<em>Abstract</em>.—Despite major declines in distribution and abundance of Cutthroat Trout <em>Oncorhynchus clarkii </em>across their native range since European settlement, substantial morphological and genetic diversity remains. For example, recent molecular investigations revealed the presence of six discrete lineages of Cutthroat Trout native to the Southern Rocky Mountains rather than four as previously thought. These include the previously recognized Yellowfin Cutthroat Trout <em>O. c. macdonaldi </em>(extinct) and Rio Grande Cutthroat Trout <em>O. c. virginalis</em>, as well as the true native of the South Platte River basin, located east of the Continental Divide, which we continue to refer to as Greenback Cutthroat Trout. Within the range of Colorado River Cutthroat Trout <em>O. c. pleuriticus</em>, which is located west of the Continental Divide, we highlight two divergent clades that historically occupied upstream, coldwater reaches of the Green River and Colorado River basins. Both are also found outside their historical ranges as well, due to extensive, mostly undocumented stocking in the early 20th century that served to conceal native diversity in the region. An additional clade closely aligned with those two Colorado River groups historically occupied the San Juan River basin. In this chapter, we discuss both molecular and morphomeristic evidence that indicates distinct lineages are aligned with major drainage basins, information that guides ongoing conservation actions.
Climate-driven disturbances in the San Juan River sub-basin of the Colorado River