Recent genomic studies have suggested that ancient introgression may facilitate rapid diversification. The cave-dwelling group (TCG) of Triplophysa sensu lato, cave fishes endemic to the karst regions of southwestern China, exhibits high diversity and rapid evolution, representing a compelling potential example of rapid speciation during the evolution of karst landscapes. Here, we investigated the complex evolutionary history of the TCG by sampling 24 species and analysing whole-genome resequencing data. We reconstructed the phylogeny using different methods and quantified introgression to infer speciation and dispersal processes, which collectively confirm extensive historical gene flow both between TCG and Claea, as well as among TCG species. Our study demonstrated that, against the backdrop of widespread phylogenetic discordance within the TCG, interspecific introgression has played a more significant role than incomplete lineage sorting. Genomic regions with the highest levels of introgression (top 1% of fdM values) are enriched for Gene Ontology terms related to circadian behaviour, phenotypic plasticity, lipid metabolism, oxygen transport and reproduction. Demographic simulations further suggest that geoclimatic factors, together with the unique genetic attributes of the group, likely promoted founder effects, inbreeding, and subsequent declines in effective population size, resulting in two distinct demographic trajectories. Additionally, our results indicate that the origin and speciation of the TCG were closely synchronised with the rapid uplift of the Qinghai-Tibet Plateau and associated climatic transitions. We further identify three distinct stages of lineage diversification, characterised by alternating accelerations and declines driven by tectonic-climate interactions that were synchronised with major Asian orogenic events and monsoon cycles.

A new species of the genus Claea, Claea dafangensis sp. nov., is described from Yuchong Township, Dafang County, Guizhou Province, China. This species can be distinguished from its four congeners by a combination of the following characteristics: body pigmentation present; normal eyes with a diameter of 10.9-21.0% of head length (HL); processus dentiformis prominent, covering the lower jaw when the mouth is shut; 8-9 branched pectoral-fin rays; 16 branched caudal-fin rays; caudal-peduncle depth 6.1-8.7% of standard length (SL); interorbital width 23.6-39.0% HL; tip of maxillary barbel reaching the posterior margin of the eyes; outrostral barbel extending backward beyond the anterior nostrils; and anal-fin base length 4.0-5.5% SL. Mitochondrial Cyt b analysis further supports the distinctiveness of this population, revealing that it forms an independent phylogenetic lineage with a minimum genetic distance of 2.6% from C. wulongensis. The description of this new species suggests that Claea dabryi represents a species complex containing multiple distinct lineages, the diversity of which requires further evaluation.

Despite a recent mass extinction, a few species have bounced back from the brink, but little is known about their intrinsic mechanisms. Hainan gibbons (Nomascus hainanus) feature a mysterious rebound, from ~13 individuals in 2003 to 42 currently. Using reliable genomic data from the fecal samples of 18 gibbons, generated through a systematically established pipeline, and from four museum specimens, our analyses reveal that Hainan gibbons have the smallest effective population size and low genetic diversity but, unexpectedly, low inbreeding and genetic load among threatened primates assessed thus far. This results from a millennial expansion mitigating bottleneck effects and a high local recombination maintaining selection efficiency. Notably, we uncover two cryptic lineages, whose recent crosses led to new family groups with increased heterozygosity. Our study reveals the importance of demographic history, genome architecture, and behavioral regulation in the recovery of endangered species and highlights the great potential of fecal genomic research in conservation biology.

