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Title: Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data
Abstract Many evolutionary relationships remain controversial despite whole-genome sequencing data. These controversies arise, in part, due to challenges associated with accurately modeling the complex phylogenetic signal coming from genomic regions experiencing distinct evolutionary forces. Here, we examine how different regions of the genome support or contradict well-established relationships among three mammal groups using millions of orthologous parsimony-informative biallelic sites (PIBS) distributed across primate, rodent, and Pecora genomes. We compared PIBS concordance percentages among locus types (e.g. coding sequences (CDS), introns, intergenic regions), and contrasted PIBS utility over evolutionary timescales. Sites derived from noncoding sequences provided more data and proportionally more concordant sites compared with those from CDS in all clades. CDS PIBS were also predominant drivers of tree incongruence in two cases of topological conflict. PIBS derived from most locus types provided surprisingly consistent support for splitting events spread across the timescales we examined, although we find evidence that CDS and intronic PIBS may, respectively and to a limited degree, inform disproportionately about older and younger splits. In this era of accessible wholegenome sequence data, these results:1) suggest benefits to more intentionally focusing on noncoding loci as robust data for tree inference and 2) reinforce the importance of accurate modeling, especially when using CDS data.  more » « less
Award ID(s):
1942273
PAR ID:
10282230
Author(s) / Creator(s):
;
Editor(s):
Townsend, Jeffrey
Date Published:
Journal Name:
Molecular Biology and Evolution
Volume:
38
Issue:
6
ISSN:
1537-1719
Page Range / eLocation ID:
2306 to 2318
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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