The Foothill Yellow-Legged Frog (Rana boylii) is a threatened river-dwelling amphibian endemic to California and Oregon. Determining the genetic structure of populations that have not yet declined is an important tool for their conservation. In this study, molecular markers were used to asses the genetic structure of R. boylii. The ND2 region of the mitochondrial genome and Random Amplified Polymorphic DNA (RAPD) markers were examined amongst 51 individuals collected from seven relatively pristine tributaries branching off the Eel River in Northern California. Both markers exhibited significant genetic differentiation among tributaries; however, the RAPD markers revealed a positive correlation between geographic distance and genetic distance. Cluster analysis illustrated a distinct separation between northern and southern tributaries within the study site. In contrast, relatively little geographic structure was apparent when mtDNA haplotypes were examined. Discordance may be caused by the number of loci examined in the mitochondrial and nuclear genomes, recent divergence, and sex-biased dispersal.
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