Integrative taxonomy detects cryptic and overlooked fish species in a neotropical river basin

Abstract

The great freshwater fish diversity found in the neotropical region makes management and conservation actions challenging. Due to shortage of taxonomists and insufficient infrastructure to deal with such great biodiversity (i.e. taxonomic impediment), proposed remedies to accelerate species identification and descriptions include techniques that combine DNA-based identification and concise morphological description. The building of a DNA barcode reference database correlating meristic and genetic data was developed for 75 % of the Mucuri River basin's freshwater fish. We obtained a total of 141 DNA barcode sequences from 37 species belonging to 30 genera, 19 families, and 5 orders. Genetic distances within species, genera, and families were 0.74, 9.5, and 18.86 %, respectively. All species could be clearly identified by the DNA barcodes. Divergences between meristic morphological characteristics and DNA barcodes revealed two cryptic species among the Cyphocharax gilbert and Astyanax gr. bimaculatus specimens, and helped to identify two overlooked species within the Gymnotus and Astyanax taxa. Therefore, using a simplified model of neotropical biodiversity, we tested the efficiency of an integrative taxonomy approach for species discovery, identification of cryptic diversity, and accelerating biodiversity descriptions.

Cytonuclear discordance in the Florida Everglades invasive Burmese python (Python bivittatus) population reveals possible hybridization with the Indian python (P. molurus)

“…The CO1 genetic distance (5.4%) was also greater than the distances for the two species published in BOLD (4.1%). In the literature, CO1 nucleotide diversity values lower than 4.1% have been used as a minimum threshold to distinguish intraspecific variation from interspecific divergence (Gomes, Pessali, Sales, Pompeu, & Carvalho, ; Ratnasingham & Hebert, ). In contrast to the strong mitochondrial differentiation signals, minimal divergence was detected between the three Bayesian clusters at nuclear microsatellites ( F ST ≤ 0.029).…”

DNA barcoding confirms the occurrence of Rhamdia branneri and Rhamdia voulezi (Siluriformes: Heptapteridae) in the Iguaçu River Basin

“…In specific groups, such as the Neotropical fish, studies have used the barcoding threshold (approximately 2%) proposed by Ward (2009) to delimit a wide-range of species (Rosso et al, 2012;Bellafronte et al,. 2013;Pereira et al, 2013;Gomes et al, 2015;Shimabukuro-Dias et al, 2016;Díaz et al, 2016). Nonetheless, given the great diversity of 6 e160147 [6] species, particularly related to life histories and complexity of environment, a fixed threshold value can under-or overestimate the correct number of MOTUs (Brown et al, 2012).…”

“…The integration between the molecular and traditional taxonomic identification is a relevant association and can promote the identification of a greater number of species than currently described (Steinke, Hanner, 2011). Presently, there is a range of studies addressing the Neotropical ichthyofauna through DNA barcoding, suggesting and revealing several new species (Pereira et al, 2011;Rosso et al, 2012;Gomes et al, 2015;Ramirez, Galetti Jr., 2015;Melo et al, 2016). However, the success of the identification of species from molecular data depends on the precise taxonomic identification and availability of reference sequences (Ward et al, 2009)…”

Insight into the population structure of hardhead silverside, Atherinomorus stipes (Teleostei: Atherinidae), in Belize and the Florida Keys using nd2

“…Additionally, the Florida and Barbados populations differed by 2.3%. These levels of intraspecific divergence are considered to be relatively large and could indicate that A. stipes from within each of these island‐groups represent independent evolutionary lineages (Gomes, Pessali, Sales, Pompeu, & Carvalho, 2015). …”