Jaime R. Alvarado Bremer

Life History and Stock Structure of Atlantic Bluefin Tuna (Thunnus thynnus)

Our understanding of the biology of Atlantic bluefin tuna (Thunnus thynnus) has increased profoundly in the last decade, and the progress is attributed to the development and application of a variety of novel tools. Here we provide a comprehensive examination of available data on the life history and stock structure of T. thynnus by re-examining current databases and literature and highlighting findings from recent studies using approaches such as archival tags and natural markers (e.g., genetics, otolith chemistry). The present review provides a detailed synthesis on the reproductive biology, feeding ecology, growth, mortality, migration, and stock structure of T. thynnus. In addition to characterizing key life history attributes and discussing stock-specific (east versus west) differences, the implication of trans-Atlantic movement and mixing are addressed. We also identify significant data needs that still exist and must be addressed to promote effective management and rapid recovery of T. thynnus populations.

Consequences of the historical demography on the global population structure of two highly migratory cosmopolitan marine fishes: the yellowfin tuna (Thunnus albacares) and the skipjack tuna (Katsuwonus pelamis)

BackgroundYellowfin and skipjack tuna are globally distributed in the worlds tropical and sub-tropical oceans. Since little, if any, migration of these fishes occurs between the Atlantic and Indo-Pacific Oceans, one might expect to see genetic differences between sub-populations in these ocean basins. However, yellowfin and skipjack tuna have extremely large population sizes. Thus, the rate of genetic drift should be slower than that observed for other tunas.ResultsLow levels of genetic differentiation were observed between Atlantic and Pacific samples of yellowfin tuna. In contrast, no genetic differentiation was observed between Atlantic and Pacific samples of skipjack tuna.ConclusionMuch lower levels of genetic differentiation were found among sub-populations of yellowfin tuna compared to those observed for other large tunas, probably due to the large population size of yellowfin tuna. Since skipjack tuna appear to have even larger population sizes, it is not surprising that no genetic differentiation was detected between Atlantic and Pacific samples of these fish.

Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L.)

Previous genetic studies of Atlantic swordfish (Xiphias gladius L.) revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs) within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise F ST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish.

Methodological streamlining of SNP discovery and genotyping via high-resolution melting analysis (HRMA) in non-model species

The exponential growth of genetic resources is fueled by continued advances in genomic technologies and the adoption of single nucleotide polymorphisms (SNPs) for population studies. Concomitant to these developments, there is growing need for rapid screening and subsequent genotyping of SNPs in non-model organisms. Here we provide a rapid and low-cost workflow utilizing high-resolution melting analysis (HRMA) for nuclear marker development and genotyping of 774 Atlantic and Mediterranean swordfish (Xiphias gladius) that is amendable to other species. Preliminary HRMA screening of amplicons (>290bp) for 10 nuclear loci revealed the presence of nucleotide polymorphisms, however, length and variability precluded diagnostic genotyping. Two variants of HRMA were therefore utilized to provide diagnostic genotyping assays. Short-amplicon HRMA (SA-HRMA), in which primers flank closely a SNP of interest, was identified as a low cost, rapid, closed-tube diagnostic genotyping assay that could distinguish between homozygous genotypes by ΔTm, and heterozygous genotypes by heteroduplex melting curve profiles. When the patterns of sequence variation were not suitable for SA-HRMA, unlabeled probe (UP)-HRMA was utilized. UP-HRMA has the advantage of being capable of genotyping multiple linked SNPs in a single closed-tube assay without Bayesian haplotype reconstruction, and can identify new SNPs while genotyping populations. Almost 37% of the SNPs genotyped via UP-HRMA were discovered while genotyping populations and not from preliminary screening. Analysis of swordfish in the North Atlantic (NA, n=419), South Atlantic (SA, n=296), and Mediterranean (MED, n=59) found no significant linkage disequilibrium. To assess whether deviations in HWE could be the result of genotyping error rather than population admixture only swordfish from reported spawning areas in the NA (n=49), MED (n=59), and SA (n=42) were analyzed and all loci were in Hardy-Weinberg equilibrium. Significant genetic differentiation (P<0.001) was identified among populations.