Y Chromosome DNA Variation in Cutthroat Trout

Y chromosome DNA sequences are relatively slowly-evolving but show informative variation among cutthroat trout subspecies.  Such sequences are only found in males and provide an interesting phylogenetic counterpart to the maternally-inherited mitochondrial DNA sequences.  The Y-DNA sequences which we have compared evolve between 3 and 13 times slower than the mitochondrial DNA sequences.  A region of about 1,200 base pairs located near the trout sex-determining locus showed variation among and within cutthroat trout subspecies, and patterns of relationship that were generally congruent with those detected based on protein and mitochondrial DNA variation.  The westslope, coastal and Lahontan subspecies appeared to be closely related, and the other subspecies appear to represent a subspecies complex with affinities to the Yellowstone cutthroat.  Although the Y marker used in our studies did not reveal sequence differences capable of distinguishing populations, or some subspecies, adjacent (uncharacterized) Y-DNA sequences may contain some rare population-specific SNPs characteristic of the inheritance of non-recombining patrilineal chromosome sequences.  The different reproductive patterns of males as compared to females have apparently led to distinctive patterns for Y chromosome markers in rainbow trout and such patterns may still be identified in cutthroat trout populations.