DOI: 10.5061/dryad.f09rh
title: Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish

description: Data from a large-scale restriction site associated DNA (RAD-Seq) study of
 nine butterflyfish species in the Red Sea and Arabian Sea provided a means
 to test the utility of a recently published draft genome (Chaetodon
 austriacus) and assess apparent bias in this method of isolating nuclear
 loci. We here processed double-digest restriction-site (ddRAD) associated
 DNA sequencing data to identify single nucleotide polymorphism (SNP)
 markers and their associated function with and without our reference
 genome to see if it improves the quality of RAD-Seq markers. Our analyses
 indicate (1) a modest gap between the number of non-annotated versus
 annotated SNPs across all species, (2) an advantage of using genomic
 resources for closely related but not distantly related butterflyfish
 species based on the ability to assign putative gene function to SNPs, and
 (3) an enrichment of genes among sister butterflyfish taxa related to
 calcium transmembrane transport and binding. The latter result highlights
 the potential for this approach to reveal insights into adaptive
 mechanisms in populations inhabiting challenging coral reef environments
 such as the Red Sea, Arabian Sea, and Arabian Gulf with further study.
description: Chaetodon_austriacus_denovo_batch_1_filtered.vcfFiltered denovo_map.pl RAD reads in .vcf format for Chaetodon austriacusChaetodon_fasciatus_denovo_batch_1_filtered.vcfFiltered denovo_map.pl RAD reads in .vcf format for Chaetodon fasciatusChaetodon_larvatus_denovo_batch_1_filtered.vcfFiltered denovo_map.pl RAD reads in .vcf format for Chaetodon larvatusChaetodon_melapterus_denovo_batch_1_filtered.vcfFiltered denovo_map.pl RAD reads in .vcf format for Chaetodon melapterusChaetodon_mesoleucos_denovo_batch_1_filtered.vcfFiltered denovo_map.pl RAD reads in .vcf format for Chaetodon mesoleucosChaetodon_paucifasciatus_denovo_batch_1_filtered.vcfFiltered denovo_map.pl RAD reads in .vcf format for Chaetodon paucifasciatusChaetodon_pictus_denovo_batch_1_filtered.vcfFiltered denovo_map.pl RAD reads in .vcf format for Chaetodon pictusChaetodon_semilarvatus_denovo_batch_1_filtered.vcfFiltered denovo_map.pl RAD reads in .vcf format for Chaetodon semilarvatusChaetodon_trifascialis_denovo_batch_1_filtered.vcfFiltered denovo_map.pl RAD reads in .vcf format for Chaetodon trifascialisCtenochaetus_striatus_denovo_batch_1_filtered.vcfFiltered denovo_map.pl RAD reads in .vcf format for Ctenochaetus striatusChaetodon_austriacus_refmap_batch_1_filtered.vcfFiltered ref_map.pl RAD reads in .vcf format for Chaetodon austriacusChaetodon_fasciatus_refmap_batch_1_filtered.vcfFiltered ref_map.pl RAD reads in .vcf format for Chaetodon fasciatusChaetodon_larvatus_refmap_batch_1_filtered.vcfFiltered ref_map.pl RAD reads in .vcf format for Chaetodon larvatusChaetodon_melapterus_refmap_batch_1_filtered.vcfFiltered ref_map.pl RAD reads in .vcf format for Chaetodon melapterusChaetodon_mesoleucos_refmap_batch_1_filtered.vcfFiltered ref_map.pl RAD reads in .vcf format for Chaetodon mesoleucosChaetodon_paucifasciatus_refmap_batch_1_filtered.vcfFiltered ref_map.pl RAD reads in .vcf format for Chaetodon paucifasciatusChaetodon_pictus_refmap_batch_1_filtered.vcfFiltered ref_map.pl RAD reads in .vcf format for Chaetodon pictusChaetodon_semilarvatus_refmap_batch_1_filtered.vcfFiltered ref_map.pl RAD reads in .vcf format for Chaetodon semilarvatusChaetodon_trifascialis_refmap_batch_1_filtered.vcfFiltered ref_map.pl RAD reads in .vcf format for Chaetodon trifascialisCtenochaetus_striatus_refmap_batch_1_filtered.vcfFiltered ref_map.pl RAD reads in .vcf format for Ctenochaetus striatus