The Tibetan wild donkey (Equus kiang) is an endemic equid species inhabiting the Qinghai-Tibet Plateau, exhibiting remarkable chromosomal diversity within the Equus genus. Here we present a chromosome-level, telomere-to-telomere genome assembly for E. kiang generated using Illumina short reads, PacBio HiFi long reads, and Hi-C sequencing data. The final assembly spans 4.02 Gb and comprises 27 pseudochromosomes. Specifically, 8 chromosomes are gapless, 8 chromosomes have one gap, 7 chromosomes have 2-4 gaps, and the remaining 4 chromosomes have five or more gaps. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis indicated 96.7% completeness, demonstrating high assembly quality. Comparative genome collinearity with the domestic horse (E. caballus) showed that 11 E. kiang chromosomes displayed a simple one-to-one chromosome-scale correspondence. We further characterized genomic features associated with these regions, including the enrichment of tandem repeats near recombination breakpoints. This high-quality genome assembly provides a foundational resource for studies of chromosome evolution, speciation, and genomic architecture in Equus and other mammals.

Six Gram-stain-positive, coccobacilli, non-motile, oxidase-negative, catalase-positive strains, designated HY-051T, HY049, HY190T, HY1757, HY647T and HY359, were isolated from the faeces of Tibetan wild asses (Equus kiang) in Tibet, China, and from fruit bat (Rousettus leschenaultii) faeces in Yunnan, China. All strains are strictly aerobic. Optimal growth for all strains occurred at 28.0 °C, pH 7.0 and with 1.0% (w/v) NaCl. While 16S rRNA gene analysis confirmed their placement within the genus Rhodococcus, phylogenomic analyses revealed that strains HY-051T/HY049, HY190T/HY1757 and HY647T/HY359 represent distinct lineages. Notably, the digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between these strains and their closest relatives were well below the species delineation thresholds (70% dDDH and 95-96% ANI). Chemotaxonomically, all three groups differ from their closest phylogenetic neighbours by the absence of C15 : 0 and C16 : 1 fatty acids and the presence of Summed Feature 3. Additionally, distinct whole-cell sugar patterns (ribose/arabinose or glucose/galactose), differential menaquinone profiles and API ZYM and 50CH biochemical profiles (e.g. aesculin hydrolysis and carbohydrate utilization) further distinguish them from known species. Based on polyphasic taxonomic analyses, strains HY-051T and HY049 constitute a novel species of the genus Rhodococcus, for which the name Rhodococcus huquni sp. nov. is proposed, with strain HY-051T (=JCM 34841T=CGMCC 1.19145T) as the type strain; strains HY190T and HY1757 constitute a novel species of the genus Rhodococcus, for which the name Rhodococcus quanlei sp. nov. is proposed, with strain HY190T (=JCM 34842T=CGMCC 1.19375T) as the type strain; and strains HY647T and HY359 constitute a novel species of the genus Rhodococcus, for which the name Rhodococcus ruitaii sp. nov. is proposed, with strain HY647T (=JCM 34787T=CGMCC 1.19150T) as the type strain.

ABSTRACT Managing human-wildlife interactions is essential for conservation in Sanjiangyuan National Park. This study develops a scenario-based framework to explain visitors’emotional and behavioural responses. A mixed-methods design combines interviews with scenario-based visual surveys. Results show that landscape and animal behaviour jointly shape emotions: grasslands and calm animals elicit positive emotions, while vigilance or aggression induces negative emotions; Tibetan wild asses are perceived more positively than snow leopards. Behavioural intentions vary by context, with grasslands encouraging photography and roads prompting avoidance. Emotional responses further influence coping behaviours, with negative emotions associated with higher risky intentions.This study advances understanding of wildlife tourism by linking cognitive appraisal processes with behavioural outcomes. It provides practical implications for visitor management and risk mitigation in protected areas.

Abstract The Tibetan antelope chiru ( Pantholops hodgsonii ), a highly specialized ungulate endemic to the Tibetan Plateau, exhibits a unique seasonal migration of a male-dominated population to the cold, arid Changchenmo Valley in eastern Ladakh, India, raising important ecological and conservation concerns. Over three years, we examined the population structure, spatial distribution, and habitat use of chiru in relation to four sympatric ungulates: argali ( Ovis ammon ), wild yak ( Bos mutus ), Tibetan wild ass kiang, ( Equus kiang ), and bharal ( Pseudois nayaur ). Across 162 surveys covering 918.6 km, we recorded 1,670 individuals, including 710 male chiru. Chiru had a mean encounter rate of 1.19 ± 1.17 individuals/km and a typical group size of 13.69. Our results indicate that sympatric ungulates partition resources through habitat selection, facilitating summer co-occurrence, while competition intensifies in winter and spring. Chiru and kiang exhibited facilitative interactions, whereas chiru showed strong segregation from other species. Notably, we observed previously unrecorded overwintering by chiru. Despite a seemingly stable population, habitat overlap, climate change, infrastructure development, and livestock competition pose significant threats. Urgent conservation measures focusing on habitat protection, reducing human disturbance, and engaging local stakeholders are critical to ensure the long-term survival of chiru and other ungulates in this fragile Trans-Himalayan ecosystem.

ABSTRACTUnderstanding the mechanisms of competition and coexistence among sympatric species is crucial for deepening our understanding of interspecific interactions and informing the conservation of rare and endangered wildlife. In this study, we utilized DNA macro‐barcoding technology to analyze the seasonal dietary habits of Kiang (Equus kiang) and Tibetan Gazelle (Procapra picticaudata) in Shiqu County, Sichuan Province, aiming to investigate their resource partitioning strategies and potential competition for limited forage resources. The results showed that Kiang mainly consumed Cyperaceae and Polygonaceae in both seasons, while Tibetan Gazelle fed on Polygonaceae and Rosaceae in the warm season and shifted to Ephedraceae in the cold season. Both species exhibited significant seasonal differences in dietary composition, with Tibetan Gazelle showing greater individual variation and seasonal shifts. In addition, their dietary niche was broader in the warm season, and overlap remained high, with indices of 0.89 and 0.87 in the warm and cold seasons, respectively. The results indicate that although Kiang and Tibetan Gazelle exhibit partial dietary overlap, they mitigate interspecific competition and achieve sympatric coexistence through differential use of dominant forage species, adjustments in dietary proportions, and individual dietary flexibility; notably, Tibetan gazelles exhibit stronger ecological adaptability. This study highlights a competition–coexistence dynamic along the trophic niche axis in typical plateau ungulates, providing insights for effective conservation strategies and biodiversity conservation in plateau regions.

Species interactions are crucial for understanding how species will respond to future climate change. Incorporating interspecific relationships into mammalian distribution prediction models will significantly impact model outcomes, especially those for animals on the Qinghai-Tibet Plateau (QTP). Thus, we incorporated interspecific relationships into species distribution models to assess and predict the future distributions of five ungulates, including the Red deer (Cervus elaphus), the Kiang (Equus kiang), the Tibetan gazelle (Procapra picticaudata), the Tibetan antelope (Pantholops hodgsonii), and the Bharal (Pseudois nayaur). We found that (1) the suitable habitats of these five ungulates were all predicted to increase between the present and 2050; (2) the suitable distribution areas of four of these ungulates were predicted to be smaller when interspecific relationships were incorporated into the models, with the exception of the Red deer, whose suitable habitat was estimated to be larger; and (3) the centroids of suitable habitat for the five ungulates were predicted to shift to the southern part of the QTP by 2050. Our results demonstrated that interspecific relationships could influence predictions of species distributions, and thus incorporating interspecific relationships will facilitate better assessments and predictions of the future distributions of species.

As a First-Class Protected species in China, the Tibetan wild ass (Equus kiang) is endemic to the Qinghai-Tibet Plateau and exhibits remarkable adaptation to extreme high-altitude environments characterized by low oxygen, cold temperatures, and high UV radiation. To explore its genetic basis and evolutionary adaptations, we generated the first telomere-to-telomere (T2T) gapless genome using an integrated sequencing strategy that combined PacBio HiFi, ultra-long Oxford Nanopore (ONT), Hi-C, and BGI short-read technologies. The resulting 2.49 Gb assembly achieved a contig N50 of 107.02 Mb, comprising all 54 telomeres and 27 centromeres across 25 pairs of autosomes and the X/Y chromosomes, and reached 99.94% BUSCO completeness. Genome annotation predicted 907 Mb of repetitive sequences (36.52% of the genome) and 24,005 protein-coding genes. Comparative and technical analyses confirmed high assembly continuity, completeness, and accuracy, with a consensus quality value (QV) of 64.73, providing a robust genomic reference for understanding the evolutionary mechanisms and adaptive traits of this iconic high-altitude ungulate.

