DOI: 10.5061/dryad.qrfj6q5wj
title: Data from: Lack of genetic differentiation in yellowfin tuna has conservation implications in the Eastern Pacific Ocean

description: Yellowfin tuna, Thunnus albacares, is an important global fishery and of
 particular importance in the Eastern Pacific Ocean (EPO). According to the
 2019 Inter-American Tropical Tuna Commission (IATTC) assessment, yellowfin
 tuna within the EPO is a single stock, and is being managed as one stock.
 However, previous studies indicate site fidelity, or limited home ranges,
 of yellowfin tuna which suggests the potential for multiple yellowfin tuna
 stocks within the EPO, which was supported by a population genetic study
 using microsatellites. If numerous stocks are present, management at the
 wrong spatial scales could cause the loss of minor yellowfin tuna
 populations in the EPO. In this study we used double digestion RADseq to
 assess the genetic structure of yellowfin tuna in the EPO. A total of 164
 yellowfin tuna from Cabo San Lucas, México, and the Galápagos Islands and
 Santa Elena, Ecuador, were analysed using 18,011 single nucleotide
 polymorphisms. Limited genetic differentiation (FST = 0.00058–0.00328)
 observed among the sampling locations (México, Ecuador, Peru, and within
 Ecuador) is consistent with presence of a single yellowfin tuna population
 within the EPO. Our findings are consistent with the IATTC assessment and
 provide further evidence of the need for transboundary cooperation for the
 successful management of this important fishery throughout the EPO.
description: # Data from: Lack of genetic differentiation in yellowfin tuna has
 conservation implications in the Eastern Pacific Ocean Access this dataset
 on Dryad: Dataset DOI link This dataset contains raw high-throughput
 sequencing data generated for the study "Lack of genetic
 differentiation in yellowfin tuna has conservation implications in the
 Eastern Pacific Ocean", published in PLOS ONE
 ([https://doi.org/10.1371/journal.pone.0272713](https://doi.org/10.1371/journal.pone.0272713)). The data consist of unprocessed sequencing reads used as the basis for the population genetic analyses reported in the article. --- ## Description of the data and file structure This dataset consists of gzipped FASTQ files only. ## FASTQ files A collection of gzipped FASTQ files (.FASTQ.gz), spanning IDs **1424793–1424946**. The numeric IDs are not continuous and there are breaks in the sequence. This is expected, as the identifiers reflect sequencing facility–assigned file or library IDs rather than a strictly sequential series. The file manifest in this Dryad submission (the complete list of uploaded FASTQ files) represents the full and verified set of files included. Each FASTQ file contains raw sequencing reads generated from a single sequencing library. Files follow the standard FASTQ format, in which each read is represented by four lines: a read identifier, the nucleotide sequence, a separator line, and Phred-scaled quality scores. The FASTQ files contain raw, unfiltered sequencing output. No quality trimming, adapter removal, alignment, or variant calling has been applied. Sequencing artifacts and low-quality reads may be present. There are no custom missing-data codes or abbreviations beyond standard FASTQ conventions. The submission contains **98 gzipped FASTQ files** in total. Downstream bioinformatic processing and population genetic analyses derived from these data are described in the associated publication. **MD5SUMS**\ This file contains MD5 checksums for all FASTQ files included in the submission and is provided to allow users to verify file integrity after download. The checksums were generated at the time of data preparation and do not represent additional processed data or analysis outputs. --- ## Sharing/Access information Links to other publicly accessible locations of the data: * Not applicable Data was derived from the following sources: * Muñoz-Abril, L. et al. (2022). Lack of genetic differentiation in yellowfin tuna has conservation implications in the Eastern Pacific Ocean. PLOS ONE. [https://doi.org/10.1371/journal.pone.0272713](https://doi.org/10.1371/journal.pone.0272713) --- ## Code/Software No code or software files are included in this Dryad submission. Bioinformatic processing and population genetic analyses were conducted outside of Dryad and are described in the associated publication.