BackgroundDNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. Despite extensive taxonomic studies, for a variety of reasons the identification of fishes can be problematic, even for experts. DNA barcoding is proving to be a useful tool in this context. However, its broad application is impeded by the need to construct a comprehensive reference sequence library for all fish species. Here, we make a regional contribution to this grand challenge by calibrating the species discrimination efficiency of barcoding among 125 Argentine fish species, representing nearly one third of the known fauna, and examine the utility of these data to address several key taxonomic uncertainties pertaining to species in this region.Methodology/Principal FindingsSpecimens were collected and morphologically identified during crusies conducted between 2005 and 2008. The standard BARCODE fragment of COI was amplified and bi-directionally sequenced from 577 specimens (mean of 5 specimens/species), and all specimens and sequence data were archived and interrogated using analytical tools available on the Barcode of Life Data System (BOLD; www.barcodinglife.org). Nearly all species exhibited discrete clusters of closely related haplogroups which permitted the discrimination of 95% of the species (i.e. 119/125) examined while cases of shared haplotypes were detected among just three species-pairs. Notably, barcoding aided the identification of a new species of skate, Dipturus argentinensis, permitted the recognition of Genypterus brasiliensis as a valid species and questions the generic assignment of Paralichthys isosceles.Conclusions/SignificanceThis study constitutes a significant contribution to the global barcode reference sequence library for fishes and demonstrates the utility of barcoding for regional species identification. As an independent assessment of alpha taxonomy, barcodes provide robust support for most morphologically based taxon concepts and also highlight key areas of taxonomic uncertainty worthy of reappraisal.

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Systematics derived from morphological characters often does not correspond with the evolutionary processes underlying the divergence within a group of organisms. In the family Mugilidae (Teleostei) morphological similarities have resulted in inconsistencies between taxonomy and phylogeny among its species, and particularly for the genera Mugil, Liza and Chelon where both intrageneric and intergeneric phylogenetic clarifications are needed.

The fish fauna of the Pampa Plain, the southernmost distribution range of many Neotropical species, was barcoded in this study. COI sequences were analysed by means of distance (K2P/NJ) and character-based (ML) models, as well as the Barcode Index Number (BIN). K2P/NJ analysis was able to discriminate among all previously identified species while also revealing the likely occurrence of two cryptic species that were further supported by BIN and ML analyses. On the other hand, both BIN and ML were not able to discriminate between two species of Rineloricaria. Despite the small genetic divergence between A. cf. pampa and A. eigenmanniorum, a tight array of haplotypes was observed for each species in both the distance and character-based methods. Deep intraspecific divergences were detected in Cnesterodon decemmaculatus (5%) and Salminus brasiliensis (6%). For Salminus brasiliensis, these findings were further supported by character-based (ML) evidence and meristic and morphological data. Our results also showed that Pampa Plain representatives of Salminus brasiliensis, Rhamdia quelen, Hoplias malabaricus, Synbranchus marmoratus, Australoheros facetus, Oligosarcus jenynsii and Corydoras paleatus differed by more than 3% from their conspecifics from other parts of South America. Overall, this study was able to highlight the likely occurrence of a cryptic species in Salminus brasiliensis and also illustrate the strong geographical structure in the COI sequence composition of seven fish species from South America.

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Mar Chiquita, an irregularly shaped brackish-water coastal lagoon, is located in the Buenos Aires province of Argentina and considered since 1996 by the Coordination Council of the Man and Biosphere Program of UNESCO as a World Reserve of Biosphere. The present paper aims to study both the spatial and temporal variation of fish composition in this coastal lagoon and the influence of some environmental variables on the relative abundance of the main fish species. Monthly sampling surveys over a two-year period in three different areas were conducted, using a beach-seine net and three monofilament-gill nets with different mesh size. Twenty-eight species belonging to four bio-ecological categories were identified, five of them are new records for Mar Chiquita fish community. The correspondence analysis showed strong relationships between high salinity range and the abundance of Brevoortia aurea, Cynoscion guatucupa and Pomatomus saltatrix. Conversely, low salinity range corresponded to high abundance of Mugil platanus and Odontesthes argentinensis. High temperatures were corresponded with abundance of Micropogonias furnieri and Brevoortia aurea. In contrast, high abundance of both Odontesthes argentinensis and Oligosarcus jenynsii were corresponded to low temperatures. Brevoortia aurea, Mugil platanus and Odontesthes argentinensis were the most abundant species, representing more than 80% of the total capture. The group of estuarine-nondependent-marine fish presented the highest species richness. Estuarine-dependent-marine species presented for both juveniles and adults specimens the highest abundance values.

With an estimate of around 9,000 species, the Neotropical region hosts the greatest diversity of freshwater fishes of the world. Genetic surveys have the potential to unravel isolated and unique lineages and may result in the identification of undescribed species, accelerating the cataloguing of extant biodiversity. In this paper, molecular diversity within the valuable and widespread Neotropical genus Hoplias was assessed by means of DNA Barcoding. The geographic coverage spanned 40 degrees of latitude from French Guiana to Argentina. Our analyses revealed 22 mitochondrial lineages fully supported by means of Barcode Index Number, Automatic Barcode Gap Discovery and phylogenetic analyses. This mtDNA survey revealed the existence of 15 fully supported mitochondrial lineages within the once considered to be the continentally distributed H. malabaricus. Only four of them are currently described as valid species however, leaving 11 mitochondrial lineages currently “masked” within this species complex. Mean genetic divergence was 13.1%. Barcoding gap analysis discriminated 20 out of the 22 lineages tested. Phylogenetic analyses showed that all taxonomically recognized species form monophyletic groups. Hoplias malabaricus sensu stricto clustered within a large clade, excluding the representatives of the La Plata River Basin. In the H. lacerdae group, all species but H. curupira showed a cohesive match between taxonomic and molecular identification. Two different genetic lineages were recovered for H. aimara. Given the unexpected hidden mitochondrial diversity within H. malabaricus, the COI sequence composition of specimens from Suriname (the type locality), identified as H. malabaricus sensu stricto, is of major importance.

Atherinopsidae are widespread freshwater and shallow marine fish with singular economic importance. Morphological, genetical and life cycles differences between marine and estuarine populations were already reported in this family, suggesting ongoing speciation. Also, coexistence and interbreeding between closely related species were documented. The aim of this study was to infer boundaries among: (A) Odontesthes bonariensis and O. argentinensis at species level, and intermediate morphs; (B) the population of O. argentinensis of Mar Chiquita Lagoon and its marine conspecifics. To achieve this, we integrated, meristic, Geometrics Morphometrics and DNA Barcode approaches. Four groups were discriminated and subsequently characterized according to their morphological traits, shape and meristic characters. No shared haplotypes between O. bonariensis and O. argentinensis were found. Significative-meristic and body shape differences between the Mar Chiquita and marine individuals of O. argentinensis were found, suggesting they behave as well differentiated populations, or even incipient ecological species. The fact that the Odontesthes morphotypes shared haplotypes with both, O. argentinensis and O. bonariensis, but also possess meristic and morphometric distinctive traits open new questions related to the origin of this morphogroup.