Data and scripts for Mol Ecol article by Jahnke et al: Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas

This repository includes data files and scripts used in the publication "Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas" published in Molecular Ecology in 2022.

In this publication we assessed 12 sites in the native range of the European shore crab Carcinus maenas spanning >2000 km, and examined genetic structure and selection to tidal gradient using 24,000 Single Nucleotide Polymorphisms (SNPs) derived from 2b-RAD sequencing. Additionally, we performed biophysical modelling, and gene expression analyses of candidate clock genes.

Data in this repository includes final filtered vcf files for all, neutral and outlier loci. Raw sequence data is archived in GenBank's SRA: BioProject ID PRJNA797386 and BioSample IDs SAMN25002278-SAMN25002565. New population genomic and biophysical modelling script are provided as well, while scripts for the 2b-RAD bioinformatic analysis are available at: https://github.com/z0on/2bRAD_denovo, and scripts for demographic inferences are available at: https://github.com/alanlm-speciation/moments_optimization.

Abstract:

Most marine invertebrates disperse during a planktonic larval stage that may drift for weeks with ocean currents. A challenge for larvae of coastal species is to return to coastal nursery habitats. Shore crab (Carcinus maenasL.) larvae are known to show tidal rhythmicity in vertical migration in tidal areas and circadian rhythmicity in micro-tidal areas, which seems to increase successful coastal settlement.We studied genome-wide differentiation based on 24,000 SNPs of 12 native populations of shore crab sampled from a large tidal amplitude gradient from macro-tidal (ca. 8 m) to micro-tidal (ca.0.2 m).Dispersal and recruitment success of larvae was assessed with a Lagrangian biophysical model, which showed a strong effect of larval behavior on long-term connectivity, and dispersal barriers that partly coincided with different tidal environments. The genetic population structure showed a subdivision of the samples into three clusters, which represent micro-, meso- and macro-tidal areas. The genetic differentiation was mostly driven by 0.5% outlier loci, whichshowed strong allelic clines located at the limits between the three tidal areas. Demographic modelling suggested that the two genetic barriers have different origins. Differential gene expression of two clock genes (cyc and pdp1) further highlighted phenotypic differences among genetic clusters that are potentially linked to the differences in larval behaviour. Taken together, our seascape genomic study suggest that tidal regime acts as a strong selection force on shore crab population structure, consistent with larval behaviour affecting dispersal and recruitment success.