Understanding how closely related species coexist in human-influenced landscapes is critical for biodiversity conservation, as species-specific ecological differentiation can lead to contrasting responses to land use and conflict risk. Macaques (Macaca spp.), which frequently occur in sympatry and are widely involved in human-primate conflict, provide an ideal model to investigate how differential adaptation to human activities shapes coexistence in mountain systems. In this study, we investigated the coexistence mechanisms among three sympatric macaques-Assamese macaque (Macaca assamensis), white-cheeked macaque (M. leucogenys), and rhesus macaque (M. mulatta)-in the Yarlung Zangbo Grand Canyon National Nature Reserve (similar to 9200 km(2)), China, a highly heterogeneous montane-canyon system in the Eastern Himalayas. By applying species distribution models, environmental niche differentiation analyses, and diel activity modeling, we quantified multidimensional niche partitioning among the three species based on multi-source occurrence data, including a 12-year camera-trap program totaling over 54,000 camera-days. Macaques diverged in predicted suitable habitats, with niche differentiation along Human Footprint Index, distance to waterways, and precipitation of the driest month. Only M. mulatta was associated with documented human-macaque conflicts, with 42-76 incidents recorded annually during 2013-2016. Temporal niche differentiation was minimal, as species were diurnal with high activity overlap (Delta(4)>= 0.75). Our research demonstrates that spatial and environmental niche differentiation, rather than temporal segregation, suggests coexistence among closely related macaques in mountain landscapes. Species-specific adaptation to anthropogenic landscapes appears to be a key mechanism shaping coexistence, highlighting the need for spatially targeted, species-tailored conservation and human-M. mulatta conflict mitigation strategies in mountainous regions.

Aim Protected areas (PAs) are central to global biodiversity conservation, but their effectiveness in understudied regions, such as high-altitude ecosystems, remains poorly understood. Tibet contains the world's highest-elevation PA network and a remarkably diverse mammalian fauna, especially medium- and large-bodied mammals (MLM) that are of major conservation concern given their important role in ecosystem functioning and high sensitivity to human activities. The Tibetan PAs offer an opportunity to evaluate the effectiveness of PAs in protecting MLMs in extreme environments. Here, we explored spatial patterns and influencing factors of MLM diversity across Tibetan PAs and related them to PA attributes, environmental and anthropogenic factors. Location Eighty-nine PAs of Tibet, China. Methods Based on a comprehensive occurrence dataset of 77 MLM species, we quantified mammal diversity within PAs using five indices (species richness, functional diversity, phylogenetic diversity, completeness index and defaunation index) and evaluated their key influencing factors (environmental, anthropogenic and PA attribute factors) through generalised additive models. The effects of species' body size, trophic level and protection status on the defaunation index were evaluated. We further estimated the PA size threshold for effective mammal conservation. Results PA protection status and vegetation heterogeneity are significantly associated with five diversity indices; specifically, PAs with stricter management and greater habitat heterogeneity supported higher MLM diversity. Medium-bodied, herbivore species with Class I protection exhibited higher levels of defaunation, highlighting the need for urgent conservation attention. PA size threshold varies among diversity indices and trophic levels, indicating that effective protection of MLMs of different trophic levels requires different PA sizes. Main Conclusions Our findings highlight the value of integrating a multidimensional biodiversity framework and PA attributes into conservation planning. Future conservation in Tibet should focus on strengthening PA management and reducing human disturbance, with PA sizes planned according to the ecological needs of different mammal groups.

Climate change poses a severe threat to desert ecosystems; however, understanding how specialized desert species respond to changing climate remains limited. These species are confronting extreme changes, including intensified droughts, altered precipitation, and temperature patterns. Here, we integrate population and ecogenomic approaches to examine population genetic structure, demographic history, and climate adaptation in two distantly related, sympatric rodent species in arid and semi-arid regions in East Asia. We further combine genomic offset analysis, ecological niche modeling, and landscape connectivity assessments to evaluate their climate change risks. Our results reveal that the two species have diverged into five geographically distinct lineages, each associated with a different arid region. Lineage divergence times are estimated between 20 and 400 thousand years ago, with population size declines occurring around the Last Glacial Maximum. While the two species exhibited distinct climate adaptation, evidenced by different key climatic variables and associated genes identified for each species, they exhibited congruent vulnerability to future climate change. This was indicated by parallel patterns of genomic offset and niche suitability loss. Under future climate change scenarios, eastern lineages in high precipitation seasonality areas (e.g., DB lineages in Horqin Sandy Land) face a higher risk due to substantial genomic offset, habitat loss, and reduced connectivity. In contrast, lineages on the west ranges with low precipitation seasonality (e.g., QH lineages in the Qaidam Basin and HL lineage in the Changtang Plateau) appear less vulnerable, characterized by lower genomic offset and the expansion of desert habitats. Overall, this study provides a comprehensive framework for identifying vulnerable populations and predicting responses to climate changes in desert species, offering critical insights for the conservation of desert ecosystems.

