The Past is Prologue: Contemporary and Historical Genetic Variation in a Bighorn Sheep Metapopulation

Bighorn sheep (Ovis canadensis) experienced widespread population declines and extirpations during the late 19th and early 20th centuries, and recovery has been limited in scope and magnitude. We explored the molecular legacy of this history by comparing genetic diversity and structure in a native Rocky Mountain bighorn sheep (O. c. canadensis) metapopulation in central Idaho to genetic variation in samples collected from the same area up to 138 years earlier and to mitochondrial DNA haplotypes in bighorn sheep populations across western North America. The contemporary Idaho metapopulation was structured into 6 genetic groups with varying levels of admixture that largely corresponded with 5 population management units as defined by the distribution of bighorn sheep and suitable habitat. Nuclear DNA microsatellite diversity (expected heterozygosity He) was higher in historical samples from a private collection dated between 1879 and 1985 from the Lower Salmon (He 0.756) and Middle Fork Salmon populations (He 0.735) than in contemporary samples (Lower Salmon He 0.677, Middle Fork He 0.720). The Lower Salmon historical samples also had higher mitochondrial DNA (mtDNA) haplotype diversity (Hd 0.972), and more private microsatellite alleles (11) than contemporary samples from Lower Salmon (Hd 0.792, 0 private alleles). Thirteen Idaho mtDNA haplotypes were assigned to a haplogroup containing desert (O. c. nelsoni, O. c. mexicana, O. c. weemsi) and Sierra Nevada (O. c. sierrae) bighorn sheep lineages, consistent with gene flow between Rocky Mountain and desert sheep subspecies. This haplogroup contained 35