Sanjiangyuan National Park (SNP), the first national park established in China, plays a pivotal role in conserving biodiversity on the Qinghai-Tibet Plateau. This study investigates the habitat suitability and projected future distribution of four key species: the Tibetan antelope (Pantholops hodgsonii), kiang (Equus kiang), Tibetan gazelle (Procapra picticaudata), and wild yak (Bos mutus). Utilizing 358 occurrence records and the MaxEnt model, we predicted current and future suitable habitats under different climate scenarios for the years 2050 and 2070. Our findings indicate that suitable habitats are significantly influenced by factors such as elevation, temperature, and vegetation health. Among the species studied, the Tibetan gazelle exhibits the most extensive suitable habitat, followed by the kiang, Tibetan antelope, and wild yak. Specifically, the Tibetan antelope’s habitat is anticipated to shift northward, while the kiang and wild yak may experience further habitat fragmentation, thereby increasing risks to their populations. Additionally, the results highlight the importance of integrating climate considerations into future conservation planning to ensure the long-term survival of these species. By identifying regions with optimal environmental conditions, conservation strategies can be more effectively directed to maintain and improve these habitats, thereby preserving biodiversity within the Sanjiangyuan region.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-23536-4.

Environmental factors, including climatic and habitat conditions, not only critically sustain ecosystem functioning and community stability but also serve as key determinants of species distributions. Research on the instant effects of environmental factors impacts remains limited. Although traditional methods, such as species distribution model, are commonly applied to assess environmental effects, they frequently overlook interspecific interactions that may determine distribution patterns. In this study, we employed a joint species distribution model and a generalized additive model to analyze the lagged responses of 2022-2023 geographic distribution patterns to historical habitat conditions (2001-2019) in four widespread high-elevation ungulates (Equus kiang, Pantholops hodgsonii, Procapra picticaudata, and Bos mutus) on the Tibetan Plateau, defining this delayed response of animal distributions to environmental changes as the distribution lag effect (DLE). Our analysis revealed that while climate strongly influenced species distributions, habitat change drove most observed delays in distribution responses. In terms of community ecology, dispersed communities exhibited shorter time lags than concentrated groups. Analyses of lag duration revealed a 5-6-year DLE in high-altitude ungulate distributions. Our results provide valuable insights into sustainable alpine steppe management by highlighting the importance of maintaining habitat quality and mitigating resource competition over time. Furthermore, it offers guidance for the long-term conservation of high-altitude ungulate species.

Ecological adaptation mechanisms of plateau ungulates to seasonal nomadic pastoralism on the eastern Qinghai-Tibetan plateau

Spatial dimensions play a significant role in niche differentiation, facilitating species coexistence. Understanding how sympatric ungulates optimize habitat utilization and how they co-exist in resource-limited environments is essential for effective wildlife conservation and reserve management. Tibetan antelope (chiru, Pantholops hodgsonii), Tibetan wild ass (kiang, Equus kiang), and wild yak (Bos grunniens) are sympatric ungulates co-evolving over generations across the Tibetan Plateau, but limited information is available on their spatial partitioning and the key variables affecting both single-species and multi-species distributions. In this study, using a combination of maximum entropy model, joint species distribution models, and random forest analysis, we examined the spatial partitioning of the three ungulates and identified the critical factors influencing their distributions with their spatial distribution data collected from the Arjin Shan National Nature Reserve in the Tibetan Plateau. Our key findings: (i) Notable differences were observed in the spatial distributions of the three ungulates, with only 16% overlap in their suitable habitats. Temperature had a stronger influence on the habitat selection by chiru and kiang, whereas precipitation played a more significant role in determining the distributions of kiang and wild yak. (ii) During summer, the interspecific relationships between chiru and wild yak, and between chiru and kiang exhibited positive correlations, while the relationship between wild yak and kiang was negatively correlated. In winter, all interspecific relationships were negatively correlated. (iii) Temperature seasonality and mean temperature of the driest quarter emerged as the most critical variables influencing multi-species habitat selection. Human interference had a significantly negative impact on all three ungulate species. Our findings underscore the importance of spatial heterogeneity in facilitating species coexistence under both climatic and anthropogenic pressures, offering valuable insights for multi-species conservation planning in resource-limited ecosystems.

