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.

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.

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.

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.