Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps

Hejase, H. A., Salman-Minkov, A., Campagna, L., Hubisz, M. J., Lovette, I. J., Gronau, I., Siepel, A. (December 2020) Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proc Natl Acad Sci U S A, 117 (48). pp. 30554-30565. ISSN 0027-8424 (Print)0027-8424

DOI: 10.1073/pnas.2015987117


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 light on the complex manner in which natural selection shapes genome sequences during speciation.

Item Type: Paper
Additional Information: 1091-6490 Hejase, Hussein A Salman-Minkov, Ayelet Orcid: 0000-0001-6031-6996 Campagna, Leonardo Orcid: 0000-0001-8408-8553 Hubisz, Melissa J Lovette, Irby J Gronau, Ilan Orcid: 0000-0001-8536-4062 Siepel, Adam Orcid: 0000-0002-3557-7219 R35 GM127070/GM/NIGMS NIH HHS/United States Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Proc Natl Acad Sci U S A. 2020 Dec 1;117(48):30554-30565. doi: 10.1073/pnas.2015987117. Epub 2020 Nov 16.
Uncontrolled Keywords: *ancestral recombination graph *machine learning *speciation *sweeps
Subjects: bioinformatics
bioinformatics > computational biology > algorithms
bioinformatics > computational biology
bioinformatics > computational biology > algorithms > machine learning
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matthew Dunn
Date: 1 December 2020
Date Deposited: 19 Apr 2021 17:30
Last Modified: 30 Jan 2024 20:50
PMCID: PMC7720181
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