Note: This metadata section includes description of a related dataset (sanger-sequenced a mitochondrial locus (COI) that was generated as part of this study. See "Related Datasets" section for metadata and NCBI Genbank accession identifiers in that dataset.

Diopatra cuprea were sampled from 19 locations on the United States east coast, from Duxbury MA (the genus’ northern limit) to St. Teresa Beach FL. Tubes were excavated with a shovel, the worm removed, and antennae clipped off and preserved in 95% ethanol for later DNA extraction. Twenty-five randomly selected individuals from each population were extracted for DNA, with the exception of Broad River Estuary populations from which 20 and 22 samples were collected. Approximately 25 mg of tissue wet weight was rinsed of ethanol with deionized water and extracted with the Qiagen DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) following the manufacturer’s extraction protocol. Extractions were screened with 1.5% agarose gels and DNA was quantified using a NanoDrop 200 spectrophotometer (Thermo Scientific, Waltham, MA, USA) to obtain concentration values and purity.

A portion of the COI gene was then PCR amplified using the protocol in Berke, et al. (2010, doi:10.1111/j.1466-8238.2009.00509.x). These were cleaned with an EXO-SAP-IT protocol and sent for Sanger sequencing with these same primers at a private company.

Double digest restriction-associated DNA sequencing (or ddRADSeq) library was prepared on 312 samples following the protocol in Parchman et al. (2012,doi: 10.1111/j.1365-294X.2012.05513.x). Briefly, we digested gDNA with two restriction enzymes, EcoRI and MseI, and ligated adaptors containing unique 8 to 10 bp barcodes to the digested DNA of each individual. The products were then PCR amplified in two independent reactions with standard Illumina primers. All amplicons were pooled and shipped to the University of Texas Genomic Sequencing and Analysis Facility or the Tufts University Core Facility, which used Pippin Prep^® to isolate the 300–450 bp fraction. This fraction was then single-read sequenced (100 basepairs) with Illumina HiSeq 4000 machine. FASTQ sequences were demultiplexed using custom Unix code. 510 million reads contained barcode sequence (range = 39 to 6.8 million (M) reads per sample; mean = 1.6 M reads), and 234 individuals had at least 200 K reads that were analyzed.

FASTQ files were uploaded to the NCBI's Sequence Read Archive (SRA) that were generated as described above. See the "Related Datasets" section for SRA metadata and accessions.

Organism identifier (Life Science Identifier (LSID)):
Diopatra cuprea, Bosc, 1802, LSID(urn:lsid:marinespecies.org:taxname:157339)