Hybridization and polymorphic microsatellite markers for two lagomorph species (Genus Sylvilagus): implications for conservation

Eastern cottontails (Sylvilagus floridanus) are a prolific and popular game species in North America but have declined within the core of their range. Swamp rabbits (S. aquaticus) are sympatric with eastern cottontails and are a species of concern at the northern fringe of their range in Illinois. Although hybridization between these species may be a potential factor affecting their declines, no studies have yet been conducted to address this issue. We examined the potential for hybridization between sympatric eastern cottontails and swamp rabbits in Illinois by sequencing a portion of the mitochondrial 12S gene in 17 individuals of each species. Additionally, we developed six microsatellite markers for the eastern cottontail (7–13 alleles/locus) that also amplify in swamp rabbits (3–5 alleles/locus). We found fixed differences between species with haplotypes forming well-differentiated clades indicating a lack of hybridization. Hybridization between eastern cottontails and swamp rabbits does not appear to be affecting their declines. Misidentification due to ambiguous morphological characteristics of the two species occurred in an earlier study and in our own. We suggest the mitochondrial 12S gene may be a convenient molecular marker for the resolution of species identity questions. Information on microsatellites, occurrence of natural hybridization, and a molecular marker for species resolution will be useful for developing management plans for lagomorphs and focusing further research on factors affecting population status.