ArticlePLoS genetics2016
Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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91 citing papers in PubMed.
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- Genome-Wide Analysis Successfully Resolves Population Structure Shaped by Recent Divergence in the Endangered Bagrid CatfishEcology and evolution · 2026Article
- Neural posterior estimation for population genetics.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
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- Estimating Linkage Disequilibrium and Effective Population Size Across Generations in Holstein Cattle.Veterinary medicine and science · 2025Article
- Article
- Positive selection on rare variants of IGF1R and BRD4 underlying the cold adaptation of wild boar.Genetics, selection, evolution : GSE · 2025Article
- Going New Places: Successful Adaptation and Genomic Integrity of Grain Amaranth in India.Evolutionary applications · 2025Article
- Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data.Heredity · 2025Article
- Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes.Current biology : CB · 2025Article
- Population History Across Timescales in an Urban Archipelago.Genome biology and evolution · 2025Article
31 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.
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