DOI: 10.5061/dryad.rxwdbrvnc
title: Data from: Genome divergence between European anchovy ecotypes fuelled by structural variants originating from trans-equatorial admixture

description: The European anchovy (Engraulis encrasicolus) is known to be subdivided
 into marine and coastal ecotypes, and their divergence shows patterns that
 are consistent with SVs. Here, we present the first genome-scale study
 investigating genetic structure in the E. encrasicolus species complex. We
 generated a reference genome and produced whole-genome resequencing data
 for anchovies from the North-East Atlantic and Mediterranean Sea, as well
 as from South Africa. We complemented this approach with the analysis of
 RAD-seq data in order to study ecotypic structure across the entire
 distribution range. We found that genetic diversity is not only
 characterised by the presence of two genetic clusters, namely the marine
 and coastal ecotypes, but also by a third ancestry which corresponds to a
 southern Atlantic lineage. Genomic landscapes of differentiation showed
 evidence for large regions of high linkage disequilibrium, likely
 representing SVs that differentiate the three anchovy lineages. 
description: # Data from: Genome divergence between European anchovy ecotypes fuelled
 by structural variants originating from trans-equatorial admixture Dataset
 DOI: [10.5061/dryad.rxwdbrvnc](10.5061/dryad.rxwdbrvnc) ## Description of
 the data and file structure The European anchovy (Engraulis encrasicolus)
 presents distinct marine and coastal forms, but the genetic basis behind
 this split has remained unclear. We used whole-genome and RAD sequencing
 to study populations across the species’ range. ### Files and variables
 #### File: Anchovy_ecotypes_2025_Supp_Appendix.html **Description:** This
 report includes results about the alignment of RAD and WGS data, PCA
 conducted on different genomic regions, and the SVs that were genotyped.
 It contains the following tabs and variables: 1\) *Samples*: The first row
 contains the sample table (also provided in ".txt" format),
 where background colours indicate ancestry proportions as RGB values (see
 Fig. 1 in the main text). Below the table, there is an interactive map
 with sample locations. 2\) *WGS mapping* tab: Statistics from alignment
 with BWA, with 'Presentation' describing all stats in detail.
 Plots shown: Distribution, Percentage, Reads mapped, Reads mapped &
 paired, Reads unmapped, Reads properly paired, Average length, Average
 quality, Insert size average, Paired different chromosomes, Paired
 different chromosomes (%), Percent paired other orientation, Percentage
 properly paired reads, Insert size, Coverage plot, GC coverage, Insertion
 data, Deletion data. 3\) *RAD mapping* tab: Statistics from alignment with
 BWA, with 'Presentation' describing all stats in detail. Plots
 shown: Distribution, Percentage, Reads mapped, Reads unmapped, Duplication
 rate, Average length, Average quality, Coverage plot, Insertion data,
 Deletion data. 4\) *WGS PCA* tab: PCA performed on the WGS dataset, using
 markers from across the entire genome ('Genome-wide PCA') or
 markers from single chromosomes only (24 plots). Sample colours reflect
 their ancestry proportions as in the sample table. 5\) *RAD PCA* tab: PCA
 performed on the RAD dataset, using markers from across the entire genome
 ('Genome-wide PCA') or markers from single chromosomes only (24
 plots). Sample colours reflect their ancestry proportions as in the sample
 table. #### File: Sample_table.txt **Description:** Sample table with
 following columns: Sample, WGS, RAD, Basin, Latitude, Longitude, Location,
 Admixture, Habitat, Genetic class #### File: Eencr_WGS_dataset.vcf.gz
 **Description:** Whole-genome resequencing dataset, containing 5.9M SNPs
 in 39 individuals. #### File: Eencr_RAD_dataset.vcf.gz **Description:**
 RAD-sequencing dataset, containing 3906 SNPs in 385 individuals. ##
 Code/software HTML report can be opened using an internet browser. ##
 Access information Data was derived from the following sources: * Sequence
 reads for whole-genome resequencing data have been deposited in the
 GenBank Sequence Read Archive under the accession codes BioProject ID
 PRJNA311981 (for RAD samples) and BioProject ID PRJNA777424 (WGS samples).
 - Accessions of RAD samples: SAMN48731832 to SAMN48732074:
 [https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=311981](https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=311981) * Accessions of WGS samples: SAMN48800104 to SAMN48800125, SAMN48746249 to SAMN48746268: [https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=777424](https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=777424)