Overhunting of Svalbard reindeer
Overharvest can lead to near-extirpation of a species and can therefore drastically impact its genetic diversity and gene pool, threatening its future adaptability. Overharvest has extensively happened in the past, but remains a contemporary issue especially for Arctic mammals, which now confront the fastest changing environment on Earth due to climate change. The high-Arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to the Svalbard archipelago, experienced a harvest-induced bottleneck that occurred throughout the 17th to 20th centuries. We here investigate changes in genetic diversity, population structure and gene-specific differentiation before, during, and after this overharvesting event. Using shotgun sequencing, we generated the first ancient nuclear and mitochondrial genomes from Svalbard reindeer (n = 18, up to 4000 BP). Together with  a large collection of modern genomes (n = 90), we were able to infer temporal changes. Our results indicate that hunting triggered drastic genetic changes and restructuring in reindeer populations. Median heterozygosity was reduced by 23%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to a complex post-harvest recolonization process and low diversity already in ancient times. This population structuring post-harvest happened during a period in which the reduced formation of sea-ice was further isolating these reindeer populations, such that altered climatic conditions worsened the consequences of overharvesting. Near-extirpation also altered the allele frequencies of important genes contributing to a variety of basic biological systems (e.g., cardiovascular, pulmonary, immune, reproductive, digestive, and central nervous systems). The genomic erosion and genetic isolation of Svalbard reindeer populations will likely play a major role in how metapopulation dynamics (i.e., extirpation, recolonization) of the species will cope with further climate change, thus for Svalbard reindeer conservation we stress the need to understand the long-term interplay of harvesting recovery and increasing landscape fragmentation.