Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next‐generation sequencing

Abstract

The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species' stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n = 326), and from these, 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (F = 0.008, p = .034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts.

Determining natal origin for improved management of Atlantic bluefin tuna

“…Despite the good performance of our assignment panel (89% and 98% of the samples with an assignment score above 80% were correctly assigned to the Gulf of Mexico or Mediterranean Sea, respectively) compared to previous endeavors (Puncher et al . ), there were samples that appeared to originate from a different region than that where they were collected, which was consistent with the pattern observed in the PCA of allele frequencies of our baseline samples (Figure b). Interestingly, the 95% confidence ellipses of each spawning component showed lower overlap as compared to those observed using otolith chemistry (Rooker et al .…”

“…Panel validation conducted on a reference set of samples excluded from SNP discovery or selection resulted in 81% and 83% of the Gulf of Mexico and Mediterranean Sea origin samples being correctly assigned, 10% and 2% incorrectly assigned, and 9% and 15% unassigned, respectively (Figure 2a). Despite the good performance of our assignment panel (89% and 98% of the samples with an assignment score above 80% were correctly assigned to the Gulf of Mexico or Mediterranean Sea, respectively) compared to previous endeavors (Puncher et al 2018), there were samples that appeared to originate from a different region than that where they were collected, which was consistent with the pattern observed in the PCA of allele frequencies of our baseline samples (Figure 2b). Interestingly, the 95% confidence ellipses of each spawning component showed lower overlap as compared to those observed using otolith chemistry (Rooker et al 2008(Rooker et al , 2014, suggesting that SNP markers have higher discriminant power for assigning ABFT origin.…”

The genetic population structure ofThunnus thynnus(Linnaeus, 1758) in the Mediterranean Sea, a controversial issue

“…The (Boustany et al, 2008;Carlsson et al, 2007;Puncher et al, 2018;Riccioni et al, 2017), in fact, it may represent a challenging task due to the difficulty of YOY sampling, which it also represents a …”

“…The hypothesis is that genetic signature might be difficult to detect in species with large population sizes and high gene flow due to allele homoplasy when using highly polymorphic loci (O'Reilly, Canino, Bailey, & Bentzen, 2004;) and neutral molecular markers (Gagnaire et al, 2015). For a species with high migratory potential such as ABFT the problem is the definition of population from the genetic point of view, since the individuals sampled at sea may correspond to a mixture of individuals from different reproductive units; this is the reason why sampling scheme of ABFT for genetic population analysis should include samples at larval stage, YOY or adults during spawning (Boustany et al, 2008;Puncher et al, 2018;Viñas et al, 2011). For a species with high migratory potential such as ABFT the problem is the definition of population from the genetic point of view, since the individuals sampled at sea may correspond to a mixture of individuals from different reproductive units; this is the reason why sampling scheme of ABFT for genetic population analysis should include samples at larval stage, YOY or adults during spawning (Boustany et al, 2008;Puncher et al, 2018;Viñas et al, 2011).…”

“…The high commercial value of this species has attracted so far deep investigations on several biological and life history issues. In particular, the study of the population structure, pivotal to management and conservation measures, has been approached through genetic studies (Alvarado-Bremer, Viñas, Mejuto, Ely, & Pla, 2005;Carlsson, McDowell, Carlsson, & Graves, 2007;Carlsson et al, 2004;Puncher et al, 2018;Riccioni, Landi, Ferrara, Milano, & Cariani, 2010;Riccioni et al, 2013;Vella et al, 2016;Viñas et al, 2011) and investigations on the migratory behaviour, using also modern techniques by otolith chemistry and electronic and natural tags such as parasites Rodríguez-Marín, Barreiro, Montero, & Carbonell, 2008;Rooker et al, 2008;Rooker, Secor, Zdanowicz, Metrio, & Relini, 2003).…”