The Qinling-Daba Mountains, serving as the natural boundary between the Oriental and Palaearctic regions, represent a critical ecological transition zone. Previous studies have demonstrated how this mountain range acts as a geographical barrier for the northward expansion of Oriental species and vice versa. However, the role of the Qinling-Daba Mountains in shaping the distribution of species distributed across the Oriental-Palaearctic region remains poorly understood. Here we performed comparative phylogeographic analysis to investigate three species of the exclusively aquatic holometabolan order Megaloptera, i.e., Protohermes xanthodes, Acanthacorydalis orientalis, and Neochauliodes rotundatus, which are co-distributed in a broad range over the Oriental and Palaearctic regions. Our results show that except for the northeastern population of P. xanthodes, the three species do not exhibit clear geographic boundaries in their population genetic structure. The ancestral distributions of these species are primarily located within western Central China, North China, and Northeast China. Notably, populations from western Central China appear to have served as the source for subsequent dispersals to surrounding areas, with the Qinling-Daba Mountains emerging as a crucial dispersal corridor. Thus, the present overlapping distribution of these three species was formed by multidirectional dispersals in each species. All three species have undergone population contraction from the Last Glacial Maximum to the present, with their suitable habitats likely shrinking due to Pleistocene climate fluctuations, and temperature acting as a key factor influencing their distribution ranges. Our study investigates the phylogeography of aquatic insect species across the Oriental-Palaearctic boundary, providing novel insights into how complex terrain influences the distribution of species.

Geographic barriers and geological historical events may play pivotal roles in driving allopatric divergence among closely related species. Here, we investigate the genomic divergence patterns and ecological niche separation of the Willow Tit Poecile montanus and the Marsh Tit P. palustris species groups in China, and their ecological niche separation across East Asia. Through comprehensive genomic sequencing, population genomic analysis, and integration of public occurrence data, we unveil striking parallels in the geographic divergence patterns between these two species groups. Notably, both species exhibit multiple divergent lineages in China, with similar spatial distributions of gene flow barriers. Furthermore, our analysis reveals unique evolutionary histories in the southwestern clades of both species groups, highlighting the intricate interplay between historical distribution dynamics, ecological preferences, and genetic divergence. Our study significantly enhances our understanding of the processes underlying the diversification of closely related widespread species within the framework of shared geographical constraints, and stresses the need for a taxonomic revision.

The Hindu Kush Himalayan (HKH) region sustains the headwaters of major Asian rivers and harbors unique alpine biodiversity, yet it is highly sensitive to climate change. Biodiversity organization and community assembly processes across trophic levels within its river ecosystems remain poorly understood. Here, we employed multi-marker environmental DNA (eDNA) metabarcoding targeting four biological groups (cyanobacteria, diatoms, invertebrates, and vertebrates) to assess multi-trophic biodiversity patterns in two alpine rivers of the region: the Yellow River source region (YR) and the middle–upper Nujiang River (NJ). These two systems differ markedly in geography, hydroclimate, vegetation, and human disturbance intensity. We identified 1695 operational taxonomic units and revealed pronounced differences in biodiversity pattern and community composition between rivers. Phototrophs and invertebrates exhibited higher α diversity in NJ, whereas vertebrates were richer in YR. β diversity was mainly driven by species turnover in both rivers, with a stronger distance–decay pattern in YR. Correlations between environmental variables and α and β diversity varied across groups and rivers, with geographic and climatic factors exerting stronger effects in NJ. iCAMP and pNST analyses revealed that stochastic processes dominated community assembly in both rivers, whereas deterministic processes were relatively stronger in YR compared to NJ. Accordingly, co-occurrence networks revealed cohesive communities in YR but more modular ones in NJ, indicating contrasting ecological stability regimes. Overall, our study provides an integrated, multi-trophic perspective on how environmental gradients shape riverine biodiversity and ecological interactions, informing adaptive conservation strategies under accelerating environmental change in the HKH region.

