title: Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting.
abstract: Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird species-collared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman'sρ= 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable.
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Dutoit
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors.forename: Nagarjun
authors.initials: N
authors.lastname: Vijay
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors.forename: Carina F
authors.initials: CF
authors.lastname: Mugal
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors.forename: Christen M
authors.initials: CM
authors.lastname: Bossu
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors.forename: Reto
authors.initials: R
authors.lastname: Burri
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.|Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Wolf
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden hans.ellegren@ebc.uu.se.
authors.forename: Hans
authors.identifier: 0000-0002-5035-1736
authors.initials: H
authors.lastname: Ellegren
mesh_terms: D000818:Animals; D046368:Crows / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D059785:Karyotype; D009711:Nucleotides / Q000235:genetics*; D011995:Recombination, Genetic; D020308:Songbirds / Q000235:genetics*; D026801:Synteny
chemical_list: D009711:Nucleotides
keywords: birds; linked selection; nucleotide diversity; recombination rate