Abstract:

Genetic diversity within species is the foundation of evolutionary adaptation and resilience to environmental change, and also provides an overview of population genetic health. Genetic diversity can be reduced by anthropogenic events causing large population reductions. We estimated the genetic diversity of select deep-sea fishes (Family Myctophidae: Ceratoscopelus warmingii, Diaphus dumerilii, Lepidophanes guentheri) by generating and analyzing DNA sequences and genome-scale single nucleotide polymorphisms. These datasets were generated from fishes collected in the Atlantic and northern Gulf of Mexico on DEEPEND cruises (DP01 through DP04) conducted from July 2011 to August 2016.

Suggested Citation:

Bernard, Andrea; Finnegan, Kimberly; Eytan, Ron; Shivji, Mahmood. 2020. Genetic diversity of deep-sea fishes (Family: Myctophidae) collected aboard multiple cruises in the Atlantic and Gulf of Mexico from 2011-07-12 to 2016-08-10. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-67wg-mz19

Purpose:

To assess the temporal genetic diversity of deep-sea fishes.

Data Parameters and Units:

The dataset contains DEEPEND Myctophid Genetic Diversity Data Spreadsheet Name "RADSeq_myctophid_Summary" Spreadsheet Tab: Sample Data Sample ID#: Genetic sample identification number; Field ID#: Additional field identification number if different than sample ID; Phylum: Taxonomic phylum of specimen; Class: Taxonomic phylum name of specimen; Order: Taxonomic order name of specimen; Family: Taxonomic family name of specimen; Genus: Taxonomic genus name of specimen; Species: Taxonomic species name of specimen; COI GenBank Accession #: National Center for Biotechnology Information (NCBI) record number or identifier for the sample’s DNA barcode sequence of the mitochondrial protein-coding gene Cytochrome c oxidase subunit I where available; File Name: Raw fastq file name that contains specimen data; Illumina Index: Illumina library identifier sequence; Adapter Sequence: Sample adapter barcode sequence; Collection Date: Specimen collection date; Start Lat: Starting latitude of sample collection trawl in decimal degrees; Start Lon: Starting longitude of sample collection trawl in decimal degrees; Notes: Any additional relevant information pertaining to the sample; Spreadsheet tab: Adapter Sequences Adapter Name: Name of adapter sequence used; Adapter Sequence: Nucleotide sequence of adapter used (5’-3’); Reference: Scientific citation for adapter sequence; Spreadsheet Tab: PCR primers Index Name: Name of Illumina Index; Index Sequence: Nucleotide sequence of index (5’-3’); Reference: Scientific citation for Illumina index sequence;

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

Individual Files: