Antlers represent the only known example of complete annual organ regeneration in mammals. Despite this unique regenerative capacity, the genetic mechanisms driving antler origin and morphological diversification across Cervidae remain poorly understood. This study assembled six high-quality chromosome-level genomes of cervids spanning four distinct tribes, including the first genomic reference for the tufted deer ( Elaphodus cephalophus). Comparative analyses across the Cervidae lineage identified signatures of positive selection on gene networks governing stem cell differentiation and bone metabolism, with elevated expression of these genes detected in antler developmental and regenerative tissues. Tribe-specific selective pressures in Cervini and Odocoileini further revealed convergent evolution targeting core developmental pathways, notably the RAS/MAPK pathway, implicating these pathways in both the emergence and enhancement of antler traits. In contrast, relaxed selective constraints in the antlerless Chinese water deer ( Hydropotes inermis) revealed disruptions in gene modules associated with tumor suppression and skeletal homeostasis, suggesting a rewiring of regulatory homeostasis. These findings highlight how antler evolution reshaped physiological trade-offs, including reduced oncogenic susceptibility and enhanced tissue regeneration and cyclic bone remodeling. This study advances current understanding of antler evolution and diversification, while providing genomic resources for mammalian regenerative biology.

Gastropod diversification represents one of the most spectacular evolutionary radiations, underpinned by a fundamentally asymmetric body plan and diverse pigmentation patterns. To understand the genetic underpinnings of these cardinal traits, we constructed a chromosome-level genome assembly for the rainbow abalone, Haliotis iris . Integrating comparative genomics, histoembryology, and molecular assays, we identify a conserved regulatory association between the long non-coding RNA lncRNA1 and pitx that is associated with asymmetric mantle development. In H. iris , this association is supported by chromatin-contact evidence and exploratory data suggesting a possible miRNA-associated post-transcriptional component. Furthermore, we identify a wnt-mitf-tyr framework for melanogenesis and show that the mantle is the primary site of melanin synthesis. Concurrently, we identify mantle-enriched prestin genes that are vibration-responsive, consistent with a possible sensory specialization of the mantle. These findings provide molecular insight into asymmetry, pigmentation, and mantle multifunctionality in gastropods.

Rumen ciliates are major contributors to enteric methane emissions from ruminant animals, yet the underlying mechanisms remain poorly understood. We present a catalog of 450 rumen ciliate genomes, with 87% newly generated. Using this resource, we quantified methane emissions from 100 cows and analyzed 1877 rumen metagenomic and metatranscriptomic datasets, which revealed correlations among ciliate abundance, methanogen abundance, and methane emissions. We further demonstrated that taxon-specific effects of rumen ciliates on methane production arise from a single-membrane, hydrogen-producing organelle called the hydrogenobody (HB), which is distinct from canonical hydrogenosomes in other protists. HBs are positioned near ciliary basal bodies and harbor specific hydrogenases and oxygen reductases. We found that Vestibuliferida ciliates, which have more abundant HBs than do Entodiniomorphida, exhibit enhanced hydrogen production and oxygen-scavenging capacity, thereby strongly promoting methanogenesis.

INTRODUCTION:Viruses are abundant biological entities within the gastrointestinal tract (GIT) of ruminants. Current understanding is extensive for bacterial and archaeal communities, but limited for viral communities. OBJECTIVES:The study aimed to investigate viral diversity, virus-host interactions and ecological functions of viruses across GIT regions and ruminant species. METHODS:We collected 373 short-read and long-read metagenomes from 10 GIT regions of seven ruminant species, combining Illumina, PacBio HiFi, and Nanopore sequencing. Viral contigs were identified using sequence homology, viral hallmark gene and machine learning, and employed to uncover community assembly of spatial heterogeneity by analyzing virus-host linkage, lifestyle, and auxiliary metabolic genes (AMGs). RESULTS:We constructed a Ruminant Gastrointestinal Virome Catalog (RGVC) comprising 43,981 vOTUs, revealing that viral communities were remarkably diverse and mainly driven by the GIT regions rather than by the ruminant species. Virus-host linkage analysis identified 4603 putative prokaryotic hosts across 34 classes for 5954 host-linked viruses, along with robust correlation (R2 = 0.91) observed between abundances of prokaryotic hosts and host-linked viruses across GIT regions. The lysogenic lifestyle was a dominant feature, with integrases being the predominant lysogenic-specific genes. We identified 864 high-confidence AMGs in lysogenic viruses that are annotated as key genes for polysaccharide degradation, glycolysis, and the Wood-Ljungdahl pathway, indicating a putative role for the viruses in supporting these host metabolic functions. The metabolic features of host-linked viruses were further verified by genomic context of selected AMGs of GH10, GPI and FHS with target function. CONCLUSION:These findings suggest that the GIT viral communities exhibit spatial heterogeneity with distinct virus-host interactions, and offer new perspectives on maintenance of complex ecological and nutritional functions in ruminant GIT.

