bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

1 The genomic formation of Tanka people, an isolated “Gypsies in water” in the coastal region of 2 Southeast China 3 4 Guanglin He1,2,#,*, Yunhe Zhang3,#, Lan-Hai Wei1,8, #,*, Mengge Wang4,5, Xiaomin Yang1, Jianxin Guo1, , 5 Rong Hu1, Chuan-Chao Wang1,6,7,*, Xian-Qing Zhang1,* 6 7 1Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data 8 Science in Health and Medicine, State Key Laboratory of Cellular Stress Biology, School of Life 9 Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, 10 China 11 2School of Humanities, Nanyang Technological University, Nanyang Avenue, 639798, Singapore 12 3School of Public Administration, Zhejiang Gongshang University, Hangzhou, 310018, China 13 4Guangzhou Forensic Science Institute, Guangzhou, 510080, China 14 5Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 15 510080, China 16 6School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, 310000, China 17 7Institute of Asian Civilizations, Zhejiang University, Hangzhou, 310000, China 18 8B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, 200438, 19 China 20 21 #These authors contributed equally to this work. 22 *Correspondence: [email protected] (GLH); [email protected] (LHW); 23 [email protected] (CCW); and [email protected] (XQZ) 24 25 ABSTRACT 26 Objectives: Three different hypotheses proposed via the controversial evidence from cultural, 27 anthropological and uniparental genetic analysis respectively stated that Tanka people probably 28 originated from Han Chinese, ancient Baiyue tribe, or the admixture of them. Therefore, the 29 genetic origin and admixture history of the Tanka people, an isolated “Gypsies in water” in the 30 coastal region of Southeast China, are needed to be genetically clarified. 31 Materials and methods: To elucidate the genetic origin of the Southeast Tanka people and explore 32 their genetic relationship with surrounding indigenous Tai-Kadai and Austronesian people and 33 Neolithic-to-historic ancients from the Yellow River Basin (YRB) and Fujian, we conducted a large- 34 scale population genomic study among 1498 modern and ancient Eurasians, in which 73 Tanka 35 and 4 Han people were first reported here. Both allele-shared and haplotype-based statistical 36 methods were used here, including PCA, ADMIXTURE, f-statistics, ALDER, qpGraph-/TreeMix 37 and qpAdm/qpWave, ChromoPainter and FineSTRUCTURE 38 Results: We found a specific genetic cline in PCA plots and detected the Tanka-specific 39 homogeneous ancestry in model-based ADMIXTURE results, suggesting differentiated 40 demographic history between Tanka and surrounding Hans. Formal tests based on sharing allele 41 patterns showed a close relationship between Tanka people and Han Chinese, but the Tanka 42 population harbored more southern East Asian ancestry related to Austronesian and Tai-Kadai 43 people compared with southern Hans. Besides, the reconstructed differentiated demographic 44 history revealed that southern Xinshizhou Tanka harbored more ancestry related to the Tai-Kadai 45 or coastal ancient Neolithic to Bronze Age East Asians compared with northern Shacheng Tanka. 46 The qpGraph-/TreeMix-based phylogenetic framework, qpAdm/qpWave-based admixture modeling 47 and FineSTRUCTURE-based dendrogram among ancient northern and southern East Asians 48 further demonstrated that the primary ancestry of modern Tanka derived from ancient millet 49 farmers in the YRB with additional admixture from multiple southern East Asian sources. 50 Discussion: Sharing ancestry estimated from the f-statistics and sharing haplotypic landscape 51 inferred from the ChromoPainter and FineSTRUCTURE showed that Southeast Tanka people not 52 only had a close genetic relationship with both Northern Hans and YRB millet farmers but also 53 possessed more southern East Asian ancestry related to Austronesian, Tai-Kadai and Hmong-Mien 54 people. Our genomic data and fitted admixture models supported modern Tanka originated from 55 ancient North China and obtained additional gene flow from ancient southern East Asians in the 56 processes of southward migrations. 57 58 Keywords, Tanka people, genetic history, admixture events, population genomics, molecular 59 anthropology bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

60 INTRODUCTION 61 The overwhelming southward population dispersal from the central plain around the Yellow River Basin 62 (YRB) of North-East Asia in the past two thousand years resulted in the formation of Han populations 63 in southern China (Guang‐Lin He et al., 2021; G. He et al., 2020; J. Sun et al., 2021). Meanwhile, it is 64 also generally accepted that this process was accompanied by a large scale of integration with the 65 southern aborigines (Guang‐Lin He et al., 2021; G. He et al., 2020; J. Sun et al., 2021). There are many 66 different local clans of Han populations in different geographic regions of southern China. Some of these 67 people have very special cultural traditions so that scholars speculate that they may be descendants of 68 remote sub-branches of the ancestor of Han populations or have a high proportion of genetic elements 69 from the southern indigenous people (S. Liu et al., 2018; J. Sun et al., 2021; Wen et al., 2004), such 70 minority groups including Chuanqing, Gejia, Dongjia, Xijia, etc. (Lu et al., 2020; Jin Sun et al., 2020). 71 The Tanka people, also called the “Gypsies in water” in the coastal region of southeastern China, were 72 also considered as a special clan of Han populations. Further population genetic study focused on the 73 origin of these minority populations will assist in exploring the detailed genetic history to better 74 understand the population demographic history in South China, as well as better reconstructing the 75 formation process of Han populations in the past two thousand years. 76 77 There are long debates about the ancient origin of Tanka people, mainly focused on three hypotheses of 78 the northern Han Chinese origin, southern indigenous Baiyue origin, and the mixture of them (Luo et al., 79 2020). Modern Tanka people are widely scattered in the coastal region of Southeast China, ranging from 80 Zhejiang province to Guangxi province. Historically documented evidence showed that Tanka people 81 were the decedents of the ancient Baiyue tribe and subsequently continuously stimulated by the 82 southward migrated Han Chinese populations from the central plain, which was further confirmed via 83 physical anthropological features. Supporting evidence of the ancient Baiyue origin of the Tanka people 84 was also provided in the perspective of uniparental genetic legacy (Luo et al., 2020). Luo et al. genotyped 85 both maternally and paternally informative SNPs in Fujian Tanka people and explored their patrilineal 86 and matrilineal genetic history (Luo et al., 2020). This uniparental genetic legacy investigation found 87 two predominant Y-chromosome lineages of O1a1a-P203 and O1b1a1a-M95 and three maternal 88 founding lineages of F2a, M7c1 and F1a1. Patterns of genetic affinity via clustering technique of 89 principal component analysis revealed the contentious relationships: a close relationship with Tai-Kadai 90 speakers based on paternal genetic variations, but an affinity with Han Chinese based on the maternal 91 genetic variations. Other analyses of divergence times based on Tanka-specific haplotypes suggested 92 their ancient indigenous origin approximately 1000 years ago, which is not consistent with its admixture 93 model with two sources related to the southward Han and southern indigenous people. However, the 94 genetic legacy from the autosomal perspectives and their ancient relationship with modern and ancient 95 East Asians keeps in its infancy. 96 97 Advances in ancient DNA studies in East Asia also provided new insights into the formation of modern 98 and ancient East Asian populations. Wang et al. recently reconstructed one deep evolutionary framework 99 and found that the deep paleolithic coastal migration route dispersed one deeply diverged lineages related 100 to South Asian Onge Hunter-Gatherer people, which also widely distributed in modern and ancient 101 Tibetans, Jomon and southeastern coastal Hanben people with a variable proportion (C. C. Wang et al., 102 2021). Further three Holocene expansions from Amur River Basin, YRB, and Yangtze River Basin 103 dispersed East Asia’s language, farming and people, which reshaped the patterns of the modern mosaic 104 genetic landscape of East Asia (Ning et al., 2020; C. C. Wang et al., 2021; Yang et al., 2020). Ancient 105 DNA research further demonstrated significant southward migration of millet farmers from YRB to 106 South China, as well as southward migration of southern Chinese agriculturists to the Island and 107 Mainland of Southeast Asia, which further complicated the following molecular patterns of the 108 population genomic diversity in ancient southern Chinese indigenous people and Southeast Asians 109 (Larena et al., 2021; Lipson et al., 2018; McColl et al., 2018; Yang et al., 2020). These genetic legacy 110 investigations provided better proxies or surrogates of the ancient sources for modeling the formation of 111 modern East Asians. 112 113 Thus, we obtained the genome-wide SNPs data from the southeastern region of China and merged them 114 with all available modern and ancient East Asians (Guanglin He et al., 2020; Lipson et al., 2018; D. Liu 115 et al., 2020; McColl et al., 2018; Ning et al., 2020; C. C. Wang et al., 2021; Yang et al., 2020) to perform 116 population genomic studies focused on the exploration of the genetic origin of Tanka people and their 117 interaction with modern and ancient surrounding populations. We identified one unique ancestry 118 composition in the Tanka people, which can be modeled as the admixture result of the southern sources 119 related to the coastal Austronesian-speaking Ami/ancient Hanben, and northern sources related to bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

120 Northern Han or Neolithic YRB farmers. Clustering results showed their relatively isolated position in 121 PCA, and unique admixture signatures in ADMIXTURE, and a closer relationship with southern 122 indigenes than with southern Han Chinese populations. Besides, f4-statistics, qpAdm, qpGraph and 123 FineSTRUCTURE results further revealed that Tanka not only harbored a close relationship with modern 124 southern Han Chinese but also had a close connection with ancient Yellow River Basin farmers, as well 125 as southern Late Neolithic to Iron Age Hanben, which can be modeled as the result of major northern 126 East Asian ancestry related to millet farmers and minor southern East Asian ancestry related to Hanben. 127 Our genomic evidence supported the ‘admixture hypothesis’ with one source related to the northern East 128 Asians and the other related to the southern indigenes. 129 130 MATERIALS AND METHODS 131 Sample collections, genotyping and quality control 132 We collected 77 saliva samples from unrelated healthy individuals from three populations in Fujian 133 province, southeastern China. We performed this study strictly followed by the regulations of the Human 134 Genetic Resources Administration of China (HGRAC) and the recommendations of the Helsinki 135 Declaration of 2000 (Association, 2001). The research protocol has been approved via the Medical Ethics 136 Committee of Xiamen University (XDYX201909). The informed consent was signed before sample 137 collections. We used the DP-318 Kit (Tiangen Biotechnology, Beijing) to isolate the genomic DNA based 138 on the manufactures’ instructions. Genotype data of approximately 700K genome-wide SNPs were 139 sequenced via the Illumina Infinium® Global Screening Array (GSA). Missing SNPs and missing 140 individuals were checked using the Plink 1.9 (Purcell et al., 2007) with the two parameters (mind: 0.01 141 and geno: 0.01). We then merged the quality-controlled data with previously published modern and 142 ancient Eurasian populations included in the Human Origin dataset or 1240K dataset publicly shared 143 from Reich Lab and other published genetic studies (Chen et al., 2021; Guanglin He et al., 2020; He et 144 al., 2021; Lipson et al., 2018; D. Liu et al., 2020; Y. Liu et al., 2021; Lu et al., 2020; McColl et al., 2018; 145 Ning et al., 2020; C. C. Wang et al., 2021; Q. Wang et al., 2020; Yang et al., 2020; Yao et al., 2021). 146 147 Sharing allele-based analyses from PCA, ADMIXTURE, f-statistics and TreeMix 148 Plink 1.9 (Purcell et al., 2007) was used to prune a dataset with strong linkage disequilibrium (--indep- 149 pairwise 200 25 0.4) and calculated the pairwise genetic distance of Fst index to evaluate the genetic 150 similarities between three Fujian populations and other eastern Eurasians. Principal component analysis 151 (PCA) among eastern modern and ancient Eurasians or their subsets was performed using smartpca 152 package in the EIGENSOFT (Patterson et al., 2012) with two parameters (lsqproject: YES and 153 numoutlieriter: 0). Unsupervised model-based ADMIXTURE analyses were carried out using 154 ADMIXTURE 1.3.0 (Alexander, Novembre, & Lange, 2009) and pruned datasets with the predefined 155 ancestral populations ranging from two to twenty. 156 157 All formal tests of allele-shared analysis using different packages in ADMIXTOOLS (Patterson et al., 158 2012). The genetic affinity between the studied Fujian populations and other Eurasian references was 159 measured via outgroup-f3-statistics in the form f3(Eurasian modern and ancients, Fujian populations; 160 Mbuti) using the qp3pop package. Admixture signals were explored via admixture-f3(Eurasian source1, 161 Eurasian source2; Fujian populations). Symmetrical-f4-statistics in the form of f4(Eurasian reference 162 population1, Eurasian reference population2; Fujian populations, Mbuti) and f4(Predefined ancestral 163 source proxy, Fujian populations, Eurasian reference population, Mbuti) were calculated qpDstat 164 package in ADMIXTOOLS (Patterson et al., 2012) with f4Mode (f4: YES). Population splits and gene 165 flow events among southern modern and ancient East Asians were constructed via TreeMix (Pickrell & 166 Pritchard, 2012) and further explored via the qpGraph (Patterson et al., 2012) with more complex models 167 based on different Paleolithic, Neolithic and modern genetic variations. We also used qpWave/qpAdm 168 packages in ADMIXTOOLS (Patterson et al., 2012) to evaluate the admixture proportion in our 169 predefined three-way admixture models with northern East Asian ancients from the YRB, southern 170 coastal East Asians from Fujian and inland East Asians from Vietnam as three source proxies. Dates of 171 admixture events were estimated via Admixture-induced Linkage Disequilibrium for Evolutionary 172 Relationships (ALDER) (Loh et al., 2013) based on the fitted decay rate of linkage disequilibrium. 173 Haplogroups of Y-chromosome and mitochondria DNA were assigned via the in-house scripts. 174 175 Sharing-haplotype-based IBD and finer-scale population dendrograms inferred from 176 FineSTRUCTURE 177 We phased genome-wide dense SNP data using ShapeIT and then calculated shared Identity by Descent 178 (IBD) between Fujian Tanka and other reference populations using the Refined IBD(Browning & 179 Browning, 2011). We painted the Tanka’s genomes using all our predefined donor chromosomes via the bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

