Abstract
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.
Highlights
As cosmopolitan fishes with large absolute population sizes and a remarkable propensity for trans-oceanic movement, tunas fit the life history of species that are not expected to show population structuring (Funk et al, 2012)
Subsequent quality filtering for loci identified 1,373 neutral loci using the primary dataset, which consists of nine sample groups taken in the Federated States of Micronesia in 2008 (FM08), the Gilbert Islands of Kiribati in 2009 (GL09), Indonesia in 2009 (ID09), the Marshall Islands in 2009 (MH09), in Papua New Guinea in 2007, 2009, 2011, and 2012 (PG07, PG09, PG11, and PG12, respectively), and in Palau in 2008 (PW08)
Number of neutral loci remaining after each quality-filtering step for primary dataset is listed in Table 2, while results for auxiliary datasets are presented in Supplementary Table S2
Summary
As cosmopolitan fishes with large absolute population sizes and a remarkable propensity for trans-oceanic movement, tunas fit the life history of species that are not expected to show population structuring (Funk et al, 2012). Growing evidence suggests that yellowfin tuna (Thunnus albacares) has the potential for genetic population structuring (Dammannagoda et al, 2008; Kunal et al, 2013; Grewe et al, 2015; Pecoraro et al, 2016), given their capacity for precise homing using a geomagnetic sensory organ (Walker et al, 1984), stronger than expected regional fidelity (Schaefer et al, 2007), and long-term coordinated movements of small groups (Klimley and Holloway, 1999) that may represent co-dispersal of kin (Anderson et al, 2019). There is only limited discussion about the potential for population structure in skipjack tuna (Katsuwonus pelamis), and little evidence to merit its expectation
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