DNA was extracted from teeth or phalanx. Firstly, we conducted 2 hours UVirradiation on the samples, and removed a layer of surface using a sterile dentistry trill, then again irradiated with 1 hour UV-light on the samples. We drilled out ~80 mg of bone powder for every sample with the sterile dentistry trill, and only do 2 samples at one time (include following procedures until performing sequencing; samples from different archaeological sites were never handled together) to avoid potential individual cross-contamination. Using the 80 mg bone powder, we performed DNA extraction following the silica suspension protocol from an early report (Rohland and Hofreiter 2007), which was modified afterwards (Allentoft, et al. 2015) for customizing recovering of more shorter DNA fragments, that finally resulting a total of 100 μl aliquots for each sample. In brief, the bone powder was digested over night with proteinase K in 0.5M EDTA plus 10% N-Laurylsarcosyl suspension, then the released DNA was absorbed in solution which includes PB buffer, 5M sodium acetate, 5M sodium chloride and SiO2 suspension, and followed by three times of purification using 80% ethyl alcohol. Finally, after airing, the DNA was eluted with 100 μl EB buffer. Next, to perform preliminary aDNA preservation situation screening, using 20μl DNA aliquots of each sample, we built the double strand library (DSL) with no Uracil- DNA-Glycosylase (UDG) treatment under a single indexing with commercial kit (cat no: E7370) from New England Biolabs (Ipswich, MA) following the manufacturer’s guidelines, as previously reported (Meyer and Kircher 2010) that includes end prep, adaptor ligation, purification, PCR amplification and size selection steps. PCRs were conducted in a final volume of 50 μl using AmpliTaq Gold 360 DNA Polymerase (AmpliTaq Gold, Life Technologies Applied Biosystems) which is able to well amplify across uracils, preserve the DNA damage pattern that induced by deamination, which indicating of authentic aDNA (Krause, et al. 2010). We performed all the sequencing (also the following captured library sequencing) on the Illumina HiSeq X Ten (PE-150) platform ( https://www.illumina.com.cn/systems/sequencing-platforms/hiseq-x.html ). The calculated appraise indexes of aDNA quality and preservation are shown in Table S1. Lastly, we rebuilt the DSLs with 3 hours UDG treatment using the remaining DNA extraction aliquots, which could largely remove uracil residues from DNA fragmental end to leave abasic sites, and cuts the DNA at the 5´ and 3´ sides of the abasic sites with enzyme endonuclease VIII (Endo VIII). For these libraries, we performed the mtDNA capture using myBaits® Mito-Target Capture Kits as previous report (Enk, et al. 2014). Briefly, we used the biotinylated RNA “baits” that are transcribed from the human genomic DNA to perform the capture in solution overnight at 65°C, then mixed in streptavidin-coated magnetic beads and sequestered the targets with a magnetic stand. The PCRs for both pre-capture and post-capture are performed using KAPA HiFi Hot start Polymerase (KAPA BIOSYSTEMS).
QI Xuebin
Hanging coffin burial is a kind of burial custom in which the coffin is placed on the cliff, cave and crevice. Hanging coffin burials are widely distributed in the Yangtze River Valley and the south of China, as well as in Southeast Asia and even the Pacific Islands. With the natural weathering and man-made destruction, there are fewer and fewer such relics. As a kind of peculiar and ancient archaeological cultural remains and funeral custom, hanging coffin culture has been widely concerned by archaeologists. Dating method: the wood samples on the hanging coffin were sent to beta analytical testing laboratory in Miami, USA for C14 determination. Methods: 4 in house NEC accelerator mass spectrometers (AMS) and 4 thermo IRMSS under strict chain of custom and quality control using ISO / IEC 17025:2005 testing accreditation pjla accreditation protocols Results: the dating results show that the earliest hanging coffin burial site is located in Wuyishan area of Fujian Province, 3600 years ago, which is equivalent to the Shang and Zhou dynasties in China. Wuyishan area in Fujian Province is considered to be the birthplace of the hanging coffin burial custom, which later spread to other areas in South China, Southeast Asia and the Pacific Islands. Located in the Jinsha River Valley of South Sichuan and Northeast Yunnan, the hanging coffin burial is the latest cultural remains of hanging coffin burial in mainland China (late Ming Dynasty), and also the West pole of the distribution of hanging coffin burial sites in China. There is a hanging coffin group in the mountainous area of Northwest Thailand, 2100-1200 years ago.