Ruminants thrive in diverse ecosystems by leveraging their rumen microbiome to ferment fibrous plants. However, the spatial biogeography of rumen microbiome and the genetic diversity of the ventral rumen epithelium remain unknown. Here, we present a multi-omics study in roe deer, sika deer, and sheep, integrating region-resolved microbiome and metabolome across 11 ruminal sacs, as well as single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and bulk RNA sequencing (RNA-seq) of ventral epithelium. We reveal species-specific microbial compositions and metabolic capacities contributing to differences in short-chain fatty acid and vitamin B production. We uncover functional divergence, genomic specialization, and metabolic changes across the microbiome of distinct ruminal sacs. Single-cell profiling reveals changes of immune responses and structural remodeling of the ruminal ventral epithelium. We demonstrate that vitamin B12 promotes epithelial growth and we identify genes enhancing stem cell differentiation. Our results highlight variation in microbial ecology and epithelial architecture among three ruminant species, offering insights to improve livestock productivity.

The maintenance of blood glucose, the body's primary source of energy, is indispensable for overall health and metabolic homeostasis. It is regulated predominantly by the glucagon receptor family which is highly conserved in vertebrates1-4. Compared with other vertebrates, avian blood glucose levels are relatively high5,6, and blood glucose regulatory mechanisms in birds have remained unclear. Here we show that high hepatic expression of the avian glucagon receptor (GCGR) in association with constitutively active Gs signalling is dependent on the interaction of different domains. In vivo experiments showed that expression of constitutively active GCGR in hepatic cells led to correspondingly high blood glucose, rapid hepatic lipid utilization and high metabolic rates via downstream signalling pathway activation in fish, reptiles, birds and mammals. Furthermore, we identified a point mutation proximal to the GCGR gene region in chicken that resulted in reduced GCGR mRNA expression and increased body weight. Overexpressing a natural human GCGR variant (HsGCGR(H339R)) with modest constitutive activity in mice demonstrated that high expression of this variant increased blood glucose concentration and reduced body weight. In sum, we find that high expression and constitutive activity of GCGR may have contributed to the evolution of flight in the ancestors of birds.

Sea anemones occupy the full depth of the oceans, yet their evolutionary patterns and adaptive strategies to the enigmatic deep sea have remained contentious and poorly resolved. Here, we assemble genomes ( n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with all publicly available actiniarian data. Phylogenomic analyses reveal a mosaic topology among deep-sea and shallow-water clades. Using a novel framework that contrasts convergent gene-loss patterns, we show that a large number of light-associated gene families— including the complete circadian toolkit—were independently deleted after lineages entered the aphotic realm, whereas comparable loss in shallow taxa is negligible, providing decisive support for a shallow-water origin followed by multiple descents. Intriguingly, some deep-sea lineages further streamline energy budgets by recurrent loss or pseudogenisation of key meiotic genes (e.g., Meiosin , Ythdc2 , Spo11 , Rad21 , Mlh3 ), indicating a shift towards asexual reproduction. Despite this extensive genomic erosion, deep-sea anemones exhibit sophisticated molecular tuning: specific amino-acid substitutions enhance protein stability and activity under deep-sea conditions, while selective expansions of gene families related to neural excitability, membrane systems, etc., likely mitigate the suppressive environmental effects on vital physiological processes. Enzyme activity assays in the yeast system confirm that the deep-sea variants exhibit superior activity and enhanced growth at 4°C. These results define a “loss-optimization-innovation” triad that underlies bathymetric adaptations and may apply to other deep-sea fauna worldwide. ### Competing Interest Statement The authors have declared no competing interest. National Key R&D Program of China, 2022YFC3400300, 2023YFC2809300, 2016YFC0304905 Northwestern Polytechnical University, D5000220464 National Natural Science Foundation of China, 32100367, 32370452 Shaanxi Postdoctoral Research Project, 2023BSHGZZHQYXMZZ53

