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

Puncher GN, Arrizabalaga H, Alemany F, Cariani A, Oray IK, Karakulak FS, Basilone G, Cuttitta A, Mazzola S, Tinti F - PLoS ONE (2015)

Bottom Line: 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.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.Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods.

View Article: PubMed Central - PubMed

Affiliation: Dept. of Biological, Geological and Environmental Sciences / Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy.

ABSTRACT
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.

No MeSH data available.


Map of the Mediterranean Sea and surrounding area with three larvae sampling sites: A) Strait of Sicily, B) Ionian Sea and C) Levantine Sea.
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pone.0130407.g001: Map of the Mediterranean Sea and surrounding area with three larvae sampling sites: A) Strait of Sicily, B) Ionian Sea and C) Levantine Sea.

Mentions: Larval tows were performed by Istituto per l’Ambiente Marino Costero of the National Research Council of Italy (IAMC-CNR) in the waters off Sicily’s southern coast (35°30’N-38°90’N, 12°38’E-15°10’E; Fig 1[A]), on board the R/V “Urania”, during 17–21 July 2011 and 5–19 July 2012 using two Bongo nets with 40 and 90cm diameters equipped with 1 mm black mesh. Bongo nets were towed obliquely from the surface to 100 m and back to the surface at two knots. All larvae were preserved in 96% ethanol and transported to the laboratory where they were identified to family, genus or species level when possible; using various taxonomic keys [54–58]. A total of 88 larvae with a mean length of 4.9 ± 1.5 mm and provisionally identified as tunas were sent to the GenoDREAM laboratory at the University of Bologna for genetic barcoding. An additional 4 non-scombrid larvae were also provided as outliers.


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

Puncher GN, Arrizabalaga H, Alemany F, Cariani A, Oray IK, Karakulak FS, Basilone G, Cuttitta A, Mazzola S, Tinti F - PLoS ONE (2015)

Map of the Mediterranean Sea and surrounding area with three larvae sampling sites: A) Strait of Sicily, B) Ionian Sea and C) Levantine Sea.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493144&req=5

pone.0130407.g001: Map of the Mediterranean Sea and surrounding area with three larvae sampling sites: A) Strait of Sicily, B) Ionian Sea and C) Levantine Sea.
Mentions: Larval tows were performed by Istituto per l’Ambiente Marino Costero of the National Research Council of Italy (IAMC-CNR) in the waters off Sicily’s southern coast (35°30’N-38°90’N, 12°38’E-15°10’E; Fig 1[A]), on board the R/V “Urania”, during 17–21 July 2011 and 5–19 July 2012 using two Bongo nets with 40 and 90cm diameters equipped with 1 mm black mesh. Bongo nets were towed obliquely from the surface to 100 m and back to the surface at two knots. All larvae were preserved in 96% ethanol and transported to the laboratory where they were identified to family, genus or species level when possible; using various taxonomic keys [54–58]. A total of 88 larvae with a mean length of 4.9 ± 1.5 mm and provisionally identified as tunas were sent to the GenoDREAM laboratory at the University of Bologna for genetic barcoding. An additional 4 non-scombrid larvae were also provided as outliers.

Bottom Line: 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.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.Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods.

View Article: PubMed Central - PubMed

Affiliation: Dept. of Biological, Geological and Environmental Sciences / Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy.

ABSTRACT
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.

No MeSH data available.