprocally monophyletic groups: a south-western clade, a central clade and a Taiwanese clade. Taiwanese and Vietnamese samples had fixed differences at several nuclear loci, but the south-western and central samples shared haplotypes at all nuclear loci. The mtDNA gene tree topology differed from the species tree topology. The species tree suggested sister relationships between Taiwanese and Vietnamese operational taxonomic units (OTUs) and between south-western and central OTUs. Diversification within the green-backed tit was relatively recent, probably within the last 0.9 million years. Extended Bayesian skyline plots suggested rapid population expansion in the south-western and central phylogroups after the Last Interglacial, and this result was consistent with ecological niche models.
Our results suggest that genetic diversification within the green-backed tit was affected by the later Pleistocene climate fluctuations. Ecological niche models indicated that the present-day vegetation distribution was, in many ways, more similar to that of the Last Glacial Maximum than it was to that of the Last Interglacial. Continental populations of the green-backed tit experienced unusual demographic and range expansion that is likely to have occurred during the cooling transition between the Last Interglacial and the Last Glacial Maximum. We found incongruence between the mtDNA gene tree and the species tree, which underscores the importance of using both mitochondrial and nuclear markers when estimating the evolutionary history of populations.