180 Chromopaintor2 and explored the finer-scale genetic structure based on the coancestry matrix using the 181 FineSTRUCTURE v4(Lawson, Hellenthal, Myers, & Falush, 2012). And finally, we identified the 182 ancestry sources and dated corresponding admixture models using GLOBETROTTER(Hellenthal et al., 183 2014). 184 185 RESULTS AND DISCUSSION 186 Overview of genetic structure and general population relationship 187 We newly generated genome-wide single nucleotide polymorphism (SNP) data approximately 700,000 188 genetic markers in 77 southern Chinese individuals, including 73 officially ethnically unrecognized 189 Tanka people from Shacheng (34) and Xinshizhou (39) and four Han Chinese individuals from Fujian 190 province. We merged the new-obtained data with 997 modern eastern Eurasian from 105 191 geographically/linguistically diverse populations (9 Austroasiatic, 12 Austronesian, 8 Hmong-Mien, one 192 Japonic, and one Koreanic, 12 Sinitic, 14 Tai-Kadai, 18 Mongolic, and 24 Tibeto-Burman), as well as 193 424 ancient genomes from 70 archaeologic sites or genetic groups from southern Siberia, Mongolia, 194 China, Japan, Nepal and China. We first evaluated the genetic relationships among our included 1,498 195 ancient and present-day individuals using PCA. We identified two parallel genetic clines that were 196 stretched out along PC2 (Figure 1A) in the two-dimensional plots: Northern East Asian genetic cline 197 consisted of Mongolian ancients and modern Tungusic/Mongolic speakers at one end and Tibeto- 198 Burman-speaking populations at the other; Southern East Asian genetic cline comprised 199 Austronesian/Austroasiatic people at one end and inland Hmong-Mien speakers at the other. The third 200 genetic cline located between southern Tai-Kadai and northern lowland Tibeto-Burman or Sinitic along 201 PC1 linked the aforementioned northern and southern East Asian genetic clines, which is referred to as 202 the Han Chinese related cline. This intermediate cline included our newly-genotyped Tanka people who 203 were localized close with modern southern Han Chinese but showed a deviation toward inland Hmong- 204 Mien-speaking Hmong and PaThen. A clear genetic landscape of substructure could be arranged along 205 PC3 (Figure 1B): High-altitude Tibeto-Burman-speaking Tibetan and Sherpa were separated from others, 206 and Austroasiatic people from the Mainland of Southeast Asia were separated from the island 207 Austronesian. Here, Fujian Tanka people showed a genetic affinity with modern Austronesian and ancient 208 Iron Age Hanben people. After excluded ancient populations from the Mongolian Plateau, the 209 aforementioned genetic clusters/clines were visualized clearly via the top three components (Figure 210 3C~D). Finally, we focused on populations from southern East Asia and Southeast Asia (Figure 3E~F). 211 Four genetic sub-clines (Hmong-Mien cline, mainland Austroasiatic cline, inland Austronesian cline, and 212 northern mainland Sinitic cline) and one Tai-Kadai genetic cluster were identified. Tanka people were 213 grouped closely with Sinitic speakers, not with southern Chinese indigenous populations. We also found 214 that Xinshizhou Tanka has deviated from the Shacheng Tanka and southern Han Chinese. 215 216 Model-based clustering via ADMIXTURE among 1,498 Eurasian individuals from 178 modern and 217 ancient individuals was conducted to further explore the genetic diversity and ancestry composition 218 (Figure S1~2). Cross-validation results showed that the model with eight predefined ancestral sources 219 was the best-fitted one (Figure 2). Four northern East Asian ancestry components were identified 220 respectively existed in Boisman_MN, Mongolia_N_North, Late-Xiongnu-Sarmatian and 221 Mebrak_2125BP with a maximized proportion. Four southern East Asian ancestry components were 222 respectively maximized in Taiwan_Gongguan, Hmong, Mlabri and Htin. Shacheng Tanka was modeled 223 as the admixture result of 0.256 coastal Gongguan-related or Austronesian-related ancestry, 0.299 inland 224 Hmong-Mien-related, and 0.320 high-altitude Mebrak-related ancestries. The other two studied 225 populations also could be fit well with these three sources of ancestry: Hmong-Mien-related, 226 Austronesian-related, and Tibeto-Burman-related, in respective proportions of 0.320, 0.274, and 0.311 227 (Xinshizhou Tanka); and 0.291, 0.215, and 0.338 (Fujian Han). Interestingly, we found a homogeneous 228 Tanka-specific blue ancestry when the assumed ancestry sources increased (K≥9). Tanka-dominant 229 ancestry played an important role in the Austroasiatic, Tai-Kadai, Hmong-Mien, and Sinitic speakers, 230 which were rare or no proportion in Austronesian-speaking populations. Compared with Tanka people, 231 geographically close Han harbored more Tibetan-dominant ancestry from North China. 232 233 The genomic affinity of Tanka people in the context of modern and ancient eastern Eurasian 234 We next calculated two statistical parameters for evaluating the genetic similarities and differences 235 between Fujian Han and Tanka people relative to other modern and ancient eastern Eurasian reference 236 populations. The unbiased pairwise genetic distance of Fst was measured between three populations and 237 other 65 southern East Asians or Southeast Asians, the smaller value between Tanka people and Han 238 Chinese populations indicated a closer genetic relationship (Table S1). We observed northern Shacheng 239 Tanka possessed the smallest genetic distance with new-studied Fujian Han (0.0055), followed by bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

240 Zhejiang Han (0.0059) and previously published Fujian Han (0.0061). For ancient southern coastal 241 ancient populations, Shacheng Tanka harbored a closer genetic relationship with the Taiwan Iron Age 242 Hanben population (0.0444), followed by the Late Neolithic Xitoucun (0.1776) and Tanshishan (0.1993). 243 Southern Xinshizhou Tanka harbored the smallest genetic relationship with two Fujian Han Chinese 244 populations among modern reference populations as well as possessed stronger affinity with Hanben and 245 Late Neolithic Fujian populations among ancient reference groups. Newly-studied Fujian Han showed 246 the most genomic affinity with all northern and southern Han Chinese than two geographically close 247 Tanka groups, consistent with the clustering pattern of the previously published Fujian Han. Our result 248 indicated that although a genetic affinity between Tanka people and Han Chinese could be identified, 249 Tanka people have more shared genetic ancestry with southern indigenous Austronesian, Tai-Kadai and 250 Hmong-Mien populations compared with southern Han Chinese. Shared genetic drift between three 251 Fujian populations and 427 Eurasian modern and ancient populations was further evaluated via the 252 outgroup-f3(Eurasian reference populations, three studied populations; Mbuti). Lager f3-values indicated 253 a closer genetic affinity (Figure 3A~B). After excluding the overlapping SNP loci less than 10000, we 254 observed consistent patterns of genetic affinity with East Asians, in which Tanka people shared more 255 genetic drift with southern Han Chinese (Table S2). Among ancient populations, Tankan people shared 256 the strongest genetic drift not only with southern Iron Age Taiwan indigenous people (Hanben and 257 Gongguan) and Vanuatu Neolithic populations but also with the northern YRB Neolithic-to-modern 258 people (Figure 2A~B), which suggested the strongest genetic link between North China, Southeast China 259 and Vanuatu via the ancient genetic legacy of southeastern farmer elites 260 261 Evidence for different genetic features of Tanka people relative to geographically close Han Chinese was 262 further provided via admixture-f3(Source1, Source2; Focused populations). This type of allele-sharing- 263 based f-statistics was widely used to explore the possible ancestral source candidates for one targeted 264 population, in which statistically significant f3-values (Z-scores less than negative three) indicated 265 obvious admixture signature. As shown in Figure 3C, we observed admixture signals in the new studied 266 Fujian Han Chinese population with one source from northern East Asia associated with Tibeto-Burman- 267 speaking populations (Tibetan and Qiang) and the other source candidates from southern East Asia 268 related to Austronesian- or Tai-Kadai-speaking populations, such as f3(Ami, Tibetan_Chamdo; 269 Han_Fujian)= -5.26*SE, which is consistent with the previous population genetic analyses focused on 270 southern and central Han Chinese (G. He et al., 2020; G. L. He et al., 2020). We also found ancient 271 northern East Asians, including the Early Iron Age SlabGrave people from Eastern Eurasian steppe, 272 Neolithic Shimao, Jinchankou, Lajia, Wanggou and others combined with southern sources can produce 273 negative f3-values, suggested the spatiotemporally northern East Asians contributed the genetic material 274 into modern Fujian Hans. Similarly, southern ancient East Asians associated with Hanben, Tanshishan 275 and Xitoucun combined with northern sources also could produce admixture signals for Fujian Han. 276 However, we did not identify statistically significant admixture signatures in the admixture f3-statistics 277 focused on Xinshizhou and Shacheng Tanka people, which is consistent with the observed homogenous 278 genetic structure in our model-based ADMIXTURE result with ancestral sources larger than eight 279 (Figure 2). We also observed 48 source pairs that possessed negative-f3-values in Shacheng Tanka and 280 10 pairs showed as negative-f3-values in Xinshizhou Tanka. These weak signals also provided clues that 281 suggested more genetic interaction between Shacheng Tanka people with their geographical neighbors 282 than it in Xinshizhou Tanka. 283 284 Genetic continuity and admixture of southeastern Chinese Tanka people 285 We following validated the genetic homogeneity observed in PCA and ADMIXTURE results using f4- 286 statistics. No statistical deviations were observed among f4(Tanka_Shacheng, Tanka_Xinshizhou; 287 Eastern Eurasian ancients, Mbuti), in which 75 ancient populations were used here, suggesting the 288 genetic cladality between two geographic different Tanka populations. If we settled the threshold of the 289 absolute Z-score as two, we could find the status that northern East Asians shared more alleles with 290 geographically northern Shacheng Tanka relative to the southern Xinshizhou Tanka people, such as 291 Neolithic Miaozigou people with f4(Tanka_Shacheng, Tanka_Xinshizhou; Miaozigou_MN, 292 Mbuti)=2.401*SE and Iron Age Zhalainuoer people with f4(Tanka_Shacheng, Tanka_Xinshizhou; 293 Zhalainuoer_IA, Mbuti)=2.90*SE. Similarly, we observed Xinshizhou Tanka harbored more Hanben- 294 related ancestry compared with Fujian Han. Compared with 134 modern populations, Austronesian 295 speakers shared more derived alleles with two Tanka people relative to Fujian Han with the negative Z- 296 scores smaller than -2 in f4(Han_Fujian, Tanka_Xinshizhou/Tanka_Shacheng; Austronesian speakers, 297 Mbuti). Summarily, Tanka people shared more southern East Asian ancestry related to Austronesian or 298 Tai-Kadai-speaking populations compared with southern Han Chinese, suggesting the different genetic 299 history between Tanka and their neighbor of Hans. bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

300 301 We further explored the genomic affinity between three newly-genotyped populations between other 302 ancient and present-day eastern Eurasian populations via f4(208Eurasian1, 208Eurasian2; three studied 303 populations, Mbuti). Compared with northern East Asians, three Fujian populations shared a more 304 common genetic ancestry component related to modern southern East Asian, Southeast Asian and 305 modern Sinitic speakers, as statistically negative f4-values were observed in f4(Northern East Asians, 306 Southern East Asians; Tanka or Han in Fujian, Mbuti). Focused on southern populations (Figure 4 and 307 S4), strong genetic affinity was observed between northern Shacheng Tanka and four populations 308 (Han_Shanghai, She, Han_Fujian and Han_Hubei), followed by other Sinitic speakers, Tai-Kadai, 309 Hmong-Mien-speaking Miao, Austronesian-speaking Ami and Kankanaey and lowland Tibeto-Burman- 310 speaking Tujia. Xinshizhou Tanka showed a similar pattern of genomic affiliation (Figure S4). 311 Compared with inland southern East Asians, Tanka people shared more ancestry with southeastern 312 coastal East Asians, especially for Austronesian speakers with statistically negative values in f4(Dai, Ami; 313 Tanka_Shacheng, Mbuti). Compared with Bronze Age steppe pastoralists (Afanasievo and Sintashta), 314 Tanka people shared most derived alleles with southern Hanben and northern late medieval Mongolian 315 people. Compared with Fujian Late Neolithic Tanshishan population, three studied populations shared 316 more alleles with the Late Neolithic Longshan people from the Yellow River basin due to the observed 317 positive values in f4(Yellow River farmers, Tanshishan; Tanka, Mbuti) (Z-Scores: Tanka_Xinshizhou, 318 2.432; Tanka_Shacheng, 2.447; Tanka_Fujian, 2.627). Results from the affinity-f4 statistics showed 319 Tanka people shared more alleles with Han Chinese populations compared with southern Chinese 320 minority populations. Our findings also showed that Tanka people shared more alleles related to the 321 southern Chinese Tai-Kadai or Austronesian people compared with southern Han Chinese, suggesting 322 that the Tanka people not only had a strong genetic affinity with Han people but also harbored additional 323 gene flow from surrounding indigenous populations. 324 325 Additionally, to explore the genetic contribution to modern Tanka’s gene pool, we performed 326 f4(Reference populations, Tanka people; Southern modern and ancient populations, Mbuti). If we 327 included southern modern and ancient populations as the direct ancestors or their ancestral proxies, 328 significant negative f4-values would be expected observed. As showed in Figure 5 and S5, signatures of 329 genetic contributions (blue color indicated genomic affinity with Tanka people) were observed not only 330 when we assumed southern East Asians as the Tanka’s ancestral sources but also identified when we 331 assumed northern modern Tibeto-Burman speakers and northern East Asians as their ancestral 332 contributors. When we hypothesized northern Neolithic-to-Iron Age East Asian people as their ancestor 333 (Northern East Asian origin hypothesis), we also identified too many blue signals evidenced for the 334 genetic contribution from southern East Asians. These identified shared alleles suggested a strong 335 phylogenetic correlation between Tanka people and both northern and southern East Asians. To further 336 validated some unique ancestral sources directly contributed to the Tanka people, we analyzed f4-statistics 337 in the new form f4(Ancestral sources, Tanka people; reference populations, Mbuti). Non-f4-values 338 showed the statistical significance (Absolute Z-Scores larger than three) were identified in 339 f4(Chuanyun_H/Miaozigou_MN/Haojiatai_LN/Tujia_HGDP/Han_Chongqing/Han_Fujian/Han_Zhejia 340 ng, Tanka people; Reference populations, Mbuti) showed the genomic affinity between Tanka people and 341 southern Han Chinese as well as the Yellow River late Neolithic ancient of Haojiatai people (forming 342 one genetically indistinguishable clade), which was consistent with the expected patterns if their northern 343 China Origin is the true history model. Following, we used other YRB millet farmers as their director 344 ancestors, we identified additional admixture signatures from southern East Asians in 345 f4(Jiaozuoniecun_LBIA/Jinchankou_LN/Wadian_LN/Xiaowu_MN/Haojiatai_LBIA/Pingliangtai_LN, 346 Tanka people; southern Chinese populations, Mbuti), suggesting additional mixture events occurred in 347 the past, which is consistent with the identified marginal negative-f3-values in admixture-f3-statistics. 348 Similar patterns were identified when we used the southern East Asians as their direct ancestor, 349 suggesting additional gene flow contributed to the formation of the Tanka people also from northern East 350 Asians. Formal tests in f4-statistics demonstrated both northern East Asians and southern East Asians 351 participated in the formation of the Tanka people, and it also possessed more southern indigenous 352 ancestry related to Austronesian or Tai-Kadai speakers compared with Fujian Han. 353 354 Phylogenetic history reconstruction and quantification of the mixed ancestry 355 We constructed one unrooted phylogenetic framework (Figure 6A) among southern Chinese Hmong- 356 Mien, Tai-Kadai, Austroasiatic, and Austronesian modern people, as well as ancient southern coastal East 357 Asians (Neolithic Tanshishan and Xitoucun, and Iron Age Hanben). PCA results among TreeMix-used 358 populations showed three genetic clines among these included populations: Austronesian and ancient 359 Taiwanese-related, Austroasiatic-related and others (Figure 6B), consistent with the patterns in previous bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

