|
Post by Admin on Feb 26, 2021 22:06:52 GMT
317 The individuals from the ~5000 BCE Neolithic Boisman culture and the ~1000 BCE 318 Iron Age Yankovsky culture together with the previously published ~6000 BCE data 319 from Devil’s Gate cave19 are genetically very similar, documenting a continuous 320 presence of this ancestry profile in the Amur River Basin stretching back at least to 321 eight thousand years ago (Figure 2 and Figure S2). The genetic continuity is also 322 evident in the prevailing Y chromosomal haplogroup C2b-F1396 and mitochondrial 323 haplogroups D4 and C5 of the Boisman individuals, which are predominant lineages 324 in present-day Tungusic, Mongolic, and some Turkic-speakers. The Neolithic 325 Boisman individuals shared an affinity with Jomon as suggested by their intermediate 326 positions between Mongolia_East_N and Jomon in the PCA and confirmed by the 327 significantly positive statistic f4 (Mongolia_East_N, Boisman; Mbuti, Jomon). 328 Statistics such as f4 (Native American, Mbuti; Test East Asian, 329 Boisman/Mongolia_East_N) show that Native Americans share more alleles with 330 Boisman and Mongolia_East_N than they do with the great majority of other East 331 Asians in our dataset (Table S5). It is unlikely that these statistics are explained by 332 back-flow from Native Americans since Boisman and other East Asians share alleles 333 at an equal rate with the ~24,000-year-old Ancient North Eurasian MA1 who was 334 from a population that contributed about 1/3 of all Native American ancestry31. A 335 plausible explanation for this observation is that the Boisman/Mongolia Neolithic 336 ancestry was linked (deeply) to the source of the East Asian-related ancestry in Native 337 Americans3,31. We can also model published data from Neolithic and Early Bronze 338 Age individuals around Lake Baikal7 as sharing substantial ancestry (77-94%) with 339 the lineage represented by Mongolia_East_N, revealing that this type of ancestry was 340 once spread over a wide region spanning across Lake Baikal, eastern Mongolia, and 341 the Amur River Basin (Table S7). Some present-day populations around the Amur 342 River Basin harbor large fractions of ancestry consistent with deriving from more 343 southern East Asian populations related to Han Chinese (but not necessarily Han 344 themselves) in proportions of 13-50%. We can show that this admixture occurred at 345 least by the Early Medieval period because one Heishui_Mohe individual (I3358, 346 directly dated to 1050-1220 CE) is estimated to have harbored more than 50% 347 ancestry from Han or related groups (Table S8).
|
|
|
Post by Admin on Feb 27, 2021 21:18:38 GMT
349 The Tibetan Plateau, with an average elevation of more than 4,000 meters, is one of 350 the most extreme environments in which humans live. Archaeological evidence 351 suggests two main phases for modern human peopling of the Tibetan Plateau. The 352 first can be traced back to at least ~160,000 years ago probably by Denisovans32 and 353 then to 40,000-30,000 years ago as reflected in abundant blade tool assemblages33. 