A genetic history of migration, diversification, and admixture in Asia

Yang, Melinda A.

doi:10.47248/hpgg2202010001

Cited by 7 publications

(4 citation statements)

References 96 publications

(245 reference statements)

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“…These factors include population structure, changes in connectivity and in population size, selection, social structure (mating systems), among others [11, 41, 24, 42]. Major progress in human population genetics and genomics, including paleogenomics, have revolutionized our understanding of present-day and past genetic variation [43, 44]. Ideas and methods coming from human population genetics have influenced our understanding of the genetic diversity of other species [45, 46, 6, 14].…”

Section: Discussionmentioning

confidence: 99%

On the demographic history of chimpanzees and some consequences of integrating population structure in chimpanzees and other great apes

Steux,

Couloigner,

Arredondo

et al. 2024

Preprint

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Reconstructing the evolutionary history of great apes is of particular importance for our understanding of the demographic history of humans. The reason for this is that modern humans and their hominin ancestors evolved in Africa and thus shared the continent with the ancestors of chimpanzees and gorillas. Common chimpanzees (Pan troglodytes) are our closest relatives with bonobos (Pan paniscus) and most of what we know about their evolutionary history comes from genetic and genomic studies. Most evolutionary studies of common chimpanzees have assumed that the four currently recognised subspecies can be modelled using simple tree models where each subspecies is panmictic and represented by one branch of the evolutionary tree. However, several studies have identified the existence of significant population structure, both within and between subspecies, with evidence of isolation-by-distance (IBD) patterns. This suggests that demographic models integrating population structure may be necessary to improve our understanding of their evolutionary history. Here we propose to usen-island models within each subspecies to infer a demographic history integrating population structure and changes in connectivity (i.e.gene flow). For each subspecies, we use SNIF (structured non-stationary inference framework), a method developed to infer a piecewise stationaryn-island model using PSMC (pairwise sequentially Markovian coalescent) curves as summary statistics. We then propose a general model integrating the four subspecies metapopulations within a phylogenetic tree. We find that this model correctly predicts estimates of within subspecies genetic diversity and differentiation, but overestimates genetic differentiation between subspecies as a consequence of the tree structure. We argue that spatial models integrating gene flow between subspecies should improve the prediction of between subspecies differentiation and IBD patterns. We also use a simple spatially structured model for bonobos and chimpanzees (without admixture) and find that it explains signals of admixture between the two species that have been reported and could thus be spurious. This may have implications for our understanding of the evolutionary history of theHomogenus.

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Section: Discussionmentioning

confidence: 99%

On the demographic history of chimpanzees and some consequences of integrating population structure in chimpanzees and other great apes

Steux,

Couloigner,

Arredondo

et al. 2024

Preprint

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“…East Asia has a long history of human occupation, dating back to at least 45 kya ( 4 ). During the Holocene, various regions around the Yellow, Huai, and Yangtze Rivers in China were important centers for the domestication of rice, broomcorn millet, and foxtail millet, beginning ~8–9 kya ( 88 ).…”

Section: East Asia and Mainland Southeast Asiamentioning

confidence: 99%

“…Assuming that the homeland of the original farming group can be identified and that these people were genetically different from the groups into whose territory they expanded, then genetic investigations can reveal the extent to which modern groups have farmer-derived vs. indigenous (pre-farming) ancestry (here we use the term ancestry to refer in a general way to the genetic contributions to populations; for a discussion of the use and misuse of this term, see refs. 3 and 4 ). Beginning with the seminal work of Cavalli-Sforza and colleagues on the role of cultural vs. demic expansions in the spread of agriculture and IE languages across Europe ( 5 ), genetic investigations have been used to address the same question for the spread of farming and/or language families elsewhere.…”

mentioning

confidence: 98%

Genomic perspectives on human dispersals during the Holocene

Stoneking

Arias

Liu

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Nearly 20 y ago, Jared Diamond and Peter Bellwood reviewed the evidence for the associated spread of farming and large language families by the demographic expansions of farmers. Since then, advances in obtaining and analyzing genomic data from modern and ancient populations have transformed our knowledge of human dispersals during the Holocene. Here, we provide an overview of Holocene dispersals in the light of genomic evidence and conclude that they have a complex history. Even when there is a demonstrated connection between a demographic expansion of people, the spread of agriculture, and the spread of a particular language family, the outcome in the results of contact between expanding and resident groups is highly variable. Further research is needed to identify the factors and social circumstances that have influenced this variation and complex history.

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“…Despite these obstacles, lithic and fossil records attest to multiple hominin groups successfully crossing Wallace's Line in the late Pleistocene (3)(4)(5), with AMH arriving by at least 50 kya as part of a wider radiation of our species beyond Africa that culminated in the peopling of Sahul around the same time (6)(7)(8).…”

Section: Introductionmentioning

confidence: 99%

The genetic origins and impacts of historical Papuan migrations into Wallacea

Purnomo,

Kealy,

O’Connor

et al. 2024

Preprint

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The tropical archipelago of Wallacea was first settled by anatomically modern humans (AMH) by 50 thousand years ago (kya), with descendent populations thought to have remained genetically isolated prior to the arrival of Austronesian seafarers around 3.5 kya. Modern Wallaceans exhibit a longitudinal countergradient of Papuan- and Asian-related ancestries widely considered as evidence for mixing between local populations and Austronesian seafarers, though converging multidisciplinary evidence suggests that the Papuan-related component instead comes primarily from back-migrations from New Guinea. Here, we reconstruct Wallacean population genetic history using more than 250 newly reported genomes from 12 Wallacean and three West Papuan populations and confirm that the vast majority of Papuan-related ancestry in Wallacea (∼75–100%) comes from prehistoric migrations originating in New Guinea and only a minor fraction is attributable to the founding AMH settlers. Mixing between Papuan and local Wallacean lineages appear to have been confined to the western and central parts of the archipelago and likely occurred contemporaneously with the widespread introduction of genes from Austronesian seafarers—which now comprise between ∼40–85% of modern Wallacean ancestry—though dating historical admixture events remains challenging due to mixing continuing into the Historical Period. In conjunction with archaeological and linguistic records, our findings point to a dynamic Wallacean population history that was profoundly reshaped by the spread of Papuan genes, languages, and culture in the past 3,500 years.

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A genetic history of migration, diversification, and admixture in Asia

Cited by 7 publications

References 96 publications

On the demographic history of chimpanzees and some consequences of integrating population structure in chimpanzees and other great apes

On the demographic history of chimpanzees and some consequences of integrating population structure in chimpanzees and other great apes

Genomic perspectives on human dispersals during the Holocene

The genetic origins and impacts of historical Papuan migrations into Wallacea

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