A paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies

Abstract

Overharvest can severely reduce the abundance and distribution of a species andthereby impact its genetic diversity and threaten its future viability. Overharvestremains an ongoing issue for Arctic mammals, which due to climate change nowalso confront one of the fastest changing environments on Earth. The high-arcticSvalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experi-enced a harvest-induced demographic bottleneck that occurred during the 17–20thcenturies. Here, we investigate changes in genetic diversity, population structure,and gene-specific differentiation during and after this overharvesting event. Usingwhole-genome shotgun sequencing, we generated the first ancient and historical nu -clear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000BP) and integrated these data with a large collection of modern genome sequences(n = 90) to infer temporal changes. We show that hunting resulted in major geneticchanges and restructuring in reindeer populations. Near- extirpation followed by pro-nounced genetic drift has altered the allele frequencies of important genes contribut-ing to diverse biological functions. Median heterozygosity was reduced by 26%, whilethe mitochondrial genetic diversity was reduced only to a limited extent, likely due toalready low pre-harvest diversity and a complex post-harvest recolonization process.Such genomic erosion and genetic isolation of populations due to past anthropogenicdisturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic casestudy therefore emphasize the need to understand the long-term interplay of past,current, and future stressors in wildlife conservation. ancient DNA, bottleneck, conservation genomics, genomic erosion, population genomics,Svalbard reindeer