354 However, it is only in the last ~3,600 years that there is evidence for continuous 355 permanent occupation of this region with the advent of agriculture34. We grouped 17 356 present-day populations from the highlands into three categories based on genetic 357 clustering patterns (Figure S3): “Core Tibetans” who are closely related to the ancient 358 Nepal individuals such as Chokopani with a minimal amount of admixture with 359 groups related to West Eurasians and lowland East Asians in the last dozens of 360 generations, “northern Tibetans” who are admixed between lineages related to Core 361 Tibetans and West Eurasians, and “Tibeto-Yi Corridor” populations (the eastern edge 362 of the Tibetan Plateau connecting the highlands to the lowlands) that includes not just 363 Tibetan speakers but also Qiang and Lolo-Burmese speakers who we estimate using 364 qpAdm4,35 have 30-70% Southeast Asian Cluster-related ancestry (Table S9). We 365 computed f3 (Mbuti; Core Tibetan, non-Tibetan East Asian) to search for non-Tibetans 366 that share the most genetic drift with Tibetans. Neolithic Wuzhuangguoliang, Han and 367 Qiang appear at the top of the list (Table S10), suggesting that Tibetans harbor 368 ancestry from a population closely related to Wuzhuangguoliang that also contributed 369 more to Qiang and Han than to other present-day East Asian groups. We estimate that 370 the mixture occurred 60-80 generations ago (2240-1680 years ago assuming 28 years 371 per generation36 under a model of a single pulse of admixture (Table S11). This 372 represents an average date and so only provides a lower bound on when these two 373 populations began to mix; the start of their period of admixture could plausibly be as 374 old as the ~3,600-year-old date for the spread of agriculture onto the Tibetan plateau. 375 These findings are therefore consistent with archaeological evidence that expansions 376 of farmers from the Upper and Middle Yellow River Basin influenced populations of 377 the Tibetan Plateau from the Neolithic to the Bronze Age as they spread across the 378 China Central plain37,38, and with Y chromosome evidence that the shared common 379 haplogroup Oα-F5 between Han and Tibetans coalesced to a common ancestry less 380 than 5,800 years ago39.
382 In the south, we find that the ancient Taiwan Hanben and Gongguan culture 383 individuals dating from at least a span of 1400 BCE - 600 CE are genetically most 384 similar to present-day Austronesian speakers and ancient Lapita individuals from 385 Vanuatu as shown in outgroup f3-statistics and significantly positive f4-statistics 386 (Taiwan_Hanben/Gongguan, Mbuti; Ami/Atayal/Lapita, other Asians) (Table S8). 387 The similarity to Austronesian-speakers is also evident in the Iron Age dominant 388 paternal Y chromosome lineage O3a2c2-N6 and maternal mtDNA lineages E1a, 389 B4a1a, F3b1, and F4b, which are widespread lineages among Austronesian- 390 speakers40,41. We compared the present-day Austronesian-speaking Ami and Atayal of 391 Taiwan with diverse Asian populations using statistics like f4 (Taiwan Iron 392 Age/Austronesian, Mbuti; Asian1, Asian2). Ancient Taiwan groups and Austronesian- 393 speakers share significantly more alleles with Tai-Kadai speakers in southern 394 mainland China and in Hainan Island42 than they do with other East Asians (Table 395 S8), consistent with the hypothesis that ancient populations related to present-day Tai- 396 Kadai speakers are the source for the spread of agriculture to Taiwan island around 297 5000 years ago43. The Jomon share alleles at an elevated rate with ancient Taiwan 398 individuals and Ami/Atayal as measured by statistics of the form f4 (Jomon, Mbuti; 399 Ancient Taiwan/Austronesian-speaker, other Asians) compared with other East Asian 400 groups, with the exception of groups in the Amur Basin Cluster (Table S8)44.