The rumen microbiome plays a critical role in nutrient metabolism and adaptation of the yak (Bos grunniens), an import livestock animal of the Qinghai-Tibet Plateau renowned for their superior plant fiber degradation capacity. However, the microbiome among the different ecological niches within yak's rumen remains unelucidated. Through shotgun sequencing of rumen solid and liquid fractions from five yaks, we identified significant differences in the microbial communities and their genetic functions between the solid and liquid fractions. Solid fractions exhibited dominance by Ruminococcus, Succiniclasticum, and Aspergillus, while Prevotella, Paludibacter, Parabacteroides, and Bacteroides prevailed in liquid fractions. Comparative CAZyme profiling revealed solid fractions were significantly enriched in cellulose/hemicellulose-targeting enzymes (GH5, GH11, and CBM63), implicating their specialization in breaking down the fibrous grasses. In contrast, liquid fractions showed higher abundances of starch-degrading enzymes (GH13, CBM48) and host-glycan utilizers (GH92), suggesting roles in soluble nutrient extraction and host-microbe interactions. Comparative analysis of 574 metagenome-assembled genomes suggested that Methanomethylophilaceae_UBA71 and nitrate-respiring Ruminococcaceae_Firm-04 preferentially colonized in the solids, whereas propionate-producing Quinella and animal glycan-degrading Bacteroides were more prevalent in the liquids. Moreover, compared to Hu sheep, yak's rumen microbiome showed significantly enhanced utilization of plant polysaccharide capacity. Comparative analysis across 10 ruminant species further highlighted host phylogeny as a key driver of rumen microbiome variation. These findings advance our understanding of niche differentiation and functional specialization within the unique yak rumen ecosystem.

Antler blastema progenitor cells (ABPCs) are a distinct population of skeletal mesenchymal stem cells found in regenerating deer antlers, with strong stemness and renewal capacity in vitro. Stem cell-derived extracellular vesicles (EVs) are emerging as potential therapeutic candidates that can mediate donor cells’ beneficial effects. Here, we tested the effects of ABPC-derived EVs (EVsABPC) on aging in mice and rhesus macaques (Macaca mulatta). We identified a variety of unique factors in EVsABPC and showed that in vitro, EVsABPC attenuated phenotypes of senescence in bone marrow stem cells. In aged mice and macaques, EVsABPC substantially increased femoral bone mineral density. Further, intravenous EVsABPC improved physical performance, enhanced cognitive function and reduced systemic inflammation in aged mice, while reversing epigenetic age by over 3 months. In macaques, EVABPC treatment was also neuroprotective, reduced inflammation, improved locomotor function and reduced epigenetic age by over 2 years. Our findings position ABPCs as an emerging and practical source of EVs with translational value for healthy aging interventions. Inspired by the regenerative capacity of deer antlers, Hao and colleagues report that antler blastema progenitor cell-derived extracellular vesicle treatment counteracts bone loss and epigenetic aging and is neuroprotective in mice and macaques.

Crabs encompass the infra-orders Brachyura and Anomura, collectively constitute the clade Meiura within order Decapoda. Despite their considerable diversity, genomic resources for crabs remain scarce, hindering our understanding of their phylogeny and genetic mechanisms underlying such unique traits as carcinization. To address these questions, here we sequenced genomes of 10 crab species covering all currently controversial taxonomies at section level. Our whole-genome phylogenetic results support Raninoida is closer to Eubrachyura rather than Dromiacea, challenging the traditional classifications. Notably, the freshwater crab subsection Potamoida, represented by S. planum, is found to be more closely related to subsection Thoracotremata than to Heterotremata as previously suggested, indicating that crab classification based solely on morphology may be misleading. Our results also clarify that the family Gecarcinidae should be classified into Thoracotremata, contrary to previous placements in Heterotremata. Comparative genomic analyses identified lineage-specific families related to crab traits, including ionotropic glutamate receptors, neurotransmitters, and energy metabolism. Additionally, transcriptomic studies of Chinese mitten crab larval stages suggest that some lineage-specific genes such as ghrA, and TCB2, may account for the prominent carcinization in brachyurans. This study not only significantly expands the genomic repository for crabs, but also provides insights into the phylogeny and trait evolution of crabs.

