BackgroundThe increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB for marine fish of Portugal.Methodology/Principal FindingsSpecimens (n = 659) representing 102 marine fish species were collected along the continental shelf of Portugal, morphologically identified and archived in a museum collection. Samples were sequenced at the barcode region of the cytochrome oxidase subunit I gene (COI-5P). Resultant DNA barcodes had average intra-specific and inter-specific Kimura-2-parameter distances (0.32% and 8.84%, respectively) within the range usually observed for marine fishes. All specimens were ranked in five different levels (A–E), according to the reliability of the match between their species identification and the respective diagnostic DNA barcodes. Grades A to E were attributed upon submission of individual specimen sequences to BOLD-IDS and inspection of the clustering pattern in the NJ tree generated. Overall, our study resulted in 73.5% of unambiguous species IDs (grade A), 7.8% taxonomically congruent barcode clusters within our dataset, but awaiting external confirmation (grade B), and 18.7% of species identifications with lower levels of reliability (grades C/E).Conclusion/SignificanceWe highlight the importance of implementing a system to rank barcode records in RLDB, in order to flag taxa in need of taxonomic revision, or reduce ambiguities of discordant data. With increasing DNA barcode records publicly available, this cross-validation system would provide a metric of relative accuracy of barcodes, while enabling the continuous revision and annotation required in taxonomic work.

BackgroundDNA 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.Methodology/Principal FindingsA 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.Conclusion/SignificanceWe 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.

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suMMARY: though whole otoliths are commonly adopted in age assignment of black scabbardfish, this study showed that sectioned otoliths are more appropriate because growth increments are more evident and ageing of larger specimens is easier. Vertebrae are not the most appropriate structure for ageing but, in the absence of otoliths, this structure may be useful in age assignment of this species. to verify possible differences between age and growth among specimens from the southern ne Atlantic, 1075 sectioned otoliths from specimens from mainland Portugal, 436 from Madeira and 107 from the Azores were analysed and the distribution of length-at-age obtained for each sex and region was determined. significant differences were obtained in the comparison of the distribution of length-at-age between Madeira, the mainland and the Azores. the von Bertalanffy growth model was applied to back-calculated mean length-at-age data from Madeira (L t = 1586 [1 -e -0.119(t+2.282) ] females; L t = 1461 [1 -e -0.146(t+1.441) ] males) and mainland (L t = 1354 [1 -e -0.170(t+2.040) ] females; L t = 1240 [1 -e -0.208(t+1.654) ] males), and significant differences in the growth equations were obtained. Furthermore, a regression tree model was used to investigate how growth is conditioned by reproduction. the results showed a clear separation between individuals from the two areas, both females and males from the mainland (non-reproductive individuals) being characterised by a lower gonadosomatic index and a lower age.Keywords: Aphanopus carbo, black scabbardfish, whole and sectioned otoliths, vertebrae, precision estimators, age and growth.ResuMen: Edad y crecimiento en el sable negro (AphAnopus cArbo Lowe, 1839) del sur de Atlántico nordeste. -A pesar de que los otolitos enteros son adoptados normalmente en lecturas de edad del sable negro, este estudio mostró que los otolitos seccionados son más apropiados porque los incrementos de crecimiento son más evidentes y facilita la asignación de edad en los peces de mayor talla. las vértebras no son las estructuras más apropiadas para asignar la edad del sable negro, pero en ausencia de otolitos, esta estructura puede resultar de utilidad en dicho proceso. Para verificar posibles diferencias entre la edad y el crecimiento de especimenes viviendo en el sur del Atlántico nordeste, 1075 otolitos seccionados de ejemplares de sable negro de Portugal continental, 436 de Madeira y 107 de Azores fueron analizados, y se obtuvieron las distribuciones de tallas por edad por sexo, en cada región. Fueron observadas diferencias significativas en la comparación de las distribuciones de talla por edad entre Madeira, continente y Azores. el modelo de crecimiento de von Bertalanffy fue aplicado a los datos retrocalculados de talla media por grupo de edad de Madeira (L t = 1586 [1 -e -0.119(t+2.282) ] hembras; L t = 1461 [1 -e -0.146(t+1.441) ] machos) y continente (L t = 1354 [1 -e -0.170(t+2.040) ] hembras; L t = 1240 [1 -e -0.208(t+1.654) ] machos), y fueran encontradas diferencias significativas en...

The study of the Portuguese marine ichthyofauna has a long historical tradition, rooted back in the 18th Century. Here we present an annotated checklist of the marine fishes from Portuguese waters, including the area encompassed by the proposed extension of the Portuguese continental shelf and the Economic Exclusive Zone (EEZ). The list is based on historical literature records and taxon occurrence data obtained from natural history collections, together with new revisions and occurrences. It comprises a total of 1191 species, distributed among 3 superclasses, 4 classes, 42 orders, 212 families and 617 genera. If considering only the EEZ and present territorial waters, this list represents an increase of 230 species (27.8%) and of 238 species (29.0%), when compared to the information available in FishBase (2012) and in the last checklist of marine and estuarine fishes of Portugal (1993), respectively. The order Perciformes shows the highest diversity, with 54 families, 162 genera and 299 species. Stomiidae (80 species), Myctophidae (71 species) and Macrouridae (37 species) are the richest families. From the listed species, 734 are present off mainland Portugal, 857 off the Azores and 766 off Madeira. Within the limits of the examined area, three species are reported for the first time in mainland Portugal and twenty-nine records are identified as doubtful. A total of 133 species have been recorded from the extended Portuguese continental shelf (2 off mainland Portugal, 117 off the Azores and 14 off Madeira), two of which are common to the Azores and Madeira extensions. Biogeographically, the Atlantic group is the most important (548 species – 46.01%), followed by the Lusitanian group (256 species – 21.49%), the African group (71 species – 5.96%), the Boreal group (34 species – 2.85%), the Mediterranean group (31 species – 2.60%), the Macaronesian group (21 species – 1.76%), the Atlantic/African group (19 species – 1.60%) and the Mediterranean/African and the Arctic groups, each with only 1 species (0.08%). Regarding the preferences for vertical habitat, the demersal fishes are the most important group (305 species – 25.61%), followed by the mesopelagic group (228 species – 19.14%), the bathypelagic group (164 species – 13.77%), the benthopelagic group (147 species – 12.34%), the bathydemersal group (115 species – 9.66%), the reef-associated group (88 species – 7.39%), the pelagic group (74 species – 6.21%), the epipelagic group (58 species – 4.87%) and 1 species (0.08%) of the benthic group. The oceanic habitat is the best represented group comprising 446 species (37.45%), followed by the shelf group (199 species – 16.71%), the slope group (164 species – 13.77%), the inner shelf group (89 species – 7.47%), the coastal group (70 species – 5.88%), the outer shelf group (29 species – 2.43%) and the oceanic/shelf group (7 species – 0.59%).