DOI: 10.5061/dryad.zgmsbccdz
title: Shared and distinct patterns of genetic structure in two sympatric large decapods

description: Aim: Comparing genetic structure in species with shared spatial ranges and
 ecological niches can help identify how dissimilar aspects of biology can
 shape differences in population connectivity. Similarly, where species are
 widely distributed across heterogeneous environments and major topographic
 barriers, knowledge of the structuring of populations can help reveal the
 impacts of factors that limit dispersal and/or drive divergence, aiding
 conservation management. Location: European seas of the northeast
 Atlantic and Mediterranean. Taxa: European clawed lobster (Homarus
 gammarus) and European crawfish (Palinurus elephas), two sympatric,
 heavily-fished decapods with extensive dispersal potential.
 Methods: By RAD-sequencing 214 H. gammarus from 32 locations, and
 349 P. elephas from 15 locations, we isolated 6,340 and 7,681 SNP loci,
 respectively. Using these data to characterise contemporary population
 structuring, we investigate potential spatial and environmental drivers of
 genomic heterogeneity. Results: We found higher levels of
 differentiation among clawed lobsters than crawfish, both globally and
 within basins, and demonstrate where known hydrographic and topographic
 barriers generate shared patterns of divergence, such as a genetic break
 between the Atlantic and Mediterranean basins. Genetic structure not
 common to both species is principally apparent in the Atlantic portions of
 their range, where clawed lobster exhibits a genetic cline and increased
 differentiation towards range margins, while crawfish appear effectively
 panmictic throughout this region. Main Conclusions: We attribute
 the comparative lack of crawfish population structuring to their greater
 dispersal tendencies via a longer pelagic larval duration and sporadic
 adult movements. In contrast, genetic connectivity in clawed lobster is
 relatively restricted, with the correlation of site of origin and
 temperature to geographic heterogeneity at many divergent loci indicative
 of both neutral and adaptive processes. Our results help inform how
 contemporary management can account for likely demographic connectivity
 and marry the conservation of genomic variation with sustainable fisheries
 in these ecologically and economically important crustaceans.
description: RADseq derived SNP data obtained from rangewide samples of two
 lobster species, European lobster (<em>Homarus gammarus</em>)
 and European spiny lobster (<em>Palinurus elephas</em>), and R
 scripts for the subsequent analytical pipeline used to address questions
 of population genetic diversity, structure, selection and
 adaptation.
description: R and numerous R packages (all open-source).
description: # Shared and distinct patterns of genetic structure in two sympatric large
 decapods \#START This README file was generated by Charlie Ellis on
 19-03-2023, and updated on 24/01/2024 Files and materials herein should
 ensure the analytical pipeline undertaken for the relevant study is fully
 reproducible (or adaptable to your own datasets of the same format). ###
 GENERAL INFORMATION 1. Citation of linked publication: Ellis CD, MacLeod
 KL, Jenkins TL, Rato LD, Jézéquel Y, Pavičić M, Díaz D, Stevens JR.
 (2023). Shared and distinct patterns of genetic structure in two sympatric
 large decapods. Journal of Biogeography.
 2. Contact Information: Lead
 & Corresponding Author; Name: Charlie Ellis Institution: University of
 Exeter Address: Department of Biosciences, Faculty of Health and Life
 Sciences, University of Exeter, Exeter, UK Email:
 3. Principal Investigator / Group Leader;
 Name: Jamie Stevens Institution: University of Exeter Address: Department
 of Biosciences, Faculty of Health and Life Sciences, University of Exeter,
 Exeter, UK Email: 4. Citation of this
 Dataset: Ellis, Charlie D. et al. (2023) Shared and distinct patterns of
 genetic structure in two sympatric large decapods [Dataset]. Dryad.