QI Xuebin
The complete mitochondrial DNA sequences of 41 human remains from 13 hanging coffin sites 2500-660 years ago in Weixin and Yanjin, Zhaotong, Yunnan, Huacun, Baise, Guangxi and bangmapa, Thailand were analyzed by using the ancient DNA analysis technique. They found that the maternal genetic diversity of the hanging coffin people in Northwest Yunnan was very high, while the genetic diversity of the hanging coffin people in northern Thailand was relatively low. This result is consistent with the view that the hanging coffin burial custom originated in southern China and spread southward to Southeast Asia. In addition, a small number of matrilineal lineages were shared among the hanging coffin people in different regions of Asia, indicating that there is a very close relationship between different hanging coffin people. Combining the results of genetic analysis with the evidences of archaeology, physical anthropology, folklore and history, they speculated that the hanging coffin burial custom originated in the Baiyue ethnic group in the southeast coastal areas of China (such as Wuyishan area) about 3600 years ago, and they are the ancestors of the Dai ethnic group with many ethnic groups. After that, the custom of hanging coffin was widely spread in South China by means of people migration and flow. However, about 2000 years ago (the earliest time of hanging coffin burial in Thailand), a very small number of inheritors of hanging coffin burial spread the custom to some aboriginal groups in Southeast Asia, such as northern Thailand, by means of cultural diffusion. This study only makes a preliminary discussion from the perspective of maternal genetic lineage. For the hanging coffin culture which has spread for more than 3000 years in South China, Southeast Asia and the vast area of the Pacific Islands, the origin and development of its culture and the history of its inheritors may be more complex. In the future, more representative samples of human remains buried in a hanging coffin will be used, from the perspective of genomic DNA and paternal Y-DNA, combined with interdisciplinary research, which will provide more systematic evidence support for a more comprehensive display of the historical and cultural features of the hanging coffin burial custom.
QI Xuebin
1) Data content: this data is the chromatin open group data of umbilical cord endothelial cells of Plateau Tibetan and plain Han people generated during the implementation of the project, including 5 cases of Plateau Tibetan umbilical cord endothelial cell chromatin open group data and 5 cases of plain Han umbilical cord endothelial cell chromatin open group data. The amount of chromatin open group data of each cell is > 15g sequencing depth, which can be used to study the high-risk factors The chromatin opening pattern and gene expression regulation pattern of the original Tibetan population and the plain Han population in high altitude hypoxia environment. 2) Data sources and processing methods: Based on our own data, we used the 150 BP pair end sequencing method of Illumina x-ten. 3) Data quality: > 15g data volume, q30 > 90%. 4) Data application achievements and prospects: the data are used to verify the open mode of cell chromatin and gene expression change mode of high altitude hypoxia adaptation genes under hypoxia environment.
QI Xuebin
The whole mitochondrial genomes of 68 Tibetan samples were sequenced by high-throughput second-generation sequencing. The average depth of sequencing was 1000 ×, ensuring that the mitochondrial genome of each sample was completely covered (100%). Based on the phylogenetic analysis, we control the quality of these data to ensure that there is no sample pollution and other quality problems. According to the phylogenetic tree, each individual was allocated into haplogroups. The results showed that in Lhasa Tibetan population, M9a1c1b1a was the highest (19.12%), followed by G2 (13.23%), M13a (11.76%), C4a (7.35%), D4 (7.35%), A11a1a (5.88%), M9a1b (5.88%), and F1c, F1g, B4, F1d, M62b, F1a, F1b, G1, M11, M8a, U7a, Z3a. These haplogroups have different originations, including Paleolithic components (M13a, M62b, M9a1b, etc.), northern China millet farmers’ components (M9a1c1b1a and A11a1a), components distributed mainly in southern East Asia (F1a, etc.), northern East Asian haplogroups (C4a, D4, etc.). It is worth noting that the maternal component of Lhasa Tibetans is mainly composed of millet agricultural population in northern China, indicating the important impact of genetic input of millet agricultural population in northern China on the genetic structure of the population in this area. Taken together, the maternal genetic structure of Lhasa Tibetan population exhibits time stratification, which may represent the genetic imprint of different population entering the region in different periods.
