Conservation Genetics 4: 393–404, 2003. © 2003 Kluwer Academic Publishers. Printed in the Netherlands. 393 Significance of caribou (Rangifer tarandus) ecotypes from a molecular genetics viewpoint R´ ehaume Courtois 1,3∗ , Louis Bernatchez 2 , Jean-Pierre Ouellet 3 & Laurier Breton 1 1 Soci´ et´ e de la faune et des parcs du Qu´ ebec, Direction de la recherche sur la faune, 675, boul. Ren´ e-L´ evesque, est (11 e ´ etage), Boîte 92, Qu´ ebec, Qu´ ebec G1R 5V7, Canada; 2 Universit´ e Laval, D´ epartement de biologie, Pavillon Vachon, Sainte-Foy, Qu´ ebec G1K 7P4, Canada; 3 Universit´ e du Qu´ ebec ` a Rimouski, D´ epartement de biologie, 300, All´ ee des Ursulines, Rimouski, Qu´ ebec G5L 3A1, Canada ( ∗ Author for correspondence, e-mail: rehaume.courtois@fapaq.gouv.qc.ca) Received 19 April 2002; accepted 24 August 2002 Key words: caribou, ecotype, genetic diversity, metapopulation, microsatellite loci Abstract Three caribou ecotypes are present in eastern North America: the mountain caribou which is found south of the St. Lawrence River, the barren-ground caribou which calves in the tundra, and in between, the forest-dwelling ecotype which lives all year long in the boreal forest. Blood and muscle samples were collected from seven populations and characterized at eight microsatellite loci to test the hypotheses that forest-dwelling and barren-ground ecotypes constitute a single metapopulation and that geographical isolation results in reduced genetic diversity. The mean number of alleles per locus, allelic richness, and observed and expected heterozygosity declined from north to south and were the smallest in isolated forest-dwelling populations. Correspondence analysis showed three groups of samples corresponding to the three ecotypes. Gene flow estimates were moderate or high among all forest- dwelling populations and particularly between those <200 km apart. Our results suggest that the three caribou ecotypes represent three distinct genetic entities and that the forest-dwelling populations in the continuous range form a metapopulation. Genetic diversity was lower in isolated populations but does not seem to be of immediate concern for conservation. We propose that management strategies should favor increase in caribou numbers in order to avoid extinction due to stochastic events and to maintain local biodiversity. In the continuous range, conservation strategies of caribou populations must be planned on a large scale to maintain occasional exchanges between populations, thus preserving genetic diversity. Introduction Five subspecies of caribou are usually recognized in North America: the Grant’s caribou in Alaska (Rangifer tarandus granti), the Canadian barren- ground caribou in Nunavut and Northwest Territories (R. t. groenlandicus), the Peary caribou in the Arctic (R. t. pearyi), the Queen Charlotte archipelago caribou (R. t. dawsoni), which has been extinct since 1910, and finally, the woodland caribou (R. t. caribou), found from Newfoundland and Labrador and northern Québec through British Columbia and southern Yukon (Banfield 1961). The first two subspecies could have descended from a population that survived the last glaciation in the Beringia refugium in Alaska-Yukon or in northern Europe; R. t. pearyi could have survived in refugia north of the continental ice-sheets in arctic Canada or northern Greenland while wood- land caribou are believed to have descended from populations that took refuge south of the continental ice-sheet, from New Jersey to Iowa and the moun- tainous region of New Mexico and Nevada (Banfield 1961; Roed et al. 1991). Banfield’s classification (1961), however, was based on craniometrical measurements and is not unanimously accepted. Geist (1991, 1998) has proposed the existence of seven North American subspecies using coat color, social behavior and