DOI: 10.5061/dryad.9tt31dg
title: Data from: Unraveling hierarchical genetic structure in a marine metapopulation: a comparison of three high-throughput genotyping approaches

description: Marine metapopulations often exhibit subtle population structure that can
 be difficult to detect. Given recent advances in high-throughput
 sequencing, an emerging question is whether various genetic approaches, in
 concert with improved sampling designs, will substantially improve our
 understanding of genetic structure in the sea. To address this question,
 we explored hierarchical patterns of structure in the coral reef fish
 Elacatinus lori using a high-resolution approach with respect to both
 genetic and geographic sampling. Previously, we identified three putative
 E. lori populations within Belize using traditional genetic markers and
 sparse geographic sampling: barrier reef and Turneffe Atoll; Glover’s
 Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals
 at ~10 km intervals throughout these reefs (1,129 individuals from 35
 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs;
 89 microsatellites; and 57 non-repetitive nuclear loci. At broad spatial
 scales, the markers were consistent with each other and with previous
 findings. At finer spatial scales, there was new evidence of genetic
 substructure, but our three marker sets differed slightly in their ability
 to detect these patterns. Specifically, we found subtle structure between
 the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most
 effectively. We also documented isolation by distance within the barrier
 reef. Sensitivity analyses revealed that the number of loci (and alleles)
 had a strong effect on the detection of structure for all three marker
 sets, particularly at small spatial scales. Taken together, these results
 illustrate empirically that high-throughput genotyping data can elucidate
 subtle genetic structure at previously-undetected scales in a dispersive
 marine fish.
description: Field sampling
 coordinatesLocations of all field
 sampling sites from a 2014 expedition around the Belize barrier reef. For
 each sampling location, we provide the site id, the UTM zone and
 coordinates, and the total number of individual tissue samples collected
 from the site.DAloia_goby_sampling_coordinates.csvGoby mitochondrial genotypesGenotype table for 29 fragments of the Elacatinus lori mitochondrial genome, generated using amplicon sequencing. Each row is a locus (i.e. a fragment); each column starting with the second is an E. lori individual. For these haploid markers, individuals are assigned one haplotype per locus. Missing data (e.g. due to low reads) are indicated by a period. For each locus, haplotypes are uniquely labeled with numbers. Associated raw sequence data have been deposited to the NCBI Sequence Read Archive (BioProject ID: PRJNA551399).goby_genotypes_mtdna.txtGoby SNP GenotypesGenotype table for 2,418 SNPs. Individuals have two alleles per locus, separated by a "/". Missing data (e.g. due to low reads) are indicated by a period. Associated raw sequence data have been deposited to the NCBI Sequence Read Archive (BioProject ID: PRJNA551399).goby_genotypes_SNP.txtGoby microsatellite genotypesGenotype table for 89 sequenced microsatellites generated using amplicon sequencing. Each row is a microsatellite locus; each column starting with the second is an E. lori individual. For these diploid markers, individuals have two alleles per locus, separated by a "|". Missing data (e.g. due to low reads) are indicated by a period. For each locus, haplotypes are uniquely labeled with numbers. Associated raw sequence data have been deposited to the NCBI Sequence Read Archive (BioProject ID: PRJNA551399).goby_genotypes_msats.txtGoby non-repetitive nuclear genotypesGenotype table for 57 sequenced non-repetitive nuclear loci generated using amplicon sequencing. Each row is a locus; each column starting with the second is an E. lori individual. For these diploid markers, individuals have two alleles per locus, separated by a "|". Missing data (e.g. due to low reads) are indicated by a period. For each locus, haplotypes are uniquely labeled with numbers. Associated raw sequence data have been deposited to the NCBI Sequence Read Archive (BioProject ID: PRJNA551399).goby_genotypes_nonrepetitive.txt