Phylogeny of Cutthroat Trout ( Oncorhynchus clarkii ) Based on Full Mitochondrial Genomes With Comments on Species Delimitation and Taxonomy

ABSTRACT Despite the important role that species concepts and taxonomy play in understanding the evolution of species, taxonomists have struggled to describe the relationship between many organisms. Here, using Cutthroat Trout as a case study, we illustrate how full mitochondrial genomes and broad taxonomic sampling can provide further insight on disputed taxonomic relationships, and aid in management and conservation decisions of different species. Inconsistencies in the taxonomy of Cutthroat Trout inspired a special workshop at the 2015 annual meeting of the American Fisheries Society that emphasized the need for revision. To further resolve the relationship between different Cutthroat Trout groups, we sequenced and assembled full mitochondrial genomes from 123 Cutthroat Trout from across their native range. We used maximum likelihood and Bayesian phylogenetic approaches to examine the evolutionary relationships between all named Cutthroat Trout subspecies. Through these analyses, we find eight lineages of Cutthroat Trout that diverged more than one million years ago, and at least 12 lineages that diverged more than 790 thousand years ago, highlighting that despite the ancient split with Rainbow Trout at around ten million years ago, the modern diversity seen within the Cutthroat Trout Species Complex is much more recent. We do not find that Coastal, Westslope, or Lahontan Cutthroat Trout are substantially more different than the lineages in the Yellowstone complex. As such, we continue to recognize a single Cutthroat Trout species ( Oncorhynchus clarkii ) comprised of eleven distinct subspecies level clades, maintaining consistency with ongoing conservation efforts, management plans and ESA‐related decisions, while also preserving stability associated with historical nomenclature. Overall, we highlight that using full mitochondrial genomes can increase phylogenetically informative information and that the consistent nature of mitochondrial genomes across the tree of life allows for a valuable and measurable comparison of different species concepts in closely related taxa.