Weasels represent the most widely distributed and diverse lineage within the family Mustelidae. They have experienced adaptive radiation and have long been the subject of significant taxonomic debates. This study undertakes a comprehensive study of this group, employing morphological measurements, mitochondrial genomes, nuclear genes, and single copy orthologs extracted from whole genome data. Based on the outcomes of phylogenetic tree construction using orthologous genes, it is ultimately verified that the genera Mustela and Neogale are independent genera, thereby resolving the controversy regarding the species they encompass. Through molecular systematics and morphological studies, a putative Mustela species collected from Mabian Dafengding National Nature Reserve in Sichuan is confirmed as a new species, designated Mustela mopbie sp. nov. This new species exhibits molecular phylogenetic affinity with M. altaica and M. nivalis, yet shares morphological similarities with M. kathiah, M. nivalis and M. aistoodonnivalis. Notably, it is considerably smaller than these species and possesses distinctive body coloration and tail morphology. This study provides a detailed description of this new species and demonstrates that larger datasets yield more robust phylogenetic signal. Furthermore, we observed substantial incongruence between mitochondrial and nuclear gene trees, suggesting potential genomic introgression between this new species and its closely related congeners (M. altaica and M. nivalis).

The wild rats in the genus Rattus represent a group of murids characterized by rapid lineage diversification but limited morphological variation. Within this genus, there are several commensal species with high invasive capacity, such as Rattus norvegicus and R. rattus, which pose a global threat. Investigating the mechanisms behind their adaptive evolution is of utmost importance. In this study, we conducted morphological study and whole-genome sequencing on Rattus species distributed in China and adjacent regions to gain insights into morphological differentiation, as well as genomic divergence and gene flow using assembled mitochondrion genome and high-quality single nucleotide polymorphisms. Despite their morphological similarity and large overlap in morphospace, our analyses revealed significant genetic differentiation at the genomic level among Rattus species in China and adjacent regions. Specifically, intraspecific differentiation was observed in R. nitidus, R. norvegicus, and R. tanezumi, which may be related to habitat heterogeneity and geographic isolation. We hypothesize that as invasive rats expand their habitat, the diversification of ecological environments might lead to more environmentally adapted evolution and accelerated genetic differentiation. Furthermore, Dsuite and TreeMix analyses detected substantial introgression among different Rattus species, particularly evident between R. norvegicus and R. tanezumi. Strong gene flow signals suggest frequent hybridization events among these species, which may facilitate the acquisition of new environmental adaptability during their expansion into new territories. This study provides a preliminary analysis that serves as a foundation for a more comprehensive investigation into the rapid lineage diversification and adaptive introgression among Rattus species.

Pygmy jerboas are one of the smallest taxa of rodents. They exhibit distinctly different morphological and biological characteristics from other subfamilies, such as more restricted distribution, species richness, reproductive ability, and population size. Agricultural expansion and the development of new energy projects in recent years lead to sharp decline of their natural populations. Here, we assembled and annotated the first reference genome for the subfamily Cardiocraniinae using Illunima and Nanopore sequencing from the thick-tailed pygmy jerboa, Salpingotus crassicauda. The final genome is 2.44 Gb in size, with a contig N50 length of 13.71 Mb and a BUSCO completeness of 96.35%. A total of 23,344 protein-coding genes were annotated in the final genome. We also determined the mitochondrial genome of this species and annotated 13 protein-coding genes, 22 tRNAs, and 2 rRNA. These genomic assemblies provide resources in studying phylogeny and adaptive evolution of Dipodidae, as well as implementing conservation management of jerboas.

As an endemic species of the Qinghai-Tibet Plateau, the Plateau Pika (Ochotona curzoniae) exhibits adaptation to the extremely high-altitude environment and possesses a number of distinct physiological characteristics. In order to explore potential mechanisms underlying the adaptation of plateau pikas, we investigate transcriptomic differences across tissues (heart, liver, spleen, lung, kidney, muscle, cerebellum, left brain, and right brain) of the Plateau Pika, in a comparative framework. We analyze possible mechanisms of adaptive evolution by including a transcriptome analysis across the 9 tissues from 3 male and 4 female O. curzoniae and contrasting results with the 8 male and 4 female Gansu Pika (O. cansus) that inhabits the lower middle altitudes. Differential expression and protein-protein interaction network analyses were used to identify the differentially expressed genes and their primary functions. By analyzing interspecific differences, we identified significant adaptive transcriptional changes in the heart, lung, and spleen of the Plateau Pika. Specifically, upregulated genes in these tissues not only show a substantial association with apoptosis and DNA damage repair, but also demonstrate apparent enrichment in biological pathways related to energy metabolism and immune regulation. The majority of downregulated genes exhibit decreased activity in metabolic pathways particularly in muscle, spleen, kidney, and brain tissues. We further reveal the pivotal gene interaction networks of the 9 tissues. Our study provides valuable insight into adaptive mechanisms underlying evolution of Plateau Pika at extreme altitudes. This study elucidates the adaptive evolutionary mechanisms of the Plateau Pika (Ochotona curzoniae) in high-altitude environments. Utilizing transcriptomic analysis across various tissues, significant adaptive transcriptional changes were identified in the heart, lungs, and spleen involving processes such as apoptosis, DNA damage repair, energy metabolism, and immune regulation. These findings provide crucial insights into the survival mechanisms of the Plateau Pika on the Qinghai-Tibet Plateau.

Conservation planning in areas prone to human–wildlife interactions requires strong integration between biodiversity protection and other human society needs. Livestock depredation by felids is one of the most reported human–wildlife conflicts in Tibet, reinforced by expanding rangeland and rebounding of wildlife populations. Tibet harbors the richest felid diversity in China; nevertheless, only two protected areas were designated targeting this emblematic group. Here, we combined species distribution modeling and systematic conservation planning approaches to identify priority areas for felid conservation in Tibet. Specifically, we assessed conservation priorities based on three complementary biodiversity indexes (taxonomic, functional, and phylogenetic) integrated with livestock density, land use, and human disturbances. Based on the most comprehensive dataset of felid species, we found that large parts of Tibet remain poorly studied and most of the felid populations inhabit unprotected Tibetan lands. In addition, we detected that livestock density is positively related to large-sized felid distributions, reflecting the long-term conflict in this region. Our prioritization analyses identified large priority areas for felid conservation in Tibet. Worrisomely, approximately 76% of them lie outside of existing and planned protected areas, with four noteworthy gaps. The largest extension of these key regions for felid conservation is located in southeastern Tibet close to the border with India, Bhutan, and Nepal, revealing the need for transnational conservation efforts across the Pan-Himalaya region. Our study represents the first attempt of systematic conservation planning for Tibetan felids taking into account the balance between multiple conservation values and competing land use for societal development.

The microbiome of mammals has profound effects on host fitness, but the process, which drives the assembly and shift of mammalian micro- biome remains poorly understood. To explore the patterns of small mammal microbial communities across host species and geographical sites and measure the relative contributions of different processes in driving assembly patterns, 2 sympatric desert rodent species ( Dipus sagitta and Meriones meridianus) were sampled from 2 geographically distant regions, which differed in the environment, followed by 16S rRNA gene sequencing. The microbiomes differed significantly between D. sagitta and M. meridianus, and linear mixed modeling (LMM) analysis revealed that microbial diversity was mostly affected by species rather than the environment. For each rodent species, the microbiome diversity and structure differed across geographical regions, with individuals from lower rainfall environments exhibiting greater diversity. The null modeling results suggested dispersal limitation and ecological drift rather than differential selective pressures acting on the microbiome. In addition, each group had a different core genus, suggesting that the taxonomic composition of the microbiome was shaped most strongly by stochastic processes. Our results suggest that variation in the microbiome between hosts, both within and among geographic rodent populations, is driven by bacterial dispersal and ecological drift rather than by differential selective pressures.These results elucidated the diversity patterns and assembly processes of bacterial microbiomes in small desert mammals. Deciphering the processes shaping the assembly of the microbial community is a premise for better understanding how the environment-host-microbe interactions of mammals are established and maintained, particularly in the context of increased environmental disturbances and global changes.

