Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans ...

• Main Authors: Viricel, Amélia, Pante, Eric, Dabin, Willy, Simon-Bouhet, Benoît
• Format: Dataset
• Language: English
• Published: Dryad 2013
• Subjects: Genomics/Proteomics; Delphinus delphis; Phocoena phocoena
• Online Access: https://dx.doi.org/10.5061/dryad.mk364; https://datadryad.org/stash/dataset/doi:10.5061/dryad.mk364

Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbor porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analyzing individuals from the distinct families compared to analyses restricted to intra-specific comparisons (i.e., within D. delphis). Despite ... : Description of files deposited to DryadDescription of files deposited to DryadDryad_File_descriptions.txtR script: 1_SlacksThis script allows testing multiple values for two stacks parameters used in the denovo_map command: M and n. It runs both denovo_map and populations commands.1_Slacks.RR script: 2_RAD_Parse_tagsThis script was used to retrieve and sort sequences from the stacks outputs (after applying the populations command) into variable versus invariable sequences. These sequences were then blasted using Blast2GO.2_RAD_Parse_tags.RR script: 3_RAD_Similarity_evalue_blastnThis script retrieves the similarity scores from Blast results obtained using Blast2GO, calculates the median and range, and builds a histogram of these similarity values.3_RAD_Similarity_evalue_blastn.RR script: 4_RAD_Parse_blast_xml_Pp_DdThis script was used to summarize Blast hits results from Blast2GO (number of hits belonging to each organism) and to retrieve and export in fasta format the whole sequence from the best hits (these ...