Abstract
<title>Abstract</title> <p>Phylogenomic conflict is increasingly recognized through the continued collection of genomic data sets combined with sophisticated computational approaches. To date, most studies examining the causes and consequences of discordance have focused on relatively deep evolutionary questions with particular emphasis on conflict between gene trees and a proposed species tree. Using a geographically widespread species complex, sagebrush lizards of the Sceloporus graciosus group, we demonstrate extreme instability of species trees across the genome using full likelihood-based techniques that account for incomplete lineage sorting and weak phylogenetic information at a given locus. Both random sets of loci and reference-guided ordered locus sets cannot consistently recover a single topology that best accounts for history, having major implications for contemporary phylogenomic analyses. We propose that widespread introgression across the genome is partly responsible for the conflict and find that the best representation of evolutionary history contains multiple gene flow events. Population structure in the complex was likely generated by geographic distance and major biogeographic barriers. We discuss implications of our results in light of current phylogeographic and species delimitation workflows. Taxonomically, our results support a system that underwent rapid divergence into multiple geographic lineages, many of which should be recognized as distinct species.</p>