360 southern PCA with ancient samples projected. Tanka people were clustered closely with Han Chinese 361 but not with Tai-Kadai or Austronesian speakers. In accordance with the genetic clustering in 362 ADMIXTURE and PCA results, four branches were identified in the TreeMix-based phylogenetic 363 framework. Hmong-Mien branch was clustered close with the Sinitic branch, which diverged from the 364 common ancestor of Tai-Kadai, Austronesian and Austroasiatic speakers. Three studied populations were 365 grouped closely and firstly clustered with neighboring Han (Fujian and Guangdong) and Chuanqing and 366 She people. To further validated the Sinitic-affinity or North China Origin hypothesis of primary ancestry 367 of Tanka people, we reconstructed the phylogenetic trees based on the f-statistics (f2, f3 and f4) using 368 qpGraph. As shown in Figure 7, we used Neolithic populations from Mongolia Plateau (MNE), Qinghai- 369 Tibetan Plateau (Chokhopani) and Yellow River Basin (Xiaowu_MN) as the ancient northern East Asian 370 source, and used mainland late Neolithic Tanshishan and Iron Age Hanben as the ancient southern East 371 Asian source to construct the basic phylogenetic framework. Tanka people could be modeled as the main 372 ancestry from ancient northern East Asians: Xinshizhou Tanka derived 91% of their ancestry from 373 Xiaowu Yangshao millet farmer and the reminding from the deep diverged eastern Eurasian related to 374 Onge in the deep admixture model (Figure 7A), and it can be also modeled via 64% Xiaowu-related 375 ancestry and 36% Tanshishan-related ancestry in the recent admixture model (Figure 7B). We further 376 used different northern and southern sources to estimate the date of these admixture events via the decay 377 of the linkage disequilibrium (Figure 7C~D). We found that major admixture events mainly occurred 378 during the Late Neolithic to medieval times with different predefined ancestral sources, which was 379 consistent with the estimated dates from GLOBETROTTER. 380 381 Finally, we used qpAdm/qpWave and the three-way admixture model to evaluate the fine-scale ancestral 382 proportion from the southern sources. Here, we used late Neolithic Tanshishan people as the proxy of 383 southern coastal ancestral populations and used Bronze Age NuiNap and late Neolithic ManBac from 384 Vietnam as the proxies of inland ancestral sources. Two main findings we identified from qpAdm results 385 (Figure 7E~F). Firstly, all included three modern populations could be successfully fitted via at least one 386 of we provided mixed models, even including the Han Chinese in model of Tanshishan-NuiNap- 387 Jinchankou, suggesting the complex ancestral sources of modern southern Han Chinese, which is 388 differentiated from the demographic history of present-day northern Han people. Secondly, compared 389 with southern Han, Tanka people harbored less northern East Asian-related ancestry, and Xinshizhou 390 Tanka people possessed more inland southern East Asian-related ancestry and less northern East Asian- 391 related ancestry. 392 393 Demographic history of Tanka people inferred from the sharing haplotype patterns 394 We subsequently explored the genetic similarities and differences within and between Tanka people and 395 their adjacent East Asians(Chen et al., 2021; He et al., 2021; Y. Liu et al., 2021; Lu et al., 2020; Jin Sun 396 et al., 2020; Q. Wang et al., 2020; Yao et al., 2021) based on the genetic variants of denser SNP data 397 (approximately 700K). we evaluated the pairwise Fst genetic distances again based on the denser SNP 398 dataset and found a closer relationship between Shacheng Tanka and Fujian Tanka (0.0062) than it 399 between Xinshizhou Tanka and Fujian Tanka people (0.0100), all these less than the genetic differences 400 between Shacheng and Xinshizhou Tanka people (0.0130). We conducted PCA analysis among three 401 Tanka populations and found population substructures among them. We could identify three branches 402 (one Shacheng and two Xinshizhou groups): Fujian Tankas were clustered between Xinshizhou and 403 Shacheng (Figure 8A). Although the population substructure was identified here, no statistically f4 values 404 were identified via f4(Xinshizhou1, Xinshizhou2; Reference populations, Mbuti). Thus, one population 405 label was used in the frequency-based analysis. 406 407 We following phased the successive independent SNP data to haplotype form from maternal and paternal 408 sides based on the haplotype phased statistical methods. Fine-scale population structures were further 409 comprehensively characterized based on the haplotype data. PCA results based on the coancestry matrix 410 also confirmed the aforementioned population substructure but with subtle differences for substructures 411 (Figure 8B~D). We observed the genetic homogeneity within Shacheng people and genetic 412 heterozygosity within Xinshizhou people via the scattered plots in the two-dimensional plots. We 413 subsequently explore the patterns of shared haplotype based on the ChromoPainter and 414 FineSTRUCTURE. We evaluated the demographic parameters based on the random extracted samples 415 (including the effective population size of Tanka people (Ne: 290.776) and mutation rate (mu: 416 0.0006513)). The inferred population affinity and dendrogram based on the pairwise coincidence showed 417 that eight Tankas from Shacheng, six Tankas from Xinshizhou and other 20 Shacheng Tanka people 418 clustered together and formed one genetically homogeneous population. The remaining Xinshizhou 419 Tankas people formed the other branch (Figure 8E~F). We also calculated the iHS values based on bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

420 phased haplotypes and identified some natural selection signatures from Chromosomes 6, 8, 11 and 17, 421 which respectively associated with the genes of HLA, MUC22, MSRA, LDLRAD3 and RBFOC3 422 423 We finally explored the genetic relationship between Tanka people with other 29 Chinese populations 424 based on the shared haplotypes. Plink-PCA based on the allele frequency spectrum among 32 populations 425 revealed two genetic clines consisted of Guizhou Hui people and Yunnan populations, which were 426 located distinct from others (Figure 9A). Tanks people clustered together and also showed a distinct 427 genetic relationship with geographically close Guizhou populations but close with Shaanxi Hans, which 428 further confirmed in the PCA patterns based on the coancestry matrix (Figure 9B). Population 429 dendrogram based on the pairwise coincidence and the TreeMix-based phylogenetic relationship showed 430 a close genetic relationship between Fujian Tanka and Fujian Han, as well as a close genetic relationship 431 with northern Hans from Shaanxi than inland Guizhou and Yunnan minorities (Figure 9C~E). Results 432 from the pairwise IBD showed Fujian Han harbored the longest shared IBD with Tanka from Xinshizhou 433 (20.373) and Shacheng (19.571), following by Ankang Hans, Chuanqing and other Shaanxi populations. 434 Tanka people not only shared the longest IBD within populations but also shared relatively longer IBD 435 with both northern Hans and southern Hmong-Mien speakers, suggesting Tanka people received gene 436 fluence from both northern and southern East Asians (Figure 9F). Pairwise Fst also showed a close 437 relationship between Fujian populations with Chongqing Miao and Tujia and northern Shaanxi Hans. 438 Clustering patterns based on the Fst matrix showed Fujian Han clustered with other Han populations, but 439 Tanks people clustered with Guizhou Manchu, Mongolian and other Hmong-Mien-speakers (Figure 9G). 440 441 Uniparental genetic legacy 442 We genotyped paternally and maternally phylogenetic information SNPs in Tanka males at a higher 443 resolution. Overall, the main founding paternal lineage in Tanka people in this study were O1a1a1a1a1a1- 444 M119-F492, O1b1a1a1a1b1b-M95-CTS651, O1b1a2a1-Page59, O2a1c1a1a1a1d1-F325-F930, and 445 O2a4b1a1a1.These observed paternal haplogroup types are also the main patrilineal types of people in 446 southern China, but the patrilineal composition between the two groups is quite different. Lineages of 447 O1a1a1a1a1a1-F492 and O1b1a1a1a1b1b-M95-CTS651 exited in Shacheng Tanka with a high 448 proportion (50%, 17/34), but these two types do not exist in Xinshizhou Tanka. Similarly, 449 O2a1c1a1a1a1d1-F325-F930 and O2a2b1a1a4a-F5-Z25853 accounted for a high proportion of 450 Xinshizhou Tanka people (36%,14/39), but they did not exist among Shacheng Tanka people. 451 Haplogroup O1b1a2a1-M268-P59 is the only shared patrilineal type among the two groups. Patriline 452 O1a--M119 is one of the main patrilineal types of Austronesian and Tai-Kadai speakers, and there is also 453 a certain proportion in geographically close Han populations. O1b1a1a1a1b1b-M95 is the major 454 patrilineal type of the Hmong-Mien, Tai-Kadai, and Austroasiatic speakers, and it also has a high 455 proportion in the Han ethnic group in South China. The downstream branch of O2-M122 is the main 456 patrilineal type of the Han people. In short, the patrilineal genetic structure of the Tanka population 457 observed here shows a strong association between the Tai-Kadai-speaking population and the southern 458 Han populations. In terms of maternal lineage, the six main haplogroup types are identified, including 459 M7b (21.9%, 16/73), M7c (9.59%, 7/73), F1a (9.59%, 7/73), FxF1a (8.22%, 6/73), D4 (8.22%, 6/73), 460 M9a1a1 (6.85%, 5/73). Among these types, F1a and FxF1a have a higher proportion in the southern 461 indigenous groups, while the other types have a higher proportion in the Han populations. In short, 462 although the patrilineal lineages of the Tanka also show a significant connection with the Austronesian 463 and Tai-Kadai groups in south China, it has a higher genetic similarity with the matrilineal lineages of 464 the Han people. 465 466 CONCLUSION 467 We generated genome-wide autosomal, paternal and maternal data of Tanka people to resolve the 468 controversial hypotheses of the origins of Tanka People (Han origin, Ancient Baiyue origin, or admixture 469 origin). We provided robust genetic evidence for the admixture original hypothesis of Tanka people based 470 on the comprehensive population genetic reconstruction. Paternal genetic evidence found that Y-lineage 471 haplogroup O1-M119 lineage reached a high frequency (35.2%,12/34) in Shacheng Tanka, which is 472 higher than it in other southern Chinese Han populations. But this patrilineal genetic composition in 473 Xinshizhou Tanka was almost the same as that of the southern Han. In the maternal genetic structure, a 474 higher proportion of southern dominant maternal types could be observed. From the genetic variations 475 from the autosomal genome-wide data, PCA and model-based ADMIXTURE results showed that Tanka 476 people had their unique genetic structure, but kept a close relationship with geographically close southern 477 Han Chinese populations. Shared genetic drift revealed from the outgroup-f3-statistic and admixture-f3- 478 statistics further not only showed a stronger Han Chinese affinity but also displayed the marginal 479 admixture signatures from the sources from southern and northern China, in which Tanka people could bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

480 be modeled as the major ancestry related to the northern East Asian and minor ancestry related to Tai- 481 Kadai-related populations. Thus, our results from the genome-wide data supported that Tanka people 482 gave rise from the admixture between southward migration Han Chinese and southern indigenous people. 483 484 Conflicts of interest 485 The authors declare no conflict of interest. 486 Acknowledgments 487 We are grateful to all sample donors. This study was supported by the National Natural Science 488 Foundation of China (31222030), China Postdoctoral Science Foundation (2021M691879). The funders 489 had no role in study design, data collection and analysis, decision to publish, or preparation of the 490 manuscript. 491 Data availability 492 The raw genome-wide data can be obtained via corresponding authors. 493 494 References 495 Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in 496 unrelated individuals. Genome Res, 19(9), 1655-1664. doi:10.1101/gr.094052.109 497 Association, W. M. (2001). World Medical Association Declaration of Helsinki. Ethical principles for 498 medical research involving human subjects. Bulletin of the World Health Organization, 499 79(4), 373. 500 Browning, B. L., & Browning, S. R. (2011). A fast, powerful method for detecting identity by descent. 501 Am J Hum Genet, 88(2), 173-182. doi:10.1016/j.ajhg.2011.01.010 502 Chen, J., He, G., Ren, Z., Wang, Q., Liu, Y., Zhang, H., . . . Huang, J. (2021). Genomic Insights Into 503 the Admixture History of Mongolic- and Tungusic-Speaking Populations From 504 Southwestern East Asia. Frontiers in Genetics, 12(880). doi:10.3389/fgene.2021.685285 505 Guang‐Lin He, Li, Y. X., Wang, M. G., Zou, X., Yeh, H. Y., Yang, X. M., . . . Chuan‐Chao, W. (2021). 506 Fine‐scale genetic structure of Tujia and central Han Chinese revealing massive genetic 507 admixture under language borrowing. Journal of Systematics and Evolution, 59(1), 1-20. 508 He, G., Wang, M., Li, Y., Zou, X., Yeh, H. Y., Tang, R., . . . Wang, C. C. (2020). Fine‐scale north‐to‐ 509 south genetic admixture profile in Shaanxi Han Chinese revealed by genome ‐wide 510 demographic history reconstruction. Journal of Systematics and Evolution, 0-. 511 doi:10.1111/jse.12715 512 He, G., Wang, Z., Guo, J., Wang, M., Zou, X., Tang, R., . . . Hou, Y. (2020). Inferring the population 513 history of Tai-Kadai-speaking people and southernmost Han Chinese on Hainan Island 514 by genome-wide array genotyping. Eur J Hum Genet, 28(8), 1111-1123. 515 doi:10.1038/s41431-020-0599-7 516 He, G. L., Li, Y. X., Wang, M. G., Zou, X., Yeh, H. Y., Yang, X. M., . . . Wang, C. C. (2020). Fine‐scale 517 genetic structure of Tujia and central Han Chinese revealing massive genetic admixture 518 under language borrowing. Journal of Systematics and Evolution, 59(1), 1-20. 519 doi:10.1111/jse.12670 520 He, G. L., Wang, M. G., Li, Y. X., Zou, X., Yeh, H. Y., Tang, R. K., . . . Wang, C. C. (2021). Fine‐scale 521 north‐to‐south genetic admixture profile in Shaanxi Han Chinese revealed by genome‐ 522 wide demographic history reconstruction. Journal of Systematics and Evolution, 0-. 523 doi:10.1111/jse.12715 524 Hellenthal, G., Busby, G. B. J., Band, G., Wilson, J. F., Capelli, C., Falush, D., & Myers, S. (2014). A 525 genetic atlas of human admixture history. Science, 343(6172), 747-751. 526 doi:10.1126/science.1243518 527 Larena, M., Sanchez-Quinto, F., Sjodin, P., McKenna, J., Ebeo, C., Reyes, R., . . . Jakobsson, M. (2021). bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

