title: Hidden histories of gene flow in highland birds revealed with genomic markers.
abstract: Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these 'hidden histories' using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation-with-bouts-of-gene-flow will turn out to be a common mode of speciation.
authors.affiliation: Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA.
authors.forename: Eugenia
authors.initials: E
authors.lastname: Zarza
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.
authors.forename: Brant C
authors.identifier: 0000-0002-1943-0217
authors.initials: BC
authors.lastname: Faircloth
authors.affiliation: Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA.
authors.forename: Whitney L E
authors.initials: WL
authors.lastname: Tsai
authors.affiliation: Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA.|Burke Museum of Natural History and Culture and Department of Biology, University of Washington, Seattle, WA, 98195, USA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Bryson
authors.affiliation: Burke Museum of Natural History and Culture and Department of Biology, University of Washington, Seattle, WA, 98195, USA.
authors.forename: John
authors.initials: J
authors.lastname: Klicka
authors.affiliation: Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA. mccormack@oxy.edu.
authors.forename: John E
authors.initials: JE
authors.lastname: McCormack
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics; D051456:Gene Flow; D049810:Genetic Speciation; D005828:Genetics, Population; D023281:Genomics; D008800:Mexico; D008957:Models, Genetic; D046109:Passeriformes / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: ancient introgression; divergence-with-gene-flow; introgression; mito-nuclear discordance