Data from: SNPs reveal a genetic cline across the northeast Atlantic and enable powerful population assignment in the European lobster ...

Resolving stock structure is crucial for fisheries conservation to ensure that the spatial implementation of management is commensurate with that of biological population units. To address this in the economically important European lobster (Homarus gammarus), genetic structure was explored across t...

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Bibliographic Details
Main Authors: Jenkins, Tom L, Ellis, CD, Triantafyllidis, A, Stevens
Format: Dataset
Language:English
Published: Dryad 2019
Subjects:
Traceability
Homarus gammarus
genetic cline
Fluidigm EP1
marine connectivity
European lobster
Northeast Atlantic
Online Access:https://dx.doi.org/10.5061/dryad.2v1kr38
https://datadryad.org/stash/dataset/doi:10.5061/dryad.2v1kr38
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Summary:Resolving stock structure is crucial for fisheries conservation to ensure that the spatial implementation of management is commensurate with that of biological population units. To address this in the economically important European lobster (Homarus gammarus), genetic structure was explored across the species’ range using a small panel of single nucleotide polymorphisms (SNPs) previously isolated from restriction-site associated DNA sequencing; these SNPs were selected to maximise differentiation at a range of both broad- and fine-scales. After quality control and filtering, 1,278 lobsters from 38 sampling sites were genotyped at 79 SNPs. The results revealed a pronounced phylogeographic break between the Atlantic and Mediterranean basins, while structure within the Mediterranean was also apparent, partitioned between lobsters from the central Mediterranean and the Aegean Sea. In addition, a genetic cline across the northeast Atlantic was revealed using both putatively neutral and outlier SNPs, but the ... : Raw SNP GenotypesRaw SNP genotypes called by the Fluidigm EP1 Genotyping Software.Lobster_SNP_Raw_Genotypes.csvR script: quality controlR script used to explore and filter data. Includes analyses of missing data, Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and heterozygosity.quality_control_2019.RR script: genetic differentiationR script used to analyse genetic differentiation. Analyses include global and pairwise Fst and Jost's D, calculating least-cost distances between sampling sites using Marmap, and Mantel tests.differentiation_stats.RR script: DAPCR script used to run discriminant analysis of principal components (DAPC).dapc_2019.RR script: snapclustR script used to run snapclust analyses.snapclust_2019.RSTRUCTURE data filesZip file containing raw STRUCTURE output files from the Atlantic hierarchical analysis and the input file.STRUCTURE_data_files.zipAssignment data filesData files used in the assignment analyses.Assignment_genotype_data.zipR script: assignmentR script used to ...

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