Data from: Common coral cultivation techniques can produce abundant chimeras

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The prevalence and persistence of chimeras in aquaculture-based coral restoration efforts is poorly resolved. Aquaculture-propagated coral spat were settled on coral seeding devices and deployed in the field for approximately two years. Upon retrieval of seeding devices, triplicate tissue samples were collected from each of 114 coral colonies, and we undertook SNP analysis using reduced-representation sequencing. Coral samples (12-15 mg; total n = 373; n = 343 triplicates from 22-month-old survivors; n = 16 eggs; n = 14 pooled sperm samples; noting that 152 eggs were sent for sequencing but DNA quantity was insufficient to proceed for all but 16) were sent to Diversity Arrays Technology Pty Ltd. (DArT, Canberra, Australia) for DNA extraction and genotyping of single nucleotide polymorphisms (SNPs). Genomic DNA was extracted following DArT proprietary protocols (Kilian et al. 2012) and sequenced using DArTseqTM, a combination of genome complexity reduction methods followed by fragment sequencing with the Illumina HiSeq 2500 next-generation sequencing platforms (Kilian et al., 2012). Sequencing data were returned pre-processed by a DArT proprietary pipeline in a scored format (0 for homozygous reference allele, 1 for homozygous alternate allele, 2 for heterozygous). Software/equipment used to manipulate/analyse the data: SNP filtering and statistical analysis was conducted in R (version 2026.01.0+392). The R script is attached to this data record.