title: One size fits all? Direct evidence for the heterogeneity of genetic drift throughout the genome.
abstract: Effective population size (Ne) is a central parameter in population and conservation genetics. It measures the magnitude of genetic drift, rates of accumulation of inbreeding in a population, and it conditions the efficacy of selection. It is often assumed that a single Ne can account for the evolution of genomes. However, recent work provides indirect evidence for heterogeneity in Ne throughout the genome. We study this by examining genome-wide diversity in the Danish Holstein cattle breed. Using the differences in allele frequencies over a single generation, we directly estimated Ne among autosomes and smaller windows within autosomes. We found statistically significant variation in Ne at both scales. However, no correlation was found between the detected regional variability in Ne, and proxies for the intensity of linked selection (local recombination rate, gene density), or the presence of either past strong selection or current artificial selection on traits of economic value. Our findings call for further caution regarding the wide applicability of the Ne concept for understanding quantitatively processes such as genetic drift and accumulation of consanguinity in both natural and managed populations.
authors.affiliation: Bioinformatics Research Center (BiRC), Aarhus University, Aarhus, Denmark INRA, UMR1313 Génétique animale et biologie intégrative, 78350 Jouy-en-Josas, France AgroParisTech, UMR1313 Génétique animale et biologie intégrative, 16 rue Claude Bernard, 75231 Paris 05, France.
authors.forename: Belén
authors.initials: B
authors.lastname: Jiménez-Mena
authors.affiliation: Bioinformatics Research Center (BiRC), Aarhus University, Aarhus, Denmark.
authors.forename: Paula
authors.initials: P
authors.lastname: Tataru
authors.affiliation: Department of Haematology, Aalborg University Hospital, 9000 Aalborg, Denmark.
authors.forename: Rasmus F
authors.initials: RF
authors.lastname: Brøndum
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark.
authors.forename: Goutam
authors.initials: G
authors.lastname: Sahana
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark.
authors.forename: Bernt
authors.initials: B
authors.lastname: Guldbrandtsen
authors.affiliation: Bioinformatics Research Center (BiRC), Aarhus University, Aarhus, Denmark tbata@birc.au.dk.
authors.forename: Thomas
authors.identifier: 0000-0002-4730-2538
authors.initials: T
authors.lastname: Bataillon
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D040961:Genetic Drift; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D007178:Inbreeding; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
keywords: Holstein breed; effective population size; genetic drift; linked selection; quantitative trait loci