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.

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 > 60% individuals; ii) MAC (minimum allele count) ≥ 3; iii) conformance to Hardy-Weinberg expectations (i.e. SNPs with significant FIS values (P < 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.

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