Dataset Submitted

ddRADseq data for population genomic analyses of deep-sea fish species

Authors: Pedro A. Peres; Heather Bracken-Grissom
Identified On: Sep 08 2021 14:04 UTC
DOI: https://doi.org/10.7266/58Y0D6NM
UDI: NO.x959.000:0001
Project Information

Funded By:
National Oceanic and Atmospheric Administration

Research Group:
DEEPEND/RESTORE Trends and drivers of faunal abundance of the offshore Gulf of Mexico

Point of Contact

Pedro Peres
Florida International University
pedro.peres27@gmail.com

Data Collection Period
2018-07-20
to
2023-05-11
Theme keywords

ddRAD-seq, Myctophidae, Mesopelagic

Abstract:

This dataset includes fastq files of the raw data resulted from Illumina sequencing of ddRAD-seq libraries and individual sequencing files resulted from libraries demultiplexing for deep-sea fish. The dataset contains samples from research cruises DP06, DP07, and DP09.

Suggested Citation:

Pedro A. Peres; Heather Bracken-Grissom. ddRADseq data for population genomic analyses of deep-sea fish species. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/58Y0D6NM

Purpose:

This dataset was used to investigate temporal changes in genomic diversity of the lanternfishes (Myctophidae) Diaphus dumerilii, Ceratoscopelus warmingii, and Lepidophanes guentheri

Data Parameters and Units:

Spreadsheet Name "ddRADSeq_dp07-dp08-dp09_fish" Voucher#: Voucher number from Florida International University Fish Collection (FIFC) of specimen; Phylum: Taxonomic phylum of specimen; Class: Taxonomic phylum name of specimen; Order: Taxonomic order name of specimen; Family: Taxonomic family name of specimen; Species: Taxonomic species name of specimen; Cruise ID: DEEPEND|RESTORE cruise during which specimen was collected; Depth (m): Depth in meters in which specimen was collected; Latitude: Starting latitude of sample collection trawl in decimal degrees; Longitude: Starting longitude of sample collection trawl in decimal degrees; Index: Illumina library identifier sequence; Barcode: Sample adapter barcode sequence; File Name: Raw fastq file name that contains specimen data;

Methods:

Restriction-site associated DNA sequencing of samples was performed as outlined in Peterson et al. (2012). PLoS ONE 7(5):e37135.

Provenance and Historical References:

Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. PLoS ONE, 7(5), e37135. doi:10.1371/journal.pone.0037135