ArticleProceedings of the National Academy of Sciences of the United States of America2020
Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 71 citations in OpenAlex.
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- Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.Molecular ecology · 2025Article
- Population Genetic Structure, Historical Effective Population Size, and Dairy Trait Selection Signatures in Chinese Red Steppe and Holstein Cattle.Animals : an open access journal from MDPI · 2025Article
- Revisiting the species problem in Northeast Pacific ribbon kelp lineages (genus Alaria): Lessons learned using whole genome data.Journal of phycology · 2025Article
- A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle system.BMC biology · 2025Article
- Genetic Differentiation is Constrained to Chromosomal Inversions and Putative Centromeres in Locally Adapted Populations With Higher Gene Flow.Molecular biology and evolution · 2025Article
- High-recombining genomic regions affect demography inference based on ancestral recombination graphs.Genetics · 2025Article
- Likelihoods for a general class of ARGs under the SMC.bioRxiv : the preprint server for biology · 2025Article
- The genetic origins of species boundaries at subtropical and temperate ecoregions in the North American racers (Coluber constrictor).Heredity · 2025Article
- Pangenome graphs and their applications in biodiversity genomics.Nature genetics · 2025Review
- Testing the genomic overlap between intraspecific mating traits and interspecific mating barriers.Evolution letters · 2024Article
- Genetic Basis and Evolution of Structural Color Polymorphism in an Australian Songbird.Molecular biology and evolution · 2024Article
- Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus.GigaScience · 2024Article
- Article
- Versatile Detection of Diverse Selective Sweeps with Flex-Sweep.Molecular biology and evolution · 2023Article
- High heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of mitonuclear co-introgression.Heredity · 2023Article
- Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species.PLoS genetics · 2022Article
- The evolutionary history and mechanistic basis of female ornamentation in a tropical songbird.Evolution; international journal of organic evolution · 2022Article
- Avian Introgression Patterns are Consistent With Haldane's Rule.The Journal of heredity · 2022Review
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7 authors at 3 institutions in 2 countries.
Funding
Abstract
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.
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