The upper Himalayan region's wild and domesticated animals have unique morphological, physiological, and dietary adaptations that allow them to survive in harsh weather. Specialized evolutionary mechanisms that promote thermoregulation, effective metabolic activities, and optimal nutrition assimilation are required because to the interplay of altitude, oxygen availability, temperature change, and unique dietary resources in these harsh environments. Yak (Bos grunniens), Churu, and Tibetan Wild Ass (Equus kiang) are among the 32 wild and 8 domestic animal species whose adaptive tactics are extensively examined in this analysis. These animals are resilient in high-altitude environments because of unique genetic and physiological changes they have experienced. Conservation biology, livestock management, and maintaining human populations that rely on these animals for agriculture all depend on an understanding of these adaptations. Understanding these adaptations is crucial for conservation biology, livestock management, and sustaining human populations dependent on these animals for agriculture, transportation, and ecological equilibrium in the region.

BackgroundThe Hetian Gray donkey, characterized by its large stature and gray coat color, is a relatively recently identified breed. This breed plays an important role in local agricultural practices and cultural heritage. However, with the widespread adoption of mechanization, its use as a draft animal has gradually diminished. Additionally, the insufficient development of its meat and milk products has contributed to a continuous decline in its population, making its conservation increasingly urgent. Despite its significance, research on the origin and ancestral composition of the Hetian Gray donkey remains limited, which is essential for developing effective conservation strategies. To address this, whole-genome resequencing data of 208 donkeys from seven Chinese indigenous donkey breeds, Equus africanus somaliensis, and Equus kiang were analyzed to investigate the relationships between the Hetian Gray donkey and other breeds in the present study. The findings of this study will provide valuable scientific evidence for preserving the genetic diversity and unique characteristics of the Hetian Gray donkey.ResultsThe analysis revealed that wild donkeys had no significant impact on the formation of the Hetian Gray donkey. Among the breeds studied, the Xinjiang donkey and the Guanzhong donkey exhibit the closest genetic affinity with the Hetian Gray donkeys. Additionally, genome-wide selection signature analysis between the Hetian Gray donkey and the Xinjiang donkey identified positive selection for genes associated with body size traits.ConclusionIn summary, the results confirm that geographical distance plays a crucial role in determining the genetic relationships among the Hetian Gray donkey and other populations. The Xinjiang donkey and the Guanzhong donkey played an important role in the formation of the Hetian Gray donkey, and genes related to body size were positively selected during development of the breed.

Bridging climate refuges for climate change adaptation: A spatio-temporal connectivity network approach

Understanding the change in the habitat distributions and abundance of wildlife in space and time is critical for the conservation of biodiversity and mitigate human–wildlife conflicts (HWCs). Tibetan antelope or chiru (Pantholops hodgsonii), Tibetan gazelle or goa (Procapra picticaudata), Tibetan wild ass or kiang (Equus kiang), and Wild yak (Bos mutus) have been sympatric on the Qinghai–Tibetan plateau (QTP) for numerous generations. However, reviews on the habitat distributions and abundance of these four wild herbivores (WHs), as well as the methods examining the changes in these aspects, are still lacking. Here, we firstly review the distributions and abundance of four major WHs on the QTP across different periods, examining the underlying causes of changes and HWCs. Furthermore, we critically compare three aspects of methods: transect surveys, machine learning (ML), and deep learning (DL) methods of studying WHs. The results show that since the 1990s, the distributions and abundance of WHs have exhibited a trend of initial decline followed by recovery, largely attributed to global climate warming and a decrease in illegal hunting. However, in recent years, the primary challenge has shifted from wildlife protection to balancing the human and wildlife interests within the constraints of limited resources. In the future, we should focus on enhancing the ecological functions of habitats to achieve harmonious coexistence between humans and nature, as well as establishing a scientific compensation mechanism to mitigate human–wildlife conflicts. In order to accurately calculate the changes, we should select appropriate models to analyze the habitats of wildlife based on their specific characteristics and the environmental conditions. Additionally, with the advancement of large models, AI (artificial intelligence) should be utilized for precise and rapid wildlife conservation. The findings of this study also provide guidance and reference for addressing the issues related to wildlife habitats and abundance in other regions globally.

