Explore the vast range of titles available.

Vulnerable populations of wild yak (Bos mutus), the wild ancestral species of domestic yak, survive in extremely cold, harsh and oxygen-poor regions of the Qinghai-Tibetan Plateau (QTP) and adjacent high-altitude regions. In this study, we sequenced and assembled its genome de novo. In total, six different insert-size libraries were sequenced, and 662 Gb of clean data were generated. The assembled wild yak genome is 2.83 Gb in length, with an N50 contig size of 63.2 kb and a scaffold size of 16.3 Mb. BUSCO assessment indicated that 93.8% of the highly conserved mammal genes were completely present in the genome assembly. Annotation of the wild yak genome assembly identified 1.41 Gb (49.65%) of repetitive sequences and a total of 22,910 protein-coding genes, including 20,660 (90.18%) annotated with functional terms. This first construction of the wild yak genome provides a variable genetic resource that will facilitate further study of the genetic diversity of bovine species and accelerate yak breeding efforts.Measurement(s)DNA • genome • sequence_assembly • sequence feature annotationTechnology Type(s)DNA sequencing assay • sequence assembly process • sequence annotationSample Characteristic - OrganismBos mutusSample Characteristic - EnvironmentQinghai-Tibetan PlateauMachine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11778669

The wild yak Bos mutus was believed to be regionally extinct in Nepal for decades until our team documented two individuals from Upper Humla, north‐western Nepal, in 2014. The International Union for Conservation of Nature (IUCN) seeks further evidence for the conclusive confirmation of that sighting. We conducted line transects and opportunistic sign surveys in the potential wild yak habitats of Humla, Dolpa, and Mustang districts between 2015 and 2017 and collected genetic samples (present and historic) of wild and domestic yaks Bos grunniens. We also sighted another wild yak in Upper Humla in 2015. Phylogenetic and haplotype network analyses based on mitochondrial D‐loop sequences (~450 bp) revealed that wild yaks in Humla share the haplotype with wild yaks from the north‐western region of the Qinghai‐Tibetan Plateau in China. While hybridization with domestic yaks is a major long‐term threat, illegal hunting for meat and trophy put the very small populations of wild yaks in Nepal at risk. Our study indicates that the unprotected habitat of Upper Humla is the last refuge for wild yaks in Nepal. We recommend wild yak conservation efforts in the country to focus on Upper Humla by (i) assigning a formal status of protected area to the region, (ii) raising awareness in the local communities for wild yak conservation, and (iii) providing support for adaptation of herding practice and pastureland use to ensure the viability of the population. Our study carries a global relevance as it presents phylogenetic and haplotype network analyses of wild and domestic yak samples to reveal that the wild yaks in Humla, Nepal, share the haplotype with wild yaks from the north‐western region of the Qinghai‐Tibetan Plateau in China, providing validation to the wild yak rediscovery in Nepal that was based on morphology and behavior of the sighted animals. We also derive phylogeographical inference for the wild yaks in the Nepalese Transhimalayas and discuss their hybridization status while also outlining the conservation implications for the wild yaks that are critically endangered in the country.

Understanding the use of small bridges and culverts by wildlife to cross the Qinghai–Tibet railway will aid in the design of wildlife crossing structures for similar transportation infrastructure. From 2014 to 2016, 36 infrared cameras were placed inside 14 small bridges and 11 culverts along the Qinghai–Tibet railway to determine the structures’ effectiveness as wildlife passages. Thirteen species of mammals were found to use the small bridges and culverts to cross the railway. The crossing rates for all mammals were significantly higher for small bridges than for culverts. Tibetan antelope ( Pantholops hodgsonii ), Tibetan gazelle ( Procapra picticaudata ), kiang ( Equus kiang ), and wild yak ( Bos mutus ) preferred small bridges over culverts to cross the railway. In contrast, mountain weasel ( Mustela altaica ) and Asian badger ( Meles leucurus ) preferred culverts to cross the railway. The crossing rates of all mammals, particularly Tibetan gazelle and woolly hare, were positively influenced by structure width. Structure height had a positive influence on wild yak, but structure length had a negative influence on kiang. The distance to the highway had a positive influence on the crossing rates of all mammals, particularly wild yak and woolly hare. Human use of the structures had no influence on the crossings of most mammals except for common wolf. We suggest that road design schemes include large and open crossing structures to benefit most species with limitations on human activities near wildlife passages.

Wild yak ( Bos mutus ) and domestic yak ( Bos grunniens ) are adapted to high altitude environment and have ecological, economic, and cultural significances on the Qinghai-Tibetan Plateau (QTP). Currently, the genetic and cellular bases underlying adaptations of yak to extreme conditions remains elusive. In the present study, we assembled two chromosome-level genomes, one each for wild yak and domestic yak, and screened structural variants (SVs) through the long-read data of yak and taurine cattle. The results revealed that 6733 genes contained high-FST SVs. 127 genes carrying special type of SVs were differentially expressed in lungs of the taurine cattle and yak. We then constructed the first single-cell gene expression atlas of yak and taurine cattle lung tissues and identified a yak-specific endothelial cell subtype. By integrating SVs and single-cell transcriptome data, we revealed that the endothelial cells expressed the highest proportion of marker genes carrying high-FST SVs in taurine cattle lungs. Furthermore, we identified pathways which were related to the medial thickness and formation of elastic fibers in yak lungs. These findings provide new insights into the high-altitude adaptation of yak and have important implications for understanding the physiological and pathological responses of large mammals and humans to hypoxia. The genetic bases of yak adaptations to extreme conditions remains elusive. This study compares yak and cattle at a genomic and transcriptomic level, revealing a new type of endothelial cell and candidate genes related with elastic fiber formation in yak lungs that might contribute to high altitude adaptation.

