Fish was an important component of (pre)historical consumption products. The study of (pre)historical fish products has been impeded by the morphological identifications in zooarchaeological research, based on poorly preserved fish bones. In this study, we applied the Bulk Bone Shotgun Metagenomic (BBSM) approach to unidentifiable bone fragments excavated from the Kongsangqiao site (dated to 652-768 CE) located on the southern slope of the central Himalayas. Among other species, the low-land South Asian fish species Rohu (Labeo rohita) was identified, marking the first discovery of a South Asian fish species on the high-altitude Tibetan Plateau. This new evidence suggests that fish may have been carried by travelers departing from South Asia to provide necessary nutritional sustenance and energy for their long-distance journeys, or was exported from the low-land South Asian plain to the Tibetan Plateau along the ancient Tubo-Nepal Road. The results also show the great potential of ancient DNA analysis on unidentifiable bone fragments in enhancing our understanding of the history of fish utilization.

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.

Wild aurochs(Bos primigenius)were once widespread across Eurasia and North Africa but became extinct around the 17th cen-tury[1].Aurochs are considered the ancestor of modern taurine(B.taurus taurus)and indicine(B.t.indicus)cattle,which were inde-pendently domesticated within regions restricted to Southwest Asia and South Asia,respectively[2,3].Extensive gene flow from local aurochs to domestic cattle has been well documented in Southwest Asia,Europe,and Africa[3,4],raising questions about the mechanisms underlying both the domestication and dispersal of early cattle.The introduction of taurine cattle from Southwest Asia,along with other domestic ruminants in ancient China～3900 years before present(a BP)and their arrival on the south-emmost Tibetan Plateau～2500 a BP,is supported by archaeologi-cal and ancient DNA(aDNA)evidence[5-7].

Extant Old World camels (genus Camelus) contributed to the economic and cultural exchanges between the East and West for thousands of years.1,2 Although many remains have been unearthed,3,4,5 we know neither whether the prevalent hybridization observed between extant Camelus species2,6,7 also occurred between extinct lineages and the ancestors of extant Camelus species nor why some populations became extinct while others survived. To investigate these questions, we generated paleogenomic and stable isotope data from an extinct two-humped camel species, Camelus knoblochi. We find that in the mitochondrial phylogeny, all C. knoblochi form a paraphyletic group that nests within the diversity of modern, wild two-humped camels (Camelus ferus). In contrast, they are clearly distinguished from both wild and domesticated (Camelus bactrianus) two-humped camels on the nuclear level. Moreover, the divergence pattern of the three camel species approximates a trifurcation, because the most common topology is only slightly more frequent than the two other possible topologies. This mito-nuclear phylogenetic discordance likely arose due to interspecific gene flow between all three species, suggesting that interspecific hybridization is not exclusive to modern camels but a recurrent phenomenon throughout the evolutionary history of the genus Camelus. These results suggest that the genomic complexity of Old World camels’ evolutionary history is underestimated when considering data from only modern species. Finally, we find that C. knoblochi populations began declining prior to the last glacial maximum and, by integrating palaeoecological evidence and stable isotope data, suggest that this was likely due to failure to adapt to a changing environment.

The domestication of livestock from their wild progenitors was essential in the process of the Neolithic Revolution.Aurochs(Bos primigenius)are considered to be the ancestors of modern cattle(B.taurus).They were once widespread across Eurasia and North Africa but became extinct approximately 400 years ago[1].As an indigenous aurochs population,East Asian aurochs had coexisted with introduced taurine cattle(B.t.taurus)for thousands of years in North China(Fig.1)[2-5].In the absence of ancient genome-wide data on East Asian aurochs,it remains unclear whether cattle-aurochs hybridization,which has been well documented in West Eurasia[6,7].also occurred in East Asia.Recently,Hou et al.