Wildlife crossing structures (WCSs) are an important measure to protect biodiversity and reduce human-wildlife conflict, especially for bundled linear infrastructure. The aim of this study was to evaluate two “management and behavioral” factors (salt blocks and feces) in relation to two “structural factors” (underpasses’ dimension and distance of bundled linear infrastructure) along Qinghai-Tibet bundled linear infrastructure (Qinghai-Tibet railway alignment runs parallel to the Qinghai-Tibet highway) and Gonghe-Yushu bundled linear infrastructure (Gonghe-Yushu expressway is parallel to the Gonghe-Yushu highway) using infrared cameras. Eight underpasses were monitored in the Qinghai-Tibet railway and six in the Gonghe-Yushu expressway, with half of the induced experimental group and half of the control group in each area. The monitoring shows that the Qinghai-Tibet railway area has richer species diversity than the Gonghe-Yushu expressway area. Salt block and feces induction experiments showed that the relative abundance index (RAI) of the experimental and control groups did not reveal significant differences in both areas. In addition, we found that the wider the width of the underpasses, the higher the utilization rate of kiang (Equus kiang) and wolly hare (Lepus oiostolus). And the distance from the adjacent linear infrastructure was positively correlated with the frequency of wolly hare, while no correlation was found with other species. In summary, this study found that salt block and feces induction could not improve the utilization rate of ungulates to underpasses of bundled linear infrastructure on Tibetan Plateau, and preliminary understood the factors affecting the utilization rate of underpasses.

Ungulates are essential for maintaining the health of grassland ecosystems on the Tibetan plateau. Increased livestock grazing has caused competition for food resources, threatening ungulates’ survival. The survival risk of food resources for ungulates can be quantified by the grazing pressure index, which requires accurate grassland carrying capacity. Previous research on the grazing pressure index has rarely taken into account the influence of wild ungulates, mainly due to the lack of precise spatial data on their quantity. In this study, we conducted field investigations to construct high-resolution spatial distributions for the four endemic ungulates on the Tibetan plateau. By factoring in the grazing consumption of these ungulates, we recalculated the grassland carrying capacity to obtain the grazing pressure index, which allowed us to assess the survival risks for each species. The results show: (1) Quantity estimates for Tibetan antelope (Pantholops hodgsonii), Tibetan wild donkey (Equus kiang), Tibetan gazelle (Procapra picticaudata), and wild yak (Bos mutus) of the Tibetan plateau are 24.57 × 104, 17.93 × 104, 7.16 × 104, and 1.88 × 104, respectively; they mainly distributed in the northern and western regions of the Tibetan plateau. (2) The grassland carrying capacity of the Tibetan plateau is 69.98 million sheep units, with ungulate grazing accounting for 5% of forage utilization. Alpine meadow and alpine steppe exhibit the highest grassland carrying capacity. (3) The grazing pressure index on the Tibetan plateau grasslands is 2.23, indicating a heightened grazing pressure in the southern and eastern regions. (4) The habitat survival risk analysis indicates that the high survival risk (the grazing pressure index exceeds 1.2) areas for the four ungulate species account for the following proportions of their total habitat areas: Tibetan wild donkeys (49.76%), Tibetan gazelles (47.00%), Tibetan antelopes (40.76%), and wild yaks (34.83%). These high-risk areas are primarily located within alpine meadow and temperate desert steppe. This study provides a quantitative assessment of survival risks for these four ungulate species on the Tibetan plateau grasslands and serves as a valuable reference for ungulate conservation and grassland ecosystem management.