Golden wild yak is a rare and unique Yak subspecies in China. In this study, we first identified the complete mitochondrial genome sequence of golden wild yak. The complete mitogenome was 16,323 bp in length, with 37 typical animal mitochondrial genes (22 transfer RNA, 2 ribosomal RNA and 13 protein-coding genes) and one non-coding region (D-loop), and its contents of A, T, G, and C were 33.71%, 27.26%, 13.21%, 25.82, respectively. The phylogenetic analysis showed that the golden wild yak is closer with Pali yak, and it might be a mutant type of Yak living in Qinghai-Tibetan Plateau area.

The Kunlun Mountain type wild yak ( Bos mutus ) is one of the most charismatic members of the Tibet/Qinghai Plateau, but its population is reduced. In this study, the complete mitochondrial genome of Kunlun Mountain type wild yak has been determined by polymerase chain reaction method for the first time. The circular genome was 16,325 base pairs (bp), containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding control region. The base composition of the genome was A (33.70%), C (25.81%), G (13.22%) and T (27.28%) with an A+T content of 60.98%. A phylogenetic analysis based on complete mitochondrial genome sequences showed that Kunlun Mountain type wild yak ( Bos mutus ) was closer to domesticated yaks ( Bos gruuniens ) and bison ( Bison bison ).

Bovine leukemia virus (BLV), an oncogenic member of the Deltaretrovirus genus, is closely related to human T-cell leukemia virus (HTLV-I and II). BLV infects cattle worldwide and causes important economic losses. In this review, we provide a summary of available information about commonly used diagnostic approaches for the detection of BLV infection, including both serological and viral genome-based methods. We also outline genotyping methods used for the phylogenetic analysis of BLV, including PCR restriction length polymorphism and modern DNA sequencing-based methods. In addition, detailed epidemiological information on the prevalence of BLV in cattle worldwide is presented. Finally, we summarize the various BLV genotypes identified by the phylogenetic analyses of the whole genome and env gp51 sequences of BLV strains in different countries and discuss the distribution of BLV genotypes worldwide.

Cauldrons, vessels that are simultaneously common and enigmatic, offer insights into past cultural and social traditions. While assumed to possess a special function, what these cauldrons contained is still largely mysterious. These vessels, such as those made from bronze or copper alloys, function as reservoirs for ancient organics through the antibacterial qualities provided by the metal surfaces. Here we show, through protein analysis, that cauldrons from the Final Bronze Age (ca. 2700 BP) were primarily used to collect blood from ruminants, primarily caprines, likely for the production of sausages in a manner similar to contemporary practices in Mongolia’s rural countryside. Our findings present a different function from the recent findings of cooked meat in copper-alloy vessels from the northern Caucasus 2000 years earlier, exposing the diversity in food preparation techniques. Our secondary findings of bovine milk within the cauldron, including peptides specific to Bos mutus , pushes back their regional domestication into the Bronze Age.

Climate change has significant impacts on species' distributions and diversity patterns. Understanding range shifts and changes in richness gradients under climate change is crucial for conservation. The Tibetan Plateau, home to wild yak, chiru, and kiang, contains a biome with many endemic ungulates. It is highly sensitive to climate change and a region that merits particular attention with regard to the impacts of global climate change on its biomes. Maximum entropy approaches were used to estimate current and future potential distributions, in response to climate change, for 22 ungulate species. We used three general circulation (MK3, HADCM3, MIROC3_2-MED) and three emissions scenarios (B1, A1B, A2) to derive estimated future measurements of 14 environmental variables over three time periods (2020, 2050, 2080), and then modeled species distributions using these predicted environmental measurements for each time period under two dispersal hypotheses (full and zero, respectively). This resulted in a total of 6160 prediction models. We found that these ungulates, on average, may lose 30-50% of their distributional areas, depending on the dispersal scenarios. In addition, 55-68% of the ungulate species were predicted to become locally endangered under the different dispersal assumptions, 23-32% to become locally critically endangered, and 4-7 endemic species to become globally endangered. Furthermore, ungulate species ranges may experience average poleward shifts of ~300 km. We also predict west-to-east reductions in species richness: southeastern mountainous areas currently have the highest species richness, but are predicted to face the greatest diversity losses, whereas the northern areas are predicted to see increasing numbers of ungulate species in the 21st century. Our study indicates much more severe range reductions of ungulates on the Tibetan Plateau than those anticipated elsewhere in the world, and species richness patterns will change dramatically with climate change. For conservation, we suggest (1) securing existing protected areas, and (2) establishing new nature reserves to counterbalance climate change impacts.

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.