Climate Change and Postglacial Human Dispersals in Southeast Asia (original) (raw)
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[This multi-authored paper on the use of archaeological DNA is significant to Myanmar because it is the first publication of DNA data from Myanmar derived from a database of over 500 samples collected by co-author Bob Hudson and members of the Field School of Archaeology, Pyay, in conjunction with Huddersfield University, UK. While only a small sample from Myanmar is used in this paper, further papers that focus more specifically on the archaeological genetics of Myanmar are forthcoming]. ****** ABSTRACT There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the “out-of- Taiwan” mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20 % of mtDNA lineages in the modern ISEA pool result from the “out-of-Taiwan” dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6–7 ka, where rice farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.
Title: Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia
2018
Two distinct population models have been put forward to explain present-day 57 human diversity in Southeast Asia. The first model proposes long-term continuity 58 (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer 59 model). Here, we use whole-genome capture in combination with shotgun sequencing to 60 generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from 62 Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with 63 the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic 64 farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-65 speaking populations. We also identify two further migratory events, consistent with the 66 expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, 67 and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings 68 support the Two Layer model for the early peopling of Southeast Asia and highlight the 69 complexities of dispersal patterns from East Asia. 70 71 Main Text: 72 The population history of Southeast Asia (SEA) has been shaped by interchanging 73 periods of isolation and connectivity. Anatomically modern humans first colonized SEA at 74 least 70,000 years ago (kya) (1-3). Within SEA, the complex topography and changes in sea 75 level promoted regional expansions and contractions of populations. By the late 76 Pleistocene/early Holocene, a pan-regional lithic technological culture was established across 77 mainland SEA, named Hoabinhian (4-7). Hoabinhian foragers are thought to be the ancestors 78 of present-day SEA hunter-gatherers, sometimes referred to as 'Negritos' because of their 79 comparatively darker skin colour and short stature. Today, however, the majority of people in 80 SEA are believed to be descendants of rice and millet farmers with varying degrees of East 81 Asian phenotypic affinity, suggesting that human diversity in SEA was strongly influenced by 82 population expansions from the north (4). Yet, the extent to which the movements from East 83 Asia (EA) impacted on the genetic and cultural makeup of the people of SEA remains 84 controversial. 85 Two distinct population models have been proposed to account for the biological and 86 cultural diversity of human populations in present-day SEA. The Regional Continuity model, 87 based primarily on morphological evidence, argues for a long-standing evolutionary continuity 88 without significant external gene flow and for the Neolithic transition in SEA occurring as 89 hunter-gatherer groups adopted agriculture, either independently or through cultural contact 90 (8-21). While this model does not necessarily argue for the independent domestication of crops 91 across SEA, it posits that gene flow from EA farmers was not the main mechanism behind the 92 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a
Abstract There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the “outof- Taiwan” mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20 % of mtDNA lineages in the modern ISEA pool result from the “out-of-Taiwan” dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6–7 ka, where ricefarming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.
Inland post-glacial dispersal in East Asia revealed by mitochondrial haplogroup M9a'b
BMC Biology, 2011
Background Archaeological studies have revealed a series of cultural changes around the Last Glacial Maximum in East Asia; whether these changes left any signatures in the gene pool of East Asians remains poorly indicated. To achieve deeper insights into the demographic history of modern humans in East Asia around the Last Glacial Maximum, we extensively analyzed mitochondrial DNA haplogroup M9a'b, a specific haplogroup that was suggested to have some potential for tracing the migration around the Last Glacial Maximum in East Eurasia. Results A total of 837 M9a'b mitochondrial DNAs (583 from the literature, while the remaining 254 were newly collected in this study) pinpointed from over 28,000 subjects residing across East Eurasia were studied here. Fifty-nine representative samples were further selected for total mitochondrial DNA sequencing so we could better understand the phylogeny within M9a'b. Based on the updated phylogeny, an extensive phylogeographic analysis wa...