The phylogeny, classification, diversity, and distribution of cave species have always been difficult problems for taxonomists. In this study, we aim to clarify the phylogeny and evolutionary history of the cave-dwelling fish genus Sinocyclocheilus, a group that is not only difficult to collect but is also frequently under-recognized due to its cryptic nature, in order to elucidate its evolutionary patterns and dynamics. Our phylogeny supports the monophyly of the five current species groups (S. angularis, S. cyphotergous, S. jii, S. microphthalmus, and S. tingi groups), but a variety of evidence suggests that corresponding subgenera should be elevated. Our species delimitation analysis identified 84 species, including 18 cryptic. Molecular dating and biogeographic analyses revealed that Sinocyclocheilus originated in the late Eocene, 40.32 millions of years ago (Ma), that the most recent common ancestor inhabited the Guijiang-Hejiang River and the Nanpanjiang River, 34.61 Ma, and dispersed outward from the Nanpanjiang River Basin, and that an acceleration of speciation rates occurred during the late Eocene. A biogeographic dynamic meta-analysis showed that lineage divergence and in situ diversification began at 38 Ma and increased sharply at 24 Ma, with two peaks at 15 and 2.5 Ma and a valley at 2.5 Ma. Dispersal events began at 28 Ma and increased sharply at 12 Ma, with a distinct peak at 5 Ma. The speciation rate increased rapidly between approximately 40 and 32 Ma, followed by a sustained, gradual decline. The diversity of Sinocyclocheilus has been severely underestimated and requires a comprehensive reassessment integrating both morphological and genetic evidence. The revised classification comprises seven species groups or subgenera. The origin and diversification history of the genus were likely coupled with orogenic activities and the intensification of the Asian monsoon rainfall, which facilitated the formation of extensive subterranean voids, thereby creating ecological opportunities for speciation. Early high-temperature events may have initially triggered a rapid increase in speciation rates, whereas the relatively stable and cooler conditions of cave environments likely became less conducive to subsequent speciation. Our results also suggest a four-phase model of karst cave formation in southwestern China, with accelerating and decelerating periods in each phase. These evolutionary dynamics can be viewed as a response to shifts in paleogeoclimatic events since the Eocene.

In the wild, non-human primates may experience population declines resulting from low genetic diversity and inbreeding, while the scientific planning of ecological corridors can assist in population recovery and mitigate genetic diversity loss. The Hainan Gibbon (Nomascus hainanus) is the world's most endangered primate, endemic to Hainan Island in extreme southern China. Recent conservation efforts have successfully increased the number of Hainan Gibbon individuals to more than three times that of 20 years ago and six times that of 50 years ago. Updated information on population genetic diversity is urgently needed. In this study, we collected fresh fecal samples from 25 individuals in five family groups (A, B, C, D, and E) of Hainan Gibbon using a non-invasive sampling method. We then evaluated and compared the variations in genetic diversity in Hainan Gibbon using 10 microsatellite loci. The sex identification experiment showed that the female-to-male ratio of the existing Hainan Gibbon population was 1:1.27. The population is still at a genetic bottleneck. Its dispersal mode is bisexual, and Hainan Gibbon tend to mate with individuals who have lower-than-average genetic relationships with themselves. The level of genetic diversity in family groups D and E was relatively low, while the genetic distance of D and E from family groups A, B, and C was relatively large. Currently, the Hainan Gibbon population exhibits no detectable genetic differentiation. With an effective population size of merely 13 individuals (95% confidence interval: 5.1-49.9), this critically endangered species remains at imminent risk of extinction. We suggest developing an ecological corridor between family groups A and E, which have a relatively large genetic distance.

A new species Oreonectes weii sp. nov., is described that was collected from Shanggao County, Jiangxi Province, China, located at the upper reaches of the Yangtze River Delta. This naming honors the globally distinguished conservation biologist Fu-Wen Wei for his exceptional and pioneering contributions to biodiversity conservation and research. Morphologically, the new species can be distinguished from its congeners by a combination of meristic and morphological characters, including fin-ray counts, body coloration, eye normal, number of lateral-line pores, and gill-raker counts. Genetically, it forms a distinct lineage in the mitochondrial Cyt b-based phylogeny and exhibits a genetic distance of 6.3% from its sister species, O. polystigmus. We further estimated divergence time within the genus Oreonectes, which indicates an origin in the Late Oligocene (~27.06 Ma) and a most recent common ancestor at ~13.91 Ma. Our biogeographic analyses suggest that the Guijiang-Hejiang River Basin likely served as a source area for the genus’ dispersal into adjacent basins, and that the new species probably originated from a dispersal event of its ancestral population from the Pearl River Basin to the Yangtze River Basin during the Late Miocene (~6.78 Ma). Lineage-divergence dynamics indicate that cladogenesis began around 28 Ma, accelerated markedly at ~18 Ma, peaked at ~6 Ma, and subsequently showed a gradual decline. The current diversity pattern of Oreonectes may have been shaped primarily by dispersal mediated by enhanced precipitation under the East Asian monsoon climate, with subsequent erosion-induced geographical isolation likely promoting speciation and diversification within the genus.

