ArticleNature communications2023
Haplotype-based inference of recent effective population size in modern and ancient DNA samples.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Updating the RZooRoH Package for the Analysis of Inbreeding, Identity-By-Descent and Relatedness From Genomic Data.Molecular ecology resources · 2026Article
- Layers in the sand: The genetic imprint of migration, culture, and Indus craft in the Thar Desert.HGG advances · 2026Article
- From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference.bioRxiv : the preprint server for biology · 2026Article
- Article
- Inferring hominin history with recurrent gene flow from single unphased genomes and a two-locus statistic.bioRxiv : the preprint server for biology · 2026Article
- Unraveling the genetic landscape and admixture dynamics of urban populations across Peru.Communications biology · 2026Article
- A large mass grave from the Early Iron Age indicates selective violence towards women and children in the Carpathian Basin.Nature human behaviour · 2026Article
- A hypomorphic SRD5A2 haplotype with a potential founder effect: composed of common variants in individuals with 5α-reductase type 2 deficiency from South China.Biology of sex differences · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Exploring the genomic population structure and history of Austroasiatic speakers in Mainland Southeast Asia.Communications biology · 2026Article
- Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies.Genome biology and evolution · 2026Review
- TS-IBD: An efficient ancestral recombination graph-based identity by descent segment detection method.Human population genetics and genomics · 2026Article
- Exploration of hanging coffin customs and the bo people in China through comparative genomics.Nature communications · 2025Article
- Inferring Domestic Goat Demographic History Through Ancient Genome Imputation.Genome biology and evolution · 2025Article
- Accelerated Bayesian inference of population size history from recombining sequence data.Nature genetics · 2025Article
- Power and Limitations of Inferring Genetic Ancestry.Annals of human genetics · 2025Review
- Effective Population Size Estimation in Large Marine Populations: Considering Current Challenges and Opportunities When Simulating Large Data Sets With High-Density Genomic Information.Evolutionary applications · 2025Review
- Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods.Nature communications · 2025Article
- Article
- Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden.Genome biology · 2025Article
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4 authors.
Funding
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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