TY - JOUR
T1 - No Population Genetic Structure of Skipjack Tuna (Katsuwonus pelamis) in the Tropical Western and Central Pacific Assessed Using Single Nucleotide Polymorphisms
AU - Anderson, Giulia
AU - Lal, Monal
AU - Stockwell, Brian
AU - Hampton, John
AU - Smith, Neville
AU - Nicol, Simon
AU - Rico, Ciro
N1 - Funding Information:
We gratefully acknowledge all the fisheries observers and research staff who collected tissue bank samples, and Simon Nicol and Valerie Allain for establishing the tissue bank; Sylvain Caillot, as an agent of SPC, for preparing Figure 1 ; Maria Ines Rico and Francois Roupsard for technical assistance with sample preparation; Anthony Beeching and Feleti P. Teo from the Western and Central Pacific Fisheries Commission (WCPFC) for facilitating and granting access to the Tissue Bank. Funding. The genomic analyses in this work were funded by The University of the South Pacific Strategic Research Themes intramural program project number F1006-R1001-71502-622. Funding for the tuna tissue bank is currently provided by the WCPFC as part of Project 35b.
Publisher Copyright:
© Copyright © 2020 Anderson, Lal, Stockwell, Hampton, Smith, Nicol and Rico.
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
PY - 2020/12/18
Y1 - 2020/12/18
N2 - Skipjack tuna (Katsuwonus pelamis) has historically been considered panmictic at the ocean basin scale because of the species’ life history and substantial absolute population size. However, recent advances in population genomics have enabled scientists to demonstrate population structure in other species that were likewise traditionally assumed to be panmictic. Accordingly, we used DArTseq, a proprietary platform of reduced-representation genome sequencing developed by Diversity Arrays Technology (DArTech) to genotype 222 skipjack tuna from 9 sample groups collected across 6 exclusive economic zones (EEZs) and over 6 years in the tropical Western and Central Pacific Ocean. This is one of the most fine-scale population genetics assessments of skipjack tuna to date. We found several statistically significant pairwise FST comparisons using purportedly neutral loci, but very little indication of structure based on observed and expected heterozygosity, effective population size, a Mantel test, AMOVA, numerous genetic clustering and population assignment tests, and exploration of correlation with oceanographic features. Significant pairwise FST values were often shallow and resulted in uncertainty about their biological significance. Furthermore, a test of the hypothesis that the geographic and temporal distribution of the potentially adaptive genetic diversity may depict cryptic fine scale structure using two different outlier detection methods, could not reject panmixia based on estimates of fixation indices and two clustering software. Our results support the presence of a single population of skipjack tuna in the tropical Western and Central Pacific Ocean, but highly recommend the expansion of the study area, in latitude, longitude, and seasonality, before drawing any global conclusions.
AB - Skipjack tuna (Katsuwonus pelamis) has historically been considered panmictic at the ocean basin scale because of the species’ life history and substantial absolute population size. However, recent advances in population genomics have enabled scientists to demonstrate population structure in other species that were likewise traditionally assumed to be panmictic. Accordingly, we used DArTseq, a proprietary platform of reduced-representation genome sequencing developed by Diversity Arrays Technology (DArTech) to genotype 222 skipjack tuna from 9 sample groups collected across 6 exclusive economic zones (EEZs) and over 6 years in the tropical Western and Central Pacific Ocean. This is one of the most fine-scale population genetics assessments of skipjack tuna to date. We found several statistically significant pairwise FST comparisons using purportedly neutral loci, but very little indication of structure based on observed and expected heterozygosity, effective population size, a Mantel test, AMOVA, numerous genetic clustering and population assignment tests, and exploration of correlation with oceanographic features. Significant pairwise FST values were often shallow and resulted in uncertainty about their biological significance. Furthermore, a test of the hypothesis that the geographic and temporal distribution of the potentially adaptive genetic diversity may depict cryptic fine scale structure using two different outlier detection methods, could not reject panmixia based on estimates of fixation indices and two clustering software. Our results support the presence of a single population of skipjack tuna in the tropical Western and Central Pacific Ocean, but highly recommend the expansion of the study area, in latitude, longitude, and seasonality, before drawing any global conclusions.
KW - DArTseq
KW - functional panmixia
KW - Katswonus pelamis
KW - population genetic structure
KW - skipjack tuna
KW - SNPs
KW - Western Pacific
UR - http://www.scopus.com/inward/record.url?scp=85099060434&partnerID=8YFLogxK
U2 - 10.3389/fmars.2020.570760
DO - 10.3389/fmars.2020.570760
M3 - Article
AN - SCOPUS:85099060434
SN - 2296-7745
VL - 7
SP - 1
EP - 16
JO - Frontiers in Marine Science
JF - Frontiers in Marine Science
M1 - 570760
ER -