KONG Qingpeng
It is not clear how the Tibetan people adapt to the extreme environment on the plateau. As an important phenotype, metabolism plays an important role in maintaining the normal biological function of individuals. Previous studies have shown that some small metabolic molecules can adapt to the extreme environment by regulating energy metabolism, oxidative stress and other biological processes. In view of this, the project is expected to find the relationship between human metabolism and extreme environmental adaptation by studying the unique metabolic characteristics of Tibetan people compared with plain people, and then study the plateau adaptation mechanism of Tibetan people from the perspective of metabolism. This data is the metabolomic data generated during the implementation of the project, and the current data includes the metabolomic data of 30 people in the plain. The combined analysis of these data and the subsequent metabolomic data can be used to study the metabolic characteristics of Tibetan people in the plateau hypoxia environment. This data set is the update and continuation of metabolomic data v1.0 of modern Chinese population.
LI Gonghua
The western and northeastern Yunnan is located in the southeast of the Qinghai Tibet Plateau. Previous genetic studies have shown that there are substantial genetic imprints of late Paleolithic human in this region, and these ancient genetic imprints are likely to spread further to the Qinghai Tibet Plateau. Therefore, the genetic study of the population in this area is helpful to clarify the migration history of early human settlement in the Qinghai Tibet Plateau. In this study, we studied the genetics of Dai people in different areas of Yunnan Province. The mitochondrial DNA hypervariable regions of 264 Dai individuals were sequenced by Sanger sequencing. Based on phylogenetic analysis, we control the quality of these data to ensure that there is no sample contamination and other quality problems. According to the revised Cambridge Reference Sequence, the variants were recorded. According to the phylogenetic tree of mitochondrial DNA in the world population (PhyloTree.org), each sample was allocated into certain haplogrop. Based on the published mtDNA data of Dai people in other areas, the maternal genetic structure and formation mechanism of Dai population were systematically studied. The results showed that there was a close genetic relationship among the Dai populations in different regions, and the haplogroups (F1a, M7B and B5a) shared by these populations could be traced back to southern China, suggesting that the Dai population might have originated in southern China and migrated southward to the mainland and Southeast Asia in the Iron or Bronze age. The genetic differentiation of the Dai population in different regions is consistent with the phenomenon that their language and culture have some differences, which indicates that the Dai people and the surrounding populations in the southward migration.
KONG Qingpeng
To investigate the paternal genetic structure of Tibetans from Shigatse, 434 male samples were collected from Shigatse, Tibet. Firstly, SNP genotyping was performed to allocate samples into haplogroups. To further evaluate the genetic diversity of the major Y-chromosomal haplogroup in Tibetan populations from Lhasa, eight commonly used Y-chromosomal STR (short tandem repeat) loci (DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393) were genotyped using fluorescence-labeled primers with an ABI 3130XL Genetic Analyzer (Applied Biosystems, USA). The results indicated that haplogroup O-M175 displayed highest frequency in Shigatse Tibetans (47.00%, the majority of its sublineages were O2-M122), followed by haplogroups D-M174 (40.78%, with most of the samples belonging to D-P47 (20.97%) and D-N1(16.82%)). Another relatively rare lineages in Shigatse Tibetans were C-M217 (1.84%), R1a1- M17 (1.61%), N1-LLY22G (5.76%), Q-M242 (0.69%). In combination with the data from Lhasa that released in 2019, our Y chromosome data of Tibetans from different locations on the Tibetan Plateau will be very helpful to understanding the paternal genetic structure of Tibetans. Moreover, the genetic history of Tibetans can also be dissected by phylogeographic and coalescent analyses.
