2018-02-21: The data are currently stored in the Dryad repository as the following two packages. The files may also be accessed here via the 'Get Data' button (above).
Dryad package: Kelp-rockfish genotypes, DOI: 10.5061/dryad.6cp14g8
Data from: "Larval dispersal connects marine reserves and replenishes fished populations along the central California coast." Baetscher DS, Anderson EC, Saarman E, Malone D, Carr MH, Garza JC (2018?) Molecular Ecology (in press).
NOTE: not all files are publicly available until the associated publication is published.
This data repository contains the following: Genotypes for 96 microhaplotypes - this file contains the genotypes for 6,108 kelp rockfish sequenced at 96 amplicon loci using paired-end Illumina sequencing. Genotypes were filtered for read depth (minimum 20 reads total per locus/individual) and allele balance (0.4 ratio of read depth for allele 1:allele 2 in a heterozygote). Samples with missing data at more than 10 percent of loci were excluded from this data set. Variant call format file generated using Freebayes software from 2,293 rockfish samples sequenced at 96 microhaplotype loci. Samples include four species of rockfishes: kelp (Sebastes atrovirens), copper (S. caurinus), black-and-yellow (S. chrysomelas), and gopher (S. carnatus). This file contains 1,495 variant sites across the 96 loci.
Dryad package: Rockfish microhaplotype sequences, DOI: 10.5061/dryad.5863d
Data from: Baetscher DS, Clemento AJ, Ng TC, Anderson EC, Garza JC (2017) Microhaplotypes provide increased power from short-read DNA sequences for relationship inference. Molecular Ecology Resources, https://doi.org/10.1111/1755-0998.12737
Consensus sequences and primer information for 192 targeted amplicons, the Binary Alignment/Map (BAM) files and variant call format (VCF) files for all retained regions genotype files for 144 kelp rockfish species and an R Notebook documenting all statistical analyses.
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