The onset of sedentism on the Tibetan Plateau is often presumed to be associated with the dispersal of agriculture or farmers from archaeological sites located in the low elevation margins of the plateau. Previous studies of the plateau assumed that all foragers were probably mobile, but few systematic excavations at forager sites have been conducted to inform us about their settlement patterns. Here we report the world's highest elevation sedentary way of living exhibited by the Mabu Co site at 4,446 metres above sea level, deep in the interior of the Tibetan Plateau 4,400-4,000 years ago. Our interdisciplinary study indicates that the site was occupied by Indigenous inhabitants of the plateau, representing the earliest known DNA evidence of foragers who predominantly harbour the southern plateau ancestry. The evidence shows that they had a sedentary lifestyle primarily supported by fishing at nearby lakes, supplemented by mammal and bird hunting, as well as small-scale exchanges of millet and rice crops. Ancient DNA, stable isotopes and other archaeological methods establish that humans were living at extremely high elevation on the Tibetan Plateau 4,400 years ago, maintaining sedentary lifestyles that combined fishing, hunting and crop exchange.

Over 5500 years ago, a sustainable and intensive millet-pig system emerged in northern China. This system, which included common millet (Panicum miliaceum), foxtail millet (Setaria italica), and domestic pig (Sus scrofa domesticus), played a crucial role in supporting the development of complex societies. Around 5000 years ago, the spread of these two millets to the Tibetan Plateau facilitated agriculturalization in the high-elevation river valley areas of the plateau (>2500 m above sea level). Previous studies tended to suggest that there were no domesticated pigs at the early settlements in high-elevation river valleys of the Tibetan Plateau, where subsistence strategies primarily relied on hunting wild animals and millet cultivation. Here, we report the earliest known domestic pigs identified through ancient DNA (aDNA) analysis of pig bones excavated from these high-elevation sites, dating back to approximately 4800-4100 years ago. Additionally, we conducted stable isotope analysis on pig and wild herbivore bone remains, as well as crop remains from the La Phob site. The delta C-13 and delta N-15 values provide clear evidence of intensive millet-pig agriculture, with pigs primarily consuming both common and foxtail millets, and their manure used for field fertilization. Our study demonstrates that by 4800 years ago, not only domestic pig and the two millets but also an intensive millet-pig system had spread to the high-elevation Tibetan Plateau, contributing to the early sedentary lifestyle of humans in these regions.

The domestic yak is a key animal species that facilitated prehistoric human exploring and settling on the Tibetan Plateau, particularly for permanent establishment in the high-altitude areas. It is hence well known as the "boat of the plateau" and "omnipotent livestock". As the most important livestock on the Tibetan Plateau, domestic yak has provided the herdsmen with meat, milk, transport power, fur, fuel and other necessary resources for production and life. However, limited by archaeological materials and disciplinary developments, the domestication process of yak is still not clear. Here we give an overview on the current status of yak domestication and how it is associated with human settlement on the Tibetan Plateau, from a multidisciplinary perspective mainly involving archaeological and genetic evidence, and also discuss into the possible directions for further studies concerning this issue. At present, the skeletal remains of yak unearthed from archaeological sites on the Tibetan Plateau are very limited. There are only 10 archaeological sites on the Tibetan Plateau where yak remains have been unearthed, among which the domestic yak remains unearthed from the Qugong site are the earliest and the most abundant. Available archaeological studies suggest that yak domestication occurred no earlier than 3750 years ago, and the domestication center might have been located in the Lhasa River valley, southern Tibetan Plateau. However, based on genetic analysis of mitochondrial and nuclear genomes of modern yak, its domestication can be traced back to the middle Holocene, earlier than the time indicated by archaeological evidence, and the inferred domestication center is in Changdu, southeastern Tibetan Plateau. The population size of yak is closely related to the human expansion and settlement on the Tibetan Plateau. Agriculture facilitated permanent human occupation of the high-altitude Tibetan Plateau about 3600 years ago, and a six-fold increase in population size of the domestic yak occurred during the same period. The introgression of cattle genes has a profound impact on the domestication process of yak and is an important source for the genetic diversity of yak. At the same time, the introgression of yak genes related to hypoxic adaptation promoted the adaptation of cattle to extreme environment of the Tibetan Plateau. Although ancient DNA is an ideal link between archaeology and genetics, and has been widely used in many species as a powerful means to study animal domestication, no ancient DNA study on yak has been published. Overall, it is still debatable about the timing, region, and process of yak domestication on the Tibetan Plateau, and there are obvious differences in the results of archaeological and genetic studies, mainly due to the lack of systematic zooarchaeological and ancient DNA study of high-altitude archaeological sites on the Tibetan Plateau. The formation and development of nomadic economy, the permanent settlement and the evolution of human livelihood patterns on the Tibetan Plateau have not been well answered. For future studies, the early hybridization between yak and cattle after cattle were introduced to the Tibetan Plateau will likely enable us to better understand the domestication process of yak and the promoting effect of yak domestication on the survival and establishment of prehistoric human on the Tibetan Plateau. More archaeological investigations, excavations, and zooarchaeological studies involving ZooMS and ancient DNA (both on fossil remains and sediments) studies on the Tibetan Plateau are required before we come to a stage for thoroughly addressing the detailed domestication process of yak.

