PT - JOURNAL ARTICLE AU - Ben J. G. Sutherland AU - Claire Rycroft AU - Anne-Laure Ferchaud AU - Rob Saunders AU - Li Li AU - Sheng Liu AU - Amy M. Chan AU - Sarah P. Otto AU - Curtis A. Suttle AU - Kristina M. Miller TI - Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster <em>Crassostrea gigas</em> throughout the Northern Hemisphere AID - 10.1101/847467 DP - 2019 Jan 01 TA - bioRxiv PG - 847467 4099 - http://biorxiv.org/content/early/2019/11/20/847467.short 4100 - http://biorxiv.org/content/early/2019/11/20/847467.full AB - Pacific oyster Crassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self-sustaining introduced populations (naturalized). The oyster aquaculture industry depends on commercially available seed (hatchery-farmed) or naturalized oysters that can be moved onto a farm (naturalized-farmed), making it critical to understand patterns of genetic variation among populations and farm types. Here we genotype wild or naturalized populations from France, Japan, China, and most extensively in coastal British Columbia, Canada. We also genotype cultured populations from throughout the Northern Hemisphere to compare with naturalized populations. In total, 16,942 markers were identified using double-digest RAD-sequencing in 182 naturalized, 112 hatchery-farmed, and 72 naturalized-farmed oysters (total = 362 individuals). Very low genetic differentiation was observed around Vancouver Island (mean FST = 0.0019), and low differentiation between countries in Japan, France, and Canada (France-Canada FST = 0.0024; Japan-Canada FST = 0.0060), all of which are in the same historical translocation lineage. Chinese populations had much higher FST (China-Japan FST = 0.0241). Hatchery-propagated populations had higher inter-individual relatedness suggesting family structure. Within-population inbreeding was not detected on farms, but nucleotide diversity and polymorphism rate were both lower in some farms. Moving oysters from nature onto farms did not result in strong within-generation selection. Private alleles were identified in several hatchery populations grown in BC, suggesting non-local origins. Putative domestication outliers were identified throughout the genome, with some identified consistently on multiple farms. These top outlier candidates were nearby genes involved in calcium signaling and calmodulin activity. Implications of potential introgression from hatchery-farmed oysters depends on whether naturalized populations are considered as a valuable, locally-adapted resource or as an introduced, invasive species, but given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, abiotic/biotic stressors), this remains an important question.