The long-term persistence of forest-dwelling caribou (Rangifer tarandus caribou) will probably be determined by management and conservation decisions. Understanding the evolutionary relationships between modern caribou herds, and how these relationships have changed through time will provide key information for the design of appropriate management strategies. To explore these relationships, we amplified microsatellite and mitochondrial markers from modern caribou from across the Southern Yukon, Canada, as well as mitochondrial DNA from Holocene specimens recovered from alpine ice patches in the same region. Our analyses identify a genetically distinct group of caribou composed of herds from the Southern Lakes region that may warrant special management consideration. We also identify a partial genetic replacement event occurring 1000 years before present, coincident with the deposition of the White River tephra and the Medieval Warm Period. These results suggest that, in the face of increasing anthropogenic pressures and climate variability, maintaining the ability of caribou herds to expand in numbers and range may be more important than protecting the survival of any individual, isolated sedentary forest-dwelling herd.

Migratory barren-ground caribou (Rangifer tarandus groenlandicus) provide an opportunity to examine the genetic population structure of a migratory large mammal whose movements and distribution, in some instances, have not been heavily influenced by human activities that result in habitat loss or fragmentation. These caribou have likely reached large effective population sizes since their rapid radiation during the early Holocene despite cyclic changes in abundance. Migratory barren-ground caribou are managed as discrete subpopulations. We investigated genetic variation among those subpopulations to determine the patterns of genetic diversity within and among them, and the implications for long-term persistence of caribou. We identified three distinct genetic clusters across the Canadian arctic tundra: the first cluster consisted of all fully-continental migratory barren-ground subpopulations; the second cluster was the Dolphin and Union caribou; and the third cluster was caribou from Southampton Island. The Southampton Island caribou are especially genetically distinct from the other barren-ground type caribou. Gene flow among subpopulations varied across the range. Occasional gene flow across the sea-ice is likely the reason for high levels of genetic variation in the Dolphin and Union subpopulation, which experienced very low numbers in the past. These results suggest that for most migratory caribou subpopulations, connectivity among subpopulations plays an important role in maintaining natural genetic diversity. Our analyses provide insight into the levels of microsatellite genetic diversity and patterns of gene flow that may be common to large subpopulations that historically had a continuous distribution across a large continental range. These data can also be used as a benchmark to compare the effects of habitat fragmentation and bottlenecks on other large caribou populations.

We investigated the status of caribou classified as Rangifer tarandus pearyi by DNA analyses, with an emphasis on those large-bodied caribou identified as ultra pearyi that were collected in summer 1958 on Prince of Wales Island, south-central Canadian Arctic Archipelago. Our comparative assessment reveals that the ultra pearyi from Prince of Wales Island belong to a group of pearyi and are not hybrids of pearyi x groenlandicus, as we found for the caribou occurring on nearby Banks Island and northwest Victoria Island. The ultra pearyi from Prince of Wales Island cluster with high arctic pearyi and are separated genetically from the caribou populations that we sampled on the low Canadian Arctic Islands and the Canadian mainland. Our findings reveal biodiversity below the level of subspecies or regional designations. These results support the position that to retain the biodiversity present among caribou populations on the Canadian Arctic Islands, conservation efforts should be targeted at the smaller scale level of the geographic population, rather than on a wider regional or subspecific range-wide basis.