DOI: 10.5061/dryad.mk364
title: Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans

description: 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 relatively stringent
 quality filters, 3,595 polymorphic loci were retrieved from our
 inter-familial comparison. Cetaceans have undergone rapid diversification
 and the estimated divergence time between the two families is relatively
 recent (14 to 19 My). Thus, our results showed that, for this level of
 divergence, a large number of orthologous loci can still be genotyped
 using this approach, which is on par with two recent in silico studies.
 Our findings constitute one of the first empirical investigations using
 RAD-tag sequencing at this level of divergence and highlights the great
 potential of this approach in comparative studies and to address
 evolutionary questions.
description: 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 longer sequences were subsequently used in Blast2GO).4_RAD_Parse_blast_xml_Pp_Dd.RR script: 5_Getting_info_on_best_Ttru_hit_sequencesThis script retrieves the length of the best Blast hit sequences obtained using the previous R script.5_Getting_info_on_best_Ttru_hit_sequences.RR script: 6_Annotation_analysis_DelphinusTursiops_RADtag_08-13-2013This script was used to make histograms of the Blast2GO annotation results.6_Annotation_analysis_DelphinusTursiops_RADtag_08-13-2013.Rsequence file for individual 9902012Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).9902012.fqsequence file for individual 10201010Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).10201010.fqsequence file for individual 10307073Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).10307073.fqsequence file for individual 10401011Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).10401011.fqsequence file for individual 10512077Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).10512077.fqsequence file for individual 10712131Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).10712131.fqStacks_commandsThree stacks commands: process_radtags, denovo_map, populations.Blast2GO annotation resultsThis file contains annotation results from Blast2GO.All_annotation_results_08-13-2013.csvxml output file from Blast2GO for conserved tagsblastResult_blastn_conserved.xmlxml output file from Blast2GO for variable tagsblastResult_blastn_variable.xmlxml output file from Blast2GO for conserved tags: Tursiops hitsblastResult_blastx_conserved_best_Ttru_hits.xmlxml output file from Blast2GO for variable tags: Tursiops hitsblastResult_blastx_variable_best_Ttru_hits.xmlBlast2GO result (blastn) for conserved tags: EvaluesEvalue_blastn_conserved_chart_data_20130715_1051.txtBlast2GO result (blastn) for variable tags: EvaluesEvalue_blastn_variable_chart_data_20130715_1051.txtBlast2GO result (blastn) for conserved tags: Similarity valuesSimilarity_blastn_conserved_chart_data_20130715_1037.txtBlast2GO result (blastn) for variable tags: Similarity valuesSimilarity_blastn_variable_chart_data_20130715_1036.txt