Assessment of the population structure and temporal changes in spatial dynamics and genetic characteristics of the Atlantic bluefin tuna under a fishery independent framework.

As a large and long-lived species with high economic value, restricted spawning areas and short spawning periods, the Atlantic bluefin tuna (BFT; Thunnus thynnus) is particularly susceptible to over-exploitation. Although BFT have been targeted by fisheries in the Mediterranean Sea for thousands of years, it has only been in these last decades that the exploitation rate has reached far beyond sustainable levels. An understanding of the population structure, spatial dynamics, exploitation rates and the environmental variables that affect BFT is crucial for the conservation of the species. The aims of this PhD project were 1) to assess the accuracy of larval identification methods, 2) determine the genetic structure of modern BFT populations, 3) assess the self-recruitment rate in the Gulf of Mexico and Mediterranean spawning areas, 4) estimate the immigration rate of BFT to feeding aggregations from the various spawning areas, and 5) develop tools capable of investigating the temporal stability of population structuring in the Mediterranean Sea. Several weaknesses in modern morphology-based taxonomy including demographic decline of expert taxonomists, flawed identification keys, reluctance of the taxonomic community to embrace advances in digital communications and a general scarcity of modern user-friendly materials are reviewed. Barcoding of scombrid larvae revealed important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. Using a Genotyping-by-Sequencing a panel of 95 SNPs was developed and used to characterize the population structuring of BFT and composition of adult feeding aggregations. Using novel molecular techniques, DNA was extracted from bluefin tuna vertebrae excavated from late iron age, ancient roman settlements Byzantine-era Constantinople and a 20th century collection. A second panel of 96 SNPs was developed to genotype historical and modern samples in order to elucidate changes in population structuring and allele frequencies of loci associated with selective traits

Molecular Identification of Atlantic Bluefin Tuna (Thunnus thynnus, Scombridae) Larvae and Development of a DNA Character-Based Identification Key for Mediterranean Scombrids

The Atlantic bluefin tuna, Thunnus thynnus, is a commercially important species that has been severely over-exploited in the recent past. Although the eastern Atlantic and Mediterranean stock is now showing signs of recovery, its current status remains very uncertain and as a consequence their recovery is dependent upon severe management informed by rigorous scientific research. Monitoring of early life history stages can inform decision makers about the health of the species based upon recruitment and survival rates. Misidentification of fish larvae and eggs can lead to inaccurate estimates of stock biomass and productivity which can trigger demands for increased quotas and unsound management conclusions. Herein we used a molecular approach employing mitochondrial and nuclear genes (CO1 and ITS1, respectively) to identify larvae (n = 188) collected from three spawning areas in the Mediterranean Sea by different institutions working with a regional fisheries management organization. Several techniques were used to analyze the genetic sequences (sequence alignments using search algorithms, neighbour joining trees, and a genetic character-based identification key) and an extensive comparison of the results is presented. During this process various inaccuracies in related publications and online databases were uncovered. Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology- based methods. While less than half of larvae provided were bluefin tuna, other dominant taxa were bullet tuna (Auxis rochei), albacore (Thunnus alalunga) and little tunny (Euthynnus alletteratus). We advocate an expansion of expertise for a new generation of morphology-based taxonomists, increased dialogue between morphology-based and molecular taxonomists and increased scrutiny of public sequence databases.Versión del editor4,411

Individual assignment of Atlantic bluefin tuna in the northwestern Atlantic Ocean using single nucleotide polymorphisms reveals an increasing proportion of migrants from the eastern Atlantic Ocean.

Identifying the origin of fish contained in a mixed fishery is critical for accurate stock assessments and the subsequent development of appropriate management strategies. Using a panel of 92 SNPs developed to differentiate Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning areas (Gulf of Mexico and Mediterranean Sea), we used individual assignment to determine composition of feeding aggregations in the northwestern Atlantic Ocean (Gulf of Maine, Bay of Fundy, Scotian Shelf, Gulf of St. Lawrence, coastal Newfoundland). Among the 3,163 individuals collected between 2004 and 2018, we found that among lower age groups (The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Unlocking the evolutionary history of the mighty bluefin tuna using novel paleogenetic techniques and ancient tuna remains

Using novel molecular techniques, DNA was extracted from Atlantic bluefin tuna vertebrae excavated from late Iron Age and ancient Roman settlements in coastal Iberia (Portugal and Spain, 4th-2nd century BC; n=23) and Byzantine-era Constantinople (4th-15th century AD; n=6), as well as vertebrae from the Massimo Sella archive located at the University of Bologna (Ionian, Thyrrhenian and Adriatic Seas, early 20th century; n=150). Comparisons have been made between the amount of DNA contained in each sample (measured via quantitative polymerase chain reactions), their age and the enviromental conditions which the bones have been exposed to. A high performance genotyping panel containing SNPs derived from two separate projects funded by the GBYP scientific programme has been designed for the purpose of genotyping all historical samples along with modern samples collected in the same geographic areas. Included in the panel are 76 SNPs with high similarity to a wide variety of genes associated with musculoskeletal system, development, metabolism, cellular function, osmoregulation and immune response. An additional 20 SNPs that provide significant discrimination between modern populations have been included in the panel

Species and origin of larvae identified using <i>CO1</i> and <i>ITS1</i> genetic markers, BLAST neighbour-joining reconstruction and character-based assignment.

<p>Species and origin of larvae identified using <i>CO1</i> and <i>ITS1</i> genetic markers, BLAST neighbour-joining reconstruction and character-based assignment.</p

Neighbour-joining phenogram of Mediterranean scombrid reference sequences clustered with number of unknown larvae in parentheses.

<p>The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref067" target="_blank">67</a>]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the tree. The evolutionary distances were computed using the Kimura 2-parameter model [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref065" target="_blank">65</a>] and are in the units of the number of base differences per site. The analysis involved 280 nucleotide sequences. All ambiguous positions were removed for each sequence pair. There were a total of 612 nucleotide positions in the final dataset.</p

Neighbour-joining phenogram of Mediterranean scombrid reference sequences clustered with number of unknown larvae in parentheses.

<p>The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref067" target="_blank">67</a>]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the tree. The evolutionary distances were computed using the p-distance method [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref066" target="_blank">66</a>] and are in the units of the number of base differences per site. The analysis involved 280 nucleotide sequences. All ambiguous positions were removed for each sequence pair. There were a total of 612 nucleotide positions in the final dataset.</p

Characteristic attributes for capable of distinguishing taxa of scombrids in the Mediterranean Sea.

<p>Position of each variable nucleotide is given in relation to 612bp alignment of all sequences. Diagnostic nucleotides at each locus are given in parentheses.</p><p>Characteristic attributes for capable of distinguishing taxa of scombrids in the Mediterranean Sea.</p

Neighbour-joining phenogram of reference sequences (including non-Mediterranean <i>Thunnus</i> species) clustered with number of unknown larvae in parentheses.

<p>The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref067" target="_blank">67</a>]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the tree. The evolutionary distances were computed using the p-distance method [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref066" target="_blank">66</a>] and are in the units of the number of base differences per site. The analysis involved 330 nucleotide sequences. All ambiguous positions were removed for each sequence pair. There were a total of 612 nucleotide positions in the final dataset.</p