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Cited by 27Forensic and Genetic ResearchGenetic diversity and population structurePleistocene-Era Hominins and Archaeology

A structured coalescent model reveals deep ancestral structure shared by all modern humans

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Cousins, Trevor, Scally, Aylwyn, Durbin, Richard·2025·Nature Genetics
DOI 10.1038/s41588-025-02117-1PMC PMC11985351

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Abstract

Understanding the history of admixture events and population size changes leading to modern humans is central to human evolutionary genetics. Here we introduce a coalescence-based hidden Markov model, cobraa, that explicitly represents an ancestral population split and rejoin, and demonstrate its application on simulated and real data across multiple species. Using cobraa, we present evidence for an extended period of structure in the history of all modern humans, in which two ancestral populations that diverged ~1.5 million years ago came together in an admixture event ~300 thousand years ago, in a ratio of ~80:20%. Immediately after their divergence, we detect a strong bottleneck in the major ancestral population. We inferred regions of the present-day genome derived from each ancestral population, finding that material from the minority correlates strongly with distance to coding sequence, suggesting it was deleterious against the majority background. Moreover, we found a strong correlation between regions of majority ancestry and human–Neanderthal or human–Denisovan divergence, suggesting the majority population was also ancestral to those archaic humans.

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Cited by

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Authors
Cousins, T., Scally, A., & Durbin, R.
Affiliations
University of Cambridge (GB)
Corresponding author
Durbin, Richard
ORCID
Venue
Nature Genetics
Publisher
Springer Science and Business Media LLC
Published
2025-03-18
Volume
57
Issue
4
Pages
856-864
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
DOI
10.1038/s41588-025-02117-1
PMC
PMC11985351
OpenAlex
W4408560619
Cited by
27
References
9
Citations by year
2026: 16 · 2025: 10 · 2024: 1
FWCI
15.28
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Genetics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
Wellcome Trust (207492/Z/17/Z, 108864/B/15/Z)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
Keywords
human population history, admixture, population bottleneck, hidden Markov models, Neanderthal ancestry, archaic admixture, human evolution, population size change
MeSH terms
Animals, Genetics, Population, Humans, Markov Chains, Models, Genetic, Population Density, Genome, Human, Evolution, Molecular, Neanderthals

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