title: DNA barcoding for species assignment: the case of Mediterranean marine fishes.
abstract: BACKGROUND
  DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity.
  
  
  RESULTS
  A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%), most of them of high commercial relevance, suggesting possible cryptic species.
  
  
  CONCLUSIONS
  We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity.
authors.affiliation: Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal.
authors.forename: Monica
authors.initials: M
authors.lastname: Landi
authors.affiliation: Malta Centre for Fisheries Science (MCFS), Fort San Lucjan Marsaxlokk, Malta.
authors.forename: Mark
authors.initials: M
authors.lastname: Dimech
authors.affiliation: Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, Palermo, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Arculeo
authors.affiliation: Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, Palermo, Italy.
authors.forename: Girolama
authors.initials: G
authors.lastname: Biondo
authors.affiliation: Modelling and Management Fishery Resources Division (DIV-RP), Instituto Português do Mar e da Atmosfera, Lisboa, Portugal.
authors.forename: Rogelia
authors.initials: R
authors.lastname: Martins
authors.affiliation: Modelling and Management Fishery Resources Division (DIV-RP), Instituto Português do Mar e da Atmosfera, Lisboa, Portugal.
authors.forename: Miguel
authors.initials: M
authors.lastname: Carneiro
authors.affiliation: Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, United Kingdom.
authors.forename: Gary Robert
authors.initials: GR
authors.lastname: Carvalho
authors.affiliation: Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, Palermo, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Lo Brutto
authors.affiliation: Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal.
authors.forename: Filipe O
authors.initials: FO
authors.lastname: Costa
mesh_terms: D000818:Animals; D002965:Classification / Q000379:methods; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D005399:Fishes / Q000145:classification / Q000235:genetics*; D008522:Mediterranean Sea; D010802:Phylogeny; D013045:Species Specificity