The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds

Suh, Alexander ORCID: https://orcid.org/0000-0002-8979-9992, Smeds, Linnéa, Ellegren, Hans and Penny, David (2015) The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds. PLoS Biology, 13 (8). ISSN 1545-7885

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Abstract

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.

Item Type: Article
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 11 Nov 2020 01:16
Last Modified: 06 Apr 2024 00:53
URI: https://ueaeprints.uea.ac.uk/id/eprint/77631
DOI: 10.1371/journal.pbio.1002224

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