DOI: 10.5061/dryad.2v1kr38
title: Data from: SNPs reveal a genetic cline across the northeast Atlantic and enable powerful population assignment in the European lobster

description: 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 precise driver(s) of this clinal pattern –isolation-by-distance,
 secondary contact, selection across an environmental gradient, or a
 combination of these factors– remains undetermined. Putatively neutral
 markers differentiated lobsters from Oosterschelde, an estuary on the
 Dutch coast, a finding likely explained by past bottlenecks and limited
 gene flow with adjacent North Sea populations. Building on the findings of
 our spatial genetic analysis, we were able to test the accuracy of
 assigning lobsters at various spatial scales, including to basin of origin
 (Atlantic or Mediterranean), region of origin and sampling location. The
 predictive model assembled using 79 SNPs correctly assigned 99.7 % of
 lobsters not used to build the model to their basin of origin, but
 accuracy decreased to region of origin and again to sampling location.
 These results are of direct relevance to managers of lobster fisheries and
 hatcheries, and provide the basis for a genetic tool for tracing the
 origin of European lobsters in the food supply chain.
description: 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 analyse population assignment using the package assignPOP.assignment_2019.RR script: plot allele frequenciesR script used to plot population allele frequencies.allele_freq_2019.ROutlier tests data filesData files used for outlier selection tests (OutFLANK, PCadapt and Bayescan).Outlier_tests_data_files.zipR script: outlier selection testsR script used to run outlier selection tests on the raw RAD sequencing data from Jenkins et al. (2018) https://doi.org/10.1007/s12686-018-1001-8. Raw reads archived on Dryad (https://doi.org/10.5061/dryad.2pc6v).outlier_selection_tests_2019.RMiscellaneous data filesZip file containing miscellaneous data files including post-filtered SNP genotypes in adegenet and genepop format, HWE results in RData format, and LD results in RData format.Miscellaneous_files.zip