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The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds
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.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
2015 (English)In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 13, no 8, e1002224Article in journal (Refereed) Published
Abstract [en]

The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms. Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene (K-Pg) boundary, yet the causes of the remaining genome-level irresolvabilities appear unclear. Here we show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly differential temporal prevalence of incomplete lineage sorting (ILS), i.e., the persistence of ancestral genetic variation as polymorphisms during speciation events. We found that ILS-derived incongruences are spread over the genome and involve 35% and 34% of the analyzed loci on the autosomes and the Z chromosome, respectively. Surprisingly, Neoaves diversification comprises three adaptive radiations, an initial near-K-Pg super-radiation with highly discordant phylogenetic signals from near-simultaneous speciation events, followed by two post-K-Pg radiations of core landbirds and core waterbirds with much less pronounced ILS. We provide evidence that, given the extreme level of up to 100% ILS per branch in super-radiations, particularly rapid speciation events may neither resemble a fully bifurcating tree nor are they resolvable as such. As a consequence, their complex demographic history is more accurately represented as local networks within a species tree.

Place, publisher, year, edition, pages
2015. Vol. 13, no 8, e1002224
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-263534DOI: 10.1371/journal.pbio.1002224ISI: 000360618400012OAI: oai:DiVA.org:uu-263534DiVA: diva2:858861
Funder
EU, European Research CouncilSwedish Research Council, 2007-8731 2010-5650Knut and Alice Wallenberg Foundation
Available from: 2015-10-05 Created: 2015-10-02 Last updated: 2017-12-01Bibliographically approved

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Suh, AlexanderSmeds, LinneaEllegren, Hans

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