Lungs are essential respiratory organs in terrestrial vertebrates, present in most bony fishes but absent in cartilaginous fishes, making them an ideal model for studying organ evolution. Here we analysed single-cell RNA sequencing data from adult and developing lungs across vertebrate species, revealing significant similarities in cell composition, developmental trajectories and gene expression patterns. Surprisingly, a large proportion of lung-related genes, coexpression patterns and many lung enhancers are present in cartilaginous fishes despite their lack of lungs, suggesting that a substantial genetic foundation for lung development existed in the last common ancestor of jawed vertebrates. In addition, the 1,040 enhancers that emerged since the last common ancestor of bony fishes probably contain lung-specific elements that led to the development of lungs. We further identified alveolar type 1 cells as a mammal-specific alveolar cell type, along with several mammal-specific genes, including ager and sfta2, that are highly expressed in lungs. Functional validation showed that deletion of sfta2 in mice leads to severe respiratory defects, highlighting its critical role in mammalian lung features. Our study provides comprehensive insights into the evolution of vertebrate lungs, demonstrating how both regulatory network modifications and the emergence of new genes have shaped lung development and specialization across species.

BACKGROUND:Electric eels evolved remarkable electric organs that enable them to instantaneously discharge hundreds of volts for predation, defense, and communication. However, the absence of a high-quality reference genome has extremely constrained the studies of electric eels in various aspects. RESULTS:Using high-depth, multiplatform sequencing data, we successfully assembled the first telomere-to-telomere high-quality reference genome of Electrophorus electricus, which has a genome size of 833.43 Mb and comprises 26 chromosomes. Multiple evaluations, including N50 statistics (30.38 Mb), BUSCO scores (97.30%), and mapping ratio of short-insert sequencing data (99.91%), demonstrate the high contiguity and completeness of the electric eel genome assembly we obtained. Genome annotation predicted 396.63 Mb repetitive sequences and 20,992 protein-coding genes. Furthermore, evolutionary analyses indicate that Gymnotiformes, which the electric eel belongs to, has a closer relationship with Characiformes than Siluriformes and diverged from Characiformes 95.00 million years ago. Pairwise sequentially Markovian coalescent analysis found a sharply decreased trend of the population size of E. electricus over the past few hundred thousand years. Furthermore, many regulatory factors related to neurotransmitters and classical signaling pathways during embryonic development were significantly expanded, potentially contributing to the generation of high-voltage electricity. CONCLUSIONS:This study not only provided the first high-quality telomere-to-telomere reference genome of E. electricus but also greatly enhanced our understanding of electric eels.

The rumen microbiome is critical for regulating milk synthesis in dairy livestock, yet the molecular mechanisms linking microbial functions to host lipid metabolism remain poorly understood. While host genetics and microbial composition have been studied, integrative analyses of the rumen-blood-mammary gland axis remain lacking. Here, we present the goat rumen microbial reference gene catalog and 5514 metagenome-assembled genomes (MAGs) from 160 multi-breed rumen samples. Integrating this resource with lactation data from 177 Saanen dairy goats, we identify Prevotella spp. as keystone taxa driving concurrent increases in milk yield and fat percentage. Functional and metabolomic profiling reveals that Prevotella bryantii B14 synthesizes nicotinate, which is converted to nicotinamide in circulation. Using in vitro and in vivo models, we demonstrate that nicotinamide activates the mTORC1 pathway in mammary epithelial cells via GPR109A, which upregulates transcription factors SREBP and PPAR-γ and the downstream lipogenic genes FASN, ACCα, and SCD1 to promote milk fat synthesis. In contrast, the relative deficiency of P. bryantii B14 and the associated reduction in nicotinamide levels in the rumen of poor lactating dairy goats may represent a significant contributor to impaired lactation performance. Additionally, the enhanced hydrogenotrophic methanogenesis activity may also adversely affect their lactation phenotype. Our study establishes a causal link between rumen microbial metabolism and mammary lipid synthesis mediated by nicotinamide-mTORC1 signaling and identifies Prevotella abundance as a biomarker for precision breeding. These findings advance the understanding of microbiome-host crosstalk in lactation and provide actionable strategies for enhancing dairy productivity through microbiota-targeted interventions.

