Inference of human population history from individual whole-genome sequences
Open accessAbstract
The history of human population size is important for understanding human evolution. Various studies have found evidence for a founder event (bottleneck) in East Asian and European populations, associated with the human dispersal out-of-Africa event around 60 thousand years (kyr) ago. However, these studies have had to assume simplified demographic models with few parameters, and they do not provide a precise date for the start and stop times of the bottleneck. Here, with fewer assumptions on population size changes, we present a more detailed history of human population sizes between approximately ten thousand and a million years ago, using the pairwise sequentially Markovian coalescent model applied to the complete diploid genome sequences of a Chinese male (YH), a Korean male (SJK), three European individuals (J. C. Venter, NA12891 and NA12878 (ref. 9)) and two Yoruba males (NA18507 (ref. 10) and NA19239). We infer that European and Chinese populations had very similar population-size histories before 10-20 kyr ago. Both populations experienced a severe bottleneck 10-60 kyr ago, whereas African populations experienced a milder bottleneck from which they recovered earlier. All three populations have an elevated effective population size between 60 and 250 kyr ago, possibly due to population substructure. We also infer that the differentiation of genetically modern humans may have started as early as 100-120 kyr ago, but considerable genetic exchanges may still have occurred until 20-40 kyr ago.
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All time intervals from 2 to 500 kya have more than 100 recombinations, which is above the minimum of 10 recommended for reliable PSMC inference.
“All time intervals from 2 to 500 kya have more than 100 recombinations, which is above the minimum of 10 recommended for reliable PSMC inference.46”
From Genomes of critically endangered saola are shaped by population structure and purging (2025) · cites this paper as [46]
The model-validation passage (page unavailable) supports the general point that recombination events affect PSMC reliability. It does not give a minimum of 10 recombinations or report more than 100 in every interval from 2 to 500 kya; instead, it says estimates more recent than 20 kya have reduced accuracy and large variance. (LLM, conf=0.85)
Experimental — accuracy not yet measuredNon-African populations have decreased genetic diversity as a result of bottlenecks that occurred as humans moved into Eurasia, Oceania, and the Americas.
“The increased variant count in African populations is consistent with the out-of-Africa model of human migration across the world, as well as the decreased genetic diversity in non-African populations as a result of the bottlenecks that occurred as humans moved into Eurasia, Oceania, and the Americas (Ramachandran et al. 2005; DeGiorgio et al. 2009; Li and Durbin 2011).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Li and Durbin 2011
The indexed Abstract (page not provided) reports severe out-of-Africa bottlenecks in European and East Asian populations, compared with a milder bottleneck in the Yoruba population. This supports the claim’s core for those populations, but the paper does not establish bottleneck-related decreases in genetic diversity for populations in Oceania or the Americas. (LLM, conf=0.87)
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References 32 · Cited by 2,590
Research works printed but not linked: 21
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- Authors
- Li, H., & Durbin, R.
- Affiliations
- Wellcome Sanger Institute (GB)
- Corresponding author
- Li, Heng
- Durbin, Richard
- Venue
- Nature
- Published
- 2011-07
- Volume
- 475
- Issue
- 7357
- Pages
- 493-496
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3154645
- OpenAlex
- W2091705028
- Cited by
- 2,590
- References
- 32
- Citations by year
- 2026: 250 · 2025: 250 · 2024: 265 · 2023: 234 · 2022: 230 · 2021: 238 · 2020: 218 · 2019: 139 · 2018: 137 · 2017: 107 · 2016: 133 · 2015: 132 · 2014: 114 · 2013: 64 · 2012: 62
- FWCI
- 46.93
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Wellcome Trust (077192)
- 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, effective population size, population bottleneck, dispersal out of Africa, whole genome sequencing, Yoruba, European populations, East Asian populations, African populations, population substructure, genetic exchange
- MeSH terms
- Computer Simulation, Female, Genetics, Population, Humans, Male, Models, Genetic, Population Density, Population Dynamics, Sequence Analysis, DNA, Genomics
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