Distinct phenotypes of native Cutthroat Trout emerge under a Molecular Model of lineage distributions

Bestgen, Kevin; Rogers, Kevin; Granger, Robert

Recent molecular investigations using contemporary and century‐old museum specimens questioned the traditional four‐subspecies taxonomic arrangement of Cutthroat Trout Oncorhynchus clarkii in the Southern Rocky Mountains, and revealed six lineages, including two that are likely extinct. We examined extant lineage specimens to determine if morpho‐meristic taxonomic approaches better classified Cutthroat Trout under the traditional Geographic Model that recognizes different subspecies east and west of the Continental Divide and in the Rio Grande basin, or the Molecular Model that uses genotypes to assign populations to four lineages. Molecular Model classification success was higher than the Geographic Model, whether comparisons involved single trait, principal component, or discriminant function analyses. Native east slope South Platte River trout (putative Greenback Cutthroat Trout, O. c. stomias) were distinct and correctly classified, as were 83% of Rio Grande Cutthroat Trout O. c. virginalis populations. In all, 100% of Blue Lineage Colorado River Cutthroat Trout populations (O. c. pleuriticus, putative west slope native of the White, Yampa, Green, and downstream Colorado River drainages) and 71% of Green Lineage Colorado River Cutthroat Trout populations (native to west slope Gunnison and Dolores River drainages, and Colorado River headwaters) were correctly classified (89% overall) under the Molecular Model. Green Lineage misclassifications were mainly from morphologically and genetically distinct populations located east of the Continental Divide, whose native status remains unknown. In contrast, only 63% of those east and west slope Cutthroat Trout populations were correctly classified under the Geographic Model. Cohesion of distinct phenotypes and genotypes of present‐day native Cutthroat Trout lineages was remarkable given widespread and massive early stocking of various lineages outside native ranges. Strong congruence of morphological and molecular patterns demonstrated the power of joint morphological and molecular analyses. We encourage management that preserves diversity of these rare Cutthroat Trout lineages that evolved in concert with their environment.