Abstract:

This data set includes all metadata and National Center for Biotechnology Information Support Center (NCBI) Sequence Read Archive (SRA) information for 96 individuals of Cranchia scabra, Pyroteuthis margaritifera, and Vampyroteuthis infernalis targeted for analysis of population structure between the Gulf of Mexico and Bear Seamount, in the northwestern Atlantic Ocean.

Suggested Citation:

Timm, LE. 2019. Demultiplexed ddRADseq data for population genomic analysis of cephalopod species - Cranchia scabra, Pyroteuthis margaritifera, and Vampyroteuthis infernalis. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-05f6-th15

Publications:

Timm, L. E., Bracken-Grissom, H. D., Sosnowski, A., Breitbart, M., Vecchione, M., & Judkins, H. (2020). Population genomics of three deep-sea cephalopod species reveals connectivity between the Gulf of Mexico and northwestern Atlantic Ocean. Deep Sea Research Part I: Oceanographic Research Papers, 103222. doi:10.1016/j.dsr.2020.103222

Purpose:

These data were generated to analyze population dynamics in three species of cephalopods common to the mesopelagic Gulf of Mexico.

Data Parameters and Units:

The dataset contains DNA sequence data and includes: study, bioproject_accession, biosample_accession, Sample ID, Voucher ID, Species (Cranchia scabra, Pyroteuthis margaritifera, and Vampyroteuthis infernalis), isolate (Midwater cephalopod), Collection Date (DD-Mon-YY), Location (Atlantic Ocean: Gulf of Mexico, Atlantic Ocean: Bear Seamount), Latitude (decimal degrees), Longitude (decimal degrees), Depth (meters), isolation_source (Oceanic midwater), tissue (Mantle), collected_by (H. Judkins; M. Vecchione), identified_by (H. Judkins; M. Vecchione), 16S Accession, COI Accession, 28S Accession, Index, Barcode, Raw Reads, library_ID, title (ddRADseq of Vampyroteuthis infernalis, ddRADseq of Pyroteuthis margaritifera, ddRADseq of Cranchia scabra), library_strategy (RAD-Seq), library_source (GENOMIC), library_selection (Reduces Representation), library_layout (paired), platform (ILLUMINA), instrument_model (Illumina HiSeq 4000), design_description (ddRADseq; SphI+EcoRI; tight 275bp size selection on PippinPrep), filetype (fastq), and filenames. Note: In the rows 50-78 in the file GRIIDC_Cephs_Final.xlsx, the sample collection date is October 15-22, 2014.

Instruments:

Illumina HiSeq 4000

Individual Files: