BackgroundClimate oscillation may have a profound effect on species distributions, gene flow patterns and population demography. In response to environmental change, those species restricted to montane habitats experienced expansions and contractions along elevation gradients, which can drive differentiation among sky islands.ResultsThe Shangcheng stout salamander (Pachyhynobius shangchengensis) is a cool stream amphibian restricted to high-elevation areas in the Dabie Mountains, East China. In the present study, we used mtDNA genes (Cyt b and ND2) of 193 individuals and 12 nuclear microsatellite loci genotyped on 370 individuals, representing 6 populations (JTX, KHJ, MW, TTZ, BYM and KJY) across the taxon’s distribution area, to investigate their genetic variation and evolutionary history of P. shangchengensis. Most populations showed unusually high levels of genetic diversity. Phylogenetic analyses revealed five monophyletic clades with divergence times ranging from 3.96 to 1.4 Mya. Accordingly, significant genetic differentiation was present between these populations. Bayesian skyline plot analyses provided that all populations underwent long-term population expansions since the last inter-glacial (0.13 Mya ~ 0.12 Mya). Msvar analyses found recent signals of population decline for two northern populations (JTX and KHJ) reflecting a strong bottleneck (approximately 15-fold decrease) during the mid-Holocene (about 6000 years ago). Ecological niche modelling has shown a discontinuity in suitable habitats for P. shangchengensis under different historical climatic conditions.ConclusionsOur results suggest that the niche conservatism of P. shangchengensis and sky island effects may have led to long-term isolation between populations. In sky island refuges, the mid-latitude Dabie Mountains have provided a long-term stable environment for P. shangchengensis, which has led to the accumulation of genetic diversity and has promoted genetic divergence.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1333-8) contains supplementary material, which is available to authorized users.

The Old World buntings (Aves: Emberizidae) mainly inhabit open habitats in Eurasia and Africa. It has long been debated whether the group originated in the New World or the Old World and whether their radiation is related to the expansion of open habitats and shifts in migratory behaviours. To answer these questions, we reconstructed their biogeographic histories and analysed their diversification patterns in terms of time, space and traits using a near-complete phylogeny. We found the most recent common ancestor of Emberizidae and their sisters distributed in the New World. After invasion into the eastern Palearctic through the Bering Straits Bridge in the middle Miocene, subsequent loss of migrations probably split Emberizidae into two lineages: one radiated in Afrotropical deserts and savannah and the other mainly diversified in Palearctic semi-open to open forests, the mountains of Central Asia and the Qinghai-Tibetan Plateau. This group began to diversify in the late Miocene (~10 Ma), at first rapidly, coinciding with the expansion of open habitats due to global cooling. As the available habitats were occupied, the diversification rate of buntings decreased rapidly in arid habitats, but shifts of habitat preference to open forests led to terminal radiations on the southern edge of taiga forests in the mountains of Central Asia and the eastern Palearctic. Our results provide insight into the biogeographic histories and radiation of the Old World buntings in open habitats.

The lack of distinct morphological features of cryptic species is a hard problem for taxonomy, especially when the taxa are closely related with considerable amounts of ancestral polymorphism. Lately, intensive coalescent-based analyses involving multiple loci have become the preferred method to assess the extent of genetic distinctivness in otherwise phenotypically similar populations. Previously, phylogenetic studies on Pachyhynobius shangchengensis uncovered five extremely deeply divergent clades, which suggested that this species may be a cryptic species complex. In this study, we used the complete mitochondrial genome data and samples from the entire range of stout salamander (Pachyhynobius), as well as publicly available mitochondrial genomes to assess species boundaries within this genus using a suite of diverse methodologies (e.g. general mixed Yule coalescent model, Automatic Barcode Gap Discovery). The phylogenetic relationships recovered two major groups within P. shangchengensis, with one group formed by four of the six extant populations and corresponding to the central and eastern range of the Dabie mountains, while the other group encompassed two other lineages in the north west of the Dabie mountain range. The species delimitation comparison within Pachyhynobius supported the presence of recognized species within the genus, and consensus was observed across methods for the existence of up to five cryptic species within what has been traditionally considered to be P. shangchengensis. While this implies the existence of four taxa in addition to the described P. shangchengensis species, morphological data and life history information are further required to contribute to the species definition. The observed pattern of genetic variation is likely the outcome of a discontinuous habitat combined with niche conservatism, which produced the sky-island effect observed in Pachyhynobius, and which led to formation of a hidden species diversity in this genus.

Species are the cornerstone in many domains of biology research, which make accurate species delimitation critically important. In this study, the systematics and biogeography of the Hyla chinensis group were analyzed based on phylogeny, species delimitation, and ancestral area reconstruction methods. The phylogenetic results showed that six specific clusters existed in the H. chinensis group. Bayesian Phylogenetics and Phylogeography (BPP) analysis indicated that six distinct species exist due to the high probability values (>0.95), which were also supported by the Bayes factor (BF) analysis. The divergence time of the H. chinensis group was estimated to date back to 18.84 million years ago (Mya) in the early Miocene. Combining the results of ancestral area reconstruction, the H. chinensis group might have originated from Guangxi-Hainan, then spread eastwardly and reached Nanling Mountains, Wuyi Mountains, Huangshan Mountain, and Taiwan. In right-about colonization, it was gradually extended to the Yunnan-Guizhou Plateau, Sichuan Basin, Qinling Mountains, and Dabie Mountains. Considering the geological movement from early Miocene to Pliocene, the colonization pattern of the H. chinensis group may be closely related to the progressive uplift of the Qinghai-Tibetan Plateau (QTP) and historical climate change. Our study provided evidence for species delimitation and speciation process within the H. chinensis group. Our study supported the hypothesis that the evolutionary divergence in this species group was a consequence of the progressive uplift of the QTP and environmental change.

Mitochondrial genomes have proved to be a powerful tool for studying evolutionary relationships and the evolutionary history. In this study, the complete mitochondrial genome of Emberiza pallasi (16,786 bp) was determined. It is similar in architecture to the typical vertebrate mtDNA genome, which consists of 37 genes (13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes) and one control region. Overall base composition of the mtDNA was A (29.37%), T (22.65%), C (33.23%), and G (14.75%). Phylogenetic analysis based on Emberiza mitogenomes indicated a relative close relationship among E. pallasi with E. elegans and E. siemsseni.