528 Multiple migrations to the Philippines during the last 50,000 years. Proc Natl Acad Sci U 529 S A, 118(13). doi:10.1073/pnas.2026132118 530 Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012). Inference of population structure using 531 dense haplotype data. PLoS Genet, 8(1), e1002453. doi:10.1371/journal.pgen.1002453 532 Lipson, M., Cheronet, O., Mallick, S., Rohland, N., Oxenham, M., Pietrusewsky, M., . . . Reich, D. 533 (2018). Ancient genomes document multiple waves of migration in Southeast Asian 534 prehistory. Science, 361(6397), 92-95. doi:10.1126/science.aat3188 535 Liu, D., Duong, N. T., Ton, N. D., Van Phong, N., Pakendorf, B., Van Hai, N., & Stoneking, M. (2020). 536 Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic 537 Diversity. Mol Biol Evol, 37(9), 2503-2519. doi:10.1093/molbev/msaa099 538 Liu, S., Huang, S., Chen, F., Zhao, L., Yuan, Y., Francis, S. S., . . . Xu, X. (2018). Genomic Analyses 539 from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral 540 Infections, and Chinese Population History. Cell, 175(2), 347-359 e314. 541 doi:10.1016/j.cell.2018.08.016 542 Liu, Y., Yang, J., Li, Y., Tang, R., Yuan, D., Wang, Y., . . . He, G. (2021). Significant East Asian Affinity 543 of the Sichuan Hui Genomic Structure Suggests the Predominance of the Cultural 544 Diffusion Model in the Genetic Formation Process. Front Genet, 12(834), 626710. 545 doi:10.3389/fgene.2021.626710 546 Loh, P. R., Lipson, M., Patterson, N., Moorjani, P., Pickrell, J. K., Reich, D., & Berger, B. (2013). 547 Inferring admixture histories of human populations using linkage disequilibrium. Genetics, 548 193(4), 1233-1254. doi:10.1534/genetics.112.147330 549 Lu, J., Zhang, H., Ren, Z., Wang, Q., Liu, Y., Li, Y., . . . Wang, C. C. (2020). Genome-wide analysis of 550 unrecognised ethnic group Chuanqing people revealing a close affinity with Southern Han 551 Chinese. Ann Hum Biol, 47(5), 465-471. doi:10.1080/03014460.2020.1782470 552 Luo, X. Q., Du, P. X., Wang, L. X., Zhou, B. Y., Li, Y. C., Zheng, H. X., . . . Li, H. (2020). Uniparental 553 Genetic Analyses Reveal the Major Origin of Fujian Tanka from Ancient Indigenous Daic 554 Populations. Hum Biol, 91(4), 257-277. doi:10.13110/humanbiology.91.4.05 555 McColl, H., Racimo, F., Vinner, L., Demeter, F., Gakuhari, T., Moreno-Mayar, J. V., . . . Willerslev, E. 556 (2018). The prehistoric peopling of Southeast Asia. Science, 361(6397), 88-92. 557 doi:10.1126/science.aat3628 558 Ning, C., Li, T., Wang, K., Zhang, F., Li, T., Wu, X., . . . Cui, Y. (2020). Ancient genomes from northern 559 China suggest links between subsistence changes and human migration. Nat Commun, 560 11(1), 2700. doi:10.1038/s41467-020-16557-2 561 Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., . . . Reich, D. (2012). Ancient 562 admixture in human history. Genetics, 192(3), 1065-1093. 563 doi:10.1534/genetics.112.145037 564 Pickrell, J. K., & Pritchard, J. K. (2012). Inference of population splits and mixtures from genome- 565 wide allele frequency data. PLoS Genet, 8(11), e1002967. 566 doi:10.1371/journal.pgen.1002967 567 Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., . . . Sham, P. C. (2007). 568 PLINK: a tool set for whole-genome association and population-based linkage analyses. 569 Am J Hum Genet, 81(3), 559-575. doi:10.1086/519795 570 Sun, J., Li, Y. X., Ma, P. C., Yan, S., Cheng, H. Z., Fan, Z. Q., . . . Wei, L. H. (2021). Shared paternal 571 ancestry of Han, Tai-Kadai-speaking, and Austronesian-speaking populations as revealed bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

572 by the high resolution phylogeny of O1a-M119 and distribution of its sub-lineages within 573 China. Am J Phys Anthropol, 174(4), 686-700. doi:10.1002/ajpa.24240 574 Sun, J., Zhao, J., Cheng, H.-Z., Yang, X., He, G., Guo, J., . . . Wang, C.-C. (2020). Genetic affinity and 575 substructure of Hmong-Mien speaking populations inferred from genome-wide array 576 genotyping of three unrecognized ethnic groups Dongjia, Xijia and Gejia. Mol Genet 577 Genomics. 578 Wang, C. C., Yeh, H. Y., Popov, A. N., Zhang, H. Q., Matsumura, H., Sirak, K., . . . Reich, D. (2021). 579 Genomic insights into the formation of human populations in East Asia. Nature, 591(7850), 580 413-419. doi:10.1038/s41586-021-03336-2 581 Wang, Q., Zhao, J., Ren, Z., Sun, J., He, G., Guo, J., . . . Wang, C. C. (2020). Male-Dominated 582 Migration and Massive Assimilation of Indigenous East Asians in the Formation of Muslim 583 Hui People in Southwest China. Front Genet, 11(1742), 618614. 584 doi:10.3389/fgene.2020.618614 585 Wen, B., Li, H., Lu, D., Song, X., Zhang, F., He, Y., . . . Jin, L. (2004). Genetic evidence supports demic 586 diffusion of Han culture. Nature, 431(7006), 302-305. doi:10.1038/nature02878 587 Yang, M. A., Fan, X., Sun, B., Chen, C., Lang, J., Ko, Y. C., . . . Fu, Q. (2020). Ancient DNA indicates 588 human population shifts and admixture in northern and southern China. Science, 589 369(6501), 282-288. doi:10.1126/science.aba0909 590 Yao, H., Wang, M., Zou, X., Li, Y., Yang, X., Li, A., . . . He, G. (2021). New insights into the fine-scale 591 history of western-eastern admixture of the northwestern Chinese population in the Hexi 592 Corridor via genome-wide genetic legacy. Mol Genet Genomics, 296(3), 631-651. 593 doi:10.1007/s00438-021-01767-0 594 595 Legends of Figures 596 Figure 1. The general pattern of genetic relationship among modern and ancient eastern Eurasian 597 via principal component analysis (PCA). (A~B) Clustering results of all included modern and ancient 598 eastern Eurasian populations based on the top three components. (C~D). PCA results among eastern 599 Eurasians after removing ancient Mongolian populations with western Eurasian admixture signals. (E~F). 600 Patterns of genetic affinity inferred from PCA focused on southern Chinese and Southeast Asian 601 populations. Our included ancient reference populations were projected into the modern genetic 602 framework. Modern populations were color-coded based on linguistic affinity and ancient populations 603 were color-coded via geographical division. 604 605 Figure 2. Model-based ADMIXTURE clustering analysis among eastern modern and ancient 606 Eurasian populations. Predefined ancestral numbers of eight to eleven were chosen there. The full 607 landscape of genetic structure was submitted in Supplementary Figure S3. 608 609 Figure 3. Genomic affinity and admixture signatures of our targeted populations. (A) Heatmap 610 displayed the shared genetic between Shacheng Tanka and other eastern modern and ancient Eurasian 611 populations. Red color denoted stronger affinity with Tanka people and green color denoted relatively 612 far genetic relationship with Tanka speakers (B) Top twenty populations shared strong genetic affinity 613 with Xinshizhou Tanka. The short bar showed the three-fold of standard error. (C) Admixture-f3-statistics 614 in the form of f3(Source1, Source2; Shacheng/Xinshizhou Tanka/Fujian Han) showed the top twenty pairs 615 for potential admixture sources. Red asterisk showed obvious statistically significant results with 616 absolute Z-Scores larger than three. And green circle showed no statistically significant results. 617 618 Figure 4. A formal test of genomic affinity in Shacheng Tanka people inferred from the two- 619 population comparison f4-statistics in the form f4(Reference population1, Reference population2; 620 Tanka_Shacheng, Mbuti). Red color denoted the positive f4-values, which suggested Shacheng Tanka 621 people shared more derived mutations with reference population1 (left population lists), and blue color 622 showed the negative f4-values, which suggested Shacheng Tanka people shared more alleles with 623 reference population2 (bottom population lists). Statistically significant results were marked with the ‘+’. bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

624 625 Figure 5. A formal test of genomic continuity and admixture in Xinshizhou Tanka people inferred 626 from the two-population comparison f4-statistics in the form f4(Reference population1, Reference 627 population2; Tanka_Xinshizhou, Mbuti). Red color denoted the positive f4-values, which suggested 628 Reference population2 (bottom population lists) shared more derived mutations with reference 629 population1 (left population lists), and blue color showed the negative f4-values, which suggested 630 reference population2 shared more alleles with Xinshizhou population and gray color showed no 631 statistically significant results were observed. Statistically significant results were marked with the ‘+’. 632 633 Figure 6. The TreeMix-based phylogenetic tree showed the genetic relationship between modern 634 and ancient East Asians. (A) Tree with four assumed admixture events. (B) Population relationships 635 among TreeMix-used populations without ancient populations were projected. 636 637 Figure 7. Genetic drift-based phylogenetic phylogeny showed population split and gene flow events. 638 (A) The targeted population was modeled as derived their ancestry from the Yellow River Yangshao 639 lineage and one ancient southern deep diverged eastern Eurasian lineage. (B). Tanka people were 640 modeled as the admixture of two Neolithic East Asian lineages. Genetic drift was marked as 1000 times 641 of f2 values. Dot blue lines denoted the admixture events and corresponding admixture proportions were 642 also marked. (C~D). Dates of admixture events estimated via ALDER. (E~F) QpAdm results showed 643 the admixture proportion of three-way admixture models. Admixture proportion was estimated used the 644 northern East Asian-Tanshishan_LN-NuiNap_BA three-way admixture model (E). Admixture 645 proportion was estimated when we used the Neolithic ManBac people as the inland southern East 646 Asian(F). 647 648 Figure 8. Finer-scale population structure within Fujian Tanka people using the phased haplotype 649 data. (A). Plink-based PCA showed the substructure within Tanka people based on the allele frequency 650 spectrum. (B~D). Haplotype-based PCA showed the substructures within Tanka people. (E~F) The 651 pairwise coincidence and heatmap showed the individual clustering pattern. (G) Natural selection 652 signatures inferred from the estimated iHS. 653 654 Figure 9. Finer-scale population structure between Fujian Tanka people and other 39 Chinese 655 populations using the phased haplotypes. (A~B). Patterns of the genetic relationship inferred from 656 PCA based on the allele frequency spectrum and haplotype-based coancestry matrix. (C~D) 657 FineSTRUCTURE results showed population structure based on the shared number of the haplotype 658 chunks. (E). The TreeMix-based phylogenetic tree showed the genetic relationship among 42 Chinese 659 populations. (F~G) Heatmap visualized based on the pairwise Fst and IBD matrixes. 660 661 Figure S1. Geographical positions of two Tanka populations and one Han Chinese population collected 662 from Fujian province in southeastern China. 663 Figure S2. Cross-validation error in the model-based ADMIXTURE analyses. The best model is the 664 eight-source-based mixed model with the smallest cross-validation error (0.5750). 665 Figure S3. Results of model-based ADMIXTURE analyses results with the predefined ancestral 666 sources ranging from two to twenty. 667 Figure S4. Formal test of genomic affinity in Xinshizhou Tanka people inferred from the two-

668 population comparison f4-statistics in the form f4(Reference population1, Reference population2;

669 Tanka_Xinshizhou, Mbuti). Red color denoted the positive f4-values, which suggested Xinshizhou 670 Tanka people shared more derived mutations with reference population1 (left population lists), and blue

671 color showed the negative f4-values, which suggested Xinshizhou Tanka people shared more alleles with 672 reference population2 (bottom population lists). Statistically significant results were marked with the ‘+’. 673 Figure S5. A formal test of genomic continuity and admixture in Shacheng Tanka people inferred

674 from the two-population comparison f4-statistics in the form f4(Reference population1, Reference

675 population2; Tanka_Shacheng, Mbuti). Red color denoted the positive f4-values, which suggested 676 reference population2 (bottom population lists) shared more derived mutations with reference

677 population1 (left population lists), and blue color showed the negative f4-values, which suggested bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

678 reference population2 shared more alleles with Shacheng population and gray color showed no 679 statistically significant results were observed. Statistically significant results were marked with the ‘+’. 680 Figure S6. Genetic drift-based phylogenetic phylogeny showed population split and gene flow 681 events for Shacheng Tanka. Tanka people were modeled as the admixture of two Neolithic East Asian

682 lineages. Genetic drift was marked as 1000 times of f2 values. Dot blue lines denoted the admixture 683 events and corresponding admixture proportions were also marked. 684 685 Legends of Tables 686 Table S1. Pairwise Fst genetic distance between three studied populations and other 65 reference 687 populations. 688 Table S2. Shared genetic drift between studied Tanka people and Han and other reference populations. 689 Table S3. Admixture signatures of admixture-f3 statistics focused on the new-studied Fujian Han 690 population. 691 Table S3. Genetic homogeneity examined via the symmetric-f4(Studied population1, Studied 692 population2; reference population, Mbuti). bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

0.15 A B Austroasiatic Chuanqing_Bijie Lajia_LN Cambodian Luoheguxiang_LBIA Htin_Mal Tai_Kadai Miaozigou_MN KhoMu BoY Pingliangtai_LN Kinh_HGDP CoLao Shimao_LN

0.10 Kinh_Vietnam Dai_HGDP Wadian_LN Mang Dong_Guizhou Wanggou_MN % %# ‡ * Mlabri Dong_Hunan Wuzhuangguoliang_LN $$ * $ % % * * Muong Gelao_Longlin Xiaogao_EN $%#$ %% & # ‡ %$†† % † * * Vietnamese LaChi Xiaojingshan_EN ‡ % % & ** ‡‡ ‡ $ % & *a* ‡ ‡ ‡ % %† # # # # Li_Hainan Xiaowu_MN

0.05 ‡‡ ‡ # PC3 (0.46%) PC2 (0.53%) ‡‡ ‡ Austronesian Maonan_Huanjiang Yumin_EN ‡%‡ $ $ # $ ‡ ‡ Ami Mulam_Luocheng % % % Atayal Nung Ancient_Amur_Liao River %%$%$† %$$%$$† % + a #%%‡$ + %# % + + + Cham Tay Wuqi_EN + ++ % + $ % + $ a a + Dusun Thai Banlashan_MN %† % & + + % aaaa + 0.00 † a + & + Ede Zhuang_Guangxi Erdaojingzi_LN $ $ + +++ % + + Giarai Haminmangha_MN && *#* % $ a # ‡% &&& $ a # # #* a* * ‡ % Ilocano Tibeto_Burman Longtoushan_BA %a# a ** a ‡† %& a a * * % † †‡‡‡ & a ††‡‡ † && † † Kankanaey Cong Mogushan_Xianbei_IA ‡†‡‡ % a −0.06 −0.04 −0.02 0.00 0.02‡†‡ 0.04† 0.06 ‡ % a †‡†‡‡‡ %%% ‡ Malay HaNhi Zhalainuoer_EN †† Murut Lahu_HGDP Zhalainuoer_IA −0.05 −0.06 −0.04 −0.02 0.00 0.02 0.04 −0.06 −0.04 −0.02 0.00 0.02 0.04 Tagalog LoLo PC1 (1.25%) PC1(1.25%) Visayan Naxi_HGDP Ancient_South_China C D PhuLa Chuanyun_H Hmong_Mien Qiang_Danba Liangdao1_EN Dao Qiang_Daofu Liangdao2_EN Hmong Sherpa_Nepal Qihe_EN Miao_HGDP Sila Suogang_LN PaThen Tibetan_Chamdo Taiwan_Gongguan She_HGDP Tibetan_Gangcha Taiwan_Hanben * Xijia_Kaili Tibetan_Gannan Tanshishan_LN ** Dongjia_Kaili Tibetan_Lhasa Xitoucun_LN *# * * ** Gejia_Kaili Tibetan_Nagqu *a* # # # # † Tibetan_Shannan Ancient_Japan

