ArticlePLoS genetics2013
Inferring demographic history from a spectrum of shared haplotype lengths.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers.
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109 citing papers in PubMed, 266 citations in OpenAlex.
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- Reconstructing the Network of Horizontal Gene Exchange in Bacteria to Differentiate Direct and Indirect Transfers.Genome biology and evolution · 2026Article
- GHIST 2024: The First Genomic History Inference Strategies Tournament.Molecular biology and evolution · 2025Article
- Accelerated Bayesian inference of population size history from recombining sequence data.Nature genetics · 2025Article
- The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies.Molecular biology and evolution · 2025Article
- Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data.Heredity · 2025Article
- Population History Across Timescales in an Urban Archipelago.Genome biology and evolution · 2025Article
- Population history across timescales in an urban archipelago.bioRxiv : the preprint server for biology · 2025Article
- Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.Molecular biology and evolution · 2024Article
- Modeling the mosaic structure of bacterial genomes to infer their evolutionary history.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Dynamics of bacterial recombination in the human gut microbiome.PLoS biology · 2024Article
- Haplotype-based inference of recent effective population size in modern and ancient DNA samples.Nature communications · 2023Article
- Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.eLife · 2023Article
- Isolation by distance in populations with power-law dispersal.G3 (Bethesda, Md.) · 2023Article
- A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model.Molecular ecology · 2022Article
- Linkage disequilibrium between rare mutations.Genetics · 2022Article
- Article
- Review
- The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects.Molecular biology and evolution · 2021Article
- Genomic basis for drought resistance in European beech forests threatened by climate change.eLife · 2021Article
49 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.