title: Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.
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.
authors.affiliation: Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS & MNHN & UPMC & EPHE, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France.|GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Simon
authors.initials: S
authors.lastname: Boitard
authors.affiliation: UMR CNRS 5219, Institut de Mathématiques de Toulouse, Université de Toulouse, Toulouse, France.
authors.forename: Willy
authors.initials: W
authors.lastname: Rodríguez
authors.affiliation: UMR 7206 Eco-anthropologie et Ethnobiologie, Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France.|LRI, Paris-Sud University, CNRS UMR 8623, Orsay, France.
authors.forename: Flora
authors.initials: F
authors.lastname: Jay
authors.affiliation: Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS & MNHN & UPMC & EPHE, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France.
authors.forename: Stefano
authors.initials: S
authors.lastname: Mona
authors.affiliation: UMR 7206 Eco-anthropologie et Ethnobiologie, Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Austerlitz
mesh_terms: D000483:Alleles; D000818:Animals; D001499:Bayes Theorem; D001947:Breeding; D002417:Cattle; D005828:Genetics, Population; D015810:Linkage Disequilibrium / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011156:Population Density