A test of the utility of DNA barcoding in the radiation of the freshwater stingray genus Potamotrygon (Potamotrygonidae, Myliobatiformes)

Abstract

DNA barcoding is a recently proposed global standard in taxonomy based on DNA sequences. The two main goals of DNA barcoding methodology are assignment of specimens to a species and discovery of new species. There are two main underlying assumptions: i) reciprocal monophyly of species, and ii) intraspecific divergence is always less than interspecific divergence. Here we present a phylogenetic analysis of the family Potamotrygonidae based on mitochondrial cytochrome c oxidase I gene, sampling 10 out of the 18 to 20 valid species including two non-described species. Potamotrygonidae systematics is still not fully resolved with several still-to-be-described species while some other species are difficult to delimit due to overlap in morphological characters and because of sharing a complex color patterns. Our results suggest that the family passed through a process of rapid speciation and that the species Potamotrygon motoro, P. scobina, and P. orbignyi share haplotypes extensively. Our results suggest that systems of identification of specimens based on DNA sequences, together with morphological and/or ecological characters, can aid taxonomic studies, but delimitation of new species based on threshold values of genetic distances are overly simplistic and misleading.

Phylogeography and conservation genetics of the Amazonian freshwater stingray Paratrygon aiereba Müller & Henle, 1841 (Chondrichthyes: Potamotrygonidae)

“…Additionally, genetic distances within the genus Paratrygon were larger than those found among species of the rosette-spot group of Potamotrygon (cf. Toffoli et al, 2008) comprises the following species: Potamotrygon motoro, P. scobina, P. orbignyi, P. leopoldi, P. falkneri, and P. henlei. Within Paratrygon, intraclade divergences were less than 1%, as were the inter-specific divergences observed in the rosette-spot group of Potamotrygon (Table 2) (Toffoli et al, 2008).…”

“…Partial sequences from COI gene were used to estimate genetic divergences, and to identify putative lineages or species within the P. aiereba, according to the DNA barcode guidelines. Other species of Potamotrygonidae and two outgroup species (Himantura pacifica, Himantura schmardae) available in the GenBank (data from Toffoli et al, 2008) were also included in analyses.…”

“…The NJ tree topology and statistical robustness (using 2000 bootstrap replicates) were estimated in PAUP* 4.0b10 (Swofford, 2002). Sequence data of other potamotrygonid species available in the GenBank (data from Toffoli et al, 2008), were included in the analyses to calculate genetic divergence between genera and for the identification of putative lineages or species within the P. aiereba, according to the DNA barcode guidelines. The same two shark species used om Toffoli et al (2008) were used as outgroups.…”

DNA barcode of Parodontidae species from the La Plata river basin - applying new data to clarify taxonomic problems

“…The basic principle that sustains the DNA barcoding methodology is related to the premise that a short standardized DNA sequence -Cytochrome c Oxidase I (COI), can distinguish species through the interspecific genetic variation, which exceeds intraspecific variation (Hajibabaei et al, 2007;Toffoli et al, 2008). Although the use of DNA barcoding is very controversial for using a single mitochondrial gene for species identification, it is believed to be a powerful tool (Ward et al, 2009).…”

Reevaluation of RAPD markers involved in a case of stingray misidentification (Dasyatidae: Dasyatis)

“…Generally, these techniques involve tissue sampling of specimens/fishery products and subsequent laboratory work. Currently, some of the most used techniques are DNA barcoding (Holmes et al, 2009;Santander-Neto et al, 2011; but see Toffoli et al, 2008), polymerase chain reaction (PCR)-restriction fragment length polymorphism (Mendonça et al, 2009), and multiplex PCR (Mendonça et al, 2010). In addition to these recent techniques, several older molecular marker techniques have been used in fisheries (Carvalho and Pitcher, 1995).…”