Dataset Information

A Useful SNP Panel to Distinguish Two Cockle Species, Cerastoderma edule and C. glaucum, Co-Occurring in Some European Beds, and Their Putative Hybrids.

ABSTRACT: Cockles are highly appreciated mollusks and provide important services in coastal areas. The two European species, edible (Cerastoderma edule) and lagoon (Cerastoderma glaucum) cockles, are not easily distinguishable, especially when young. Interestingly, the species show different resistance to Marteilia cochillia, the parasite responsible for marteiliosis outbreaks, which is devastating cockle production in some areas. C. edule is severely affected by the parasite, while C. glaucum seems to be resistant, although underlying reasons are still unknown. Hybrids between both species might be interesting to introgress allelic variants responsible for tolerance, either naturally or through artificial selection, from lagoon into edible cockle. Here, we used 2b restriction site-associated DNA sequencing (2b-RAD) to identify single nucleotide polymorphisms (SNP) diagnostic for cockle discrimination (fixed for alternative allelic variants). Among the nine diagnostic SNPs selected, seven were validated using a SNaPshot assay in samples covering most of the distribution range of both species. The validated SNPs were used to check cockles that were suggested to be hybrids by a claimed diagnostic tool based on the internal transcribed spacers of the ribosomal RNA. Although these were shown to be false positives, we cannot rule out the fact that hybrids can occur and be viable. The SNP tool here developed will be valuable for their identification and management.

SUBMITTER: Maroso F

PROVIDER: S-EPMC6826453 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Publications

A Useful SNP Panel to Distinguish Two Cockle Species, Cerastoderma edule and C. glaucum, Co-Occurring in Some European Beds, and Their Putative Hybrids.

Maroso Francesco F Gracia Celia Pérez de CP Iglesias David D Cao Asunción A Díaz Seila S Villalba Antonio A Vera Manuel M Martínez Paulino P

Genes 20190927 10

Cockles are highly appreciated mollusks and provide important services in coastal areas. The two European species, edible (Cerastodermaedule) and lagoon (Cerastodermaglaucum) cockles, are not easily distinguishable, especially when young. Interestingly, the species show different resistance to Marteilia cochillia, the parasite responsible for marteiliosis outbreaks, which is devastating cockle production in some areas. C.edule is sev ...[more]

PMID: 31569787

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Project description:Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9309 SNPs localized in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to analyse the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual/interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (F ST = 0.0240; p < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental correlates suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome. Two main genetic groups were identified, northwards and southwards of French Brittany. Larval dispersal modelling suggested a barrier for larval dispersal linked to the Ushant front that could explain these two genetic clusters. Further genetic subdivision was observed using outlier loci and considering larval advection. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for the management of cockles, designing conservation strategies, founding broodstock for depleted beds and producing suitable seed for aquaculture production.

Project description:BackgroundThe cockle is available to numerous fishing villages in Europe, especially Portugal. In the Ria de Aveiro, there is a lack of a fisheries management program and the need for new ecological studies on cockle biology, ecology, and conservation. We shared local ecological knowledge (LEK) highlights about the cockle-Cerastoderma edule (Linnaeus 1758) in the Ria de Aveiro in favor of adaptive management of this bioresource.MethodsSemi-structured interviews with sixty shellfishers in this coastal lagoon were carried out during April and May 2021. LEK data on the biology and ecology of the cockle were analyzed using an ethical-emic approach and the model of integration of different individual skills. These informal data were compared with previously published data for the species, the Fish Base, and GBIF databases.Results and discussionThe average minimum size of the cockle for capture was 23.4 mm, and the average capture per tide was 137.12 kg. The areas with the highest productivity and the most shellfish were RIAV1 and RIAV2. Cockles inhabit areas of sand and mud at an average depth of 2.71 cm. Feeds are mainly small particles, plankton, mud, and algae. The main predators were crabs, European plaice, and bird species. Cockles spawn primarily in late spring and summer. As of 2010, there was a slight decrease in cockle stocks in the Ria de Aveiro due to overfishing, increased rainfall, and changes in the sediment. Considering and analyzing this knowledge is essential for a better understanding of the environmental context the cockles thrive in the view of users of the natural resource.ConclusionInformal data shared by shellfishers in the Ria de Aveiro were typical of filter-feeding bivalves. LEK may assist in planning future management plans for cockles, and unrefuted data may serve as untestable hypotheses. Ethnobiological studies in the Ria de Aveiro lagoon with other species may improve the management of this system since multiple fisheries are carried out in this coastal area.

Dataset Information

A Useful SNP Panel to Distinguish Two Cockle Species, Cerastoderma edule and C. glaucum, Co-Occurring in Some European Beds, and Their Putative Hybrids.

Publications

A Useful SNP Panel to Distinguish Two Cockle Species, <i>Cerastoderma edule</i> and <i>C. glaucum</i>, Co-Occurring in Some European Beds, and Their Putative Hybrids.

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