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Genome of a middle Holocene hunter-gatherer from Wallacea.

ABSTRACT: Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA¹. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4-4.2 kyr cal BP)¹. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia-New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3-7.2 kyr cal BP at the limestone cave of Leang Panninge² in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the 'Toalean' technocomplex^3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago⁵. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.

SUBMITTER: Carlhoff S

PROVIDER: S-EPMC8387238 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

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Genome of a middle Holocene hunter-gatherer from Wallacea.

Carlhoff Selina S Duli Akin A Nägele Kathrin K Nur Muhammad M Skov Laurits L Sumantri Iwan I Oktaviana Adhi Agus AA Hakim Budianto B Burhan Basran B Syahdar Fardi Ali FA McGahan David P DP Bulbeck David D Perston Yinika L YL Newman Kim K Saiful Andi Muhammad AM Ririmasse Marlon M Chia Stephen S Hasanuddin Pulubuhu Dwia Aries Tina DAT Suryatman Supriadi Jeong Choongwon C Peter Benjamin M BM Prüfer Kay K Powell Adam A Krause Johannes J Posth Cosimo C Brumm Adam A

Nature 20210825 7873

Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA<sup>1</sup>. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in ...[more]

PMID: 34433944

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Project description:BackgroundThe Windover mortuary pond dates to the Early Archaic period (6,800-5,200 years ago) and constitutes one of the earliest archaeological sites with intact and well-preserved human remains in North America. Unlike many prehistoric egalitarian hunter-gatherers, the Windover people may not have practiced a sex-based division of labor; rather, they may have shared the load. We explore how mobility and subsistence, as reconstructed from archaeological data, influenced hand and foot bone morphology at Windover.MethodsWe took length and width measurements on four carpal bones, four tarsal bones, and load-bearing tarsal areas (calcaneus load arm, trochlea of the talus). We analyzed lateralization using side differences in raw length and width measurements. For other hypothesis testing, we used log transformed length-width ratios to mitigate the confounding effects of sexual dimorphism and trait size variation; we tested between-sex differences in weight-bearing (rear foot) and shock-absorbing (mid foot) tarsal bones and between-sex differences in carpal bones.ResultsWe identified no significant between-sex differences in rear and midfoot areas, suggesting similar biomechanical stresses. We identified no significant between-sex differences in carpal bones but the test was under-powered due to small sample sizes. Finally, despite widespread behavioral evidence on contemporary populations for human hand and foot lateralization, we found no evidence of either handedness or footedness.DiscussionThe lack evidence for footedness was expected due its minimal impact on walking gait but the lack of evidence for handedness was surprising given that ethnographic studies have shown strong handedness in hunter-gatherers during tool and goods manufacture. The reconstructed activity patterns suggested both sexes engaged in heavy load carrying and a shared division of labor. Our results support previous findings-both sexes had stronger weight-bearing bones. Male shock-absorbing bones exhibited a trend towards greater relative width (suggesting greater comparative biomechanical stress) than females which may reflect the typical pattern of male hunter-gatherers engaging in walking greater distances at higher speeds than females. While there were no significant between-sex differences in carpal bones (supporting a shared work load model), females exhibited greater variation in index values, which may reflect a greater variety of and specialization in tasks compared to males. Because carpals and tarsals are so well-preserved at archaeological sites, we had surmised they might be useful proxies for activity in the absence of well-preserved long bones. Tarsals provide a stronger signal of past activity and may be useful in the absence of, or in addition to, preferred bones. Carpals, however, may not be useful as the effect size of biomechanical stress (in this study at least) is low and would require larger samples than may be possible at archaeological sites.

Dataset Information

Genome of a middle Holocene hunter-gatherer from Wallacea.

Publications

Genome of a middle Holocene hunter-gatherer from Wallacea.

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