Inferring population size history from large samples of genome-wide molecular data - an approximate Bayesian computation approach
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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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The pattern of domestic populations undergoing sharper decreases than wild populations was also observed in the analysis of PopSizeABC.
“This pattern was also observed in the analysis of PopSizeABC (Boitard et al. 2016) (supplementary fig. S8, Supplementary Material online).”
From Genomic Analyses Unveil Helmeted Guinea Fowl (<i>Numida meleagris</i>) Domestication in West Africa (2021) · cites this paper as Boitard et al. 2016
The Results (Application to NGS samples in cattle; page unavailable) report population declines in four domestic cattle breeds and a sharper decrease in their shared ancestral history. That sharper decrease began before domestication, however, and the paper does not compare the declines of domestic populations with those of wild populations. (LLM, conf=0.86)
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- Authors
- Boitard, S., Rodríguez, W., Jay, F., Mona, S., & Austerlitz, F.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Université Paris-Sud (FR)
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2016-03-04
- Volume
- 12
- Issue
- 3
- Pages
- e1005877
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC4778914
- OpenAlex
- W2292463482
- Cited by
- 190
- References
- 73
- Citations by year
- 2026: 16 · 2025: 13 · 2024: 30 · 2023: 22 · 2022: 13 · 2021: 23 · 2020: 15 · 2019: 11 · 2018: 25 · 2017: 17 · 2016: 5
- FWCI
- 15.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by)
- HAL (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Indian National Science Academy
- Agence Nationale de la Recherche (ANR-10-GENM-0014, ANR-12, ANR-10, ANR-12-BSV7-0012)
- Université de Toulouse
- Centre National de la Recherche Scientifique
- Institut National de la Recherche Agronomique
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- approximate Bayesian computation, linkage disequilibrium, whole genome sequencing, cattle breeds, population decline, domestication
- MeSH terms
- Alleles, Animals, Bayes Theorem, Breeding, Cattle, Genetics, Population, Population Density, Linkage Disequilibrium, Polymorphism, Single Nucleotide
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