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A spatially-explicit model of stabilizing selection for improving phylogenetic inference

Jeremy M. Beaulieu, Brian C. O’Meara, Michael A. Gilchrist
doi: https://doi.org/10.1101/2020.05.12.091744
Jeremy M. Beaulieu
aDepartment of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701 USA
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  • For correspondence: jmbeauli@uark.edu
Brian C. O’Meara
bDepartment of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996-1610 USA
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Michael A. Gilchrist
bDepartment of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996-1610 USA
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Abstract

Ultraconserved elements (UCEs) are stretches of hundreds of nucleotides with highly conserved cores flanked by variable regions. Although the selective forces responsible for the preservation of UCEs are unknown, they are nonetheless believed to contain phylogenetically meaningful information from deep to shallow divergence events. Phylogenetic applications of UCEs assume the same degree of rate heterogeneity applies across the entire locus, including variable flanking regions. We present a Wright-Fisher model of selection on nucleotides (SelON) which includes the effects of mutation, drift, and spatially varying, stabilizing selection for an optimal nucleotide sequence. The SelON model assumes the strength of stabilizing selection follows a position dependent Gaussian function whose exact shape can vary between UCEs. We evaluate SelON by comparing its performance to a simpler and spatially invariant GTR+Γ model using an empirical dataset of 400 vertebrate UCEs used to determine the phylogenetic position of turtles. We observe much improvement in model fit of SelON over the GTR+Γ model, and support for turtles as sister to lepidosaurs. Overall, the UCE specific parameters SelON estimates provide a compact way of quantifying the strength and variation in selection within and across UCEs. SelON can also be extended to include more realistic mapping functions between sequence and stabilizing selection as well as allow for greater levels of rate heterogeneity. By more explicitly modeling the nature of selection on UCEs, SelON and similar approaches can be used to better understand the biological mechanisms responsible for their preservation across highly divergent taxa and long evolutionary time scales.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted October 29, 2020.
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A spatially-explicit model of stabilizing selection for improving phylogenetic inference
Jeremy M. Beaulieu, Brian C. O’Meara, Michael A. Gilchrist
bioRxiv 2020.05.12.091744; doi: https://doi.org/10.1101/2020.05.12.091744
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A spatially-explicit model of stabilizing selection for improving phylogenetic inference
Jeremy M. Beaulieu, Brian C. O’Meara, Michael A. Gilchrist
bioRxiv 2020.05.12.091744; doi: https://doi.org/10.1101/2020.05.12.091744

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