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How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Konstanz, Dept Biol, D-78457 Constance, Germany.ORCID iD: 0000-0002-4805-5575
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
2019 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 212, no 1, p. 277-285Article in journal (Refereed) Published
Abstract [en]

There is an increasing awareness that selection affecting linked neutral sites strongly influences on how diversity is distributed across the genome. In particular, linked selection is likely involved in the formation of heterogenous landscapes of genetic diversity, including genomic regions with locally reduced effective population sizes that manifest as dips in diversity, and "islands" of differentiation between closely related populations or species. Linked selection can be in the form of background selection or selective sweeps, and a long-standing quest in population genetics has been to unveil the relative importance of these processes. Here, we analyzed the theoretically expected reduction of diversity caused by linked selection in the collared flycatcher (Ficedula albicollis) genome and compared this with population genomic data on the distribution of diversity across the flycatcher genome. By incorporating data on recombination rate variation and the density of target sites for selection (including both protein-coding genes and conserved noncoding elements), we found that background selection can explain most of the observed baseline variation in genetic diversity. However, positive selection was necessary to explain the pronounced local diversity dips in the collared flycatcher genome. We confirmed our analytical findings by comprehensive simulations. Therefore, our study demonstrates that even though both background selection and selective sweeps contribute to the heterogeneous diversity landscape seen in this avian system, they play different roles in shaping it.

Place, publisher, year, edition, pages
GENETICS SOCIETY AMERICA , 2019. Vol. 212, no 1, p. 277-285
Keywords [en]
diversity, background selection, selective sweeps, flycatcher
National Category
Genetics Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-383847DOI: 10.1534/genetics.119.301991ISI: 000466802000018PubMedID: 30872320OAI: oai:DiVA.org:uu-383847DiVA, id: diva2:1317986
Funder
Swedish Research Council, 2013-8271Knut and Alice Wallenberg FoundationAvailable from: 2019-05-24 Created: 2019-05-24 Last updated: 2019-05-24Bibliographically approved

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Rettelbach, AgnesEllegren, Hans

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