DOI: 10.5061/dryad.xpnvx0kmr
title: Heterogeneous microgeographic genetic structure of the common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean: biogeographic barriers and environmental factors

description: Knowledge of genetic structure at the finest level is essential for
 conservation of genetic resources. Despite no visible barriers limiting
 gene flow, significant genetic structure has been shown in marine species.
 The common cockle (Cerastoderma edule) is a bivalve of great commercial
 and ecological value inhabiting the Northeast Atlantic Ocean. Previous
 population genomics studies demonstrated significant structure both across
 the Northeast Atlantic, but also within small geographic areas,
 highlighting the need to investigate fine-scale structuring. Here, we
 analysed two geographic areas that could represent opposite models of
 structure for the species: 1) the SW British Isles region, highly
 fragmented due to biogeographic barriers, and 2) Galicia (NW Spain), a
 putative homogeneous region. 9,250 SNPs genotyped by 2b-RAD on 599
 individuals from 22 natural beds were used for the analysis. The entire
 SNP dataset mostly confirmed previous observations related to genetic
 diversity and differentiation, however, neutral and divergent SNP outlier
 datasets enabled disentangling physical barriers from abiotic
 environmental factors structuring both regions. While Galicia showed a
 homogeneous structure, the SW British Isles region was split into four
 reliable genetic regions related to oceanographic features and abiotic
 factors, such as sea surface salinity and temperature. The information
 gathered supports specific management policies of cockle resources in SW
 British and Galician regions also considering their particular
 socio-economic characteristics; further, these new data will be added to
 those recently reported in the Northeast Atlantic to define sustainable
 management actions across the whole distribution range of the species.
description: Sample area and
 oceanography Two geographic areas along the Northeast
 Atlantic coast were investigated (Fig. 1). The first was focused on the
 British Isles and English Channel (hereafter called the SW British Isles
 region), where previous, though incomplete information, supported
 significant genetic sub-structuring (e.g. Coscia et al. 2020; Vera et al.
 2022). The second area was Galicia (Northwest Spain), which may be
 genetically homogeneous according to information in other mollusc species
 (Diz and Presa 2009; Vera et al. 2016). 
 Over the cockle reproductive
 season (May to September; Mahony et al. 2020), the coastline of Galicia is
 characterised by wind-driven upwelling of cold waters resulting in sea
 surface temperatures (SSTs) that are several degrees colder than off-shore
 SSTs (Supplementary Fig. 1b). Also driven by the predominantly northerly
 winds in the summer months, the Portugal coastal current transports waters
 southwards along the coastline of Iberia (Teles-Machado et al. 2016) with
 residual current strengths along the Galician coastline exceeding 0.15 m/s
 (Supplementary Fig. 1d). The SW British Isles region is divided into
 distinct oceanographic regions (the English Channel, the Celtic Deep, the
 Celtic Sea and the Irish Sea) by diverging current or seasonal frontal
 systems (Galparsoro et al. 2014). Several tidal mixing fronts separate
 seasonally stratified and mixed waters (Supplementary Fig. 1a): the Ushant
 Front (Group “Grepma”, 1988), the Celtic Sea Front, and the Irish Sea
 Front (Simpson and Pingree, 1978). The Celtic Sea is characterised by
 northward flow along the western coast of Cornwall which merges into the
 Celtic Sea Front jet and links into the Irish Coastal Current which
 transports water clockwise along the south and west coast of Ireland
 (Supplementary Fig. 1c; Brown et al. 2003; Fernand et al. 2006). Northward
 currents along the Ushant Front link the Amoricain Shelf with the Celtic
 Sea. The southern English Channel coast is dominated by northeastward
 flow, with the strongest currents occurring around the Cotentin
 Peninsula.  Sample collection
 A total of 374 cockles from 14
 wild natural beds were collected across the aforementioned two regions in
 the period 2017-2020 and stored in 100% ethanol for analyses (Table 1).
