Dataset: Population genomics (RADseq-derived SNP genotypes) of the amphipod Ampithoe valida from collections in Japan, North America, and South America in 2015

Individuals were collected by hand from eelgrass beds and from algae (primarily Ulva lactuca, Gracilaria vermiculophylla and Fucus vesiculosus) on docks, mudflats, and sandy/rocky shores. They were immediately euthanized and stored in 95% ethanol until use. Genomic DNA was extracted from amphipod tissue using either a Qiagen DNeasy spin-column kit following the manufacturer’s protocol for animal tissues or a Macherey-Nagel Nucleospin Tissue kit. For individuals that were less than approximately one centimeter in length or severely degraded, the entire individual was used; otherwise only half of the individual was used in the extraction. We genotyped single nucleotide polymorphisms (SNPs) using a restriction-site associated genotype-by-sequencing on DNA extractions from 350 individuals. Eleven individuals sampled for mtDNA, but not included in the RADseq library did not have a sufficient amount of DNA extraction product to be included. Genomic DNA was digested with two restriction enzymes, EcoRI and MseI. Pooled fragments for each individual were ligated with customized adaptor sequences containing the Illumina adaptors and primer sequences and unique 8–10 bp barcodes to allow for the in silico identification of individuals. DNA fragments were amplified by PCR twice and size selected (300–450 bp) using a Blue Pippin. The final library was sequenced using a single-end 100 bp protocol within a lane of an Illumina HiSeq 2500 sequencer at the University of Texas at Austin Genome Sequencing and Analysis Facility (GSAF).

Organism name, Life Science Identifier (LSID):
 Ampithoe valida, urn:lsid:marinespecies.org:taxname:102005