DNA barcodes discriminate freshwater fishes from the Paraíba do Sul River Basin, São Paulo, Brazil

Abstract

Background and aims: Considering the promising use of DNA barcoding for species identification, the importance of the freshwater fish fauna of the Paraíba do Sul River Basin, and its advanced stage of degradation, the present study evaluated the effectiveness of DNA barcoding to identify the fish species in this basin. Materials and methods: A total of 295 specimens representing 58 species belonging to 40 genera, 17 families, and 5 orders were sequenced. Results: The DNA barcodes discriminated all species analyzed without ambiguity. The results showed a pronounced difference between conspecific and congeneric pair-wise sequence comparisons, demonstrating the existence of a "barcode gap" for the species analyzed. The nearest-neighbor distance analysis showed only three cases with Kimura two-parameter values lower than a 2% divergence threshold. However, the patterns of divergence observed in each case remained sufficient to discriminate each species, revealing the accuracy of DNA barcoding even cases with relatively low genetic divergence. At the other extreme, three species displayed high genetic sequence divergence among conspecifics. For two cases, Characidium alipioi and Geophagus proximus, barcoding proved effective at flagging possible new species. For another case, Astyanax bimaculatus, the use of DNA barcoding of the comparison of shared freshwater fish fauna between different basins revealed itself as highly useful in disclosing that the previously identified A. bimaculatus "cluster A" probably represents the species Astyanax altiparanae. Conclusion: The present study is among the first to assess the efficiency of barcoding for the Brazilian freshwater fishes. The results demonstrate the utility of barcoding to identify the fauna from this basin, contribute to an enhanced understanding of the differentiation among species, and to help flag the presence of overlooked species.

Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River

“…Originally, Hebert et al (2003) proposed that a divergence of 2-3% in the DNA barcode represents the threshold for the definition of species status in a lot of taxonomic groups. Several studies with fish groups have documented a larger range of genetic divergence (8-10%) between congeneric species (Ward et al, 2005(Ward et al, , 2009Hubert et al, 2008;Lara et al, 2010;De Carvalho et al, 2011;Pereira et al, 2011). Similar levels of divergence were found herein among Hoplias malabaricus haplogroups, what can be interpreted as indicative of speciation event.…”

Knodus moenkhausii (Characiformes: Characidae): one fish species, three hydrographic basins - a natural or anthropogenic phenomenon?

“…All specimens of K. moenkhausii from the three among the three hydrographic basins and the haplotypes of both genes were shared among the three hydrographic basins revealing a complete lack of population structure. The genetic distance from congeners ranged from 8.6% to 11.0 and 9.3% to 11.0% for COI and CytB genes, respectively: values consistent with those found in other DNA barcoding surveys that showed average genetic distances between congeners ranging from 7% to 11% in more than 90% of comparisons [28,30,31,47,48]. Similarly, these other studies report genetic divergences within species of about 0.5%, a similar value to that found in the present survey.…”

“…org), and in some studies the successful identification rate can exceed 90% [30,31]. The GYMC analysis [32] uses maximum-likelihood statistics and a time-calibrated gene tree to delimit species using sequences from a single locus.…”

Pimelodus maculatus (Siluriformes, Pimelodidae): complete mtDNA sequence of an economically important fish from the São Francisco river basin

“…Several genetic studies of partial mitochondrial and nuclear regions of P. maculatus have found a high degree of genetic diversity among populations (Garcia & Moreira Filho 2005;Paiva & Kalapothakis 2008;Carvalho et al 2011;Lundberg et al 2011;Pereira et al 2011;Ribolli et al 2012;Ferreira et al 2014;Frantine-Silva et al 2015). Here, we provide the first description of the complete mitochondrial DNA (mtDNA) sequence for P. maculatus, which could support the development of molecular markers studies to aid wildlife forensics, evolutionary approaches, and conservation and management studies.…”