|
|
|
Post by Admin on Mar 4, 2021 3:53:39 GMT
402 The Han Chinese are the world’s largest ethnic group. It has been hypothesized based 403 on the archaeologically documented spread of material culture and farming 404 technology, as well as the linguistic evidence of links among Sino-Tibetan languages, 405 that one of the ancestral populations of the Han might have consisted of early farmers 406 along the Upper and Middle Yellow River in northern China, some of whose 407 descendants also may have spread to the Tibetan Plateau and contributed to present- 408 day Tibeto-Burmans45. Archaeological and historical evidence document how during 409 the past two millennia, the Han expanded south into regions inhabited by previously 410 established agriculturalists46. Analysis of genome-wide variation among present-day 411 populations has revealed that the Han Chinese are characterized by a “North-South” 412 cline47,48, which is confirmed by our analysis. The Neolithic Wuzhuangguoliang, 413 present-day Tibetans, and Amur River Basin populations, share significantly more 414 alleles with Han Chinese compared with the Southeast Asian Cluster, while the 415 Southeast Asian Cluster groups share significantly more alleles with the majority of 416 Han Chinese groups when compared with the Neolithic Wuzhuangguoliang (Table 417 S12, Table S13). These findings suggest that Han Chinese may be admixed in variable 418 proportions between groups related to Neolithic Wuzhuangguoliang and people 419 related to those of the Southeast Asian Cluster. To determine the minimum number of 420 source populations needed to explain the ancestry of the Han, we used qpWave4,49 to 421 study the matrix of all possible statistics of the form f4 (Han1, Han2; O1, O2), where 422 “O1” and “O2” are outgroups that are unlikely to have been affected by recent gene 423 flow from Han Chinese. This analysis confirms that two source populations are 424 consistent with all of the ancestry in most Han Chinese groups (with the exception of 425 some West Eurasian-related admixture that affects some northern Han Chinese in 426 proportions of 2-4% among the groups we sampled; Table S14 and Table S15). 427 Specifically, we can model almost all present-day Han Chinese as mixtures of two 428 ancestral populations, in a variety of proportions, with 77-93% related to Neolithic 429 Wuzhuangguoliang from the Yellow River basin, and the remainder from a 430 population related to ancient Taiwan that we hypothesize was closely related to the 431 rice farmers of the Yangtze River Basin. This is also consistent with our inference that 432 the Yangtze River farmer related ancestry contributed nearly all the ancestry of 433 Austronesian speakers and Tai-Kadai speakers and about 2/3 of some Austroasiatic 434 speakers17,20 (Figure 4). A caveat is that there is a modest level of modern 435 contamination in the Wuzhuangguoliang we use as a source population for this 436 analysis (Online Table 1), but this would not bias admixture estimates by more than 437 the contamination estimate of 3-4%. The average dates of West Eurasian-related 438 admixture in northern Han Chinese populations Han_NChina and Han_Shanxi are 32- 439 45 generations ago, suggesting that mixture was continuing at the time of the Tang 440 Dynasty (618-907 CE) and Song Dynasty (960-1279 BCE) during which time there 441 are historical records of integration of Han Chinese amd western ethnic groups, but 442 this date is an average so the mixture between groups could have begun earlier.
|
|
|
Post by Admin on Mar 4, 2021 23:23:25 GMT
444 To obtain insight into the formation of present-day Japanese archipelago populations, 445 we searched for groups that contribute most strongly to present-day Japanese through 446 admixture f3-statistics. The most strongly negative signals come from mixtures of Han 447 Chinese and ancient Jomon (f3(Japanese; Han Chinese, Jomon)) (Table S16). We can 448 model present-day Japanese as two-way mixtures of 84.3% Han Chinese and 15.7% 449 Jomon or 87.6% Korean and 12.4% Jomon (we cannot distinguish statistically 450 between these two sources; Table S17 and Table S18). This analysis by no means 451 suggests that the mainland ancestry in Japan was contributed directly by the Han 452 Chinese or Koreans themselves, but does suggest that it is from an ancestral 453 population related to those that contributed in large proportion to Han Chinese as well 454 as to Koreans for which we do not yet have ancient DNA data.
