Distinct Phenotypes of Native Cutthroat Trout Emerge under a Molecular Model of Lineage Distributions

Abstract

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 whether morpho‐meristic taxonomic approaches better classified Cutthroat Trout under (1) the traditional Geographic Model, which recognizes different subspecies east and west of the Continental Divide and in the Rio Grande basin; or (2) the Molecular Model, which uses genotypes to assign populations to four lineages. Classification success of the Molecular Model was higher than that of the Geographic Model, whether comparisons involved single‐trait, principal components, or discriminant function analyses. Native east slope South Platte River trout (putative Greenback Cutthroat Trout O. clarkii stomias) were distinct and correctly classified, as were 83% of Rio Grande Cutthroat Trout O. clarkii virginalis populations. In all, 100% of the Blue Lineage populations of Colorado River Cutthroat Trout O. clarkii pleuriticus (putative west slope native of the White, Yampa, Green, and downstream Colorado River drainages) and 71% of the Green Lineage populations of Colorado River Cutthroat Trout (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 slope 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 of their 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.

Predicting Persistence of Rio Grande Cutthroat Trout Populations in an Uncertain Future

“…, ) and morphological (Bestgen et al. ) diversity they display but also for the potential ecological diversity that is yet unmeasured (e.g., thermal tolerance). In contrast, a different strategy may be needed for populations in the Rio Grande Headwaters GMU ( n = 43 populations), where 15 populations have an over 50% chance of persistence.…”

“…Therefore, conservation in these two GMUs might focus on reintroductions to other streams where conditions will support long-term persistence. Maintaining these peripheral populations is important (Haak and Williams 2012), not only for the genetic (Pritchard et al 2007a(Pritchard et al , 2009) and morphological (Bestgen et al 2019) diversity they display but also for the potential ecological diversity that is yet unmeasured (e.g., thermal tolerance). In contrast, a different strategy may be needed for populations in the Rio Grande Headwaters GMU (n = 43 populations), where 15 populations have an over 50% chance of persistence.…”

“…; Bestgen et al. ). At present, management of RGCT genetic risk is focused on maintaining pure stocks that are free or nearly free of nonnative alleles (Allendorf et al.…”

“…Outbreeding depression is also a concern, as Rainbow Trout O. mykiss (a sister taxon) readily hybridize with Cutthroat Trout O. clarkii, reducing their fitness (Muhlfeld et al 2009a) and leaving populations susceptible to extinction through hybridization (Rhymer and Simberloff 1996;Muhlfeld et al 2017). Other taxa of commonly stocked nonnative Cutthroat Trout (e.g., Yellowstone Cutthroat Trout O. c. bouvieri and Colorado River Cutthroat Trout O. c. pleuriticus) also hybridize readily with RGCT, infusing nonnative alleles into otherwise pure populations (Pritchard et al 2007b;Bestgen et al 2019). At present, management of RGCT genetic risk is focused on maintaining pure stocks that are free or nearly free of nonnative alleles , in part because the USFWS considered only RGCT populations with less than 10% admixture as contributing to the viability of the subspecies in recent listing decisions (USFWS 2014).…”

Wild, Native, or Pure: Trout as Genetic Bodies

“…The discovery that decades of greenback cutthroat trout recovery had been based on a case of mistaken identity proved disorienting to the scientists, wildlife officials, and anglers who had been studying, managing, or catching these fish for years. In little more than a decade, the observation-based biology that had long guided fisheries management faced challenges by laboratory tests that could ascertain tiny differences in the lineage and genetic composition of trout and other organisms (see Bestgen, Rogers, and Granger [2019] for a comparison of approaches). As a result, the scientific understanding of cutthroat trout has been effectively reconstructed from one based in direct experiences with fish in particular places to more abstracted DNA analyses of fish tissue or environmental samples (e.g., Tautz et al 2003; Blaxter 2004; Metcalf et al 2007, 2012).…”