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 of files deposited to Dryad
Description of files deposited to Dryad
Dryad_File_descriptions.txt
R script: 1_Slacks
This 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.R
R script: 2_RAD_Parse_tags
This 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.R
R script: 3_RAD_Similarity_evalue_blastn
This 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.R
R script: 4_RAD_Parse_blast_xml_Pp_Dd
This 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.R
R script: 5_Getting_info_on_best_Ttru_hit_sequences
This script retrieves the length of the best Blast hit sequences obtained using the previous R script.
5_Getting_info_on_best_Ttru_hit_sequences.R
R script: 6_Annotation_analysis_DelphinusTursiops_RADtag_08-13-2013
This script was used to make histograms of the Blast2GO annotation results.
6_Annotation_analysis_DelphinusTursiops_RADtag_08-13-2013.R
sequence file for individual 9902012
Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
9902012.fq
sequence file for individual 10201010
Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
10201010.fq
sequence file for individual 10307073
Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
10307073.fq
sequence file for individual 10401011
Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
10401011.fq
sequence file for individual 10512077
Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
10512077.fq
sequence file for individual 10712131
Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
10712131.fq
Stacks_commands
Three stacks commands: process_radtags, denovo_map, populations.
Blast2GO annotation results
This file contains annotation results from Blast2GO.
All_annotation_results_08-13-2013.csv
xml output file from Blast2GO for conserved tags
blastResult_blastn_conserved.xml
xml output file from Blast2GO for variable tags
blastResult_blastn_variable.xml
xml output file from Blast2GO for conserved tags: Tursiops hits
blastResult_blastx_conserved_best_Ttru_hits.xml
xml output file from Blast2GO for variable tags: Tursiops hits
blastResult_blastx_variable_best_Ttru_hits.xml
Blast2GO result (blastn) for conserved tags: Evalues
Evalue_blastn_conserved_chart_data_20130715_1051.txt
Blast2GO result (blastn) for variable tags: Evalues
Evalue_blastn_variable_chart_data_20130715_1051.txt
Blast2GO result (blastn) for conserved tags: Similarity values
Similarity_blastn_conserved_chart_data_20130715_1037.txt
Blast2GO result (blastn) for variable tags: Similarity values
Similarity_blastn_variable_chart_data_20130715_1036.txt