Possible Ancestral Structure in Human Populations
Open accessAbstract
Determining the evolutionary relationships between fossil hominid groups such as Neanderthals and modern humans has been a question of enduring interest in human evolutionary genetics. Here we present a new method for addressing whether archaic human groups contributed to the modern gene pool (called ancient admixture), using the patterns of variation in contemporary human populations. Our method improves on previous work by explicitly accounting for recent population history before performing the analyses. Using sequence data from the Environmental Genome Project, we find strong evidence for ancient admixture in both a European and a West African population (p approximately 10(-7)), with contributions to the modern gene pool of at least 5%. While Neanderthals form an obvious archaic source population candidate in Europe, there is not yet a clear source population candidate in West Africa.
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There is evidence for superarchaic gene flow into Denisovans, into Neanderthal-Denisovan ancestors, and into Africans.
“There is evidence for superarchaic gene flow into Denisovans 13,21,22 , into Neanderthal-Denisovan ancestors 27 , and into Africans 4 .”
From The Genetic Legacy of Introgression from Two Deeply Divergent Lineages in the Genus <i>Homo</i> (2026) · cites this paper as [21]
The citation is attached to the claim about gene flow into Africans, not the claims about Denisovans. The Abstract reports strong evidence for ancient admixture in a West African population, but says its source population is unknown. The Discussion likewise describes an admixture signal in West Africans; neither passage identifies the source as superarchaic. (LLM, conf=0.87)
Experimental — accuracy not yet measuredUnusually large variation in LD within the human genome suggests that ancient human populations were subdivided.
“Unusually large variation in LD within the human genome already suggests that ancient human populations were subdivided111,112”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [112]
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“S* score identifies divergent haplotypes in a target population that carry derived variants in strong linkage disequilibrium (LD) while being absent in the reference population 5,13,66 .”
- Authors
- Plagnol, V., & Wall, J. D.
- Affiliations
- University of Southern California (US)
- Corresponding author
- Plagnol, Vincent
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2006-07-28
- Volume
- 2
- Issue
- 7
- Pages
- e105
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC1523253
- OpenAlex
- W2033913430
- Cited by
- 275
- References
- 1
- Citations by year
- 2026: 13 · 2025: 6 · 2024: 5 · 2023: 7 · 2022: 6 · 2021: 12 · 2020: 14 · 2019: 16 · 2018: 15 · 2017: 12 · 2016: 25 · 2015: 9 · 2014: 13 · 2013: 10 · 2012: 16
- FWCI
- 9.87
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Figshare (submittedVersion, cc-by)
- Funders
- National Science Foundation (0423123)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- Neanderthals, human evolution, archaic human admixture, European populations, West African populations, human population structure
- MeSH terms
- Animals, Biological Evolution, Fossils, Genetic Markers, Genetics, Population, Humans, Genetic Variation, Hominidae, Models, Statistical, Linkage Disequilibrium, Population Groups
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