 1. Method Types and Data
 Generation: \-- RADseq derived SNP data obtained from rangewide samples of
 two lobster species, European lobster (*Homarus gammarus*) and European
 spiny lobster (*Palinurus elephas*) \-- BioOracle environmantal data; raw
 asci files of marine environmental parameters obtained via
 BioOracle's open source digital data repository, via
 \-- Reproducable scripts in R for the
 subsequent analytical pipeline used to address questions of population
 genetic diversity, structure, selection and adaptation. 1. Usage Notes: R
 / R Studio; and numerous R packages; BioOracle environmental dataset
 downloads (all open-source). 1. Funding: European Commission, Award:
 ENG4300 European Commission, Award: 05R16P00366 ### SHARING & ACCESS
 INFORMATION 1. Licenses/restrictions placed on the data: CC0 1.0 Universal
 (CC0 1.0) Public Domain 2. Links to publications that cite or use the
 data: Ellis CD, MacLeod KL, Jenkins TL, Rato LD, Jézéquel Y, Pavičić M,
 Díaz D, Stevens JR. Shared and distinct patterns of genetic structure in
 two sympatric large decapods. Journal of Biogeography. 2023 May 2.
 3. The raw RAD sequence data
 from which SNP loci were derived are available via the NCBI SRA
 repository, at 
 ### FILE AND DATA OVERVIEW This data archive consists of: 1. this README
 file 2. Ellis-etal2022_JBiogeog_CrawfishPelephasDataAnalysis.zip folder
 with analytical resources for European spiny lobsters (*Palinurus
 elephas*) 3. Ellis-etal2022_JBiogeog_LobsterHgammarusDataAnalysis.zip
 folder with analytical resources for European lobsters (*Homarus
 gammarus*) 4. BioOracleEnvData.zip folder containing raw ASCI files of
 marine environmental parameters used in Redundancy Analysis Each
 Ellis-*DataAnalysis.zip folder (b & c, above) contains sufficient
 resources to undertake analytical investigation of the RADseq derived SNP
 genotypes, and reproduce the analytical pipeline of Ellis et al, 2023,
 via: * populations.snps*.gen -- a file with raw SNP genotype data output
 from the Stacks v2.0 pipeline, in a 'Genepop' format, used by R
 script 01 to generate an initial unfiltered genind object; * other raw
 files required to run parts of the analysis pipeline; * coord*.csv -- a
 .csv table of latitude and longitud coordinates corresponding to the
 location of sites, denoted by their site ID codes, as used in R scripts
 05c and 06. * plot_bayescan_function.txt -- a .txt file containing a
 function to call from R script 03 in order to plot the results of Bayescan
 analyses, using the BaysOut*_fst.txt file outputs created by Bayescan (run
 on external HPC) * a series of 13 R scripts, with descriptive filenames
 prefixed with a numeral that denotes the ascending order in which they
 should be run, with comprehensive annotation and explanation of the
 analytical pipeline inherent; * 01 InitialImport_*.R * a script to input
 Stacks-derived genotype file, convert it to a Genind file, filter for
 missing data (via individuals and loci) and inspect basic statistics * 02
 DAPC_fulldata_*.R * a script to produce a Discriminant Analysis of
 Principal Components and associated plot, using the full SNP dataset * 03
 OutlierDetection_*.R * a script to detect outliers using Bayescan (via a
 HPC) and OUTflank, and highlight the overlap between detection methods *
 04a DAPC_neutral_*.R\ a script to produce a Discriminant Analysis of
 Principal Components and associated plot, using only neutral SNPs * 04b
 DAPC_outliers_*.R * a script to produce a Discriminant Analysis of
 Principal Components and associated plot, using only outlier SNP candidate
 loci * 05a RDA_geneticdata_*.R * a script to reformat SNP genotype data
 into allele frequency data, formatted for use in Redundancy Analysis * 05b
 RDA_envirodata_*.R * a script to reformat environmental data (obtained
 from BioOracle) into site-specific environmental gradients, formatted for
 use in Redundancy Analysis * 05c prelimlc_distances.R * a preliminary
 script (to be run prior to the other 05c*.R script) to calculate a matrix
 of least-cost marine distance paths between sites * 05c
 RDA_spatialdata_*.R * a script to convert pairwise geographic site
 distances as distance-based MEMs, for use in Redundancy Analysis * 05d
 RDA_GEA_*.R * a script to perform a basic Genotype Environment Association
 analysis, in which correlations between genotypic and environmental
 gradients are assessed via Redundancy Analysis * 05e RDA_dbMEMs_*.R * a
 script to perform a full distance-based Redundancy Analysis, in which
 genotypic gradients are correlated to both environmental and spatial
 variables, controlled as factors. * 06 FstIBD_*.R * a script to calculate
 and plot classic population genetic differentiation statistics, the
 fixation index (Fst) and isolation by distance (IBD) * 07 Snapclust_*.R *
 a script to run Snapclust algorithms, to assess the optimal number of
 ancestral populations (k) and assign membership of individuals to the
 resulting compartmentation of ancestral populations. A series of other
 .txt .csv and .RData files which are created by the R scripts workflow,
 and are included to demonstrate repeatability of our analysis, and to
 provide example file structures for others. * outlierBAY*.csv * a comma
 separated data table file created in R script 03, giving the locus IDs of
 outlier SNPs identified as selection candidates by Bayescan, for
 downstream identification of the outlier (and neutral) loci data subset *
 allele_freqs_filt.csv * a comma separated data table file created in R
 script 05a, giving the minor allele frequencies of filtered SNP loci, for
 downstream use in redundancy analyses * lc_distances_km.csv * a comma
 separated data table file created in R script 05c, giving a matrix of
 least cost seaward distances between pairwise sites, for downstream use in
 redundancy analyses and calculations of Isolation By Distance *
 BaysOutfst.txt * a text file created by Bayescan (run separately on a HPC)
 with the results of all SNP loci across all samples, for downstream
 plotting and interrogation of outlier SNP loci. * BaysOutATL_fst.txt * a
 text file created by Bayescan (run separately on a HPC) with the results
 of all SNP loci across only Atlantic-origin samples, for downstream
 plotting and interrogation of outlier SNP loci. * BaysOutMED_fst.txt * a
 text file created by Bayescan (run separately on a HPC) with the results
 of all SNP loci across only Mediterranean-origin samples, for downstream
 plotting and interrogation of outlier SNP loci. * Pelephas.RData * a
 genind object created in R script 01 featuring genotypes of all crawfish
 samples at all filtered SNP loci, used by several other R scripts
 downstream * LobPopGen_.RData * a genind object created in R script 01
 featuring genotypes of all lobster samples at all filtered SNP loci, used
 by several other R scripts downstream * Pelephas_ATL.RData * a genind
 object created in R script 02 featuring genotypes of Atlantic-origin
 crawfish samples at all filtered SNP loci, used by several other R scripts
 downstream * LobPopGen_ATL*.RData * a genind object created in R script 02
 featuring genotypes of Atlantic-origin lobster samples at all filtered SNP
 loci, used by several other R scripts downstream * Pelephas_MED*.RData * a
 genind object created in R script 02 featuring genotypes of
 Mediterranean-origin crawfish samples at all filtered SNP loci, used by
 several other R scripts downstream * LobPopGen_MED*.RData * a genind
 object created in R script 02 featuring genotypes of Mediterranean-origin
 lobster samples at all filtered SNP loci, used by several other R scripts
 downstream * NeutralData_.RData * a genind object created in R script 03
 featuring genotypes of all samples at only neutral filtered SNP loci
 (without those flagged as outliers), used by several other R scripts
 downstream * Outlier.RData * a genind object created in R script 03
 featuring genotypes of all samples at only filtered SNP loci identified as
 outliers, used by several other R scripts downstream. For each species,
 there are several of these Outlier*.RData genind objects, each with
 different naming that reflects the different selection of samples and
 detection methodologies used to identify them. ### SOFTWARE AND
 REPRODUCABILITY \--- All analyses were run in R v4.0.0, using R Studio
 \--- For version numbers used of individual R software packages, please
 see the Methods section of the published study, via
 \--- For any compatability
 issues or queries / troubleshooting relating to reproducability, please
 contact Charlie Ellis - \#END