The transition of human societies from high mobility to sedentary lifestyles had a profound impact on subsistence, technology, and the origin of civilization. Sedentism was influenced by various factors such as climate change, population growth, resource pressure, and technological innovation. The Tibetan Plateau, due to its alpine and hypoxic conditions, is an ideal region to study human adaptation to extreme environments. However, the prehistoric process of sedentism on the Tibetan Plateau is unclear and the chronological sequence and driving mechanism of sedentism on the Tibetan Plateau are still controversial. Previous studies have focused on the diffusion of agriculture from low to high elevation areas, with little attention given to the role of animal resources in sedentism. Seasonality analysis using animal remains is crucial in determining whether a site was occupied year-round. To establish the seasonal calendar of animal resource utilization, it is recommended to create a database of skeletal morphology, whole genome, and proteome of contemporary Tibetan Plateau fauna to aid in the identification of animal remains from archaeological sites. Thus, intricate web of human-animal-environment relationship and the role of animal resources in human sedentism on the Tibetan Plateau can then be evaluated.

Tigers ( Panthera tigris ) are flagship big cats and attract extensive public attention due to their charismatic features and endangered status. Despite this, little is known about their prehistoric lineages and detailed evolutionary histories. Through palaeogenomic analyses, we identified a Pleistocene tiger from northeastern China, dated to beyond the limits of radiocarbon dating (greater than 43 500 years ago). We used a simulated dataset and different reads processing pipelines to test the validity of our results and confirmed that, in both mitochondrial and nuclear phylogenies, this ancient individual belongs to a previously unknown lineage that diverged prior to modern tiger diversification. Based on the mitochondrial genome, the divergence time of this ancient lineage was estimated to be approximately 268 ka (95% CI: 187–353 ka), doubling the known age of tigers' maternal ancestor to around 125 ka (95% CI: 88–168 ka). Furthermore, by combining our findings with putative mechanisms underlying the discordant mito-nuclear phylogenetic placement for the South China tigers, we proposed a more complex scenario of tiger evolution that would otherwise be missed using data from modern tigers only. Our study provides the first glimpses of the genetic antiquity of tigers and demonstrates the utility of aDNA-based investigation for further understanding tiger evolution.

The extinct Camelus knoblochi is known as the largest camel in genus Camelus, but its relationship to modern Camelus species remains unclear. In this study, we reported the first mitochondrial and nuclear analyses of seven Late Pleistocene C. knoblochi samples from Northeastern China. We found that they are inseparable to wild Bactrian camel on the matrilineal side, but belong to a distinct cluster on the biparental nuclear side. Further admixture proportion analyses suggested hybrid ancestry between both the ancestors of the modern wild and domesticated Bactrian camels, with ~65% contribution from the former and ~35% from the later. By calculating the coalescence time for three Camelus species above, we estimated the hybridization event occurred between approximately 0.8 and 0.33 Ma. We also used Bayesian skyline to reconstruct the maternal demographic trajectories for different Camelus to better compare their evolutionary histories. Our results provide molecular insights into C. knoblochi and fill in a vital piece in understanding the genus Camelus.

Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta. Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62–2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.

我国鹿类资源丰富,鹿亚科(Cervinae)动物有7个种在中国有分布.鹿亚科的种内系统发育研究很多,但是各物种之间进化关系仍有待进一步研究,其中从分子水平对古代材料的报道更为鲜见.对采集自黑龙江的两个距今分别为3800和5100 a的古代鹿亚科动物亚化石材料开展了古DNA研究.通过古DNA提取、古DNA双链文库构建、高通量测序及数据分析,得到了两条长度分别为16475 bp (GenBank收录号:MT784751,序列完整度:99.83％)和16167 bp (GenBank收录号:MT784752,序列完整度:97.96％)的线粒体基因组序列,对两个样品进行了分子鉴定.结合GenBank中现生鹿亚科动物的线粒体同源序列,构建了系统发育树.结果 表明:1)二代测序DNA片段末端碱基特性分析说明序列来自古代样品;2)两个样品代表的个体在系统发育树中均与马鹿聚类,在物种归属中被分子鉴定为马鹿(Cervuselaphus);3)黑龙江的两个古代样品与现生马鹿阿拉善亚种(C.elaphus alxaicus)亲缘关系最近,而与现生马鹿东北亚种(C.elaphus xanthopygus)亲缘关系较远.结合样品年代信息,说明两例样品代表的黑龙江古代马鹿种群,不是现生马鹿东北亚种的直系母系祖先.

BACKGROUND:Old World porcupines (Family: Hystricidae) are the third-largest rodents and inhabit southern Europe, Asia, and most regions of Africa. They are a typical indicator of warm climate and their distribution is restricted to tropical and subtropical zones. In China, porcupines are widely distributed in southern areas of the Yangtze River. However, fossil remains have been identified in a few sites in northern China, among which Tianyuan Cave-near Zhoukoudian site-represents the latest known porcupine fossil record. So far, studies have focused mainly on porcupines' husbandry and domestication but little is known about their intrafamilial phylogenetic relationships and evolutionary history.RESULTS:In this study, we sequence partial mitochondrial 12S rRNA and cyt b genes for seven Late Pleistocene porcupine individuals from Northern, Southern and Central China. Phylogenetic analyses show that the Tianyuan Cave porcupines, which had been morphologically identified as Hystrix subcristata, have a closer relationship to Hystrix brachyura.CONCLUSION:Together with morphological adaptation characteristics, associated fauna, and climate change evidence, the molecular results reveal that a Late Quaternary extirpation has occurred during the evolutionary history of porcupines.

选用低黏度的双酚A型环氧树脂E-44、E-51与酚醛改性胺室温固化剂,开发了一种室温固化无溶剂岩芯胶粘剂.探究主体胶粘剂配方,并研究各助剂及用量对主体胶粘剂性能的影响.研究结果表明:在m(E-44)∶m(E-51)∶m(酚醛改性胺)=70∶30∶100的配方下,主体胶粘剂配方的综合性能较好;m(E-44)∶m(E-51)∶m(固化剂)∶m(增韧剂DOP)∶m(偶联剂KH-550)∶m(硅微粉)∶m(碳酸钙)=70∶30∶100∶15∶3∶4∶12时,该胶粘剂体系剪切强度最大,达到了16.10 MPa.选取该最大剪切强度胶粘固化体系进行其他测试,得到胶粘剂体系的接触角达到了79.4°;热失重结果显示,其在200℃之后才开始分解,耐热性较好.另外,该配方的凝胶时间及流平性均可满足实际操作要求,固化物不会造成岩芯污染,为该胶粘剂在岩芯上的应用提供科学依据.

There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95% CI: 0.86-1.24 Ma), and the two Old World lineages (I & II) split at 0.88 Ma (95% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species. (C) 2020 Elsevier Ltd. All rights reserved.

Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis a slow increase in female effective population size of C. bactrianus from 5000 years ago, which to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.