 Additionally, 231 cockles from eight beds previously analysed (Vera et al.
 2022: identified as IDA_18, IDC_18, WDE_17, WBY_17, FBS_17, FAR_17, SNO_17
 and SLO_17, where 17 and 18 in the codes represent 2017 and 2018,
 respectively) were included in the analysis to achieve a comprehensive
 picture of the areas studied, thus providing an overall total of 605
 cockles. To avoid generation overlapping, all samples belonged to the 0+
 year age class of their sampling year. No temporal replicates were
 included considering the temporal genetic stability previously reported by
 Vera et al. (2022).  Single Nucleotide Polymorphism (SNP)
 genotyping Total DNA was extracted from gills using the
 E.Z.N.A. E-96 mollusc DNA kit (OMEGA Bio-tek), following manufacturer
 recommendations. 2b-RAD libraries (~ 90 cockles per run) were constructed
 using the AlfI IIb restriction enzyme and sequenced in an Illumina NextSeq
 500 platform following Maroso et al. (2018; 2019). Bowtie 1.1.2 (Langmead
 et al. 2009) was used to align reads to the cockle’s genome (Bruzos et al.
 2022) allowing a maximum of three mismatches and a unique valid alignment
 (-v 3 -m 1). The reference-based mode with default parameters in the
 gstacks module of STACKS 2.0 (Catchen et al. 2013) was used for SNP
 calling.  For genotyping, SNPs were filtered following Vera et al. (2022):
 i) SNPs genotyped in &gt; 60% individuals; ii) MAC (minimum allele
 count) ≥ 3; iii) conformance to Hardy-Weinberg expectations (i.e. SNPs
 with significant FIS values (P &lt; 0.05) in at least 25% of the
 populations were removed); and iv) the most polymorphic SNP within each
 RAD-tag was retained. Individuals with less than 250,000 reads were
 discarded.
description: All files can be opened with Notepad or similar.
description: # Vera et al. Heterogeneous microgeographic genetic structure of the
 common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean:
 biogeographic barriers and environmental factors Dataset of the manuscript
 entitled "Heterogeneous microgeographic genetic structure of the
 common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean:
 biogeographic barriers and environmental factors". SNPs were obtained
 using 2bRADseq methodology and using the software STACKS 2.0. All files
 are in "Genepop" format commonly and widely used by the
 population genetics/genomics research community. ## Description of the
 data and fiel structure: Description of files deposited in Dryad: * 8
 Genepop input files: * CEMicTot.gen: Genepop input file including all the
 beds and markers used in the study (9,250 markers). Bed codes are shown in
 Table 1 of the manuscript. * CEMicN.gen: Genepop input file including the
 beds from SW British Isles region and all markers used in the study (9,250
 markers). Bed codes are shown in Table 1 of the manuscript. *
 CEMicN_Neu.gen: Genepop input file including the beds from SW British
 Isles region with the 9,064 neutral SNP markers identified. Bed codes are
 shown in Table 1 of the manuscript. * 186DivMicN.gen: Genepop input file
 including the beds from SW British Isles region with the 186 divergent
 outliers identified using different methodologies. Bed codes are shown in
 Table 1 of the manuscript. * 35DivMicN.gen: Genepop input file including
 the beds from SW British Isles region with the 35 divergent outliers
 shared by the different methodologies used. Bed codes are shown in Table 1
 of the manuscript. * CEMicGal.gen: Genepop input file including the beds
 from Galicia region and all markers used in the study (9,250 markers). Bed
 codes are shown in Table 1 of the manuscript. * CEMicGalNeu.gen: Genepop
 input file including the beds from Galicia region with the 9,199 neutral
 markers identified. Bed codes are shown in Table 1 of the manuscript. *
 51DivCEMicGal.txt: Genepop input file the beds from Galicia region with
 the 51 divergent outliers identified using different methodologies. Bed
 codes are shown in Table 1 of the manuscript. ## Sharing/Access
 information N/A ## Code/Software N/A