Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oysterCrassostrea gigasthroughout the Northern Hemisphere

Abstract

<jats:title>ABSTRACT</jats:title><jats:p>Pacific oyster <jats:italic>Crassostrea gigas</jats:italic>, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self-sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery-farmed) or naturalized/wild oysters to move onto a farm (naturalized-farmed). It is therefore important to understand genetic variation among populations and farm types. Here we genotype naturalized/wild 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 (n = 366). Consistent with previous studies, very low genetic differentiation was observed around Vancouver Island (mean F<jats:sub>ST</jats:sub> = 0.0019), and low differentiation between countries in the Japan-Canada-France historical translocation lineage (France-Canada F<jats:sub>ST</jats:sub> = 0.0024; Japan-Canada F<jats:sub>ST</jats:sub> = 0.0060). Chinese populations were more differentiated (China-Japan F<jats:sub>ST</jats:sub> = 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 was lower in one farm population. Moving oysters from nature onto farms did not result in strong within-generation selection. Private alleles at substantial frequency were identified in several hatchery populations grown in BC, suggesting non-local origins. Tests of selection identified outlier loci consistent with selective differences associated with domestication, in some cases consistently identified in multiple farms. 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 valued as a locally-adapted resource or as an introduced, invasive species. Given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, biotic stressors), this remains an important question.</jats:p>

Socioecological factors related to aquaculture introductions and production of Pacific oysters (Crassostrea gigas) worldwide

“…Many reviews have covered introductions of C. gigas and effects of Pacific oysters as ecosystem engineers 5,6,31‐33 . Yet, given on‐going expansion of Pacific oyster aquaculture and opportunities for establishment, these reviews rapidly become outdated and incomplete.…”

From the woods to the halls of science: Louis Bernatchez’s contributions to science, wildlife conservation and people

“…The authors invited to contribute to this Special Issue include both junior and senior researchers in the broad field of evolutionary/ecological/conservation genomics, reflecting the persistent mentoring to which Louis has constantly devoted so much time and energy (Figure 2). It is worthwhile to note that several of the papers detail long‐term research projects (Bowles, Marin, Mogensen, MacLeod, & Fraser, 2020; Garant, 2020; Perrier, Rougemont, & Charmantier, 2020; Stanford, Clake, Morris, & Rogers, 2020; Veliz et al, 2020), or collective advancements of a research group (Blanchet et al., 2020; Dalziel et al., 2020; Østbye et al, 2020), along with new “perspectives” and approaches in the field (Angers, Perez, Menieucci, & Leung, 2020; Durand et al., 2020; Filteau & Derôme, 2020; Gagnaire, 2020; Hallin et al., 2020; Lu et al., 2020; Milot, Béchet, & Maris, 2020; Sutherland et al., 2020), and the use of genomics information for wildlife management and conservation (Bangs, Douglas, Brunner, & Douglas, 2020; Bourret, Albert, April, Côté, & Morissette, 2020; Capblancq, Després, & Mavárez, 2020; Delrieu‐Trottin et al., 2020; Leblanc et al, 2020; Uusi‐Heikkilä, 2020; Young, Cluney, & Weir, 2020) as well as human health (Wirth, Wong, Vandenesch, & Rasigade, 2020).…”

“…It is this specific focus of science which he passed on to his students and ranges from an understanding of evolutionary processes such as connectivity and species boundaries to wildlife management and aquaculture (Figure 2). Most of the studies presented are based on wild populations, with a great majority of them focusing on fish (Angers et al., 2020; Bangs et al., 2020; Blanchet et al., 2020; Bowles et al., 2020; Dalziel et al., 2020; Delrieu‐Trottin et al., 2020; Gagnaire, 2020; Leblanc et al., 2020; Lu et al., 2020; Østbye et al, 2020; Stanford et al., 2020; Uusi‐Heikkilä, 2020; Veliz et al, 2020; Young et al., 2020), but also other aquatic organisms (Sutherland et al., 2020), as well as birds and mammals (Garant, 2020; Yannic, Hagen, Leugger, Karger, & Pellissier, 2020), terrestrial invertebrates (Capblancq et al, 2020), plants (Durand et al., 2020), yeast (Hallin et al., 2020) and bacteria (Filteau & Derôme, 2020; Wirth et al., 2020).…”

“…2020), and the process of domestication in aquaculture (Sutherland et al. 2020), the historical and contemporary admixture process across species (Bangs et al. 2020; Lu et al.…”

“…Sutherland et al. (2020) analyse a worldwide data set of naturalized and wild populations of Pacific Oyster ( Crassostera gigas ) to understand genetic variation among populations and farmed types and propose appropriate industrial decisions around this major industry in aquaculture. They conclude that implications of potential introgression from hatchery‐farmed oysters depend on whether naturalized populations are valued as a locally adapted resource or as an introduced, invasive species.…”