RT Journal Article
SR Electronic
T1 Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.03.07.977694
DO 10.1101/2020.03.07.977694
A1 Hussein A. Hejase
A1 Ayelet Salman-Minkov
A1 Leonardo Campagna
A1 Melissa J. Hubisz
A1 Irby J. Lovette
A1 Ilan Gronau
A1 Adam Siepel
YR 2020
UL http://biorxiv.org/content/early/2020/07/29/2020.03.07.977694.abstract
AB Numerous studies of emerging species have identified genomic “islands” of elevated differentiation against a background of relative homogeneity. The causes of these islands remain unclear, however, with some signs pointing toward “speciation genes” that locally restrict gene flow and others suggesting selective sweeps that have occurred within nascent species after speciation. Here, we examine this question through the lens of genome sequence data for five species of southern capuchino seedeaters, finch-like birds from South America that have undergone a species radiation during the last ∼50,000 generations. By applying newly developed statistical methods for ancestral recombination graph inference and machine-learning methods for the prediction of selective sweeps, we show that previously identified islands of differentiation in these birds appear to be generally associated with relatively recent, species-specific selective sweeps, most of which are predicted to be “soft” sweeps acting on standing genetic variation. Many of these sweeps coincide with genes associated with melanin-based variation in plumage, suggesting a prominent role for sexual selection. At the same time, a few loci also exhibit indications of possible selection against gene flow. These observations shed new light on the complex manner in which natural selection shapes genome sequences during speciation.Significance Statement Genome-wide scans can identify differentiated loci between species that may have promoted speciation. So-called “islands of differentiation” have generally been identified and characterized using standard population genetic summary statistics (e.g., FST and dxy), which are limited in distinguishing among possible causes of differentiation, such as selection against gene flow and selective sweeps. We introduce a powerful strategy for analyzing such islands, combining new methods for inferring the full Ancestral Recombination Graph and machine learning methods for identifying selective sweeps. We applied our methods to genomic sequences from closely related southern capuchino seedeaters (Neotropical tanagers) and found signatures of recent selective sweeps around pigmentation genes, including many “soft” sweeps that acted on standing variation.Competing Interest StatementThe authors have declared no competing interest.