China’s current standard for evaluating the effectiveness of nature reserves (HJ 1203—2021) takes increases in the population size and expansion of the distribution range of flagship species as core assessment indicators. Based on an analysis of six national nature reserves in which primates are designated as flagship species, this study demonstrates that this evaluation framework has substantial limitations. Although the population dynamics of flagship species are critical to the assessment of conservation effectiveness, they cannot represent their actual functional importance within ecosystems. Many other species occupying the same ecological niche as the flagship species also play irreplaceable ecological roles. Flagship species cannot comprehensively represent the ecosystem as a whole. Ecological studies have shown that competitive interactions among sympatric species indicate that population growth of a single species is insufficient to reflect the structural and functional integrity and stability of biological communities. This paper calls for a shift away from the traditional ”single-species supremacy” assessment paradigm toward an evaluation framework centered on ecosystem function, in which community structure and ecological processes are incorporated as core indicators, thereby enabling a more scientifically grounded assessment of conservation effectiveness.

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 genus Paramesotriton Chang, 1935, comprising 15 species classified into two groups, exhibits the broadest geographical distribution among modern Asian newts, extending across southern China from west to east and representing a prominent example of adaptive radiation. Despite this success, intrageneric phylogenetic relationships among species remain unresolved, with particularly poor resolution within the Paramesotriton caudopunctatus species group (PCSG). In this study, restriction-site-associated DNA sequencing from five representative PCSG species was combined with previously published mitochondrial genomes to generate a genome-scale phylogenomic framework. The resulting analyses yielded robust support for interspecific relationships within PCSG. Gene tree discordance was primarily attributable to incomplete lineage sorting, with additional contributions from pre-speciation gene flow, as indicated by ASTRAL, HyDe, Dsuite, and PhyloNet. Evidence also supported hybridization between P. longliensis and an unidentified Paramesotriton lineage, consistent with a hybrid origin for P. zhijinensis. Comparative genomic and biogeographic inference further indicated that erosional isolation associated with exposure of carbonate sedimentary rocks facilitated allopatric divergence among PCSG lineages. Moreover, divergence timing aligned PCSG origin and diversification with Miocene paleoclimatic variability and progressive erosion of carbonate substrates, directly implicating karst landscape evolution in lineage formation within Asian warty newts. An erosion-driven speciation framework is therefore supported, in which recurrent episodes of geomorphological restructuring of karst mountain systems repeatedly imposed geographic isolation, driving successive allopatric diversification during both tectonically active and tectonically stable periods.

Chiroptera species (hereafter bats) exhibit extraordinarily long lifespans compared to non-flying mammals of similar body size, yet the underlying ecological drivers and molecular mechanisms remain poorly understood. In this study, we employed phylogenetic regression models to explain maximum longevity (MLg) variation using 24 life-history traits from 101 bat species. In parallel, we conducted comprehensive comparative genomics analyses on 39 high-quality bat genomes to identify candidate genes and biological processes involved in longevity regulation. Our results revealed that female age at sexual maturity and maximum latitude explain the greatest proportion of MLg variation within bats, and genes involved in DNA damage repair, inflammation, immunity and mitochondrial function may play critical roles in various extremely long-lived bat species. We also identified the potential importance of lipid metabolism, specifically the cholesterol metabolism pathway and APO gene family, as a previously under-appreciated mechanism in bat longevity regulation. Given the distinct ecological and physiological features, our family-specific analyses on Vespertilionidae and Pteropodidae uncovered divergent life-history predictors and genetic strategies for extended longevity. In Vespertilionidae, MLg is most strongly associated with latitude and may be regulated primarily through the maintenance of DNA stability, while MLg in Pteropodidae is best predicted by body mass and is linked to tumour suppression and immune response. Overall, our study elucidates the complex interplay between life-history factors and genomic adaptations underlying extended lifespans in bats, providing valuable insights into mammalian longevity evolution and potential targets for improving human healthspan.

