Climate oscillations may drive the divergence of ancestral species through habitat isolation, species distribution patterns, and the cessation of gene flow. However, traditional ecological niche models lack the consideration for the genetic adaptation of species, thus it’s difficult to understand how climate oscillations affect species divergence by changing their climatic suitability and historical demography. We analyzed the impact of climate change on the divergence of two langur species, François’ langur and White-headed langur, using Maxent, Genotype–Environment Association (GEA) models and genomic data. Our results indicate that 1) Climatic suitability for François’ langur and White-headed langur has separated from the Last Interglacial (LIG, 120,000-140,000 years ago) to the Last Glacial Maximum (LGM); 2) Although the effective population size for both species decreased between the LIG and the LGM, the effective population size of François’ langur increased more quickly than that of White-headed langur from the LGM to the present; 3) Historical patterns of climate change have resulted in periods of expanded and contracted climatic suitability, with each species experiencing periods of interspecific genetic isolation and periods of interspecific genetic exchange; and 4) Human activities and future climate change have contracted the range of François’ langur (in China) and White-headed langur. Climate oscillation, population isolation, and in situ evolution in refugia from the LIG to the LGM appear to have played a critical role in langur speciation and adaptive evolution. Overall, our results demonstrate how climatic oscillations and historical demography drive speciation, providing a new perspective on species divergence and conservation.

Understanding how populations diverge and new species arise is a central question in evolutionary biology. ‘Allopatric’ divergence through geographic isolation is considered to be the commonest mechanism generating species biodiversity in mountainous ecosystems. However, the underlying genomic dynamics, especially genomic islands of elevated divergence and genes that are highly diverged as a result of lineage-specific selection, remain poorly understood. Stellera chamaejasme is widely distributed on the Qinghai-Tibet Plateau and in adjacent regions, making it a good model with which to explore genomic divergence in mountainous ecosystems. We assembled a high-quality, chromosome-level genome for this species and re-sequenced the genomes of 24 populations across its distributional range. Our population genomic analyses recovered four distinct genetic lineages corresponding to geographic distributions with contrasting environments. However, we revealed that continuous gene flow occurred during the diversification of these four lineages and inter-lineage hybrids, and plastome introgressions were frequently found in regions of contact. The elevated genomic divergences were highly heterogeneous across the genome. The formation of such genomic islands showed neither correlation with rate of gene flow nor relationship to time of divergence. The lineage-specific positively selected genes potentially involved in local adaptation were found both within and outside genomic islands. Our results suggest that genomic divergence in S. chamaejasme is likely to have been triggered and further maintained by local selection in addition to geographic isolation.

 Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae).  A high-quality chromosome-level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein-coding genes annotated. Two rounds of recent independent whole-genome duplication (WGD) were revealed. More than 10% of the novel genes from the recent species-specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait.  Other contrasting gene expression between flowers included that related to flower development and color, hormones, and iridoid biosynthesis. Metabolomic analyses similarly suggested differential concentrations of both hormones and iridoids in the two types of flowers. The interactions between multiple genes may together lead to contrasting morphology and open versus closed pollination of the dimorphic flowers in this species.  A total of 56 candidate genes were identified from the known iridoid biosynthesis-related pathways. Two hub genes were found to play an essential role in transferring intermediate products between leaves and flowers during iridoid biosynthesis.

Repeated homoploid hybrid speciation (HHS) events with the same parental species have rarely been reported. In this study, we used population transcriptome data to test paraphyly and HHS events in one conifer Picea brachytyla. All analyses identified and supported non-sister relationships for the two lineages of P. brachytyla. The southern lineage was placed within the re-circumscribed P. likiangensis species complex (PLSC) while P. brachytyla sensu stricto (s.s.), comprising only the northern lineage, parallels both PLSC and the closely related P. wilsonii. In addition, both phylogenetic and coalescent analyses suggested that P. brachytyla s.s. arose from homoploid hybrid speciation between the ancestor of the PLSC before its diversification (into the current varieties or species), and P. wilsonii, through an intermediate hybrid lineage at an early stage and backcrossing to the ancestral PLSC. These two parental ancestors also produced another homoploid hybrid species, P. purpurea, in the same way but at a later stage, through the same extinct lineage but backcrossing to the other parent, P. wilsonii. We reveal the first case that backcrossing to different parents of the same extinct hybrid lineage produced two different hybrid species. Our results highlight the existence of more reticulate evolution during species diversification in the spruce genus and more complex homoploid hybrid events than have previously been identified.