Genomic Diversity and Population Structure of Semi-Domesticated Reindeer populations in Southern Norway and wild reindeer from Iceland

Abstract Reindeer and caribou (Rangifer tarandus) play key ecological, cultural, and economical roles across Arctic and Subarctic regions. However, genome-wide patterns of genetic diversity and population structure in semi-domesticated reindeer from Norway remain insufficiently characterized. Here we generated a high-quality chromosome-level genome assembly (GCA_965153185.1) for Norwegian semi-domesticated Eurasian tundra reindeer (Rangifer tarandus tarandus). The genome spans 2.54 Gb, with a scaffold N50 of 75.6 Mb, 96.1% complete BUSCOs, and 39,855 predicted protein-coding genes. Using this reference, we performed whole-genome resequencing of 175 individuals from five reindeer populations from Norway and 28 individuals from Iceland, identifying ~19.9 million genetic variants. Genetic differentiation was low among Norwegian populations (FST = 0.005–0.011), but substantially higher between Norway and Iceland (FST = 0.140–0.161). Populations from Norway exhibited similar levels of nucleotide diversity (π = 1.39–1.62 × 10−3), whereas the Icelandic population showed reduced diversity (π = 0.99 × 10−3) and approximately half as many segregating variants. Analyses of runs of homozygosity (ROH) and genome-wide heterozygosity indicated low levels of recent inbreeding across all populations, with long ROHs (>8 Mb) being rare. Despite reduced genetic diversity, the Icelandic population showed limited evidence of recent inbreeding. These patterns are consistent with contrasting demographic histories, with gene flow maintaining diversity among populations from Norway, while founder effects combined with long-term isolation have shaped the Icelandic population.