DOI: 10.5061/dryad.bn457rr
title: Data from: RADseq analyses reveal concordant Indian Ocean biogeographic and phylogeographic boundaries in the reef fish Dascyllus trimaculatus

description: Population genetic analysis is an important tool for estimating the degree
 of evolutionary connectivity in marine organisms. Here, we investigate the
 population structure of the three-spot damselfish Dascyllus trimaculatus
 in the Red Sea, Arabian Sea and Western Indian Ocean, using 1,174 single
 nucleotide polymorphisms (SNPs). Neutral loci revealed a signature of weak
 genetic differentiation between the Northwestern (Red Sea and Arabian Sea)
 and Western Indian Ocean biogeographic provinces. Loci potentially under
 selection (outlier loci) revealed a similar pattern but with a much
 stronger signal of genetic structure between regions. The Oman population
 appears to be genetically distinct from all other populations included in
 the analysis. While we could not clearly identify the mechanisms driving
 these patterns (isolation, adaptation, or both), the datasets indicate
 that population level divergences are largely concordant with
 biogeographic boundaries based on species composition. Our data can be
 used along with genetic connectivity of other species to identify the
 common genetic breaks that need to be considered for the conservation of
 biodiversity and evolutionary processes in the poorly studied Western
 Indian Ocean region.
description: SNP loci of Dascyllus
 trimaculatus from the Western Indian OceanThe dataset contains
 1,174 loci generated with ddRAD Sequencing, from single end reads, cleaned
 and trimmed to 95 bp. The format is for STRUCTURE. It contains 93
 individuals from 7 populations. These loci were obtained with a STACKS
 denovo map using these filters: Loci shared in at least 65% of individuals
 within a group (r=0.65), shared between all populations (p=7), Coverage 8x
 (m=8), minor allele frequency 1.5% (maf=0.015) (i.e., at least two
 individuals must have the unique allele) Populations 1:NRS: Northern Red
 Sea 2:DJI: Djibouti 3:OMA: Oman 4:DGA: Diego de García, Chagos 5:ZAN:
 Zanzibar 6:MAY: Mayotte 7:JDN: Juan de Nova, Scattered
 Islands67p7po8x_93_1174_maf_no_out.txtSubset of neutral loci (only) of Dascyllus trimaculatus from the Western Indian OceanThe dataset “neutral.txt” contains a subset of the 1,174 loci generated with ddRAD Sequencing, from single end reads, cleaned and trimmed to 95 bp. Thus this is a subset of data from the file “67p7po8x_93_1174_maf_no_out.txt”. The format is for STRUCTURE. The subset consists of 1,117 loci identified to be potentially neutral to selection by the FDIST method from the software Arlequin. It contains 93 individuals from 7 populations. These loci were obtained with a STACKS denovo map using these filters: Loci shared in at least 65% of individuals within a group (r=0.65), shared between all populations (p=7), Coverage 8x (m=8), minor allele frequency 1.5% (maf=0.015) (i.e., at least two individuals must have the unique allele) Populations 1:NRS: Northern Red Sea 2:DJI: Djibouti 3:OMA: Oman 4:DGA: Diego de García, Chagos 5:ZAN: Zanzibar 6:MAY: Mayotte 7:JDN: Juan de Nova, Scattered Islandsneutral.txtSubset of SNP loci potentially under positive selection, of Dascyllus trimaculatus from the Western Indian OceanThe dataset “positive.txt” contains a subset of the 1,174 loci generated with ddRAD Sequencing, from single end reads, cleaned and trimmed to 95 bp. Thus this is a subset of data from the file “67p7po8x_93_1174_maf_no_out.txt”. The format is for STRUCTURE. The subset consists of 25 loci identified to be potentially under positive selection by the FDIST method used to detect outliers, from the software Arlequin. It contains 93 individuals from 7 populations. These loci were obtained with a STACKS denovo map using these filters: Loci shared in at least 65% of individuals within a group (r=0.65), shared between all populations (p=7), Coverage 8x (m=8), minor allele frequency 1.5% (maf=0.015) (i.e., at least two individuals must have the unique allele) Populations 1:NRS: Northern Red Sea 2:DJI: Djibouti 3:OMA: Oman 4:DGA: Diego de García, Chagos 5:ZAN: Zanzibar 6:MAY: Mayotte 7:JDN: Juan de Nova, Scattered Islandspositive.txt