How ecological and evolutionary factors affect small mammal diversity in arid regions remains largely unknown. Here, we combined the largest phylogeny and occurrence dataset of Gerbillinae desert rodents to explore the underlying factors shaping present-day distribution patterns. In particular, we analyzed the relative contributions of ecological and evolutionary factors on their species diversity using a variety of models. Additionally, we inferred the ancestral range and possible dispersal scenarios and estimated the diversification rate of Gerbillinae. We found that Gerbillinae likely originated in the Horn of Africa in the Middle Miocene and then dispersed and diversified across arid regions in northern and southern Africa and western and central Asia, forming their current distribution pattern. Multiple ecological and evolutionary factors jointly determine the spatial pattern of Gerbillinae diversity, but evolutionary factors (evolutionary time and speciation rate) and habitat filtering were the most important in explaining the spatial variation in species richness. Our study enhances the understanding of the diversity patterns of small mammals in arid regions and highlights the importance of including evolutionary factors when interpreting the mechanisms underlying large-scale species diversity patterns.

Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation, thus enabling range expansion. In contrast, narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions, thus limiting their ability to expand into novel environments. However, the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood. The Niviventer niviventer species complex (NNSC), consisting of highly abundant wild rats in Southeast Asia and China, offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related. In the present study, we combined ecological niche modeling with phylogenetic analysis, which suggested that sister species cannot be both widespread and dominant within the same geographical region. Moreover, by assessing heterozygosity, linkage disequilibrium decay, and Tajima's D analysis, we found that widespread species exhibited higher genetic diversity than narrow-range species. In addition, by exploring the "genomic islands of speciation", we identified 13 genes in highly divergent regions that were shared by the two widespread species, distinguishing them from their narrow-range counterparts. Functional annotation analysis indicated that these genes are involved in nervous system development and regulation. The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.

Wildlife is reservoir of emerging viruses. Here we identified 27 families of mammalian viruses from 1981 wild animals and 194 zoo animals collected from south China between 2015 and 2022, isolated and characterized the pathogenicity of eight viruses. Bats harbor high diversity of coronaviruses, picornaviruses and astroviruses, and a potentially novel genus of Bornaviridae. In addition to the reported SARSr-CoV-2 and HKU4-CoV-like viruses, picornavirus and respiroviruses also likely circulate between bats and pangolins. Pikas harbor a new clade of Embecovirus and a new genus of arenaviruses. Further, the potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified, complicating wildlife protection and the prevention and control of these diseases in domestic animals. This study provides a nuanced view of the frequency of host-jumping events, as well as assessments of zoonotic risk.

Secondary and plantation forests are the main alternative forests remaining after the deforestation of primary forests. Understanding the conservation value of secondary and plantation forests is important for resource utilization. To explore the impact of forest conversion on biodiversity, we compared multiple diversity metrics (taxonomic, phylogenetic and functional diversity) and community structures of small mammals in the primary, secondary and plantation forests on Mt. Liangshan, Sichuan Province, China. Seven field surveys were conducted to survey local small mammal assemblages between 2016 and 2020. We found that the taxonomic, phylogenetic and functional diversity metrics of small mammals in the three forest types were similar at the landscape scale, while all diversity metrics were lowest in the plantation forest and highest in the primary forests at the site scale. The community structure analysis showed that random processes were dominant across the three forest types, and there was no difference in small mammal community structures among the three forest types. Our results indicated that secondary and plantation forests in the nature reserves, adjacent to the primary forest and exposed to little human disturbance, also can provide important habitats for small mammals.

BACKGROUND:Environmental conditions vary among deserts across the world, spanning from hyper-arid to high-elevation deserts. However, prior genomic studies on desert adaptation have focused on desert and non-desert comparisons overlooking the complexity of conditions within deserts. Focusing on the adaptation mechanisms to diverse desert environments will advance our understanding of how species adapt to extreme desert environments. The hairy-footed jerboas are well adapted to diverse desert environments, inhabiting high-altitude arid regions, hyper-arid deserts, and semi-deserts, but the genetic basis of their adaptation to different deserts remains unknown. RESULTS:Here, we sequenced the whole genome of 83 hairy-footed jerboas from distinct desert zones in China to assess how they responded under contrasting conditions. Population genomics analyses reveal the existence of three species in hairy-footed jerboas distributed in China: Dipus deasyi, Dipus sagitta, and Dipus sowerbyi. Analyses of selection between high-altitude desert (elevation ≥ 3000m) and low-altitude desert (< 500m) populations identified two strongly selected genes, ATR and HIF1AN, associated with intense UV radiation and hypoxia in high-altitude environments. A number of candidate genes involved in energy and water homeostasis were detected in the comparative genomic analyses of hyper-arid desert (average annual precipitation < 70mm) and arid desert (< 200mm) populations versus semi-desert (> 360mm) populations. Hyper-arid desert animals also exhibited stronger adaptive selection in energy homeostasis, suggesting water and resource scarcity may be the main drivers of desert adaptation in hairy-footed jerboas. CONCLUSIONS:Our study challenges the view of deserts as homogeneous environments and shows that distinct genomic adaptations can be found among desert animals depending on their habitats.

Climate adaptation and dispersal can determine a species’ response to climate change. However, quantifying how they can mitigate climate change risks remains a challenge. Here we combine ecological genomic, niche modelling and landscape genetic approaches to reveal similar population-level vulnerability for a keystone species and its two beneficiary species in an alpine grassland ecosystem in the Qinghai–Tibetan Plateau. We use climate-associated genotypes to identify population-level adaptation and model maladaptation with and without dispersal and find that contemporary populations in southwestern ranges are the most vulnerable to climate change. This vulnerability cannot be mitigated by dispersal to more suitable niches because of climate maladaptation and landscape barriers. Overall, combined multiple climate change risk estimates in coevolving species can be used to improve climate change vulnerability assessments beyond what can be learned from a single species or modelling.

Phenotypes associated with metabolism and water retention are thought to be key to the adaptation of desert species. However, knowledge on the genetic changes and selective regimes on the similar and divergent ways to desert adaptation in sympatric and phylogenetically close desert organisms remains limited. Here, we generate a chromosome level genome assembly for Northern three-toed jerboa (Dipus sagitta) and three other high-quality genome assemblies for Siberian jerboa (Orientallactaga sibirica), Midday jird (Meriones meridianus), and Desert hamster (Phodopus roborovskii). Genomic analyses unveil that desert adaptation of the four species mainly result from similar metabolic pathways, such as arachidonic acid metabolism, thermogenesis, oxidative phosphorylation, insulin related pathway, DNA repair and protein synthesis and degradation. However, the specific evolved genes in the same adaptative molecular pathway often differ in the four species. We also reveal similar niche selection but different demographic histories and sensitivity to climate changes, which may be related to the diversified genomic adaptative features. In addition, our study suggests that nocturnal rodents have evolved some specific adaptative mechanism to desert environments compared to large desert animals. Our genomic resources will provide an important foundation for further research on desert genetic adaptations.

Abstract Rare and geographically restricted species may be vulnerable to genetic effects from inbreeding depression in small populations or from genetic swamping through hybridization with common species, but a third possibility is that selective gene flow can restore fitness (genetic rescue). Climate-sensitive pikas (Ochotona spp.) of the Qinghai–Tibetan Plateau (QHTP) and its vicinity have been reduced to residual populations through the movement of climatic zones during the Pleistocene and recent anthropogenic disturbance, whereas the plateau pika (O. curzoniae) remains common. Population-level whole-genome sequencing (n = 142) of six closely related species in the subgenus Ochotona revealed several phases of ancient introgression, lineage replacement, and bidirectional introgression. The strength of gene flow was the greatest from the dominant O. curzoniae to ecologically distinct species in areas peripheral to the QHTP. Genetic analyses were consistent with environmental reconstructions of past population movements. Recurrent periods of introgression throughout the Pleistocene revealed an increase in genetic variation at first but subsequent loss of genetic variation in later phases. Enhanced dispersion of introgressed genomic regions apparently contributed to demographic recovery in three peripheral species that underwent range shifts following climate oscillations on the QHTP, although it failed to drive recovery of northeastern O. dauurica and geographically isolated O. sikimaria. Our findings highlight differences in timescale and environmental background to determine the consequence of hybridization and the unique role of the QHTP in conserving key evolutionary processes of sky island species.