Haplotype-based inference of recent effective population size in modern and ancient DNA samples
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Abstract
Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2000 years in both modern and ancient DNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe shows improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We apply HapNe to several modern populations from the 1,000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups.
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The inferred HapNe-LD curve for Rapanui shows a decreasing population size that reaches its minimum about 28 generations (about 800 years) before the Ancient Rapanui time of birth, followed by a steady increase.
“Our inferred HapNe-LD curve is pictured in Fig. 2b and Supplementary Fig. 28. It shows a decreasing population size that reaches its minimum about 28 generations (about 800 years) before the Ancient Rapanui time of birth, followed by a steady increase.”
From Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas (2024) · cites this paper as [51]
The Results section (“Overview of the HapNe algorithm”; page not available) confirms that HapNe-LD infers recent effective population size. The paper’s ancient-population results discuss other populations, not Rapanui; our copy does not support the claimed minimum 28 generations before the Ancient Rapanui birth date or the subsequent steady increase. (LLM, conf=0.80)
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- Authors
- Fournier, R., Tsangalidou, Z., Reich, D., & Palamara, P. F.
- Affiliations
- University of Oxford (GB)
- Broad Institute (US)
- Centre for Human Genetics (GB)
- Corresponding author
- Palamara, Pier Francesco
- Venue
- Nature Communications
- Published
- 2023-12-01
- Volume
- 14
- Issue
- 1
- Pages
- 7945-7945
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10692198
- OpenAlex
- W4389247739
- Cited by
- 49
- References
- 88
- Citations by year
- 2026: 14 · 2025: 23 · 2024: 10 · 2023: 2
- FWCI
- 8.13
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Howard Hughes Medical Institute
- John Templeton Foundation (61220)
- Wellcome Trust (203141/Z/16/Z, 204826/Z/16/Z, 203141, 204826)
- International Seafood Sustainability Foundation
- National Institute for Health and Care Research (203141/Z/16/Z., GM100233)
- National Institutes of Health (GM100233)
- Medical Research Council (MC_PC_17228)
- Engineering and Physical Sciences Research Council
- Biomedical Research Council
- NIHR Oxford Biomedical Research Centre
- National Human Genome Research Institute (R21HG010748, R01HG012287)
- National Institute of General Medical Sciences (R01GM100233)
- H2020 European Research Council (850869)
- Health Data Research UK
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- effective population size, ancient DNA, identical by descent, linkage disequilibrium, Iron Age Britain, underrepresented groups, population fluctuations
- MeSH terms
- DNA, Ancient, Genetics, Population, Haplotypes, Humans, Population Density, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Genomics
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