Simple SummaryShiqu County, in Sichuan Province, is the eastern edge of the distribution area of the kiang (Equus kiang) on the Tibetan Plateau. However, there is a lack of understanding about the kiang population and its habitat in this region. This study aims to assess the population and habitat status of kiangs. The results showed that the area of suitable habitat for kiangs is 3402.45 km2, with an estimated population of 1395.00 ± 272.20, and a population density of 0.41 ± 0.08/km2. These findings provide a scientific reference for the conservation of the kiang population and its habitat in the region.Shiqu County, Sichuan Province, forms the eastern edge of the distribution area of the kiang (Equus kiang). It is important to assess the population and habitat status of peripheral populations, as these play a significant role in the development of conservation strategies for kiangs. Based on field transect data collected from July to August 2023, this study predicted the suitable habitat distribution of kiangs in Shiqu County using a MaxEnt model and estimated the population size and density using the ‘Distance’ package. Additionally, it analyzed the responses of the group size of kiangs to environmental factors in Shiqu County. The results showed that the area of suitable habitat for kiangs is 3402.45 km2, accounting for 13.51% of the total area of Shiqu County. The estimated population was 1395.00 ± 272.20, with a population density of 0.41 ± 0.08/km2. Additionally, the group size of kiangs was significantly positively correlated with the distance from the road and grazing site. The distance from the grazing site, elevation, and temperature annual range are the main environmental factors affecting the distribution of kiangs. This study initially revealed the peripheral population Status and suitable habitat of the kiang on the eastern Tibetan Plateau, and the potential threat of grazing interference and road obstruction. The research results can provide a scientific reference for the population and habitat protection of kiangs in this area.

Several studies have investigated the gut bacterial composition of wild ungulates in the Qinghai–Xizang Plateau. However, the relationship between their gut microbiome dendrograms and their phylogenetic tree remains unclear. In this study, we analyzed 45 amplicons (V3–V4 region of the 16S rRNA gene) from five wild ungulates—Pseudois nayaur, Pantholops hodgsonii, Gazella subgutturosa, Bos grunniens, and Equus kiang—from the Qinghai–Xizang Plateau to clarify the relationship between their phylogenies and gut microbiome dendrograms. The unweighted pair group method with arithmetic mean analysis and hierarchical clustering analysis indicated that G. subgutturosa is closely related to P. nayaur; however, these results were inconsistent with their phylogenetic trees. Additionally, the indicator genera in the microbiome of each wild ungulate showed strong associations with the diets and habitats of their host. Thus, diet and space niche differentiation may primarily account for the differences between the gut microbiome characteristics of these wild ungulates and their phylogeny. In summary, our research provides insights into the evolutionary factors influencing the gut microbiome of wild ungulates in the Qinghai–Xizang Plateau.

The wild large herbivores inhabiting the Yellow-River-Source National Park (YRSNP) are confronted with a significant threat from climate change and human activities. In response to these detrimental influences, measures have been proposed by the government, such as the Ecological Conservation and Restoration Project in the Sanjiangyuan Region (ECRPSR) and the establishment of the Sanjiangyuan National Park (SNP). To advance species diversity, it is crucial to investigate the spatial distribution of large herbivores, identify factors influencing their distribution, and address conflicts arising from divergent plans within the YRSNP. In this study, unmanned aerial vehicles were employed for surveying the distribution of the Tibetan wild ass (Equus kiang) and Tibetan gazelle (Procapra picticaudata). The findings indicate that the optimal habitat area for Tibetan wild ass is 437.16 km2, while for Tibetan gazelle, it is 776.46 km2. Precipitation and the human footprint index emerge as the primary factors influencing the habitat distribution of large herbivores within the YRSNP. Under the influence of the ECRPSR, there was a noteworthy expansion of the habitat area for Tibetan wild ass by 791.25 km2, and for Tibetan gazelle, it expanded by 1612.94 km2. From a wildlife conservation standpoint, this study proposes the establishment of a wildlife refuge in the YRSNP, effective coordination of conflicts between various functional zones and plans, preservation of suitable habitats for large herbivores, and the provision of a scientific foundation to reconcile development and conservation conflicts in the region, while concurrently fostering biodiversity conservation.