Genotype likelihood (beagle file) and genotype (vcf) files of North Atlantic and Black Sea Harbour porpoises (Phocoena phocoena) ...

• Main Authors: Celemin Amaro, Enrique, Autenrieth, Marijke, Roos, Anna, Pawliczka, Iwona, Quintela, Maria, Lindstrøm, Ulf, Benke, Harald, Siebert, Ursula, Lockyer, Christina, Berggren, Per, Özturk, Amaha, Özturk, Bayram, Lesage, Veronique, Tiedemann, Ralph
• Format: Dataset
• Language: English
• Published: Dryad 2023
• Subjects: FOS Biological sciences; Harbour Porpoise; Genomics; genetic structure; local adaptation; Conservation; Harbour porpoise; North Atlantic; Phocoena phocoena
• Online Access: https://dx.doi.org/10.5061/dryad.4qrfj6qg6; https://datadryad.org/stash/dataset/doi:10.5061/dryad.4qrfj6qg6

The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean species primarily occurring in coastal and shelf waters across the Northern hemisphere. It inhabits heterogeneous seascapes broadly varying in salinity and temperature. Here we produced 74 whole genomes at intermediate coverage to study Harbour porpoise’s evolutionary history and investigate the role of local adaptation in the diversification into subspecies and populations. We identified ~6 million high-quality SNPs sampled at 8 localities across the North Atlantic and adjacent waters, which we used for population structure, demographic, and genotype-environment association analyses. Our results suggest a genetic differentiation between three subspecies (P.p. relicta, P.p. phocoena, and the recently proposed P.p meridionalis), and three distinct populations within the subspecies P.p. phocoena: Atlantic, Belt Sea, and Proper Baltic Sea. Effective population size and Tajima’s D levels suggest a population contraction in Black Sea and Iberian ... : # Genotype likelihood (beagle file) and genotype (vcf) files of North Atlantic and Black Sea Harbour porpoises (Phocoena phocoena) [https://doi.org/10.5061/dryad.4qrfj6qg6](https://doi.org/10.5061/dryad.4qrfj6qg6) This dataset contains resequencing data used in harbour porpoise genomics research. In this project, we analyzed population structure, demographic history, and signatures of selection. ## Description of the data and file structure Data uploaded here contain: - Genotype likelihoods of the 72 samples: 72_porpoises_unlinked.beagle - Genotypes of 72 samples: Filtered_SNPs_72_samples.vcf - Adaptive_SNPs_no_including_BLS: Pcadapt_adaptive_SNPs_unlinked_67_porpoises.vcf - Neutral_SNPs_no_including_BLS: Neutral_SNPs_unlinked_67_porpoises_in_HWE.vcf - RDA_Pcadapt_overalpping_SNPS_no_including_BLS: RDA-Pcadapt_adaptive_SNPs_unlinked_67_porpoises.vcf ## Sharing/Access information Raw sequecing data can be downloaded from the NCBI Bio Project PRJNA997110 ...