Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species‐specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia‐within‐refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large‐scale south‐to‐north post‐LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three‐step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis‐driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.

The evolution of sexual size dimorphism (SSD) is likely constrained by life history. Using phylogenetic comparative methods, we examined correlations between SSD among anurans and their life history traits, including egg size, clutch size, mating combat, and parental care behaviour. We used sexual dimorphism index (SDI = Body-sizefemale /Body-sizemale –1) as the measurement for SSD. Body size, life history and phylogenetic data were collected from published literature. Data were analysed at two levels: all anuran species and within individual families.

A molecular phylogeny of the high‐elevation Tibetan megophryid frogs was reconstructed using mitochondrial and nuclear gene sequences. Both parsimony and Bayesian analysis produced similar tree topologies, which identified the genusLeptobrachiumas a sister group toVibrissaphora, and the generaOreolalaxandScutigeras monophyletic groups. Within the latter two genera, several species groups were also clearly recognized. At least 13 megophryids display reversed sexual size dimorphism (RSSD), where males are equal to or larger than females. According to our phylogenetic hypothesis, RSSD may have independently evolved at least five times or as many as seven times in this group. The multiple origins of RSSD within this group provide an excellent opportunity for studying the relationship between body size sexual dimorphism and other life‐history traits and for determining the costs and benefits of RSSD.

Background: Mitochondrial introgression may result in the mitochondrial genome of one species being replaced by that of another species without leaving any trace of past hybridization in its nuclear genome. Such introgression can confuse the species genealogy estimates and lead to absurd inferences of species history. We used a phylogenetic approach to explore the potential mitochondrial genome introgression event(s) between two closely related green pond frog species,Pelophylax nigromaculatusandP. plancyi.Results: DNA sequence data of one mitochondrial and two nuclear genes from an extensive sampling of the two species were collected, and the genealogies of the three genes were constructed and compared. While the two nuclear genes congruently showed mutual reciprocal monophyly of both species, the mitochondrial phylogeny separated a KoreanP. nigromaculatusclade, a paraphyletic central ChinaP. plancyiassemblage, and a large well-supported introgression clade. Within the introgression clade, the mitochondrial haplotypes of the two speciesweremixed together. This reticulated pattern can be most parsimoniously explained by an ancient mitochondrial introgression event fromP. plancyitoP. nigromaculatusthat occurred at least 1.36 MYA, followed by multiple recent introgression events fromP. nigromaculatusback toP. plancyiwithin the last 0.63 MY. The re-constitution of previously co-adapted genomes inP. plancyimay be responsible for the recent rampant introgression events. The KoreanP. nigromaculatusclade likely represents the only surviving "true" mitochondrial lineage ofP. nigromaculatus, and the central ChinaP. plancyiassemblage likely represents the "original"P. plancyimitochondrial lineage. Refugia in the Korean Peninsula and central China may have played a significant role in preserving these ancient lineages.Conclusions: The majority of individuals in the two species have either introgressed (P. nigromaculatus) or reclaimed (P. plancyi) mitochondrial genomes while no trace of past hybridization in their nuclear genomes was detected. Asymmetrical reproductive ability of hybrids and continuous backcrossing are likely responsible for the observed mitochondrial introgression. This case is unique in that it includes an ancient "forward" introgression and many recent "backward" introgressions, which re-constitutes the original nuclear and mitochondrial genomes ofP. plancyi. This hybrid system provides an excellent opportunity to study cyto-nuclear interaction and co-adaptation.

Background: Understanding how organisms adapt to high-elevation environments at a genome scale provides novel insights into the process of adaptive evolution. Previous studies have mainly focused on endothermic organisms, while poikilothermic species may have evolved different mechanisms to cope with high-elevation environments. In this context, we sequenced transcriptomes of a pair of closely related anuran species, Rana chensinensis and R. kukunoris, which inhabit respective low- and high-elevation habitats. By comparing the two transcriptomes, we identified candidate genes that may be involved in high-elevation adaption in poikilothermic species. Results: Over 66 million sequence reads from each transcriptome were generated. A total of 41,858 and 39,293 transcripts for each species were obtained by de novo assembly. By comparing the orthologous transcripts, we identified 125 protein-coding genes that have likely experienced strong positive selection (Ka/Ks>1). In addition, 335 genes that may bear a signature of positive selection (1≥Ka/Ks>0.5) were also recognized. By considering their functions, fourteen candidate genes were determined to be likely involved in high-elevation adaptation, including two CYP genes, USP-1, and several others. Conclusions: We identified a set of candidate genes that may have promoted adaptation of R. kukunoris to its high-elevation environment. These include several genes that have previously been associated with oxygen binding, response to UV radiation, and repair of free radical injury. Detailed molecular, physiological, and phenotypic studies are required to better understand the roles of these genes in improving the performance of R. kukunoris in a high-elevation environment. We have evidence for both convergent and divergent evolution between endothermic and poikilothemic species, but additional research across a wide range of organisms will be necessary to comprehend the complexity of high-elevation adaptation.