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.
SNP loci of Dascyllus trimaculatus from the Western Indian Ocean
The 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 Islands
67p7po8x_93_1174_maf_no_out.txt
Subset of neutral loci (only) of Dascyllus trimaculatus from the Western Indian Ocean
The 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 Islands
neutral.txt
Subset of SNP loci potentially under positive selection, of Dascyllus trimaculatus from the Western Indian Ocean
The 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 Islands
positive.txt
