Yellowfin tuna, Thunnus albacares, is one of the most important seafood commodities in the world. Despite its great biological and economic importance, conflicting evidence arises from classical genetic and tagging studies concerning the yellowfin tuna population structure at local and global oceanic scales. Access to more powerful and cost effective genetic tools would represent the first step towards resolving the population structure of yellowfin tuna across its distribution range. Using a panel of 939 neutral Single Nucleotide Polymorphisms (SNPs), and the most comprehensive data set of yellowfin samples available so far, we found genetic differentiation among the Atlantic, Indian and Pacific oceans. The genetic stock structure analysis carried out with 33 outlier SNPs, putatively under selection, identified discrete populations within the Pacific Ocean and, for the first time, also within the Atlantic Ocean. Stock assessment approaches that consider genetic differences at neutral and adaptive genomic loci should be routinely implemented to check the status of the yellowfin tuna, prevent illegal trade, and develop more sustainable management measures.

/pdf/the-population-genomics-of-yellowfin-tuna-thunnus-albacares-1wnosu17ke.pdf

The population genomics of yellowfin tuna (Thunnus albacares) at global geographic scale challenges current stock delineation.

Isolength restriction site-associated DNA (isoRAD) sequencing is a very simple but powerful approach that was originally developed for genome-wide genotyping at minimal labor and cost, and it has recently extended its applicability to allow quantification of DNA methylation levels. The isoRAD method is distinct from other genotyping-by-sequencing (GBS) methods because of its use of special restriction enzymes to produce isolength tags (32-36 bp), and sequencing of these uniform tags can bring many benefits. However, the relatively short tags produced by the original protocol are mostly suited to single-end (SE) sequencing (36-50 bp), and therefore they cannot efficiently match the gradually increased sequencing capacity of next-generation sequencing (NGS) platforms. To address this issue, we describe an advanced protocol that allows the preparation of five concatenated isoRAD tags for Illumina paired-end (PE) sequencing (100-150 bp). The configuration of the five concatenated tags is highly flexible, and can be defined by users to work with a desired combination of samples and/or restriction enzymes to suit specific research purposes. In comparison with the original protocol, the advanced protocol has an additional digestion and ligation step, and library preparation can be completed in ∼8 h.

Serial sequencing of isolength RAD tags for cost-efficient genome-wide profiling of genetic and epigenetic variations

The red swamp crayfish (Procambarus clarkii) is one of the most economically important farmed aquatic species in China. However, it is also a famous invasive species in the world. This invasive species was dispersed most via human activities including intentional or unintentional carry in China. Thus, P. clarkii naturally distributed in China provides us a desirable mode to investigate the genetic structure of an invasive species dispersed mainly by human-mediated factors. To reveal the impact of human-mediated dispersal on genetic structure of P. clarkii in China, a total of 22,043 genome-wide SNPs were obtained from approximately 7.4 billion raw reads using 2b-RAD technique in this study. An evident pattern of population genetic structure and the asymmetrical migrational rates between different regions were observed with 22 populations based on these SNPs. This study provide a better understanding of the population genetic structure and demographic history of P. clarkii populations in China, inferring that anthropogenic factors (aquaculture or by accident) and ecological factors (e.g., complicated topography and climatic environment), as well as its special biological traits could account for the current population structure pattern and dispersal history of P. clarkii.

/pdf/characterization-of-population-genetic-structure-of-red-50386g7pfr.pdf

Characterization of Population Genetic Structure of red swamp crayfish, Procambarus clarkii, in China.

Yellowfin tuna (Thunnus albacares; YFT) is an apex marine predator inhabiting tropical and sub-tropical pelagic waters. It supports the second largest tuna fishery in the world. Here, we review the available literature on YFT to provide a detailed overview of the current knowledge of its biology, ecology, fisheries status, stock structure and management, at global scale. YFT are characterized by several peculiar anatomical and physiological traits that allow them to survive in the oligotrophic waters of the pelagic realm. They are opportunistic feeders, which allows fast growth and high reproductive outputs. Globally, YFT fisheries have expanded over the last century, progressively moving from coastal areas into the majority of sub-tropical and tropical waters. This expansion has led to a rapid increase in global commercial landings, which are predominantly harvested by industrial longline and purse seine fleets. For management purposes, YFT is divided into four stocks, each of which is currently managed by a separate tuna Regional Fisheries Management Organization. Our current understanding of YFT stock structure is, however, still uncertain, with conflicting evidence arising from genetic and tagging studies. There is, moreover, little information about their complex life-history traits or the interactions of YFT populations with spatio-temporally variable oceanographic conditions currently considered in stock assessments. What information is available, is often conflicting at the global scale. Finally, we suggest future research directions to manage this valuable resource with more biological realism and more sustainable procedures.

Putting all the pieces together: integrating current knowledge of the biology, ecology, fisheries status, stock structure and management of yellowfin tuna (Thunnus albacares)

The Pacific bluefin tuna, Thunnus orientalis, is a highly migratory species that is widely distributed in the North Pacific Ocean. Like other marine species, T. orientalis has no external sexual dimorphism; thus, identifying sex-specific variants from whole genome sequence data is a useful approach to develop an effective sex identification method. Here, we report an improved draft genome of T. orientalis and male-specific DNA markers. Combining PacBio long reads and Illumina short reads sufficiently improved genome assembly, with a 38-fold increase in scaffold contiguity (to 444 scaffolds) compared to the first published draft genome. Through analysing re-sequence data of 15 males and 16 females, 250 male-specific SNPs were identified from more than 30 million polymorphisms. All male-specific variants were male-heterozygous, suggesting that T. orientalis has a male heterogametic sex-determination system. The largest linkage disequilibrium block (3,174 bp on scaffold_064) contained 51 male-specific variants. PCR primers and a PCR-based sex identification assay were developed using these male-specific variants. The sex of 115 individuals (56 males and 59 females; sex was diagnosed by visual examination of the gonads) was identified with high accuracy using the assay. This easy, accurate, and practical technique facilitates the control of sex ratios in tuna farms. Furthermore, this method could be used to estimate the sex ratio and/or the sex-specific growth rate of natural populations.

/pdf/improvement-of-the-pacific-bluefin-tuna-thunnus-orientalis-3xqtv9f4je.pdf

Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers.

https://www.tamug.edu/rooker/pdf/Pecoraro_etal_2016.pdf

Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (Thunnus albacares).

pdf/quantifying-the-accuracy-of-shark-bycatch-estimations-in-3dqru1kgnq.pdf

Quantifying the accuracy of shark bycatch estimations in tuna purse seine fisheries

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Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (Thunnus albacares).

Quantifying the accuracy of shark bycatch estimations in tuna purse seine fisheries