PC2 (0.35%) + + PC3 (0.30%) + + $ Japonic&Koreanic ‡ Tibetan_Shigatse Japan_Jomon + +++ $ # + Japanese_HGDP Tibetan_Xinlong $ + + # Korean $ Tibetan_Xunhua Ancient_Mongolia a Tibetan_Yajiang Altai_MLBA $ % % + $ a a + Mongolic TibetanHO_Yunnan Chandman_IA % aaaa + & *#* a $ a & + Baoan_Jishishan Tujia_HGDP earlyMed_Turk $ a # # a* * $ + +++ # #* * % + + * %a # ** + Buryat_Aginsky + Vietnam_Lahu earlyMed_Uigur ‡ & a a * %‡ & † ‡†‡ &% a a * %% && ‡†‡ & ‡ Buryat_Bohansky a Yi_HGDP earlyXiongnu_rest †† † & a ‡†‡‡ % a % ‡‡ a † † Buryat_Duldurginsky earlyXiongnu_west

% −0.06 −0.04 −0.02 0.00 0.02 0.04 0.06 −0.04 −0.02 0.00 0.02 0.04%% 0.06 0.08 ‡†‡‡† % †‡†‡‡‡ Buryat_Ehirit Fofonovo_EN † Tungusic † Buryat_Selenginsky Hezhen_HGDP Khovsgol_LBA −0.06 −0.04 −0.02 0.00 0.02 0.04 −0.06 −0.04 −0.02 0.00 0.02 0.04 Buryat_Zakamensky Nanai lateMed_Khitan PC1 (0.83%) PC1 (0.83%) Kalmyk Negidal lateMed_Mongol E F Khamnegan Oroqen_HGDP lateXiongnu Mogolian_HGDP Ulchi lateXiongnu_han 0.15 Mongol_Minorities Xibo_HGDP lateXiongnu_sarmatian Mongol_Sainnoyon SlabGrave_EIA_1 0.05 Mongol_Uuld Ancient_Russia Sagly_EIA_4 Mongol_Zasagt Boisman_MN † Ulaanzukh_LBA_2 0.10 Tu_HGDP DevilsCave_N ‡ CenterWest_LBA_4 Yugur_Sunan Shamanka_EBA # Mongolia_N_East Daur_HGDP Shamanka_Ene Mongolia_N_North 0.00 $ Dongxiang_Linxia UstBelaya_Angara % Ulaanzuukh_SlabGrave

0.05 Russia_UstIda_EBA & XiongNu PC3 (0.59%) PC2 (0.63%) Sinitic Russia_UstIda_LN Han_Chongqing UstBelaya_EBA Ancient_Nepal

−0.05 Han_Fujian Chokhopani_2700BP Han_Guangdong Ancient_Yellow River Mebrak_2125BP Han_Henan Bianbian_EN Samdzong_1500BP Han_Hubei Boshan_EN Han_Jiangsu China_Tianyuan Studied Populations

−0.10 Han_Shandong Dacaozi_IA Tanka_Fujian −0.05 0.00 Han_Shanghai Haojiatai_LBIA Tanka_Shacheng Han_Shanxi Haojiatai_LN Tanka_Xinshizhou Han_SichuanHO Jiaozuoniecun_LBIA Han_Zhejiang Jinchankou_LN −0.10 −0.05 PC1 (0.87%) 0.00 0.05 −0.10 −0.05 PC1 (0.87%) 0.00 0.05 K=8 K=9 K=10 K=11 K=8 K=9 K=10 K=11 earlyMed_Uigur Chandman_IA Taiwan_Hanben earlyXiongnu_west China_Tianyuan Atayal Tibeto-Burman Austronesian earlyMed_Turk Taiwan_Gongguan Sila Kankanaey Suogang_LN Cong Tagalog Lahu_HGDP Qihe_EN Dusun

HaNhi bioRxiv preprint Murut Vietnam_Lahu Ami KhoMu Tanshishan_LN Xitoucun_LN Mang Liangdao1_EN Ilocano (which wasnotcertifiedbypeerreview)istheauthor/funder.Allrightsreserved.Noreuseallowedwithoutpermission. Htin_Mal Visayan Liangdao2_EN Ede Tibetan_Chamdo Giarai Tibetan_Shannan Tibetan_Lhasa

Mongolian Neolithic Hmong-Mien PhuLa doi: Muong Tibetan_Shigatse Sherpa_Nepal Tibetan_Nagqu Chokhopani_2700BP Thai https://doi.org/10.1101/2021.07.18.452867 Mebrak_2125BP LaChi Samdzong_1500BP Tibetan_Gangcha LoLo Qiang_Danba Malay Qiang_Daofu Cambodian Tibetan_Yajiang TibetanHO_Yunnan Cham Miaozigou_MN Tibetan_Xinlong Han_SichuanHO Naxi_HGDP Tibetan_Xunhua Han_Chongqing Yi_HGDP Jinchankou_LN Tujia_HGDP Pingliangtai_LN Shimao_LN Tungusic Austroasiatic1 Haojiatai_LBIA Lajia_LN Jiaozuoniecun_LBIA Wuzhuangguoliang_LN Luoheguxiang_LBIA Han_Jiangsu Han_Shanghai Hmong Han_Shanxi Han_Henan Gejia_Kaili Han_Shandong Dongjia_Kaili Dongxiang_Linxia PaThen Yugur_Sunan Xijia_Kaili Haminmangha_MN Tu_HGDP Zhalainuoer_IA Baoan_Jishishan earlyXiongnu_rest Mongolia_N_East Wadian_LN Tibetan_Gannan Dacaozi_IA lateXiongnu Erdaojingzi_LN Wanggou_MN

Russia_UstBelaya_Angara ; Jomon Western herder Haojiatai_LN Russia_UstIda_EBA this versionpostedJuly19,2021. Xiaowu_MN Mogolian_HGDP Russia_Shamanka_EBA UstBelaya_EBA Xibo_HGDP Russia_UstIda_LN

Japanese_HGDP Khovsgol_LBA Longtoushan_BA Boshan_EN Mongolia_LBA_4_CenterWest Korean Yumin_EN XiongNu Mongolia_N_North Bianbian_EN Mongolia_LBA_2_Ulaanzukh Xiaojingshan_EN Ulaanzuukh_SlabGrave lateXiongnu_han Fofonovo_EN Banlashan_MN Mongolia_EIA_1_SlabGrave Xiaogao_EN BoY Chuanyun_H Russia_Shamanka_Eneolithic Mlabri BoY Austroasiatic2 Tanka_Xinshizhou Japan_Jomon Nanai Han_Hubei Han_Zhejiang Boisman_MN Tanka_Fujian DevilsCave_N Han_Fujian Negidal Mogushan_Xianbei_IA

Tanka_Shacheng Ulchi The copyrightholderforthispreprint Wuqi_EN Zhalainuoer_EN Chuanqing_Bijie Oroqen_HGDP lateMed_Khitan Miao_HGDP Daur_HGDP Han_Guangdong Hezhen_HGDP She_HGDP Khamnegan Buryat_Bohansky Shamanka_EBA Tanka-related ancestry Dai_HGDP Buryat_Selenginsky Nung Buryat_Zakamensky Buryat_Duldurginsky Tay Buryat_Aginsky Kinh_Vietnam Buryat_Ehirit Kinh_HGDP Vietnamese Li_Hainan lateMed_Mongol Maonan_Huanjiang

Mulam_Luocheng Kalmyk Zhuang_Guangxi Mongol_Uuld Mongol_Zasagt CoLao Mongol_Minorities Dong_Guizhou Mongol_Sainnoyon Dong_Hunan Altai_MLBA Mongolia_EIA_4_Sagly Dao Gelao_Longlin lateXiongnu_sarmatian bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

Z-Scores f4(Reference populations1, Reference populations2; Tanka_Shacheng, Mbuti) 40

20 Group1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ilocano + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + TibetanHO_Yunnan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Qiang_Danba

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mang 0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dusun + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + HaNhi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Vietnam_Lahu + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Cong + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Qiang_Daofu + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Yajiang −20 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Sila

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Thai + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Nagqu + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Chamdo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + KhoMu

−40 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Rai_Nepal + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Shannan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Lhasa + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Shigatse

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mlabri + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Visayan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Gannan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Htin_Mal + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Xunhua + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Sherpa_Nepal + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tagalog

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Shanghai + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + She_HGDP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Fujian + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Hubei

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Zhejiang + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dong_Hunan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Jiangsu + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Miao_HGDP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Zhuang_Guangxi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Maonan_Huanjiang + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mulam_Luocheng + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tujia_HGDP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Guangdong + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dong_Guizhou

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Kankanaey + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Henan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Chongqing + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Shandong + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Nung + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoLao + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ami + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dao + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_SichuanHO + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Hmong

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + LoLo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PhuLa + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Kinh_HGDP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Lahu_HGDP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Murut + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Yi_HGDP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Naxi_HGDP

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Kinh_Vietnam + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Muong + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dai_HGDP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Vietnamese + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Shanxi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Gelao_Longlin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PaThen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Xinlong + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Li_Hainan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + LaChi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BoY + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Atayal

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Newar_Nepal

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tamang_Nepal

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ede + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Giarai

Group + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Gangcha + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Gurung_Nepal Austroasiatic + + + + + + + + + + + + + Austronesian + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Cambodian + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Malay Hmong_Mien + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Cham

Sinitic Sila Tay Dao Ede Cong Thai Ami LoLo BoY MangDusunHaNhi Nung CoLao PhuLa Murut LaChi Atayal Giarai MalayCham IlocanoYunnan KhoMu MlabriVisayan Tagalog Hmong Muong PaThen Group2 Htin_Mal Tai_Kadai Rai_Nepal Han_Hubei Kankanaey Yi_HGDP Dai_HGDP Li_Hainan Cambodian She_HGDPHan_Fujian Han_Jiangsu Tujia_HGDP Han_Henan Naxi_HGDP VietnameseHan_Shanxi Qiang_Danba Qiang_Daofu Sherpa_Nepal Han_ZhejiangDong_HunanMiao_HGDP Kinh_HGDPLahu_HGDP Newar_Nepal Vietnam_Lahu Tibetan_Nagqu Tibetan_Lhasa Han_Shanghai Dong_Guizhou Han_Shandong Kinh_Vietnam Gelao_Longlin Tamang_Nepal Gurung_Nepal Tibetan_Yajiang Tibetan_GannanTibetan_Xunhua Han_Guangdong Han_Chongqing Han_SichuanHO Tibetan_Xinlong Tibeto_Burman Tibetan_Chamdo Tibetan_ShannanTibetan_Shigatse Zhuang_GuangxiMulam_Luocheng Tibetan_Gangcha TibetanHO_ Maonan_Huanjiang bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

Group f (Reference populations1, Tanka_Xinshizhou; Reference populations2, Mbuti) Ancient populations 4 Austroasiatic Austronesian Hmong_Mien Sinitic Tai_Kadai Tibeto_Burman Reference1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dusun + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Murut + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ilocano

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Qihe_EN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Lahu_HGDP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Vietnam_Lahu + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + HaNhi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Sila

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Htin_Mal + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + KhoMu + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mlabri + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Cong + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mang

+ + + + + + + Han_Hubei + + + + + + + + + + + + + + + Han_Shanghai + + + + + + Han_Guangdong + + + Miao_HGDP + + She_HGDP + + + + Han_SichuanHO + + Longtoushan_BA Chuanyun_H Miaozigou_MN Haojiatai_LN Tujia_HGDP Han_Chongqing Han_Fujian Han_Zhejiang + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Bianbian_EN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Henan + + + + + + + + + + + + + + + + + + + + + + Han_Jiangsu + + + + + + + + + + + + + + + + + + + + + + + + Jiaozuoniecun_LBIA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Jinchankou_LN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Wadian_LN + + + + + + + + + + + + + + + + + + + + + + + + + + + + Xiaowu_MN + + + + + + + + + + + + + + + + + + + + Haojiatai_LBIA + + + + + + + + + + + + + + + + + + + + + + + Pingliangtai_LN

+ + + + + + + + + + + + + + + + + + + + + Hmong + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dong_Guizhou + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dong_Hunan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoLao

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Maonan_Huanjiang + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Li_Hainan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Zhuang_Guangxi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Nung + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + LaChi Z-Score + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mulam_Luocheng + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dao

≥10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Kankanaey + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ami + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Atayal [5,10) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Taiwan_Hanben + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PhuLa + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Kinh_HGDP [3,5) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Kinh_Vietnam + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + LoLo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Vietnamese + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Gelao_Longlin 0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dai_HGDP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Muong

+ + + + + + + + + + + Suogang_LN (-5,-3] + + + + + + + + + + + + + + + + Tanshishan_LN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BoY + + + + + + + + + + + + + + + + + + + + + + + PaThen (-10,-5] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Liangdao2_EN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Liangdao1_EN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Xitoucun_LN

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tagalog (~,-10] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Visayan

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Thai + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ede + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Giarai + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Cham + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Cambodian + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Malay

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Qiang_Daofu

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Gannan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Nagqu + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Chamdo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tibetan_Lhasa

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Yi_HGDP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Naxi_HGDP

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Banlashan_MN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Wanggou_MN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Lajia_LN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Shimao_LN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Shandong + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Han_Shanxi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Boshan_EN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Xiaojingshan_EN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Xiaogao_EN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Yumin_EN

Ede Sila TayDao Cong BoY Nung LoLoThai Ami GiaraiMalay MangChamHaNhi LaChi PhuLaCoLao DusunMurut Atayal Mlabri KhoMu Hmong PaThen Muong IlocanoTagalogVisayan Lajia_LN Htin_Mal Qihe_EN Han_Hubei Yumin_EN Yi_HGDP Cambodian Dai_HGDPLi_Hainan Kankanaey Reference2Han_Jiangsu Han_HenanHan_ShanxiHan_FujianTujia_HGDPShe_HGDP Boshan_ENWadian_LN Shimao_LNNaxi_HGDP Vietnamese Han_Zhejiang Xiaogao_ENHaojiatai_LNBianbian_EN Chuanyun_H Qiang_Daofu Xiaowu_MN Lahu_HGDP Dong_HunanMiao_HGDP Kinh_HGDP Suogang_LNXitoucun_LN Han_ShanghaiHan_Shandong Tibetan_NagquTibetan_Lhasa Banlashan_MNWanggou_MN Vietnam_LahuDong_Guizhou Kinh_Vietnam Gelao_LonglinLiangdao1_EN Liangdao2_ENTanshishan_LN Han_SichuanHOHan_Chongqing Haojiatai_LBIAJinchankou_LNMiaozigou_MN Pingliangtai_LN Tibetan_Gannan Han_Guangdong Taiwan_Hanben Xiaojingshan_ENLongtoushan_BA Tibetan_Chamdo Zhuang_GuangxiMulam_Luocheng Maonan_Huanjiang Jiaozuoniecun_LBIA bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

