Population genomics and environmental adaptation in the sea scallop, Placopecten magellanicus, detected using RAD-seq derived SNPs and experimental larval rearing

Understanding the scale of connectivity and adaptation among marine populations can inform fisheries conservation and management. We used a combination of advanced genomic techniques and experimental methods to determine the scale of connectivity and adaptation in the sea scallop, Placopecten magellanicus. Restriction-site Associated DNA sequencing genotyped 7163 SNPs in 245 individuals across 12 populations in the Northwest Atlantic. Subsequent analysis of these data identified a strong separation between populations north and south of Nova Scotia and identified an association between population structure and the coldest temperatures experienced by scallop populations. Common garden experiments on a northern and southern populations found that larvae from the north grew more quickly overall, potentially an adaptive strategy to the northern winter. These observations contribute to growing evidence of fine-scale population structure and adaptation in marine systems and support the hypothesis that a combination of limited dispersal and adaptive differentiation drives sea scallop population structure

Genomic evidence of recent European introgression into North American farmed and wild Atlantic salmon

publishedVersio

Multifaceted framework for defining conservation units: An example from Atlantic salmon (Salmo salar) in Canada

Abstract Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at‐risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units is done by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC can recognize conservation units below the species level (termed “designatable units”; DUs) if the unit has attributes that make it both discrete and evolutionarily significant. There are various ways in which a DU can meet criteria of discreteness and significance, and increasing access to “big data” is providing unprecedented information that can directly inform both criteria. Specifically, the incorporation of genomic data for an increasing number of non‐model species is informing more COSEWIC assessments; thus, a repeatable, robust framework is needed for integrating these data into DU characterization. Here, we develop a framework that uses a multifaceted, weight of evidence approach to incorporate multiple data types, including genetic and genomic data, to inform COSEWIC DUs. We apply this framework to delineate DUs of Atlantic salmon (Salmo salar, L.), an economically, culturally, and ecologically significant species, that is also characterized by complex hierarchical population structure. Specifically, we focus on an in‐depth example of how our approach was applied to a previously data limited region of northern Canada that was defined by a single large DU. Application of our framework with newly available genetic and genomic data led to subdividing this DU into three new DUs. Although our approach was developed to meet criteria of COSEWIC, it is widely applicable given similarities in the definitions of a conservation unit

Neutral Genotypes

Genepop file of neutral SNP genotype

Kontraktuele kontrolerechten en bewijsovereenkomsten

This R file contains pseudocode for the main analyses used in the publication "Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus" by Van Wyngaarden, M et al. Not all steps are included in the code but examples of the major analyses (outlier selection, PCA, RDA, and multiple linear regressions) are presented. Running this code will not repeat all the analyses used in the publication but will allow readers to see what functions were used

VanWyngaardenM_etal_GeogDistMatrix

This file contains matrices of pairwise geographic distances (km; shortest distance and estimated ocean current-based distance) between 12 populations of the sea scallop, Placopecten magellanicus, used along with 7163 RAD-seq derived SNPs to estimate isolation-by-distance and dispersal distances among populations. Population names and geographic coordinates can be found in Table 1 of the associated publication

VanWyngaardenM_etal_SeascapeGen_FinalEnvironmentalData

This file contains data for the final 90 environmental variables used to compare genetic and environmental variation among sea scallop populations as well as the latitude and longitude of all 12 sample sites. Data have been standardized to 0 mean and unit variance

GreenCrabEnvironmentalData

Environmental (temperature and salinity) data, and Cartesian coordinates for each sample site in our study

VanWyngaardenM_etal_RADseq_SNPs

This VCF file contains 7216 RAD-seq derived SNPs detected among 12 Northwest Atlantic Ocean populations of the sea scallop, Placopecten magellanicus. The program stacks v0.9999 was used to call variants; parameters can be found in Table S1 of the associated publication

VanWyngaardenM_etal_SeascapeGen_RADseq_SNPs

This VCF file contains 7216 RAD-seq derived SNPs detected among 12 Northwest Atlantic Ocean populations of the sea scallop, Placopecten magellanicus. The program stacks v0.9999 was used to call variants