The karst ecosystem in southwestern China is a global hotspot for cavefish diversity research, yet the origins and evolutionary history of this diversity remain poorly understood. To elucidate their evolutionary origins and history, we analyzed 183 cavefish species and their close relatives from ten clades. Our findings indicate that freshwater fishes began colonizing caves ~44 million years ago (Ma). Speciation was driven by in situ diversification, starting around 43.2 Ma, increasing sharply by ~35 Ma and 18 Ma, and peaking at ~8.3 Ma, 2.5 Ma, and 1.5 Ma. Distinct hydrological basins exhibited divergent diversification patterns. Dispersal between the Pearl and Yangtze River basins began by ~24.1 Ma, accelerated around 21 Ma, 13 Ma, and 9.6 Ma, and peaked at ~13 Ma, 5 Ma, and 2 Ma. We propose that river drainages in southwestern China developed stepwise from the late Eocene to early Pleistocene, with connectivity between the Pearl and Yangtze basins established by the late Oligocene ( ~ 26 Ma). The origin and diversification of cavefishes are closely linked to the evolution of karst landscapes, shaped by orogeny and monsoon-driven climate changes since the late Eocene. These insights are crucial for informing conservation strategies for these unique habitats under ongoing climate change.

Major geoclimatic events trigger clade divergence, shaping diversification patterns. However, the influence of historical geoclimatic events on the diversification of subsurface biota remains poorly understood. This study investigates the phylogeny and evolutionary history of under-recognized hypogean fishes in the Nemacheilidae family (HFN) in southwestern China, using mitogenome and nuclear gene sequencing. Our phylogeny supports the current genus-level classification but reveals conflicts between mitochondrial and nuclear gene topologies, suggesting past hybridization events. The ancestor of the HFN originated in eastern China-Korean Peninsula-Japanese Islands, north of northwest China-Mongolian Plateau, the Qinghai-Xizang (Tibetan) Plateau-Hengduan Mountains during the late Eocene (~36 million years ago [Mya]) and early Miocene (~16 Mya), and dispersed twice into the karst region of southwestern China. An ancient radiation event occurred from 22.44 Mya to 12.25 Mya. In situ diversification is the major speciation event, originating around 30 Mya and increasing sharply at ~11 Ma, with 3 peaks at ~7 Mya, ~3 Mya, and 1 Mya, and 2 valleys at ~5 Mya and ~2 Mya. Ancestral state reconstruction suggests at least 4 independent origins for the colorless, eye-blind, and troglobitic species morphs, as opposed to 2 events for the caudal adipose keel, and that these traits have undergone multiple reversals. These results highlight the role of geological processes and climatic events in the evolution of hypogean fishes and provide insights for conservation efforts, particularly in specialized cave habitats.

We describe a new species, Sinocyclocheilus panzhouensis sp. nov. , from Panzhou City, Guizhou Province, China, using morphological and genetic evidence. Phylogenetic analysis of mitochondrial cytochrome b (Cyt b ) and NADH dehydrogenase subunit 4 (ND4) sequences reveals distinct genetic divergence from related species, with genetic distances ranging from 1.7–14.2% in Cyt b and 1.2–12.6% in ND4. Morphologically, S. panzhouensis sp. nov. is characterised by absence of a horn-like structure and indistinct elevation at the head-dorsal junction; body covered with tiny scales, with irregular black markings; wide mouth, 7.8–9.3% of standard length and longer pectoral fin 17.9–30.6% of standard length; last unbranched ray of dorsal-fin with weak serrations along posterior margin; tip of pectoral fins not reaching the pelvic-fin origin; lateral line complete and curved, with pores 71–79; and eight rakers on the first gill arch. This discovery raises the number of Sinocyclocheilus species in Guizhou to 19, with five species found in the Beipanjiang River. This study highlights the need for further surveys in Guizhou to explore the full species diversity of the genus.

