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 forces. Here, we examine how different of genome support or contradict well-established among three mammal groups using millions orthologous parsimony-informative biallelic sites (PIBS) distributed across primate, rodent, and Pecora genomes. We compared PIBS concordance percentages locus types (e.g. coding sequences (CDS), introns, intergenic regions), contrasted utility over timescales. Sites derived noncoding provided more data proportionally concordant those CDS all clades. were also predominant drivers tree incongruence two cases topological conflict. most surprisingly consistent for splitting events spread timescales examined, although find evidence that intronic may, respectively a limited degree, inform disproportionately about older younger splits. In this era accessible wholegenome sequence data, these results:1) suggest benefits intentionally focusing on loci as robust inference 2) reinforce importance accurate modeling, especially when