KONG Qingpeng, QI Xuebin
We obtained the whole genome variation data of 30 Tibetan individuals. The SNP typing of 30 samples was carried out by DNA array method, and about 700000 loci (including nuclear genome, mitochondrial DNA and Y chromosome) of each sample were obtained. First, after extracting genomic DNA, DNA amplification, enzymatic fragmentation, precipitation and re suspension were carried out. After the sample was incubated overnight and hybridized with beadchip, the DNA was annealed to obtain a site-specific 50 mer probe, covalently coupled with an Infinium bead type. Then Infinium XT was used to extend the enzyme base to give the allele specificity, and then fluorescent staining was carried out. The fluorescence intensity of the beads was detected by iSCAN system, and the Illumina software automatically performed the analysis and genotype recognition. Finally, the SNP typing results of each sample were obtained. Based on the above data, relevant biological information analysis (mainly including chip site quality control analysis, Y chromosome and mitochondrial DNA haplotype analysis) was carried out. This data is helpful to analyze the genetic structure of Tibetan population from the perspective of nuclear genome, Y chromosome and mitochondrial DNA. By comparing with the data of people around the plateau, we can trace the migration and settlement history of the plateau population comprehensively.
KONG Qingpeng
This data is the distribution data of the prehistoric era sites on the Qinghai-Tibet Plateau and surrounding areas, which is derived from the Supplementary Maps of the paper: Chen, F.H., Dong, G.H., Zhang, D.J., Liu, X.Y., Jia, X., An, C.B., Ma, M.M., Xie, Y.W., Barton, L., Ren, X.Y., Zhao, Z.J., & Wu, X.H. (2015). Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 BP. SCIENCE, 347, 248-250. The Qinghai-Tibet Plateau, with an average altitude of more than 4000m, is the highestand largest plateau all around the world, and also is one of the most unsuitable areas for human life with long-term on the earth. The remains at the archaeological site are direct evidences left behind the ancient human activities. The original data of this data is digitized from the results of the Qinghai-Tibet Plateau high-textual census and archaeological survey (Qinghai Volume and Tibet Volume of the Chinese Cultural Relics Atlas). The map was digitized mainly based on the distribution maps of the sites, and the latitude and longitude coordinates and altitude were obtained. a total of 6,950 sites, most of which are distributed in the northern part of the plateau. The age range of the site is between 7000BP and 2300BP. This data set is of reference value for the research on the process and power of human diffusion to the Tibetan Plateau in the prehistoric era and other studies related to human activities in the Tibetan Plateau and the prehistoric era.
DONG Guanghui, LIU Fengwen
This data is derived from the Supplementary Tables of the paper: Chen, F. H., Welker, F., Shen, C. C., Bailey, S. E., Bergmann, I., Davis, S., Xia, H., Wang, H., Fischer, R., Freidline, S. E., Yu, T. L., Skinner, M. M., Stelzer, S., Dong, G. R., Fu, Q. M., Dong, G. H., Wang, J., Zhang, D. J., & Hublin, J. J. (2019). A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau. Nature, 569, 409-412. This research is another breakthrough made by academician Fahu Chen and his team over the years research of human activities and environmental adaptation on the Tibetan Plateau. The research team analyzed the newly discovered hominid mandible fossils in Xiahe County, Gansu Province, China, and identified it belongs to Denisovan of the Tibetan Plateau, which suggested to call Xiahe Denisovan. The team conducted a multidisciplinary analysis of the fossil, including chronology, physique morphology, molecular archaeology, living environment and human adaptation. It is the first Denisovan fossil found outside the Denisova Cave in the Altai Mountains and the earliest evidence of human activity on the Tibetan Plateau (160 kyr BP). This study provides key evidence for further study of Denisovans' physical characteristics and distribution in East Asia, it also provides evidence of a deep evolutionary history of these archaic hominins within the challenging environment of the Tibetan Plateau. This data contains 6 tables, table name and contents are as follows: t1: Distances in mm between meshes generated from CT versus photoscans (PS). t2: Measurements of the Xiahe mandible after reconstruction. t3: Comparative Dental metrics. t4: Comparative crown morphology. t5: Uniprot accession numbers for protein sequences of extant primates used in the phylogenetic analyses. t6: Specimen names and numbers.