A PaThen Dong_Guizhou Dong_Hunan Ami Dusun Murut Kankanaey Visayan Taiwan_Hanben Tanshishan_LN Xitoucun_LN Atayal Tagalog LaChi Nung Li_Hainan Ami Dusun Kinh_Vietnam Murut Kankanaey Vietnamese Visayan Dai_HGDP Taiwan_Hanben Kinh_HGDP Tanshishan_LN Muong Atayal Xitoucun_LN Tagalog Thai Mang Cham 0.000 0.005 0.010 0.015 0.020 0.025 0.030 0.035 Cambodian Htin_Mal Malay Ede Giarai KhoMu B Ami Han_Hubei Mulam_Luocheng Migration Tay Atayal Han_Jiangsu Muong BoY Han_Shandong Murut weight Zhuang_Guangxi Cambodian Han_Shanxi Nung Maonan_Huanjiang Cham Han_SichuanHO PaThen 0.5 0.10 e Chuanqing_Bijie Han_Zhejiang She_HGDP Gelao_Longlin n i CoLao Hmong Tagalog l Mulam_Luocheng c Dai_HGDP Htin_Mal Taiwan_Hanben

c Dao Japanese_HGDP Han-Fujian_New Dao i

t Dong_Guizhou Kankanaey Tanka_Shacheng a

CoLao i Dong_Hunan KhoMu Tanka_Xinshizhou s Dongjia_Kaili Kinh_HGDP Tanshishan_LN

BoY a

o Dusun Kinh_Vietnam Tay

r Miao_HGDP t Ede Korean Thai

s Gejia_Kaili LaChi Vietnamese

Han_Guangdong u Gelao_Longlin A Li_Hainan Visayan She_HGDP Giarai Malay Xijia_Kaili 0.05 Han_Fujian Mang Xitoucun_LN Tanka_Xinshizhou Han_Guangdong Maonan_Huanjiang Zhuang_Guangxi Han_Fujian_New Han_Henan Miao_HGDP Tanka_Shacheng Han_SichuanHO 0

Han_Zhejiang PC2 Han_Jiangsu Han_Shanxi Han_Shandong 0.00 e Han_Henan n li Japanese_HGDP c l Korean ta n Han_Hubei e A in u Han_Fujian t st n r Chuanqing_Bijie o on c e 10 s.e. e si Xijia_Kaili −0.05 n an i cl Dongjia_Kaili Tanka People h ine C h Gejia_Kaili t u o Hmong S

−0.05 0.00 0.05 PC1 0.10 0.15 0.000 0.001 0.002 0.003 0.004 Drift parameter with five migration events bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

f4(Mbu, Los; Ong, Xia)=2.650*SE f4(Mbu, Los; Ong, Xia)=2.650*SE Tanka_Shacheng Tanka_Xinshizhou A Final score: 20.513 B Final score: 21.808 C D Nganasan/Tanka_Xinshizhou abs(Z_Score) > 2 Han_Shandong/Zhuang_Guangxi Kinh_Vietnam/Gelao_Longlin FALSE Zhuang_Guangxi/Tibetan_Shigatse R R Maonan_Huanjiang/Dongjia_Kaili Han_Shandong/Zhuang_Guangxi TRUE Dongjia_Kaili/Nganasan Han_Shandong/Maonan_Huanjiang Xijia_Kaili/Nganasan 51 51 58 58 Ulchi/Tanka_Xinshizhou Maonan_Huanjiang/Nganasan Tibetan_Shigatse/Tanka_Xinshizhou Dao/Daur_HGDP Dai_HGDP/Tanka_Xinshizhou Dongjia_Kaili/Ulchi LaChi/Dongjia_Kaili Dao/Mongol_Uuld 23 161 312 0 23 161 0 300 Xijia_Kaili/Ulchi Daur_HGDP/Maonan_Huanjiang Tibetan_Shigatse/Dongjia_Kaili Gelao_Longlin/Tibetan_Lhasa Mongol_Uuld/Maonan_Huanjiang Mbuti Denisova Mbuti Denisova Han_Shandong/Xijia_Kaili Daur_HGDP/Dai_HGDP Gejia_Kaili/Nganasan Mongol_Uuld/Han_Shandong BCE15000 BCE10000 BCE5000 0 BCE15000 BCE10000 BCE5000 0 81 21 127 20 Tanshishan_LN NuiNap_BA Yumin_EN ManBac_LN Yumin_EN Tanka-Xinshizhou|3.83E-01 Tanka-Xinshizhou|2.80E-02 Tanka-Shacheng|6.38E-01 E Tanka-Shacheng|2.80E-02 F Han-Fujian|4.97E-01 Han-Fujian|3.00E-02 0 68 11 0 21 15 10 Shimao_LN Shimao_LN Tanka-Xinshizhou|4.14E-01 Tanka-Xinshizhou|1.83E-01 Tanka-Shacheng|7.47E-01 Tanka-Shacheng|5.48E-01 Loschbour 9 4% Loschbour 4% Han-Fujian|1.78E-01 Han-Fujian|1.51E-01 Longtoushan_BA Longtoushan_BA Tanka-Xinshizhou|3.99E-01 Tanka-Xinshizhou|6.35E-01 45 242 Tanka-Shacheng|6.16E-01 Tanka-Shacheng|8.76E-01 127 85 36 242 Han-Fujian|5.79E-01 Han-Fujian|8.60E-01 Banlashan_MN Banlashan_MN Tanka-Xinshizhou|1.07E-01 Tanka-Xinshizhou|7.86E-02 Onge Tanka-Shacheng|3.18E-01 Tanka-Shacheng|3.51E-01 2 91 96% 66 Han-Fujian|1.09E-01 Han-Fujian|2.43E-01 Dacaozi_IA Dacaozi_IA Tanka-Xinshizhou|2.92E-01 Tanka-Xinshizhou|4.79E-01 4% Onge 83 8 20 96% Tanka-Shacheng|2.94E-01 Tanka-Shacheng|4.93E-01 Han-Fujian|5.27E-01 Han-Fujian|8.29E-01 2% 6 Jinchankou_LN Jinchankou_LN 89 12 262 31 65 Tanka-Xinshizhou|2.60E-01 Tanka-Xinshizhou|2.27E-01 Tanka-Shacheng|5.67E-01 Tanka-Shacheng|5.19E-01 0 90 0 10 260 Han-Fujian|4.41E-01 Han-Fujian|5.87E-01 Lajia_LN Lajia_LN 117 Tianyuan Tanka-Xinshizhou|2.37E-01 Tanka-Xinshizhou|2.14E-01 Tanka-Shacheng|3.44E-01 Tanka-Shacheng|3.51E-01 Tianyuan Han-Fujian|5.10E-01 Han-Fujian|6.33E-01 96% 181 0 169 0 Luoheguxiang_LBIA Luoheguxiang_LBIA Tanka-Xinshizhou|8.98E-01 Tanka-Xinshizhou|8.35E-01 98% 0 193 25% 0 0 6 0 Tanka-Shacheng|9.94E-01 Tanka-Shacheng|9.87E-01 29% Han-Fujian|7.69E-01 Han-Fujian|7.60E-01 26% Jiaozuoniecun_LBIA Jiaozuoniecun_LBIA 96 71% 74% 24 0 26% Tanka-Xinshizhou|3.43E-01 Tanka-Xinshizhou|4.34E-01 Tanka-Shacheng|4.96E-01 Tanka-Shacheng|5.86E-01 93 74% 75% 21% 79% 61% 39% Han-Fujian|1.50E-01 Han-Fujian|2.27E-01 Pingliangtai_LN Pingliangtai_LN MNE Tanka-Xinshizhou|1.55E-01 Tanka-Xinshizhou|2.33E-01 Tanka-Shacheng|3.65E-01 Tanka-Shacheng|5.00E-01 MNE Han-Fujian|3.55E-01 Han-Fujian|5.43E-01 0 117 361 0 24 0 Wadian_LN Wadian_LN Tanka-Xinshizhou|5.66E-01 Tanka-Xinshizhou|5.32E-01 1 340 9 0 Tanka-Shacheng|8.44E-01 Tanka-Shacheng|8.58E-01 Chokhopani Han-Fujian|7.44E-01 Han-Fujian|7.48E-01 Xiaowu_MN Xiaowu_MN Tanka-Xinshizhou|4.75E-01 Chokhopani Hanben Tanka-Xinshizhou|7.48E-01 Tanka-Shacheng|6.37E-01 Tanka-Shacheng|8.98E-01 67% 69% 33% 31% 4 447 9% Han-Fujian|7.01E-01 Han-Fujian|8.89E-01 Xiaogao_EN Xiaogao_EN 4 444 365 1 Tanka-Xinshizhou|2.17E-01 Tanka-Xinshizhou|5.43E-01 Xiaowu_MN Tanka-Shacheng|3.96E-01 Tanka-Shacheng|8.16E-01 Han-Fujian|1.01E-01 Han-Fujian|4.97E-01 Xiaowu_MN Tanshishan_LN Boshan_EN Boshan_EN Tanka-Xinshizhou|3.02E-01 Tanka-Xinshizhou|3.02E-01 0 247 91% Tanka-Shacheng|3.99E-01 Tanka-Shacheng|3.99E-01 Han-Fujian|1.23E-01 Han-Fujian|1.23E-01 64% 36% Bianbian_EN Wanggou+_MN Hanben Tanshishan_LN Tanka-Xinshizhou|2.43E-02 Tanka-Xinshizhou|2.70E-01 Tanka-Shacheng|6.96E-02 Tanka-Shacheng|4.73E-01 Han-Fujian|8.08E-02 Han-Fujian|2.76E-01 5 10 Mongolia_N_East Mongolia_N_East Tanka-Xinshizhou|2.60E-02 Tanka-Xinshizhou|1.83E-01 Tanka-Shacheng|1.37E-01 Tanka-Shacheng|5.92E-01 Han-Fujian|4.02E-01 Han-Fujian|2.51E-01 Tanka_Xinshizhou Tanka_Xinshizhou 0 0.2 0.4 0.6 0.8 1.0 0 0.5 1.0 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.18.452867; this version posted July 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 61Han_Xian;18Han_Baoji;24Han_ Tanka_Xinshizhou664 IBD Tanka_Xinshizhou674 Tanka_Xinshizhou663 Tanka_Xinshizhou673 Tanka_Xinshizhou686 Tanka_Xinshizhou692 D F Tanka_Shacheng639 Tanka_Shacheng657 Tanka_Shacheng653 Tanka_Shacheng654 Tanka_Shacheng631 Mongolian_Bijie577 Mongolian_Bijie585 Mongolian_Bijie588 Manchu_Jinsha522 Manchu_Jinsha524 Manchu_Jinsha530 Manchu_Jinsha536 Han_Hanzhong100 Miao_Qianjiang565 Miao_Qianjiang556 Han_Nanchong205 Han_Nanchong185 Han_Nanchong175 Han_Nanchong207 Han_Nanchong167 Miao_Qianjiang557 Han_Nanchong156 Han_Nanchong197 Han_Nanchong187 Tujia_Qianjiang711 Tujia_Qianjiang704 Tujia_Qianjiang707 Tujia_Qianjiang708 Tujia_Qianjiang723 Tujia_Qianjiang726 Chuanqing_Bijie43 Chuanqing_Bijie44 Han_Shangluo216 Lahu_Lancang489 Lahu_Lancang483 Wa_Cangyuan730 Wa_Cangyuan738 Han_Xianyang320 Han_Xianyang321 Han_Xianyang323 Pumi_Lanping592 Pumi_Lanping598 Blang_Menghai18 Blang_Menghai21 Han_Lanzhou115 Han_Lanzhou126 Han_Lanzhou138 Han_Lanzhou134 Han_Lanzhou153 Han_Lanzhou152 Han_Lanzhou125 Hani_Honghe373 Hani_Honghe378 Han_Shangluo Han_Nanchong Han_Lanzhou Han_Hanzhong Han_Baoji Han_Ankang Gejia_Kaili Dongjia_Kaili Chuanqing_Bijie Blang_Menghai Bai_Heqing Manchu_Bijie514 Manchu_Bijie492 Manchu_Bijie504 Hui_Guizhou449 Hui_Guizhou477 Hui_Guizhou451 Hui_Guizhou456 Hui_Guizhou446 Hui_Guizhou455 Han_Weinan240 Han_Weinan247 Han_Weinan226 Han_Weinan231 Han_Weinan224 Han_Weinan234 Shui_Sandu606 Shui_Sandu620 Dongjia_Kaili49 Han_Ankang63 Han_Ankang72 Hui_Boshu411 Hui_Boshu385 Hui_Boshu406 Hui_Boshu418 Hui_Boshu428 Hui_Boshu407 Hui_Boshu424 Hui_Boshu412 Han_Xian293 Han_Xian304 Han_Xian257 Han_Xian248 Han_Xian278 Han_Xian308 Han_Xian305 Han_Xian299 Han_Xian315 Han_Xian280 Han_Xian261 Han_Xian266 Han_Xian251 Gejia_Kaili59 Gejia_Kaili60 Gejia_Kaili54 Han_Baoji84 Bai_Heqing9 Bai_Heqing1 Han_Baoji88

Gejia_Kaili Dongjia_Kaili

Xijia_Kaili Tanka_Shacheng657 Manchu_Jinsha Manchu_Bijie Lahu_Lancang Hui_Guizhou Hui_Boshu Hani_Honghe Han_YulinSX Han_Yanan Han_Xianyang Han_Xian Han_Weinan Manchu_Bijie 0.000 Manchu_Jinsha Tanka_Shacheng653 Tanka_Shacheng654 Tanka_Shacheng631 0.142 Chuanqing_Bijie Tanka_Xinshizhou674 0.1420.1420.142 0.142 0.367 0.0860.0000.000 Tanka_Xinshizhou663 0.6290.000 bioRxiv preprint 0.6290.000 0.000 0.367 Tanka_Xinshizhou673 0.0000.1420.0000.000 Blang_MenghaiShui_Sandu Tanka_Xinshizhou686 0.000 Tanka_Xinshizhou692 0.9940.994 0.367

0.000 Xijia_Kaili Wa_Cangyuan Tujia_Qianjiang Tanka_Xinshizhou Tanka_Shacheng Han_Fujian Shui_Sandu Pumi_Lanping Mongolian_Bijie Miao_Qianjiang Wa_Cangyuan Hui_Guizhou449 0.0000.0000.000 Hui_Guizhou477 0.0000.0000.0000.000 Hani_Honghe Hui_Guizhou451 0.8500.1580.850 Hui_Guizhou456 0.4310.431

Lahu_Lancang Weinan;39Han_Lanzhou;14Han_Xianyang;29Han_YulinSX;7Han_Shangluo;10Han_Yanan;4Han_Nanchong;1Han_Ankang;2Han_Hanzhong Hui_Guizhou446 Mongolian_Bijie 0.000 Hui_Guizhou455 0.010 0.000 (which wasnotcertifiedbypeerreview)istheauthor/funder.Allrightsreserved.Noreuseallowedwithoutpermission. Han_Xian251 Miao_Qianjiang Han_Xianyang323 A Tujia_Qianjiang Han_Weinan234 0.120 Han_Xian261 Han_Nanchong Han_Xian266 Han_Weinan224 0.120 Han_Xian280 Hui_Guizhou Han_Weinan226

