title: Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation.
abstract: Recently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated or that may cross species barriers through introgressive hybridization. Here we use a reduced-representation genomic approach to explore divergence among six species of southern capuchino seedeaters, a group of recently radiated sympatric passerine birds in the genus Sporophila. For the first time in these taxa, we discovered a small proportion of markers that appeared differentiated among species. However, when assessing the significance of these signatures of divergence, we found that similar patterns can also be recovered from random grouping of individuals representing different species. A detailed demographic inference indicates that genetic differences among Sporophila species could be the consequence of neutral processes, which include a very large ancestral effective population size that accentuates the effects of incomplete lineage sorting. As these neutral phenomena can generate genomic scan patterns that mimic those of markers involved in speciation and phenotypic differentiation, they highlight the need for caution when ascertaining and interpreting differentiated markers between species, especially when large numbers of markers are surveyed. Our study provides new insights into the demography of the southern capuchino radiation and proposes controls to distinguish signal from noise in similar genomic scans.
authors.affiliation: Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA.|Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY, 14853, USA.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Campagna
authors.affiliation: Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center (IDC), P.O. Box 167, Kanfei Nesharim St., Herzliya, 46150, Israel.
authors.forename: Ilan
authors.initials: I
authors.lastname: Gronau
authors.affiliation: Seção de Aves, Museu de Zoologia, Universidade de São Paulo (MZUSP), Caixa Postal 42.494, CEP 04218-970, São Paulo, SP, Brazil.
authors.forename: Luís Fábio
authors.initials: LF
authors.lastname: Silveira
authors.affiliation: Watson School of Biological Sciences, Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Siepel
authors.affiliation: Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA.|Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY, 14853, USA.
authors.forename: Irby J
authors.initials: IJ
authors.lastname: Lovette
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D005260:Female; D051456:Gene Flow; D056426:Genetic Loci; D049810:Genetic Speciation; D005828:Genetics, Population; D023281:Genomics; D008297:Male; D008957:Models, Genetic; D046109:Passeriformes / Q000145:classification / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013020:South America; D061350:Sympatry
keywords: RAD sequencing; drift; genomic scan; incomplete lineage sorting; outlier analysis; species flock