CHEN Fahu
This data set includes a monthly composite of 30 m × 30 m surface vegetation coverage products in the Qilian Mountain Area in 2019. In this paper, the maximum value composition (MVC) method is used to synthesize monthly NDVI products and calculate FVC by using the reflectance data of Landsat 8 and sentinel 2 red and near infrared channels. The data is monthly synthesized by Google Earth engine cloud platform, and the index is calculated by the model. The missing pixels are interpolated with good quality, which can be used in environmental change monitoring and other fields.
QI Xuebin
The data includes the runoff components of the main stream and four tributaries in the source area of the Yellow River. In 2014-2016, spring, summer and winter, based on the measurement of radon and tritium isotopic contents of river water samples from several permafrost regions in the source area of the Yellow River, and according to the mass conservation model and isotope balance model of river water flow, the runoff component analysis of river flow was carried out, and the proportion of groundwater supply and underground ice melt water in river runoff was preliminarily divided. The quality of the data calculated by the model is good, and the relative error is less than 20%. The data can provide help for the parameter calibration of future hydrological model and the simulation of hydrological runoff process.
QI Xuebin
1) Data content: this data is the placenta umbilical cord endothelial cells (HUVEC) transcriptome data of high altitude Tibetan and lowland Han population generated during the implementation of the project, including the RNA-seq data of 3 high altitude Tibetan HUVEC and 3 lowland Han placenta HUVEC. Each RNA-seq data is 6G sequencing depth, which can be used to study the effect of high altitude Tibetan population and lowland Han population for gene expression patterns at hypoxic environment. 2) Data source and processing method: own data, the pair end 150bp sequencing method using Illumina x-ten sequencing platform. 3) Data quality: 6G data depth, q30 > 90%. 4) Results and prospects of data application: the data will be used to validate the gene expression pattern of high altitude hypoxia adaptation gene to hypoxia environment at the cell level.
QI Xuebin
The average altitude of the Tibetan Plateau is more than 4000 meters. The harsh environment such as high cold and low oxygen poses a huge challenge to human survival. However, since the late Paleolithic period, Tibetan people in the plateau have reached the Plateau, and in the Neolithic period, people began to permanently settled on the high-altitude areas on a large scale. The history of population migration in this process has become the focus of different fields. In order to analyze the genetic structure of Tibetan population from the perspective of the whole genome and trace back the history of human settlement on the plateau, we obtained the whole genome variation data of 20 Tibetan individuals. The SNP typing of 20 samples was carried out by DNA array method, and about 700000 loci (including nuclear genome, mitochondrial DNA and Y chromosome) of each sample were obtained. Based on the above data, relevant biological information analysis (mainly including chip site quality control analysis, Y chromosome and mitochondrial DNA haplotype analysis) was carried out. This data is helpful to analyze the genetic structure of Tibetan population from the perspective of nuclear genome, Y chromosome and mitochondrial DNA. By comparing with the data of people around the plateau, we can trace the migration and settlement history of the plateau population comprehensively.
KONG Qingpeng
How the Tibetan people adapt to the extreme environment of the plateau is not clear at present. Metabolism, as an important phenotype, plays an important role in maintaining the normal biological function of individuals. Previous studies have shown that some small metabolic molecules can adapt to the extreme environment by regulating the biological processes such as energy metabolism and oxidative stress. In view of this, this project is to find the relationship between the human metabolism and the extreme environmental adaptation by studying the unique metabolic characteristics of Tibetan population compared with the plain population, and then study the plateau adaptation mechanism of Tibetan population from the perspective of metabolism. This data is the metabolome data generated during the implementation of this project. The current data includes the metabolome data of 30 people in the plain. The combined analysis of this data and the subsequent metabolome data can be used to study the metabolism characteristics of the Tibetan people at high altitude in the low oxygen environment.
LI Gonghua