Han_Weinan231 doi: Bai_Heqing Pumi_Lanping Han_Xian257 0.120 Han_Xianyang320 Tanka_Shacheng Han_Xian248 Han_Fujian Han_Xianyang321 Tanka_Xinshizhou Han_Xian278 https://doi.org/10.1101/2021.07.18.452867 Han_Xian308 Han_Lanzhou134 Han_Xian305 Han_Yanan Han_Xian299 0.846 Han_YulinSX Han_Lanzhou153 0.098 Han_Shangluo Han_Xian315 Han_Lanzhou152 Han_Weinan Han_Lanzhou125 Han_Weinan247 Han_Baoji84 Han_LanzhouHan_Xian Han_Weinan240 Han_Hanzhong100 Han_Xianyang Han_Lanzhou115

Han_Hanzhong Han_Xian293 Blang_Menghai23 0.098 Blang_Menghai27 Han_Lanzhou126 Han_Lanzhou138 B # Blang_Menghai24

Han_Xian304 # Hui_Boshu 0.693 Blang_Menghai30 Hui_Boshu411 0.693 Blang_Menghai19 Blang_Menghai16 Han_Ankang 0.693 Blang_Menghai29

0.693 0.693 Blang_Menghai17 Hui_Boshu385 0.693 # Blang_Menghai26 Blang_Menghai25 # Hui_Boshu406 0.693 Blang_Menghai18

0.693 Blang_Menghai22 # # Han_Baoji Hui_Boshu418 0.970 0.693 # # #

Hui_Boshu428 #

0.9880.012 # Bai_Heqing9 # Bai_Heqing1 0.0000.0000.000 Pumi_Lanping592 0.317 0.012 Blang_Menghai20 Han_Baoji Han_Ankang Hui_Boshu Han_Hanzhong Han_Xianyang Han_Lanzhou Han_Xian Han_Weinan Han_Shangluo Han_YulinSX Han_Yanan Tanka_Xinshizhou Tanka_Shacheng Han_Fujian Pumi_Lanping Bai_Heqing Hui_Guizhou Han_Nanchong Tujia_Qianjiang Miao_Qianjiang Mongolian_Bijie Lahu_Lancang Hani_Honghe Wa_Cangyuan Blang_Menghai Shui_Sandu Chuanqing_Bijie Manchu_Jinsha Manchu_Bijie Xijia_Kaili Dongjia_Kaili Gejia_Kaili Pumi_Lanping598 0.000 Blang_Menghai28 Wa_Cangyuan736 Mongolian_Bijie577 0.000 Wa_Cangyuan742

0.000 Wa_Cangyuan740 Wa_Cangyuan733 0.000 # Wa_Cangyuan728 Wa_Cangyuan729 Wa_Cangyuan735 Miao_Qianjiang565 Wa_Cangyuan738 Wa_Cangyuan739 0.000 0.000 # Wa_Cangyuan741 Wa_Cangyuan737

0.295 Wa_Cangyuan732 Mongolian_Bijie585 0.0000.984 0.000 Wa_Cangyuan730 0.727 # # #

Mongolian_Bijie588 # # # # # # #

Tujia_Qianjiang711 0.000 # Wa_Cangyuan734 Wa_Cangyuan731 # #

Tujia_Qianjiang704 Blang_Menghai21 Tujia_Qianjiang707 0.000 PC 1vs2 Lahu_Lancang485 # Tujia_Qianjiang708 # #

Tujia_Qianjiang723 Lahu_Lancang483 Lahu_Lancang479

Miao_Qianjiang556 Lahu_Lancang488 Lahu_Lancang486 0.000 # Tujia_Qianjiang726 Lahu_Lancang484 Lahu_Lancang487 # Hani_Honghe377 # Hani_Honghe382 Hani_Honghe378 Han_Nanchong205 Lahu_Lancang490 Hani_Honghe383 # Hani_Honghe381 Lahu_Lancang489 Hani_Honghe375 Hani_Honghe380 # Hani_Honghe374 Hani_Honghe372 Hani_Honghe379

Han_Nanchong185 Hani_Honghe384 Hani_Honghe371 Hani_Honghe370 # Hani_Honghe376 Lahu_Lancang481 #

Han_Nanchong175 # Lahu_Lancang480 # # # Lahu_Lancang482 # # # # Lahu_Lancang491 # #

Han_Nanchong207 # Hani_Honghe373 # # # #

Tanka_Xinshizhou664 0.367 # # #

100 200 300 Tanka_Shacheng639 0.028 # # Han_Nanchong167 # Shui_Sandu612 Shui_Sandu615 Shui_Sandu609 Shui_Sandu614 Shui_Sandu606 Shui_Sandu613 Shui_Sandu616 Shui_Sandu610 Shui_Sandu607 Shui_Sandu611 Shui_Sandu618 Dongjia_Kaili48

Han_Shangluo216 Shui_Sandu617 Shui_Sandu619 Dongjia_Kaili46 Shui_Sandu620 Shui_Sandu608 Dongjia_Kaili53 Manchu_Bijie502 Dongjia_Kaili45 Dongjia_Kaili49 Dongjia_Kaili51 Manchu_Jinsha520 Gejia_Kaili55 Manchu_Bijie517 Dongjia_Kaili50 Dongjia_Kaili47 Gejia_Kaili61 Mongolian_Bijie569 Gejia_Kaili62 Manchu_Jinsha540 Xijia_Kaili748 Gejia_Kaili58 Gejia_Kaili54 Gejia_Kaili56 ; Xijia_Kaili749 Pumi_Lanping600 Gejia_Kaili57 Manchu_Jinsha545 Xijia_Kaili747 Dongjia_Kaili52 Manchu_Jinsha530

Han_Ankang63 Manchu_Jinsha542 Manchu_Bijie503 Xijia_Kaili743 Manchu_Bijie515 Gejia_Kaili60 Bai_Heqing1 Pumi_Lanping602 Manchu_Jinsha524 Manchu_Jinsha527 Pumi_Lanping601 Manchu_Jinsha537 Manchu_Bijie514 Xijia_Kaili751 Manchu_Jinsha532 Xijia_Kaili744 Manchu_Jinsha538 Bai_Heqing10 Chuanqing_Bijie43 Pumi_Lanping605 Manchu_Jinsha522 Manchu_Jinsha544 # Manchu_Jinsha521 Manchu_Bijie505 Chuanqing_Bijie32 Manchu_Bijie511 Chuanqing_Bijie35 Manchu_Bijie509 Manchu_Jinsha526 Manchu_Jinsha525 Manchu_Jinsha541 Manchu_Jinsha536 Bai_Heqing13 # Fst Miao_Qianjiang565 Xijia_Kaili750 Manchu_Jinsha528 Bai_Heqing15 Manchu_Bijie508 Manchu_Bijie497 # Manchu_Jinsha533 Manchu_Jinsha523 Manchu_Bijie498 Bai_Heqing12 Manchu_Bijie512 Manchu_Bijie493 Xijia_Kaili745 Chuanqing_Bijie36 Bai_Heqing14 Manchu_Jinsha531 Chuanqing_Bijie40 # Pumi_Lanping598 Manchu_Bijie495 Pumi_Lanping603 Chuanqing_Bijie41 Manchu_Bijie510 Manchu_Jinsha543 Manchu_Bijie499 # Chuanqing_Bijie42 Chuanqing_Bijie38 # Manchu_Jinsha539 Tanka_Xinshizhou689 # Gejia_Kaili59 Manchu_Jinsha534 # Manchu_Bijie507

Han_Baoji88 Bai_Heqing9 # # Bai_Heqing2 Chuanqing_Bijie44 # Bai_Heqing6 Bai_Heqing8 # Chuanqing_Bijie34 Chuanqing_Bijie37 # Manchu_Bijie518 Mongolian_Bijie583 Bai_Heqing5 Pumi_Lanping604 Pumi_Lanping592 Manchu_Bijie496 Mongolian_Bijie573 # Chuanqing_Bijie39 Chuanqing_Bijie33 Pumi_Lanping594 # Tanka_Xinshizhou674 # this versionpostedJuly19,2021. # Manchu_Bijie492 Manchu_Bijie516 Pumi_Lanping593 # # Bai_Heqing11 # # Manchu_Bijie500 Chuanqing_Bijie31 # # Pumi_Lanping597 # Pumi_Lanping599 Mongolian_Bijie570 Tanka_Xinshizhou691 Tanka_Xinshizhou670 Mongolian_Bijie578 Tanka_Xinshizhou667 Mongolian_Bijie590 Mongolian_Bijie591 # Manchu_Bijie494 Mongolian_Bijie577 Bai_Heqing3 Mongolian_Bijie585 # Tanka_Xinshizhou697 Mongolian_Bijie571 # # # Bai_Heqing7 # Manchu_Bijie501 Tanka_Xinshizhou684 # Mongolian_Bijie572 # Mongolian_Bijie582 Manchu_Bijie506 # Tanka_Xinshizhou665 # Mongolian_Bijie579 Mongolian_Bijie576 Bai_Heqing4 Tanka_Xinshizhou686 Pumi_Lanping596 # Manchu_Jinsha535 Mongolian_Bijie589 Tanka_Xinshizhou680 Mongolian_Bijie568 Tanka_Xinshizhou661 Mongolian_Bijie574 Manchu_Jinsha519 Hui_Guizhou440 # Manchu_Jinsha546 # Manchu_Bijie504 Mongolian_Bijie586 # Han_Nanchong165 Tanka_Xinshizhou696 Pumi_Lanping595 Han_Nanchong163 Manchu_Bijie513 Mongolian_Bijie584 Tujia_Qianjiang714 Tanka_Xinshizhou695 # Han_Ankang72 Tanka_Xinshizhou662 Tanka_Xinshizhou681 Tanka_Xinshizhou683 # Miao_Qianjiang556 Hui_Guizhou453 Tanka_Xinshizhou671 Mongolian_Bijie588 Mongolian_Bijie580 Han_Nanchong207 Hui_Guizhou464 Mongolian_Bijie587 Manchu_Jinsha529 Miao_Qianjiang550 Han_Nanchong188 Mongolian_Bijie566 # Hui_Guizhou460 Hui_Guizhou465 # Tanka_Xinshizhou692 Mongolian_Bijie581 Hui_Guizhou449 Tujia_Qianjiang710 Hui_Guizhou470 Han_Nanchong184 # Hui_Guizhou450 Hui_Guizhou445 Tanka_Xinshizhou682 Hui_Guizhou458 # Tanka_Xinshizhou666 Miao_Qianjiang562 # Han_Nanchong202 # Hui_Guizhou473 Xijia_Kaili746 # Hui_Guizhou463 Tanka_Shacheng637 Han_Nanchong213 Tujia_Qianjiang706 # Han_Nanchong175 Han_Nanchong190 Hui_Guizhou461 Hui_Guizhou437 # Hui_Guizhou448 Miao_Qianjiang559 Han_Nanchong159 Hui_Guizhou443 Hui_Guizhou441 Tanka_Xinshizhou669 # Tujia_Qianjiang700 Han_Nanchong176 Tanka_Xinshizhou690 Hui_Guizhou456 Tanka_Shacheng627 Han_Nanchong155 Tanka_Xinshizhou678 Han_Nanchong206 Tujia_Qianjiang702 Hui_Guizhou452 Tanka_Xinshizhou673 Hui_Guizhou468 Tanka_Xinshizhou679 Tanka_Shacheng651 Tanka_Xinshizhou694 Han_Nanchong154 Han_Nanchong170 # # # Hui_Guizhou438 Miao_Qianjiang548 Han_Nanchong191 Hui_Guizhou469 Hui_Guizhou434 Tanka_Xinshizhou688 # G Han_Nanchong199 Tujia_Qianjiang727 Tanka_Xinshizhou685 Miao_Qianjiang553 Tanka_Xinshizhou668 Tanka_Xinshizhou693 Tujia_Qianjiang718 Hui_Guizhou475 Tujia_Qianjiang709 Han_Nanchong185 # # # Han_Nanchong174 # # # # Han_Nanchong167 # Hui_Guizhou477 Han_Nanchong158 Tanka_Xinshizhou660 Miao_Qianjiang563 # # Miao_Qianjiang551 Hui_Guizhou472 Hui_Guizhou444 Tanka_Xinshizhou687 Han_Nanchong156 Hui_Guizhou459 Han_Nanchong179 Miao_Qianjiang547 Tanka_Shacheng631 # Han_Nanchong205 Hui_Guizhou467 Hui_Guizhou451 Hui_Guizhou436 Han_Nanchong201 Tanka_Shacheng642 Tanka_Xinshizhou664 Tujia_Qianjiang724 Tujia_Qianjiang713 Hui_Guizhou471 Hui_Guizhou462 Han_Nanchong168 # Han_Nanchong204 Han_Nanchong160 Han_Nanchong210 Han_Nanchong161 Tujia_Qianjiang711 Hui_Guizhou447 Tujia_Qianjiang708 Tanka_Xinshizhou663 Han_Nanchong196 Han_Nanchong180 Miao_Qianjiang552 Tujia_Qianjiang698 Hui_Guizhou454 Tujia_Qianjiang720 Hui_Guizhou474 Tujia_Qianjiang722 Tanka_Shacheng649 # Tanka_Shacheng641 Tujia_Qianjiang719 # Tanka_Shacheng634 Hui_Guizhou439 Tujia_Qianjiang723 Tujia_Qianjiang717 Han_Nanchong172 Hui_Guizhou457 Tanka_Xinshizhou676 # Tanka_Xinshizhou672 Hui_Guizhou466 Tanka_Shacheng632 Miao_Qianjiang558 Miao_Qianjiang549 Tanka_Xinshizhou659 Tujia_Qianjiang716 Han_Nanchong183 # Miao_Qianjiang554 Tanka_Shacheng657 Miao_Qianjiang564 Miao_Qianjiang557 Tanka_Shacheng656 Tanka_Shacheng654 Tujia_Qianjiang707 # Hui_Guizhou478 Tujia_Qianjiang699 Miao_Qianjiang555 Tujia_Qianjiang701 # Tujia_Qianjiang715 Hui_Guizhou435 Hui_Guizhou455 # # # Tanka_Shacheng648 Tujia_Qianjiang705 Tanka_Shacheng640 Tujia_Qianjiang725 # Han_Nanchong211 # # # Tanka_Shacheng629 # Hui_Guizhou476 # Miao_Qianjiang557 Han_Nanchong203 # Tanka_Xinshizhou675 Han_Nanchong169 # # # Tujia_Qianjiang721 # Han_Nanchong166 Hui_Guizhou446 Han_Hanzhong99 # Han_Nanchong197 # Han_Nanchong208 # Tujia_Qianjiang704 Tanka_Shacheng636 Tanka_Shacheng643 # Tanka_Shacheng645 Tanka_Shacheng625 Han_Nanchong157 # # Han_Nanchong193 Tanka_Shacheng638 Han_Nanchong200 Tujia_Qianjiang703 Tanka_Shacheng652 Han_Nanchong192 Miao_Qianjiang560 Han_Hanzhong98 # # # # # Han_Nanchong189 # # # # Tanka_Shacheng644 Han_Nanchong171 Han_Nanchong195 Hui_Boshu389 Han_Nanchong186 Hui_Guizhou442 # Han_Nanchong162 Tanka_Xinshizhou677 Tujia_Qianjiang726 # Tanka_Shacheng653 # # Tanka_Shacheng655 Tanka_Shacheng650 Han_Nanchong187 Han_Nanchong178 Tanka_Shacheng626 # Han_Nanchong177 # # Tanka_Shacheng630 Hui_Boshu417 # Tujia_Qianjiang712 Hui_Boshu396 # # Tanka_Shacheng646 # # # # # Hui_Boshu399 Tanka_Shacheng639 Miao_Qianjiang561 # # # Tanka_Shacheng635 # # # Tanka_Shacheng633 # # Hui_Boshu429 # Han_Nanchong181 Han_Hanzhong106 # Han_Hanzhong105 # # # Hui_Boshu388 # # Han_Hanzhong101 # Han_Nanchong209 Han_Nanchong182 Tanka_Shacheng658 # Hui_Boshu400 Han_Hanzhong96 Han_Nanchong194 Hui_Boshu404 Han_Hanzhong104 # # Hui_Boshu414 Hui_Boshu402 Hui_Boshu424 Hui_Boshu391

