Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini)

Systematic Biology
Bryan S McleanJoseph A Cook

Abstract

Phylogenomic data sets are illuminating many areas of the Tree of Life. However, the large size of these data sets alone may be insufficient to resolve problematic nodes in the most rapid evolutionary radiations, because inferences in zones of extraordinarily low phylogenetic signal can be sensitive to the model and method of inference, as well as the information content of loci employed. We used a data set of

gt;$3950 ultraconserved element (UCE) loci from a classic mammalian radiation, ground-dwelling squirrels of the tribe Marmotini (Sciuridae: Xerinae), to assess sensitivity of phylogenetic estimates to varying per-locus information content across four different inference methods (RAxML, ASTRAL, NJst, and SVDquartets). Persistent discordance was found in topology and bootstrap support between concatenation- and coalescent-based inferences; among methods within the coalescent framework; and within all methods in response to different filtering scenarios. Contrary to some recent empirical UCE-based studies, filtering by information content did not promote complete among-method concordance. Nevertheless, filtering did improve concordance relative to randomly selected locus sets, largely via improved consistency of two-step summ...Continue Reading

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Citations

May 30, 2020·Genome Biology and Evolution·Brian Tilston SmithMichael J Andersen
Dec 14, 2018·BMC Evolutionary Biology·Nicolás Mongiardino KochGreg W Rouse
Feb 6, 2021·Molecular Phylogenetics and Evolution·Mark P Simmons, John Gatesy
May 14, 2021·Molecular Biology and Evolution·Nicolás Mongiardino Koch
Jan 4, 2022·Bioinformatics·Uyen Mai, Siavash Mirarab

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