Genetic variation and population structure of moose (Alces alces) at neutral and functional DNA loci

Genetic variation was examined for moose (Alces alces) from Riding Mountain, Isle Royale, and Pukaskwa national parks; northwestern, Nipigon, northeastern, and central Ontario; New Brunswick; and Newfoundland. The national parks were identified as maintaining potentially different local selection pressures due to the absence of hunting and the presence or absence of the parasite Parelaphostrongylus tenuis. Genetic variation was estimated using neutral DNA markers, assessed by multilocus DNA fingerprinting and five microsatellite loci, and the functional antigen binding region (ARS) (exon 2) of the major histocompatibility complex (MHC) gene DRB. There was discordance in the allelic diversity observed at the neutral loci compared with the MHC DRB locus in a number of populations. Ontario populations demonstrated higher levels of variability at the neutral loci and relatively low levels at the DRB locus. Conversely, the Isle Royale population has the lowest genetic variability, consistent with a historic small founding event, at the neutral DNA markers and relatively high variability at the MHC gene. Relatively high levels of genetic variation at the DRB locus were observed in protected park populations concomitant with the absence of white-tailed deer (Odocoileus virginianus) or the parasite P. tenuis and an absence of hunting. Gene flow was observed among the neighboring geographic regions within Ontario, including Pukaskwa National Park, with evidence of isolation-by-distance among more distant regions within Ontario. The discordant patterns between DNA markers suggest that neutral DNA markers may not accurately reflect adaptive variation present at functional loci.