ArticleProceedings of the National Academy of Sciences of the United States of America2014
Neutral genomic regions refine models of recent rapid human population growth.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed.
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- The impact of non-neutral synonymous mutations when inferring selection on nonsynonymous mutations.Genetics · 2025Article
- Estimation of demography and mutation rates from one million haploid genomes.American journal of human genetics · 2025Article
- Neolithic introgression of IL23R-related protection against chronic inflammatory bowel diseases in modern Europeans.EBioMedicine · 2025Article
- Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History.Molecular biology and evolution · 2025Article
- Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations.PLoS biology · 2024Article
- Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history.bioRxiv : the preprint server for biology · 2023Article
- Population history modulates the fitness effects of Copy Number Variation in the Roma.Human genetics · 2023Article
- Recurrent mutation in the ancestry of a rare variant.Genetics · 2023Article
- Human cooperation and evolutionary transitions in individuality.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Article
- Article
- The demographic history of Madagascan micro-endemics: have rare species always been rare?Proceedings. Biological sciences · 2021Article
- Adaptive Introgression across Semipermeable Species Boundaries between Local Helicoverpa zea and Invasive Helicoverpa armigera Moths.Molecular biology and evolution · 2020Article
- Efficiently inferring the demographic history of many populations with allele count data.Journal of the American Statistical Association · 2020Article
- A Computational Approach for Modeling the Allele Frequency Spectrum of Populations with Arbitrarily Varying Size.Genomics, proteomics & bioinformatics · 2019Article
- The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference.Molecular biology and evolution · 2019Article
- An efficient algorithm for generating the internal branches of a Kingman coalescent.Theoretical population biology · 2018Article
- Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia.PLoS genetics · 2018Article
- Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
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11 authors.
Funding
Abstract
Human populations have experienced dramatic growth since the Neolithic revolution. Recent studies that sequenced a very large number of individuals observed an extreme excess of rare variants and provided clear evidence of recent rapid growth in effective population size, although estimates have varied greatly among studies. All these studies were based on protein-coding genes, in which variants are also impacted by natural selection. In this study, we introduce targeted sequencing data for studying recent human history with minimal confounding by natural selection. We sequenced loci far from genes that meet a wide array of additional criteria such that mutations in these loci are putatively neutral. As population structure also skews allele frequencies, we sequenced 500 individuals of relatively homogeneous ancestry by first analyzing the population structure of 9,716 European Americans. We used very high coverage sequencing to reliably call rare variants and fit an extensive array of models of recent European demographic history to the site frequency spectrum. The best-fit model estimates ∼ 3.4% growth per generation during the last ∼ 140 generations, resulting in a population size increase of two orders of magnitude. This model fits the data very well, largely due to our observation that assumptions of more ancient demography can impact estimates of recent growth. This observation and results also shed light on the discrepancy in demographic estimates among recent studies.
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