Mammalian scent glands mediate species-specific chemical communication, yet the mechanistic basis for convergent musk production remain incompletely understood. Forest musk deer and muskrat have independently evolved specialized musk-secreting glands, representing a striking case of convergent evolution. Through an integrated multi-omics approach, this study identified cyclopentadecanone as a shared key metabolic precursor in musk from both forest musk deer and muskrat, although downstream metabolite profiles diverged between the two lineages. Single-cell RNA sequencing revealed that these specialized apocrine glands possessed unique secretory architecture and exhibited transcriptional profiles associated with periodic musk production, distinct from those in conventional apocrine glands. Convergent features were evident at the cellular level, where acinar, ductal, and basal epithelial subtypes showed parallel molecular signatures across both taxa. Notably, acinar cells in both species expressed common genes involved in fatty acid and glycerolipid metabolism (e.g., ACSBG1, HSD17B12, HACD2, and HADHA), suggesting a conserved molecular framework for musk precursor biosynthesis. Metagenomic analysis of musk samples further revealed parallel microbial community structures dominated by Corynebacterium and enriched in lipid metabolic pathways. These findings suggest multi-level convergence in musk biosynthesis, from molecular pathways to microbial communities, providing novel insights into mammalian chemical signaling and artificial musk production.

The remarkable morphological diversity and species abundance of teleost fishes offer a valuable resource for understanding vertebrate evolution. In phase I of the Fish10K project, genomes of 110 teleost species were sequenced and assembled, filling gaps in 3 previously unrepresented orders, and integrated with existing data to generate a 464 species whole-genome alignment spanning all teleost orders-the largest such resource beyond mammals and birds. Comparative analyses reveal distinctive genomic features, including progressive genome compaction with shortened intron lengths relative to non-teleost ray-finned fishes. Analysis of the transposable element (TE) landscape suggests a potential association between TE expansion in teleost genomes and different habitats, as well as the uniqueness of teleosts' DNA-dominated transposon composition among vertebrates. Genome-wide phylogenetic analyses refute the widely accepted monophyly of "Siluriphysi" hypothesis and support the hypothesis of a single origin of electroreception followed by secondary loss in Characiformes. A refined evolutionary timeline of teleosts by whole-genome alignment resource placed teleosts at ∼253 million years ago, predating the Permian-Triassic extinction, and delineates three diversification phases punctuated by mass extinctions, challenging continuous post-Cretaceous-Palaeogene acceleration models. This study establishes a large-scale genomic database and a foundational whole-genome alignment resource, advancing insights into the landscape of teleost genomic architecture and macroevolution.

BACKGROUND:Animal pigmentation serves as an excellent model for studying genetics, development, and evolution. Among yak breeds, the all-white yak breed (Bos grunniens) is the only indigenous variety with pristine white fur, in stark contrast to the black coat color of the wild yak and most domesticated yaks. RESULTS:Using whole-genome sequencing data from 387 yaks, we analyzed the population genetic structure of all-white yaks and discovered that they clustered into two distinct genetic groups. Further, by conducting a genome-wide association study (GWAS) based on whole-genome variants (SNPs and indels) between all-white and wild-type yaks, we identified a 14-bp deletion in the promoter of KIT, which decreased its expression in all-white yaks. The following knock-in experiments in mouse confirmed that the absence of the yak 14-bp motif decreases the expression of KIT. Deletion of a human orthologue of the yak 14-bp motif by using the CRISPR/Cas9 system reduces the melanin accumulation in human melanoma cells. CONCLUSIONS:Overall, our study revealed the genetic basis of all-white yaks and underscored the importance of studying livestock phenotypes to uncover conserved genetic regulators in mammals.

The antler is the only organ that can fully regenerate annually in mammals. However, the regulatory pattern and mechanism of gene expression and cell differentiation during this process remain largely unknown. Here, we obtain comprehensive assembly and gene annotation of the sika deer (Cervus nippon) genome. We construct, together with large-scale chromatin accessibility and gene expression data, gene regulatory networks involved in antler regeneration, identifying four transcription factors,MYC,KLF4,NFE2L2,andJDP2, with high regulatory activity across the whole regeneration process. Comparative studies and luciferase reporter assay suggest theMYCexpression driven by a cervid-specific regulatory element might be important for antler regenerative ability. We further develop a model called combinatorial TF Oriented Program (cTOP), which integrates single-cell data with bulk regulatory networks and findPRDM1,FOSL1,BACH1, andNFATC1as potential pivotal factors in antler stem cell activation and osteogenic differentiation. Additionally, we uncover interactions within and between cell programs and pathways during the regeneration process. These findings provide insights into the gene and cell regulatory mechanisms of antler regeneration, particularly in stem cell activation and differentiation.