Sexual dimorphism in dioecious plants is common in reproductive tissues. Genes expressed in these tissues often exhibit sex-bias and differ between sexes in their protein evolutionary rates. At the same time, sex-linked genes often balance their expression levels between sexes through dosage compensation. We compared gene expression between males and females in floral and leaf tissues of eight dioecious Salicaceae species whose sex chromosomes are young to understand the level of conservation and diversity of genes with sex-biased expression. Our results revealed that sexually dimorphic gene expression showed large numbers of differences among these species, with only 6% of the genes remaining conserved, exhibiting a consistent sex-biased direction in at least seven species. Protein evolutionary rates depended on their degree of conservation and the direction of sex bias in expression. Non-core sex-biased genes exhibited elevated evolutionary rates, and core male-biased genes showed higher nonsynonymous and synonymous substitutions than unbiased genes. Detailed studies in three willow species revealed that the expression dosage of most sex-linked genes was partially (0.5 < Xmale/XXfemale < 1) or excessively (Zfemale/ZZmale > 1) compensated through reducing gene expression in the homogametic sex. Our results provide novel insights into how sexually dimorphic gene expression evolves during repeated turnovers of sex chromosomes in plants and confirmed that dosage compensation mechanisms evolve relatively early in the development of sex chromosomes.

The unique geomorphology of rivers in the eastern Himalaya has long intrigued geologists, yet their drainage history remains debated. Drainage reorganization can have a significant impact on genetic differentiation in freshwater taxa. This study employs the cold-adapted fish genus Schizothorax as a biogeographic proxy to reconstruct the evolutionary history of the Yarlung Tsangpo-Brahmaputra River (YTB), with a focus on a prominent hanging valley tributary-trunk stream system. Phylogeographic analyses of mitochondrial cyt b gene sequences identified a monophyletic QTP-YGP clade comprising species from the Qinghai-Tibet Plateau (QTP) and the Yunnan-Guizhou Plateau (YGP). Within the QTP lineage, YTB species represent the earliest diverging clade. In contrast, species from the Indus and Ganges basins are more closely related to congeners from the southeastern QTP and YGP. The YTB assemblage further subdivided into two distinct clades. Molecular dating suggests that the YTB lineage diverged from the broader QTP-YGP group during the early Late Miocene, with the two YTB clades separating in the Late Miocene. We propose that a paleo-Yarlung Tsangpo-Dingba (Dibang)-Brahmaputra river and a Yigong-Parlung-Zayul (Lohit) river were established prior to the Late Miocene and were subsequently captured by the lower Yarlung Tsangpo River—via the Siang and Zhaqu, respectively—during the late Miocene and Quaternary. The modern YTB drainage configuration was established by the late Early Pleistocene. This study underscores the importance of integrating genetic and geomorphological data to understand the complex evolution of drainages in the eastern Himalayas.

Taxonomic diversity (TD) and phylogenetic diversity (PD) are two important metrics of biodiversity, but they are often mismatched in many areas across the world. This geographic mismatch, typically identified through assessing relative phylogenetic diversity (RPD), is associated with climatic conditions and is critical not only to understanding the origin and maintenance of biodiversity but also to conservation planning. Here, using a comprehensive data set of butterflies across the world, we explore geographic patterns of RPD and its relationships with climatic factors. Butterfly species assemblages used in this study are species in 12,407 grid cells across the world. We use two different metrics to measure RPD, one directly relating PD to TD (PD_dev) and the other exploring variation on phylogenetic branch length (Mishler’s RPD). We find that RPD is higher in humid subtropical and tropical regions, where butterflies originated and maintain many distinct phylogenetic lineages, and is lower in temperate and arid tropical regions as well as in geologically young mountains, where there are fewer major phylogenetic lineages and where regional radiations form clusters of closely related species. The patterns of PD_dev and Mishler’s RPD are largely similar, but PD_dev is more strongly related to temperature whereas Mishler’s RPD is more strongly related to precipitation, suggesting that these metrics capture different ways in which climate influences PD. Overall, areas with higher RPD likely hold higher evolutionary potential than areas with equivalent species richness but lower RPD, so that areas of high RPD would be of particular interest for biodiversity conservation.