0.000 Tanka_Fujian623 Hui_Boshu428

Han_Nanchong156 Hui_Boshu415 Han_Hanzhong103 Tanka_Fujian621 Hui_Boshu420 # Tanka_Fujian622 Hui_Boshu386 Han_Lanzhou107 # # Hui_Boshu395 Hui_Boshu419 Hui_Boshu412 # Hui_Boshu393 Hui_Boshu433 # # Han_Lanzhou118 Hui_Boshu416 # Hui_Boshu407 Han_Lanzhou146 # Han_Lanzhou134 # Han_Ankang67 Hui_Boshu408 Hui_Boshu387 # # Han_Hanzhong102 Hui_Boshu390 Han_Lanzhou140 Hui_Boshu403 Hui_Boshu422 Hui_Boshu409 Han_Lanzhou108 # Hui_Boshu421 Han_Lanzhou114 Han_Lanzhou141 Han_Ankang69 Hui_Boshu385 # # Han_Hanzhong95 # # # Hui_Boshu425 Hui_Boshu427 Hui_Boshu398 Hui_Boshu411 Han_Shangluo219 # Han_Nanchong212 Han_Nanchong164 # Han_Ankang72 Hui_Boshu410 Han_Xianyang328 Han_Nanchong173 # # # # Han_Shangluo216 Han_Ankang70 Han_Weinan225 # Han_Hanzhong94 Han_Lanzhou124 # # # Han_Lanzhou110 Han_Nanchong198 # Hui_Boshu392 Hui_Boshu394 Han_Xianyang321 Han_Lanzhou112 Han_Lanzhou143 Han_Lanzhou116 Han_Ankang63 Hui_Boshu430 Han_Baoji88 # # Han_Lanzhou150 Han_Hanzhong97 Han_Ankang71 # Hui_Boshu413 # # Han_Lanzhou138 Han_Shangluo215 Hui_Boshu405 # Hui_Boshu397 # # Han_Lanzhou126 # # Hui_Boshu418 # Hui_Boshu426 Han_Lanzhou151 Hui_Boshu432 Han_Hanzhong100 # # # # # Han_Lanzhou145 # # Han_Baoji74 Han_Xianyang329 Han_Xianyang323 Han_Lanzhou127 Han_Lanzhou147 Hui_Boshu406 Han_Shangluo220 # # Hui_Boshu423 Han_Lanzhou130 # Han_Xianyang325 # Hui_Boshu431 # Han_Lanzhou136 # # # # Han_Xianyang319 Han_Weinan244 Han_Xianyang324 Han_Lanzhou113 # # Han_Ankang64 # # # Han_Xianyang330 # Han_Lanzhou129 # Han_Lanzhou123 # # Han_Lanzhou142 # Han_Xianyang318 Han_Xian258 Han_Lanzhou121 Hui_Boshu401 Han_Lanzhou109 Han_Lanzhou128 Han_Xianyang326 # # Han_Lanzhou115 # # Han_Shangluo218 # # # Han_Lanzhou152 Han_Shangluo214 Han_Xianyang322 Han_Lanzhou125 # Han_Weinan241 Han_Lanzhou144 Han_Weinan237 Han_Xianyang327 # # Han_Ankang66 Han_

Han_Nanchong197 Han_Lanzhou132 # Han_Ankang68 Han_Xian298 Han_Xianyang320 # # # Han_Baoji86 # # Han_Ankang65 Han_Weinan236 Han_Shangluo221 # Han_Lanzhou122 Tanka_Fujian624 # Han_Xianyang317 # Han_Xian302 Han_Xian300 # Han_Baoji81 # Han_YulinSX350 # # # # # # Han_Lanzhou153 # # Han_Xian250 # Han_Weinan223 # # Han_Lanzhou131 # Han_YulinSX358 Han_Xian295 # Han_Xian294 Han_Weinan224 Han_Xian263 # # Han_YulinSX351 # # Han_Lanzhou149 # # Han_Xian292 Han_Xian303 Han_Lanzhou133 Han_Lanzhou111 Han_Lanzhou117 # Han_Lanzhou135 # Han_Baoji92 Han_Baoji87 # Han_Xian280 Han_Weinan228 Han_Lanzhou120 Han_YulinSX343 Han_Weinan243 Han_Xian261 # Han_Weinan245 Han_Weinan235 Han_YulinSX354 # # # # Han_Weinan240 # # Han_Yanan337 # Han_Lanzhou148 # Han_Baoji93 Han_Shangluo222 Han_YulinSX345 Han_YulinSX348 Han_Xian256 Han_Xian268 # # Han_Weinan247 Han_Weinan242 Han_Lanzhou139 # # # # Han_Yanan336 Han_Weinan227 # Han_Weinan226 Han_Yanan338 # Han_Weinan238 Han_Shangluo217 Han_YulinSX342 # Han_YulinSX361 Han_Xian301 Han_Yanan339 Han_Baoji73 Han_Lanzhou137 # Han_YulinSX357 # # # # Han_Yanan331 Han_Xian251 Han_YulinSX369 # Han_YulinSX366 # Han_Xian283 Han_Baoji78 Han_Xian274 # Han_Xian260 Han_YulinSX367 # # Han_YulinSX364 Han_Weinan231 # # # Han_Lanzhou119 # Han_Baoji80 # # Han_Xian253 Han_Xian271 Han_YulinSX352 Han_YulinSX356 Han_Xian276 # # # Han_Xian267 # Han_Yanan340 # Han_Baoji89 # # # Han_Xian282 # # Han_Weinan246 # # Han_Baoji79 # # Han_Xian266 # # # Han_Baoji91 Han_Baoji84 Han_Xian290 # # Han_Weinan233 Han_YulinSX363 Han_Xian249 # Han_Xian296 Han_Xian272 Han_YulinSX355 Han_YulinSX368 Han_YulinSX353 # Han_YulinSX359 Han_Xian307 # # # # Han_Weinan239 Han_YulinSX362 Han_Baoji77 # # Han_Xian309 # Han_Xian316 Han_Xian287 # # # Han_Xian306 Han_Xian314 Han_YulinSX365 # # # Han_Yanan334 Han_Xian281 Han_Xian254 Han_Weinan234 # Han_YulinSX347 # Han_Baoji75 Han_Xian269 # # # Han_Xian265 Han_Xian285 Han_Baoji85 # Han_Xian312 Han_Xian297 Han_Xian270 # # # Han_Xian255 # Han_Xian313 Han_YulinSX360 Han_Yanan332 # # # # Han_Xian304 Han_Baoji83 # Han_Weinan229 Han_Xian279 Han_Xian299 Han_Yanan335 Han_YulinSX349 # # # # Han_Xian310 # # # # Han_Xian277 Han_Yanan333 # Han_Baoji82 Han_Weinan230 # # # Han_Xian311 Han_Xian284 Han_Xian262 Han_Xian291 Han_Xian264 # # Han_Xian305 # Han_Xian289 Han_Xian275 Han_Xian252 # # # # Han_Xian248 # # # # # # # Han_YulinSX344 # # # # # # Han_Xian315 Han_Baoji90 # Hui_Boshu407 Han_Xian286 Han_Xian308 # # # Han_Xian259 Han_YulinSX346 # Han_Xian257 # # # # Han_YulinSX341 # # # # # Han_Xian273 # # Han_Xian288 Han_Baoji76 # # # # # # # # Han_Xian278 # # Han_Xian293 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # Weinan232 # # # # # # # # # # # # # # # # # # # # # # # # # # # #

Hui_Boshu424 # # # # # # # # # # # # # # #

Lahu_Lancang # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #

Han_Nanchong187 # # # # # # # Blang_Menghai # Hui_Boshu412 0.0000.000 Wa_Cangyuan Blang_Menghai18 0.000 Blang_Menghai21 11Manchu_Bijie;11Manchu_Jinsha Wa_Cangyuan730

Chuanqing_Bijie 7Manchu_Bijie;3Manchu_Jinsha Wa_Cangyuan738 Mongolian_Bijie Lahu_Lancang489 0.537 Lahu_Lancang483 0.5370.425 Han_Nanchong Hani_Honghe373 Hani_Honghe378 0.425 Miao_Qianjiang Shui_Sandu606 0.984 Tujia_Qianjiang Shui_Sandu620 0.152 Chuanqing_Bijie43 0.984 0.846 Chuanqing_Bijie44 0.152 0.391 0.000 Manchu_Bijie504 1Tanka_Xinshizhou 1Tanka_Xinshizhou 1Tanka_Xinshizhou 1Tanka_Xinshizhou 1Tanka_Xinshizhou Bai_Heqing 0.0000.391 1Mongolian_Bijie 2Mongolian_Bijie 1Mongolian_Bijie Han_Lanzhou Manchu_Jinsha530 0.000 0.39114Tanka_Shacheng 0.002 0.113 0.224 0.335 0.446 0.556 0.667 0.778 0.889 Manchu_Jinsha536 1Tanka_Shacheng Gejia_Kaili59 0.130 1Blang_Menghai 1Blang_Menghai 0.130 1Pumi_Lanping 1Lahu_Lancang 5Lahu_Lancang 1Hui_Guizhou 2Hui_Guizhou 2Hui_Guizhou Han_Xian Gejia_Kaili60 0.846 14Shui_Sandu Gejia_Kaili54 1

Han_Baoji Dongjia_Kaili49 1Hui_Boshu 1Hui_Boshu 3Hui_Boshu Han_Yanan Manchu_Bijie514 0.000 Han_Xianyang Manchu_Bijie492 0.435 Han_Shangluo Manchu_Jinsha522 0.000 Manchu_Jinsha524 Han_Weinan 0.000 Han_YulinSX E 10 s.e. weight Migration Hui_Boshu Population Dendrogram average chunk reporting counts 0 0.5

1Tanka_Shacheng The copyrightholderforthispreprint Miao_Qianjiang

Han_HanzhongHan_Fujian Tujia_Qianjiang 0.000

Drift parameter Drift 0.000 Chuanqing_Bijie Han_Fujian Han_Nanchong 2Tanka_Shacheng Han_Ankang Han_Hanzhong C

Mongolian_Bijie 0.142 Han_Ankang 4Tanka_Shacheng 0.142 0.142 0.142

Han_Baoji 0.142

Han_Xian Han_Shangluo 0.367 Hui_Boshu Han_Lanzhou Han_Yanan Han_Weinan Han_Xia 2Tanka_Xinshizhou 0.086 Pumi_Lanping Han_YulinSX 0.000 0.0000.000 1Tanka_Xinshizhou 0.629 Dongjia_Kaili 0.629 0.000 0.367 0.0000.000 Bai_Heqing 1Tanka_Xinshizhou 0.1420.000 0.000 Shui_Sandu Manchu_Jinsha Tanka_Shacheng Gejia_Kaili 1Tanka_Xinshizhou 0.000 0.367 Manchu_Bijie

Xijia_Kaili Xijia_Kaili 1Tanka_Xinshizhou Shui_Sandu nyang 0.9940.994 2Hui_Guizhou 0.000 0.002 0.000 Hani_Honghe Hani_Honghe 0.000 0.000 Hui_Guizhou

Tanka_Xinshizhou 5Hui_Guizhou 0.0000.000 Manchu_Bijie 0.1580.000 0.000 Manchu_Jinsha 0.8500.850 2Hui_Guizhou 0.4310.431 T 0.000 anka_Xinshizhou 0.010 0.000 Dongjia_Kaili Gejia_Kaili 14Hui_Guizhou 0.120 2Han_Lanzhou 0.1200.120 Tanka_ShachengHui_Guizhou 0.846 0.693 1Hui_Boshu 0.693 0.098 1Hui_Boshu 0.6930.6930.6930.693 0.693 0.693 1Hui_Boshu 0.098 0.693 Pumi_Lanping 1Hui_Boshu 0.970 0.9880.012 Tanka_Shacheng Hui_Guizhou Tanka_Xinshizhou Manchu_Jinsha Manchu_Bijie Hani_Honghe Shui_Sandu Xijia_Kaili Gejia_Kaili Dongjia_Kaili Pumi_Lanping Han_Ankang Han_Hanzhong Han_Fujian Hui_Boshu Han_YulinSX Han_Weinan Han_Shangluo Han_Xianyang Han_Yanan Han_Baoji Han_Xian Han_Lanzhou Bai_Heqing Tujia_Qianjiang Miao_Qianjiang Han_Nanchong Mongolian_Bijie Chuanqing_Bijie Wa_Cangyuan Blang_Menghai Lahu_Lancang 1Pumi_Lanping 0.0000.000 0.3170.0000.012 3Pumi_Lanping 0.000 Blang_Menghai 0.295

0.004 1Mongolian_Bijie 0.000 0.000 0.0000.000 0.000

Wa_Cangyuan 0.000 2Mongolian_Bijie 0.7270.984 0.000 0.000 1Mongolian_Bijie 0.000 0.000 0.367 0.028 Lahu_Lancang 6Tanka_Shacheng;6Tanka_Xinshizhou;2Tanka_Fujian 0.000 0.0000.000 1Blang_Menghai 0.000 1Blang_Menghai 1Lahu_Lancang 0.537 0.537 2Lahu_Lancang 0.425 0.425 0.846 13Hani_Honghe 0.984 0.188 0.1520.984 86.6 0.152 173 259 346 432 518 605 691 778

0 0.005 0.01 0.015 0.02 0.025 0.03 0.035 0.391 0.000 11Chuanqing_Bijie 0.0000.3910.391 0.000 0.130 0.130 0.846 7Manchu_Jinsha;2Manchu_Bijie 0.000 11Manchu_Bijie;11Manchu_Jinsha 0.000 0.435