The genus Murina Gray, 1842, recently had four new species discovered in China over the last four years, suggesting its diversity may have been previously underestimated. Herein, we describe four new species—Murina beibengensis sp. nov., Murina medogensis sp. nov., Murina milinensis sp. nov., and Murina yadongensis sp. nov.—based on morphological and genetic evidence from specimens collected during bat diversity surveys conducted in the Xizang Autonomous Region of China over the past three years. Each of these four new species forms an independent lineage on a phylogenetic tree reconstructed using the mitochondrial COI and Cyt b genes, and each is genetically distinct from its congeners. Morphologically, the new species can be distinguished from the 43 recognized congeners by features including forearm length, hair color, and skull morphology. We elevated M. huttoni rubella from a subspecies of M. huttoni to a species based on morphological and genetic evidence. The new species discussed herein increase the number of species in the genus Murina to four worldwide and from 23 to 28 in China. This study not only enriches our understanding of bat species diversity but also underscores the importance of conducting bat surveys in the specialized highland habitats of the Himalayas.

The genus Pseudohynobius exhibits a west-to-east distribution across southwestern China, spanning diverse mountain ranges and elevations. However, knowledge regarding the diversity, phylogeny, and evolutionary history of this genus remains limited. In this study, based on the concept of phylogenetic species, we identified eight phylogenetic species, including two cryptic lineages. Divergence time estimation revealed that Pseudohynobius originated approximately 14.57 million years ago (Ma), with interspecific divergence mainly occurring between 8.0 and 1.4 Ma. Biogeographic analysis indicated that its most recent common ancestor likely inhabited the Hengduan–Dalou Mountains region in southwestern China around 8.62 Ma and that the Dalou Mountains served as a source of outward dispersal and a key region for speciation between 11 and 4 Ma. The lineage divergence dynamics of this genus are coupled with orogenic movements and paleoclimatic shifts, which may have been the primary drivers of its historical diversification. This study underscores the urgency of conducting further surveys and taxonomic studies to avoid underestimating the diversity of this critically endangered genus.

The yellow boxfish ( Ostracion cubicus) exhibits a combination of derived morphological traits specialized for coral reef environments and ancestral characteristics, including a fused dermal plate. Contradictory evolutionary evidence hinders true classification of O. cubicus. To clarify its evolutionary position within Tetraodontiformes, a chromosome-level genome assembly was generated, representing the most contiguous and complete genome to date for this lineage. Notably, O. cubicus possessed the largest genome within the order Tetraodontiformes, primarily due to extensive transposable element expansion. Phylogenetic analysis based on 19 whole genomes and 131 mitochondrial genomes resolved Tetraodontiformes into three major sister groups (Ostraciidae-Molidae, Tetraodontidae, and Balistidae-Monacanthidae). Comparative genomic evidence indicated that O. cubicus diverged early from the common ancestor of modern Tetraodontiformes and retained the highest number of HOX genes among surveyed taxa. Although overall genomic architecture was largely conserved, certain genetic and environmental changes may have contributed to its phenotypic adaptations, including climate cooling during the Miocene-Pliocene Transition, recent DNA and long interspersed nuclear element (LINE) transposon bursts, lineage-specific chromosomal rearrangements, and gene family expansion. Many positively selected genes and rapidly evolving genes were associated with skeletal development, including bmp7, egf7, and bmpr2. Transcriptomic comparisons between carapace and tail skin revealed various candidate genes and pathways related to carapace formation, such as postn, scpp1, and components of the TGF-β signaling pathway. A derived amino acid substitution in eda, coupled with protein structural modeling, suggested potential molecular convergence in dermal plate formation among teleosts. These findings provide novel insights into the genomic and developmental basis of carapace evolution and coral reef-adaptation in O. cubicus, offering a strong case for evolutionary balance between genomic conservation with regulatory innovation to achieve coral reef specialization.