The gastrointestinal tract of ruminants hosts a specialized microbial ecosystem that has evolved to efficiently digest fiber. However, modern intensive farming practices, which often involve reduced dietary fiber and increased grain supplementation, are linked to metabolic disorders in ruminants. Despite this, the understanding of the taxonomic and functional adaptations of the gastrointestinal microbiome to dietary changes remains limited, largely due to the challenges in obtaining high-resolution characterization of microbial communities. This study employed genome-resolved metagenomics to examine how a starch-rich (SR) grain-based diet compares to a fiber-rich (FR) hay-based diet in shaping the composition and function of the gastrointestinal microbiome in the rumen, jejunum, and cecum of Hu sheep. A total of 10 sheep (approximately 180 d old, with a body weight of 25.6 ± 0.41 kg) were allocated to the 2 dietary groups (SR and FR groups) for a 28-d experimental period, and metagenomic sequencing was performed on digesta samples from different gastrointestinal regions. Using a representative microbial gene catalog (RGMGC) and 10,373 metagenome-assembled genomes from previous studies,microbial composition, strain-level diversity, and carbohydrate-active enzyme profiles at higher taxonomic and functional resolution were analyzed. The results showed that the transition from the FR diet to the SR diet significantly altered the fermentation patterns and the structure and function of the sheep gastrointestinal microbiota. Community analysis revealed microbial taxa such as Prevotella spp., Alistipes spp., RC9 spp., CAG-110 spp., and Akkermansia spp. with significantly altered abundances (P < 0.05), primarily associated with the reduced fiber content in the SR diet. Moreover, the gastrointestinal microbiome exhibited strain-level changes in carbohydrate degradation, leading to reduced metabolic functions necessary for fiber processing. Comparative genomics at the single-genome level pinpointed Prevotella as a core genus with strains showing significant functional differences, notably in the capacity to degrade plant polysaccharides. Overall, these findings provide new insights into microbial regulation of gastrointestinal health and offer valuable enzyme gene resources in ruminants.

Lungs, essential for terrestrial vertebrates and present in bony fishes but absent in cartilaginous fishes, provide an ideal model for studying organ origination. Our study analyzed single-cell RNA sequencing data from mature and developing vertebrate lungs, revealing substantial similarities in cell composition, developmental trajectories and gene expression pattern across species. Notably, most lung-related genes are also present in cartilaginous fishes, indicating that gene presence alone does not guarantee lung development. We identified thousands of lung regulatory elements specific to bony fishes, with higher concentrations around genes such as tbx4 and the hoxb gene cluster. These regulatory changes might contribute to lung emergence as well as the unique co-expression patterns in lung epithelial cells, such as those related to pulmonary surfactants and cell morphology. Our research also revealed that AT1 cells are specific to mammals, and we identified a mammal-specific gene, sfta2. Knockout experiments demonstrated that sfta2 deletion causes severe respiratory defects in mice, underscoring its critical role in specialized mammalian lungs. In conclusion, our results demonstrate that the origin and evolution of lungs are driven by a complex interplay of regulatory network modifications and the emergence of new genes, underscoring the multifaceted nature of organ evolution. ### Competing Interest Statement The authors have declared no competing interest.

家牦牛在史前人类定居青藏高原的过程中起到了巨大作用,但牦牛的驯化过程仍存在诸多未解决的科学问题.本文梳理了牦牛驯化的考古学和遗传学研究进展,展望了开展牦牛驯化与人类定居青藏高原过程研究的未来方向.家牦牛最早的考古学证据来自距今3750年前的青藏高原南部拉萨河谷,但现代遗传学研究显示,牦牛的驯化可追溯至全新世中期,驯化地点最有可能位于西藏东南部的昌都地区,其种群数量增长与人类大规模长年定居青藏高原高海拔地区的历史高度相关,且黄牛的基因渗入对牦牛的驯化过程产生了深刻影响.基于现有研究进展,本文建议:（1）针对青藏高原考古遗址开展系统性的动物考古学研究;（2）应用ZooMS和古DNA技术筛选和鉴定牦牛骨骼遗存,结合古环境DNA进行遗传学研究,追溯牦牛驯化的时间和地点;（3）开展野牦牛与黄牛的杂交驯化模式研究,理解牦牛驯化及其扩散对史前人类在青藏高原生存和发展的促进作用.