Consequences of the Last Glacial Period on the Genetic Diversity of Southeast Asians
Genes, 2022
The last glacial period (LGP) promoted a loss of genetic diversity in Paleolithic populations of modern humans from diverse regions of the world by range contractions and habitat fragmentation. However, this period also provided some currently submersed lands, such as the Sunda shelf in Southeast Asia (SEA), that could have favored the expansion of our species. Concerning the latter, still little is known about the influence of the lowering sea level on the genetic diversity of current SEA populations. Here, we applied approximate Bayesian computation, based on extensive spatially explicit computer simulations, to evaluate the fitting of mtDNA data from diverse SEA populations with alternative evolutionary scenarios that consider and ignore the LGP and migration through long-distance dispersal (LDD). We found that both the LGP and migration through LDD should be taken into consideration to explain the currently observed genetic diversity in these populations and supported a rapid ex...
Origin and Post-Glacial Dispersal of Mitochondrial DNA Haplogroups C and D in Northern Asia
PLoS ONE, 2010
More than a half of the northern Asian pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroups C and D, two of the most frequent haplogroups throughout northern, eastern, central Asia and America. While there has been considerable recent progress in studying mitochondrial variation in eastern Asia and America at the complete genome resolution, little comparable data is available for regions such as southern Siberia -the area where most of northern Asian haplogroups, including C and D, likely diversified. This gap in our knowledge causes a serious barrier for progress in understanding the demographic pre-history of northern Eurasia in general. Here we describe the phylogeography of haplogroups C and D in the populations of northern and eastern Asia. We have analyzed 770 samples from haplogroups C and D (174 and 596, respectively) at high resolution, including 182 novel complete mtDNA sequences representing haplogroups C and D (83 and 99, respectively). The present-day variation of haplogroups C and D suggests that these mtDNA clades expanded before the Last Glacial Maximum (LGM), with their oldest lineages being present in the eastern Asia. Unlike in eastern Asia, most of the northern Asian variants of haplogroups C and D began the expansion after the LGM, thus pointing to post-glacial re-colonization of northern Asia. Our results show that both haplogroups were involved in migrations, from eastern Asia and southern Siberia to eastern and northeastern Europe, likely during the middle Holocene.
Human Genetics, 2016
There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the “out-of-Taiwan” mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. W...
A Mitochondrial Stratigraphy for Island Southeast Asia
American Journal of Human Genetics, 2007
Island Southeast Asia (ISEA) was first colonized by modern humans at least 45,000 years ago, but the extent to which the modern inhabitants trace their ancestry to the first settlers is a matter of debate. It is widely held, in both archaeology and linguistics, that they are largely descended from a second wave of dispersal, proto-Austronesian-speaking agriculturalists who originated in China and spread to Taiwan ∼5,500 years ago. From there, they are thought to have dispersed into ISEA ∼4,000 years ago, assimilating the indigenous populations. Here, we demonstrate that mitochondrial DNA diversity in the region is extremely high and includes a large number of indigenous clades. Only a fraction of these date back to the time of first settlement, and the majority appear to mark dispersals in the late-Pleistocene or early-Holocene epoch most likely triggered by postglacial flooding. There are much closer genetic links to Taiwan than to the mainland, but most of these probably predated the mid-Holocene "Out of Taiwan" event as traditionally envisioned. Only ∼20% at most of modern mitochondrial DNAs in ISEA could be linked to such an event, suggesting that, if an agriculturalist migration did take place, it was demographically minor, at least with regard to the involvement of women.
Ancient DNA indicates human population shifts and admixture in northern and southern China
Science, 2020
Human genetic history in East Asia is poorly understood. To clarify population relationships, we obtained genome wide data from 26 ancient individuals from northern and southern East Asia spanning 9,500-300 years ago. Genetic differentiation was higher in the past than the present, reflecting a major episode of admixture involving northern East Asian ancestry spreading across southern East Asia after the Neolithic, transforming the genetic ancestry of southern China. Mainland southern East Asian and Taiwan Strait island samples from the Neolithic show clear connections with modern and ancient samples with Austronesian-related ancestry, supporting a southern China origin for proto-Austronesians. Connections among Neolithic coastal groups from Siberia and Japan to Vietnam indicate that migration and gene flow played an important role in the prehistory of coastal Asia.