Pollinators are key drivers of floral evolution and diversification. While floral traits often converge in response to shared pollinators, they may diverge following pollinator shifts. Here, we examine the evolution of floral traits in Brandisia, a hemiparasitic genus endemic to East and Southeast Asia that exhibits notable interspecific variation. We combined field observations, a literature survey of pollination systems across Orobanchaceae, measurements of 14 floral traits, and phylogenetically informed comparative analyses. Our results show that Brandisia species are primarily bird-pollinated, probably derived from the bee-pollinated condition predominant in Orobanchaceae. Their flowers show typical bird-pollination traits, including tubular corollas, exserted reproductive organs, and abundant dilute nectar. Several traits may also function to avoid antagonists through visual (e.g., red coloration inconspicuous to bees), morphological (e.g., reduced or recurved corolla lobes), or physiological (e.g., dilute nectar) barriers. Ancestral state reconstruction indicates that the common ancestor of Brandisia had moderately specialized floral traits, including solitary axillary flowers, orange-yellow coloration, short tubular corollas, and hexose-dominated nectar. From this ancestral condition, both more specialized and more generalized phenotypes evolved, involving 11 shifts across eight traits. Together, our findings indicate that Brandisia is predominantly bird-pollinated in the Asian flora. Rather than resulting from major pollinator shifts, floral trait variation in Brandisia reflects a continuum of adaptation to bird pollinators, potentially shaped by fine-scale niche partitioning. Some floral traits may also have evolved under additional selective pressures, such as avoiding bees. This study advances understanding of how bird pollinators shape floral diversification in angiosperms.

East Asia’s largest inland arid ecological region—the Tarim Basin and Hexi Corridor—serves as an independent evolutionary center for highland ichthyofauna. However, systematic studies on the evolutionary patterns of fishes in this region remain limited. In this study, we integrated mitochondrial cytochrome b (Cyt b) and nuclear SNP data to investigate the demographic structure and historical dynamics of three desert fish species: Triplophysa tenuis, Triplophysa bombifrons, and Hedinichthys yarkandensis. Our results indicate that populations in the Hexi Corridor and Tarim Basin diverged approximately 0.8 million years ago (Ma), coinciding with a period of increasing aridity, followed by alternating phases of population contraction and secondary contact. Demographic fluctuations were likely driven by westerly atmospheric circulation interacting with regional geological activity. Furthermore, this study provides evidence for the existence of an ancient South Tarim River and suggests the need for taxonomic re-evaluation of T. bombifrons. These findings offer critical insights into the evolutionary processes shaping fish diversity in arid regions of China and inform strategies for their conservation.

Dolichopetalum is a monotypic liana genus of Apocynaceae and is restricted to subtropical montane forests in Asian subtropical karst areas. In this study, we used plastome data to examine the tribal position of Dolichopetalum within the family, and four plastid and three nuclear loci to further clarify its relationship and taxonomic status. We also estimated the time of origin of Dolichopetalum and modeled its range change by estimating the potential historic and current distributions. Our family-wide phylogenetic analysis confirms that Dolichopetalum belongs in the tribe Marsdenieae. Our subsequent analyses of Marsdenieae further suggest that Dolichopetalum is a distinct genus and has a distant relationship with Marsdenia s.str., challenging the traditional viewpoint. Dolichopetalum is probably allied to Campestigma, Cionura, Harmandiella, and Gongronema-Dischidanthus-Sarcolobus, and originated at about 11 Ma and rapidly diverged with its four allies over a period of less than three million years, which might be associated with the intensified East Asian monsoon in the early Late Miocene. The distributional range of Dolichopetalum may have undergone a dramatic contraction since the Last Glacial Maximum and will likely further shrink and undergo fragmentation in the future, possibly driven by global warming and desertification in Asian subtropical karst areas. This study provides new insights into the evolutionary history of Dolichopetalum and will have important conservation implications for the unique biodiversity of Asian subtropical karst areas under climate change scenarios.

