title: Correlated patterns of genetic diversity and differentiation across an avian family.
abstract: Comparative studies of closely related taxa can provide insights into the evolutionary forces that shape genome evolution and the prevalence of convergent molecular evolution. We investigated patterns of genetic diversity and differentiation in stonechats (genus Saxicola), a widely distributed avian species complex with phenotypic variation in plumage, morphology and migratory behaviour, to ask whether similar genomic regions have become differentiated in independent, but closely related, taxa. We used whole-genome pooled sequencing of 262 individuals from five taxa and found that levels of genetic diversity and divergence are strongly correlated among different stonechat taxa. We then asked whether these patterns remain correlated at deeper evolutionary scales and found that homologous genomic regions have become differentiated in stonechats and the closely related Ficedula flycatchers. Such correlation across a range of evolutionary divergence and among phylogenetically independent comparisons suggests that similar processes may be driving the differentiation of these independently evolving lineages, which in turn may be the result of intrinsic properties of particular genomic regions (e.g. areas of low recombination). Consequently, studies employing genome scans to search for areas important for reproductive isolation or adaptation should account for corresponding regions of differentiation, as these regions may not necessarily represent speciation islands or evidence of local adaptation.
authors.affiliation: Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.|Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA.
authors.forename: Benjamin M
authors.identifier: http://orcid.org/0000-0002-7355-6005
authors.initials: BM
authors.lastname: Van Doren
authors.affiliation: Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.|Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Campagna
authors.affiliation: Animal Health and Comparative Medicine, Institute of Biodiversity, University of Glasgow, Glasgow, G12 8QQ, UK.
authors.forename: Barbara
authors.initials: B
authors.lastname: Helm
authors.affiliation: Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Campus of Mieres, Research Building, 5th Floor, c/ Gonzalo Gutiérrez Quirós s/n, 33600, Mieres, Asturias, Spain.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Illera
authors.affiliation: Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.|Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA.
authors.forename: Irby J
authors.initials: IJ
authors.lastname: Lovette
authors.affiliation: Max Planck Institute for Evolutionary Biology, AG Behavioural Genomics, August-Thienemann-Str. 2, 24306, Plön, Germany.
authors.forename: Miriam
authors.initials: M
authors.lastname: Liedvogel
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D049810:Genetic Speciation; D014644:Genetic Variation; D016678:Genome; D046109:Passeriformes / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D060047:Reproductive Isolation
keywords: 
  Ficedula
  ; 
  Saxicola
  ; differentiation peaks; genetic drift; genomic scan; linked selection; pooled sequencing