Divergence and plasticity shape adaptive potential of the Pacific oyster

Li, Li; Li, Ao; Song, Kai; Meng, Jie; Guo, Ximing; Li, Shiming; Li, Chunyan; Wit, Pierre De; Que, Huayong; Wu, Fucun; Wang, Wei; Qi, Hongsheng; Xu, Fei; Cong, Rong; Huang, Baoyu; Li, Yingxiang; Wang, Ting; Tang, Xueying; Liu, Sheng; Li, Busu; Shi, Ruihui; Liu, Youli; Bu, Chen; Zhang, Chi; He, Weiming; Zhao, Shancen; Li, Hongjun; Zhang, Shoudu; Zhang, Linlin; Zhang, Guofan

doi:10.1038/s41559-018-0668-2

Cited by 115 publications

(142 citation statements)

References 66 publications

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“…It should be noted that neutral pairwise F ST values were all close to zero within U.S. waters (Tables S12 and S13), which is not unexpected based on previous studies (Barney et al, 2017;Clucas, Kerr, et al, 2019;Kovach et al, 2010), and is typical of findings from cod and other marine species. The interpretation of very small F ST is not straightforward (Conover et al, 2006;Li et al, 2018;Waples & Gaggiotti, 2006 Figure 7).…”

Section: Implications For Stock Structurementioning

confidence: 99%

Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing

Clucas

Lou

Therkildsen

et al. 2019

Evolutionary Applications

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Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome‐wide patterns of variation, we used low‐coverage sequencing to perform a region‐wide, whole‐genome analysis of fine‐scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole‐genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter‐ and spring‐spawning populations revealed highly elevated relative (FST) and absolute (dxy) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain‐pituitary‐gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high‐resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome‐scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.

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Section: Implications For Stock Structurementioning

confidence: 99%

Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing

Clucas

Lou

Therkildsen

et al. 2019

Evolutionary Applications

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“…Although HTS has allowed the development of medium-density SNP panelsand whole genome resequencing of hundreds of individuals in oysters [47,[60][61][62], those approaches do not always scale to specific questions that only require small SNP panels. The level of precision for inferring individual ancestry for species identification requires only a handful of ancestry informative markers, typically one or two per chromosome.…”

Section: A New Flexible Tool To Differentiate the Two Oyster Resourcementioning

confidence: 99%

“…Such a different resource, if less economically interesting at present, might become more when considering the rapid evolution of the marine environment. However more studies are needed in Europe to be able to exclude phenotypic plasticity as a source of quantitative differences, which requires careful common-garden studies [79], such as performed in China where divergent adaptive strategies were observed with underlying evolutionary trade-offs between genetic adaptation and plasticity at the molecular level in the two oyster congeners [47,80,81].…”

Section: Conservation Issuesmentioning

confidence: 99%

“…However, including several of our French samples in a genome-wide analysis together with introgressed C. gigas/C. angulata Portuguese and French samples could be of interest, as a recent study on Chinese C. gigas populations, performed with the whole-genome re-sequencing of 371 oysters, provided evidence of a weak but significant differentiation among oyster populations at fine spatial scales [47].…”

Section: Confirmation Of a High Homogeneity Within The Pacific Cuppedmentioning

confidence: 99%

“…Thanks to the use of high throughput sequencing (HTS) approaches, thousands of polymorphic markers have been discovered [42,47], providing increased power to select subsets of ancestry informative loci to detect cryptic genetic subdivision and population structure [18]. For instance, a panel of 96 informative single-nucleotide polymorphisms (SNPs) allowed characterizing current ancestry patterns and temporal changes in admixture among two genetically distinct lineages of the invasive marine crab Carcinus maenas, which were independently introduced to eastern North America [48].…”

Section: Introductionmentioning

confidence: 99%

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Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels

Lapègue

Heurtebise

Cornette

et al. 2020

Genes

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The Pacific oyster, Crassostrea gigas, was voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry, following a severe disease outbreak. Since then, the two species have been in contact in southern Europe and, therefore, have the potential to exchange genes. Recent evolutionary genomic works have provided empirical evidence that C. gigas and C. angulata exhibit partial reproductive isolation. Although hybridization occurs in nature, the rate of interspecific gene flow varies across the genome, resulting in highly heterogeneous genome divergence. Taking this biological property into account is important to characterize genetic ancestry and population structure in oysters. Here, we identified a subset of ancestry-informative makers from the most differentiated regions of the genome using existing genomic resources. We developed two different panels in order to (i) easily differentiate C. gigas and C. angulata, and (ii) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic populations. Our results confirm high genetic homogeneity among Pacific cupped oyster populations in France and reveal several cases of introgressions between Portuguese and Japanese oysters in France and Portugal.

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bHLH genes polymorphisms and their association with growth traits in the Pacific oyster Crassostrea gigas

Chen

et al. 2019

J. Ocean. Limnol.

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Divergence and plasticity shape adaptive potential of the Pacific oyster

Cited by 115 publications

References 66 publications

Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing

Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing

Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels

bHLH genes polymorphisms and their association with growth traits in the Pacific oyster Crassostrea gigas

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