Thamnocalamus, a bamboo genus endemic to the Himalaya, comprises four to six species with a complex taxonomic history. Distinguishing Thamnocalamus from Fargesia based on vegetative characteristics is particularly challenging, as previous studies frequently resulted in misclassifications of species between the two genera. Leveraging subgenome-scale syntenic nuclear genes and genomic distance-based k-mer analyses through deep genome skimming, we dissected the complex phylogenetic relationships within Thamnocalamus to facilitate subsequent taxonomic revision. Our study presents: (1) an updated phylogeny improved in resolution and sampling density, (2) characterization of the evolutionary process underlying gene tree incongruence, and (3) enumeration of four Chinese Thamnocalamus species with a diagnostic morphological key. Based on a robust phylogenetic framework and morphological comparisons, we propose a new combination, T. damuniu, and further investigate potential hybridization among Thamnocalamus species. Consequently, Thamnocalamus crassinodus and T. unispiculatus were inferred to be of hybrid origin but with differential inheritance probability proportions, together with incomplete lineage sorting, which likely contributes to the gene tree incongruence and non-monophyly of T. crassinodus in k-mer-based analysis. As many poorly known bamboo species were described solely from vegetative specimens, we emphasize the necessity of integrating molecular evidence into taxonomic decisions and describing new species within the taxonomically challenging Bambusoideae, calling for reassessment of species with uncertain generic status integrating nuclear genomic data of multiple individuals per species, and detailed morphological comparisons.

Aquatic angiosperms represent an important but underexplored lineage for understanding genome evolution, particularly in species with exceptionally large genomes. Here, we present a chromosome-scale genome assembly of the endangered aquatic monocot Ottelia songmingensis (~10.8 Gb), providing a valuable genomic resource for studying genome gigantism and conservation. Using ONT and Hi-C technologies, we anchored 87.7% of the assembly to 11 pseudochromosomes and predicted 35,362 protein-coding genes. Comparative genomics revealed two whole-genome duplication events, including a more recent duplication and an ancestral triplication shared within Alismatidae. Repetitive elements constitute 94.3% of the genome, with long terminal repeat retrotransposons alone accounting for over 90%. A recent burst of LTR activity (~6 Mya) combined with a low solo-to-intact ratio (0.61) suggests inefficient transposon removal as a driver of genome expansion. Whole-genome bisulfite sequencing showed globally high DNA methylation levels (CG ~85%, CHG ~78%), particularly enriched in transposable element–rich regions, highlighting the role of epigenetic regulation in stabilizing large genomes. Population resequencing further indicated extremely low nucleotide diversity (π = 5.31 × 10⁻⁴) and long-term decline of effective population size since the Middle Pleistocene. Together, these resources provide a genomic foundation for exploring the evolutionary forces underlying genome gigantism and for guiding conservation genomics in endangered aquatic plants.

Cavefishes display pronounced troglomorphic adaptations, such as visual degeneration, depigmentation, and scale reduction, as specialized responses to subterranean environments. Among these, the cave loaches (CLS) of the family Nemacheilidae represent China’s second-most diverse cavefish group; however, their evolutionary history remains poorly understood. To bridge this knowledge gap, we conducted whole-genome resequencing of 62 CLS species and two closely related taxa, complementing these data with published genomic resources. The reconstructed phylogeny identified ancient introgression as the primary driving force behind phylogenetic discordance, with incomplete lineage sorting as a secondary contributor. Pleistocene climatic fluctuations, coupled with species-specific genetic architectures, generated four distinct demographic trajectories across populations. Additionally, we delineated four distinct phases of lineage diversification in CLS, shaped by tectonic–climatic interactions, with alternating periods of acceleration and decline synchronized with the Asian orogenic and monsoonal cycles. This study provides the first integrated genomic perspective on the evolution of the CLS, demonstrating how biotic and abiotic factors have collectively shaped subterranean biodiversity.