ArticlePLoS genetics2019
Models of archaic admixture and recent history from two-locus statistics.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Article
- Faster inference of complex demographic models from large allele frequency spectra.Bioinformatics (Oxford, England) · 2026Article
- Neural posterior estimation for population genetics.Genetics · 2026Article
- Inferring hominin history with recurrent gene flow from single unphased genomes and a two-locus statistic.bioRxiv : the preprint server for biology · 2026Article
- Neural posterior estimation for population genetics.bioRxiv : the preprint server for biology · 2026Article
- Recovering signatures of archaic introgression using ancestral recombination graphs.bioRxiv : the preprint server for biology · 2026Article
- Combining Population Genomics With Ancient DNA to Understand Island Colonisation History of the Madagascar Turtle Dove.Molecular ecology · 2026Article
- GENERAL MOMENT CLOSURE FOR THE NEUTRAL TWO-LOCUS WRIGHT-FISHER DYNAMICS.bioRxiv : the preprint server for biology · 2026Article
- Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs.bioRxiv : the preprint server for biology · 2026Article
- GHIST 2024: The First Genomic History Inference Strategies Tournament.Molecular biology and evolution · 2025Article
- Accessible, Realistic Genome Simulation with Selection Using stdpopsim.Molecular biology and evolution · 2025Article
- Accelerated Bayesian inference of population size history from recombining sequence data.Nature genetics · 2025Article
- A model for background selection in non-equilibrium populations.bioRxiv : the preprint server for biology · 2025Article
- Accessible, realistic genome simulation with selection using stdpopsim.bioRxiv : the preprint server for biology · 2025Article
- 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
- Resolving out of Africa event for Papua New Guinean population using neural network.Nature communications · 2025Article
- Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods.Nature communications · 2025Article
- Article
- A structured coalescent model reveals deep ancestral structure shared by all modern humans.Nature genetics · 2025Article
- Insufficient Evidence for a Severe Bottleneck in Humans During the Early to Middle Pleistocene Transition.Molecular biology and evolution · 2025Article
3 more citing papers are in PubMed but not listed here.
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Abstract
We learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4 - 8% genetic ancestry to individuals in world-wide populations.
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