Abstract
<em>Abstract</em>.—A Y chromosome marker shared with Rainbow Trout <em>Oncorhynchus mykiss </em>has been sequenced in many Cutthroat Trout <em>O. clarkii </em>subspecies. The marker is found in and inherited through males. It evolves more slowly than the maternally inherited mitochondrial DNA. The marker delineates the four major groups of Cutthroat Trout: the Lahontan Cutthroat Trout <em>O. c. henshawi </em>subspecies complex, the Yellowstone Cutthroat Trout <em>O. c. bouvieri</em> subspecies complex, Westslope Cutthroat Trout <em>O. c. lewisi</em>, and Coastal Cutthroat Trout <em>O. c. clarkii</em>. The paternal inheritance pattern of the Y marker makes it useful for dissecting the origins of fish with mixed ancestries. We describe a case study using both Y and mitochondrial markers in Lahontan Cutthroat Trout subspecies complex trout populations. Our results confirmed Lahontan Cutthroat Trout affinities for the Paiute Cutthroat Trout <em>O. c. seleniris</em> and Willow–Whitehorse Creek Cutthroat Trout. However, we found evidence of a complex ancestry for Guano Creek, Oregon trout, a group that has been proposed by some to be related to the Alvord Cutthroat Trout, a subspecies thought to be extinct.
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