This study reports and characterizes the complete mitogenome of Theloderma albopunctatum. The mitogenome was 15,780 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with 29.35% A, 25.17% T, 14.24% G, and 31.24% C. The original data were assembled and annotated, and the complete mitochondrial genome was mapped. The phylogenetic tree obtained in this study supports the division of the Rhacophorinae and Buergeriinae subfamilies. This mitogenome provides a valuable resource for understanding evolutionary relationships within the Rhacophoridae family.

The Boulenger’s slug snake (Pareas boulengeri Angel, 1920) has previously been documented as relatively widely distributed across the eastern, southern, and southwestern regions of China. In the present study, integrated morphological comparisons and molecular phylogenetic analyses were undertaken to reevaluate the taxonomic status of P. boulengeri and to describe two new species: Pareas dabieshanensis sp. nov. and Pareas orientalis sp. nov. Phylogenetic reconstruction based on CYTB gene sequences indicated that populations previously identified as P. boulengeri comprise three distinct lineages: true P. boulengeri, P. dabieshanensis sp. nov., and P. orientalis sp. nov. The two new species exhibit significant genetic divergence from their congeners, with uncorrected pairwise distances of 4.1–4.5%, consistent with interspecific divergence within the genus. Morphologically, P. dabieshanensis sp. nov. is distinguished by the presence of two subocular scales, the absence of preocular scales, and higher ventral (184–187) and subcaudal (68–74) counts. P. orientalis sp. nov. is characterized by a single preocular scale and fused subocular and postocular scales. The revised distributions restrict P. boulengeri to southwestern China, while the new species are confined to the Dabie Mountains (Anhui, Hubei, Henan) and eastern China (southern Anhui, Jiangsu, Jiangxi, Zhejiang), respectively. The non-overlapping ranges of P. dabieshanensis sp. nov. and P. orientalis sp. nov., bisected by the Yangtze River, suggest that this major hydrological system acted as a biogeographic barrier driving speciation. This study expands the genus Pareas to 33 recognized species (27 in China) and underscores the prevalence of cryptic diversity within morphologically conserved lineages.

We describe Oreonectes guidongensis sp. nov., a new species collected from Hezhou City, Guangxi Zhuang Autonomous Region, China. Morphologically, it is distinguished from all congeners by the following combination of characters: six branched pelvic-fin rays; seven branched dorsal-fin rays; tip of pelvic fin not reaching the anus; a well-developed posterior chamber of the air bladder; 14–16 branched caudal-fin rays; 10 inner gill rakers on the first gill arch; and a distance between the posterior base of the pectoral fin and the anterior base of the pelvic fin of 18.8–27.9% of standard length. Phylogenetic analysis based on the mitochondrial cytochrome b gene supports the distinctiveness of this species, revealing genetic distances of 5.4–8.5% from its congeners. The discovery of Oreonectes guidongensis sp. nov. underscores the need to re-evaluate O. polystigmus as a potential species complex to better understand the genus’s biodiversity.

The tube-nosed bats (genus Murina) are small insectivorous mammals that are primarily distributed in South, East, and Southeast Asia. The Qinghai-Tibet Plateau (QTP) has long been an understudied region in bat surveys, especially for species of small arboreal bats, including Murina. In 2023, we surveyed the southeastern QTP and collected seven individual specimens of Murina. The specimens were identified using combined morphological and molecular data (the mitochondrial Cyt b gene). Phylogenetic analyses identified three unknown clades: Murina sp1, Murina sp2, and Murina sp3. Murina sp1 was most closely related to M. pluvialis, with a genetic distance of 0.09. Murina sp2 was most closely related to M. shuipuensis, with a genetic distance of 0.13, and Murina sp3 was most closely related to M. chrysochaetes, with a genetic distance of 0.15. All three species delimitation methods supported the partitioning of Murina sp1, Murina sp2, and Murina sp3. Herein, we describe a new species, Murina chayuensis sp. nov. (Murina sp1.), that is similar to M. annamitica and M. lorelieae. Owing to the limited number of specimens, Murina sp2 and Murina sp3 are not described in this study. Our results highlight the overlooked diversity of bats in the southeastern QTP, and thus this group warrants further surveys and taxonomic studies.