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Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multi-modelling approach

Citation

Coscia, Ilaria et al. (2020), Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multi-modelling approach, Dryad, Dataset, https://doi.org/10.5061/dryad.ht76hdrbr

Abstract

Population dynamics of marine species that are sessile as adults are driven by oceanographic dispersal of larvae from spawning to nursery grounds. This is mediated by life-history traits such as the timing and frequency of spawning, larval behaviour and duration, and settlement success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study the fine scale spatial genetic structure in the commercially important cockle species Cerastoderma edule and compare it to environmental variables and current-mediated larval dispersal within a modelling framework. Hydrodynamic modelling employing the NEMO Atlantic Margin Model (AMM15) was used to simulate larval transport and estimate connectivity between populations during spawning months (April - September), factoring in larval duration and inter-annual variability of ocean currents. Results at neutral loci reveal the existence of three separate genetic clusters (mean FST=0.021) within a relatively fine spatial scale in the northwest Atlantic. Environmental Association analysis indicates that oceanographic currents and geographical proximity explain over 20% of the variance observed at neutral loci, while genetic variance (71%) at outlier loci was explained by sea surface temperatures extremes. These results fill an important knowledge gap in the management of a commercially important and overexploited species, bringing us closer to understanding the role of larval dispersal in connecting populations at a fine geographical scale.

Usage Notes

This repository contains the files used to run the analyses for this paper, as follows:

1. 1711Neutral_STR.str: genotypes of putatively neutral SNPs, in Structure format

2. 14Outlier_STR.str: genotypes of putatively outliers, in Structure format

3. MAF_per_population.txt: the genomic input file for the environmental association analysis

4.edges-to-nodes2.csv: the matrix of connectivity used for SEA

5.edges_weights2.csv: the weights associated to the above matrix (derived by connectivity matrices)

6.Environmental_data_by_location.csv: Environmental data used forthe environmental association analysis