456 We used qpGraph35 to explore models with population splits and gene flow, and 457 tested their fit to the data by computing f2-, f3- and f4- statistics measuring allele 458 sharing among pairs, triples, and quadruples of populations, evaluating fit based on 459 the maximum |Z|-score comparing predicted and observed values. We further 460 constrained the models by using estimates of the relative population split times 461 between the selected pairs of populations based on the output of the MSMC 462 software50. While admixture graph modeling based on allele frequency correlation 463 statistics is not able to reject a model in which ancient Taiwan individuals and 464 Boisman share substantial ancestry with each other more recently than either does 465 with the ancestors of Chokopani and Core Tibetans, this model cannot be correct 466 because our MSMC analysis reveals that Core Tibetans (closely related to Chokopani) 467 and Ulchi (closely related to Boisman) share ancestry more recently in time on 468 average than either does with Ami (related to Taiwan_Hanben). This MSMC-based 469 constraint allowed us to identify a parsimonious working model for the deep history 470 of key lineages discussed in this study (Supplementary Information section 3: 471 qpGraph Modeling). Our fitted model (Figure 5), suggests that much of East Asian 472 ancestry today can be modelled as derived from two ancient populations: one from the 473 same lineage as the approximately ~40,000-year-old Tianyuan individual and the 474 other more closely related to Onge, with groups today having variable proportions of 475 ancestry from these two deep sources. In this model, the Mongolia_East_N and Amur 476 River Basin Boisman related lineages derive the largest proportion of their ancestry 477 from the Tianyuan-related lineage and the least proportion of ancestry from the Onge- 478 related lineage compared with other East Asians. A sister lineage of 479 Mongolia_East_N is consistent with expanding into the Tibetan Plateau and mixing 480 with the local hunter-gatherers who represent an Onge-related branch in the tree. The 481 Taiwan Hanben are well modelled as deriving about 14% of their ancestry from a 482 lineage remotely related to Onge and the rest of their ancestry from a lineage that also 483 contributed to Jomon and Boisman on the Tianyuan side, a scenario that would 484 explain the observed affinity among Jomon, Boisman and Taiwan Hanben. We 485 estimate that Jomon individuals derived 45% of their ancestry from a deep basal 486 lineage on the Onge side. These results are consistent with the scenario a Late 487 Pleistocene coastal route of human migration linking Southeast Asia, the Japanese 488 Archipelago and the Russian Far East51. Due to the paucity of ancient genomic data 489 from Upper Paleolithic East Asians, there are limited constraints at present for 490 reconstructing the deep branching patterns of East Asian ancestral populations, and it 491 is certain that this admixture graph is an oversimplification and that additional 492 features of deep population relationships will be revealed through future work.
Figure 5: qpGraph modeling of a subset of East Asians. We used all available sites in the 1240K dataset, restricting to transversions only to replicate key results (Supplementary Information). We started with a skeleton tree that fits the data with Denisova, Mbuti, Onge, Tianyuan and Loschbour and one admixture event. We then grafted on Mongolia_East_N, Jomon, Taiwan_Hanben, Chokhopani, and Boisman in turn, adding them consecutively to all possible edges in the tree and retaining only graph solutions that provided no differences of |Z|>3 between fitted and estimated statistics. We used the MSMC relative population split time to constrain models (the maximum discrepancy for this model is |Z|=2.8). Drifts along edges are multiplied by 1000. Dashed lines represent admixture. Deep population splits are not well constrained due to a lack of data from Upper Paleolithic East Asians. 494 At the end of the last Ice Age, there were multiple highly differentiated populations in 495 East as well as West Eurasia, and it is now clear that these groups mixed in both 496 regions, instead of one population displacing the others. In West Eurasia, there were 497 at least four divergent populations each as genetically differentiated from each other 498 as Europeans and East Asians today (average FST=0.10), which mixed in the 499 Neolithic, reducing heterogeneity (average FST=0.03) and mixed further in the Bronze 500 Age and Iron Age to produce the present-relatively low differentiation that 501 characterizes modern West Eurasia (average FST=0.01)52. In East Eurasia, our study 502 suggests an analogous process, with the differentiation characteristic of the Amur 503 River Basin groups, Neolithic Yellow River farmers, and people related to those of 504 the Taiwan Iron Age (average FST=0.06 in our data) collapsing through mixture to 505 today’s relatively low differentiation (average FST=0.01-0.02) (Figure 6). A priority 506 should be to obtain ancient DNA data for the hypothesized Yangtze River population 507 (the putative source for the ancestry prevalent in the Southeast Asian Cluster of 508 present-day groups), which should, in turn, make it possible to test and further extend 509 these models, and in particular to understand if dispersals of people in Southeast Asia 510 do or do not correlate to ancient movements of people.
|
|