We have analyzed DNA microsatellites and the mitochondrial control region in reindeer from 31 different husbandry areas in Norway, Sweden and Finland in order to better understand the processes that underlie the genetic variability of the Nordic domestic herds. The distinct differentiation found in the nuclear markers but less so in the mitochondrial marker, gives evidence of an origin from a common ancestral population which later evolved into the two main gene pools characterizing the nuclear genomes of domestic reindeer in Finland and most of Sweden and Norway. Analyses of temporal trends in effective population size gives evidence of a rapid increase in number of reindeer before the population growth associated with the pastoral transition. This implies that the ancestry of contemporary domestic reindeer lay among a rapid growing wild population possibly located in the boreal areas of eastern Fennoscandia or European Russia. The evolution of reindeer husbandry in Finland, perhaps with input from European Russia, which later spread to northern Norway could explain the shared genomic pattern observed in these areas today.  The structured selection of productive female-centered herds may explain the genetic structure in other parts of Norway and in Sweden. The further sub-structuring of the Swedish/ Norwegian gene-pool appears to follow the traditional language borders with the South Sámi language dominating the southern- and the Central Sámi language in the more northern genetic sub-clusters. This suggests that traditional knowledge, cultural identities and herd migrations have contributed to shape the genetic structure seen today. Ecological gradients are more pronounced within as compared to between the genetic clusters, giving further evidence that historical and social-cultural processes are important drivers for the genetic differentiations found in domestic reindeer across the Nordic countries.

DNA was extracted from blood and tissue samples using DNeasy Blood and Tissue Kits (Qiagen). 904 reindeer samples from 31 reindeer herding districts in Norway, Sweden and Finland were analyzed for 18 microsatellite loci amplified by PCR and scored as product sizes.

Microsatellites without score are given as 0.