DNA barcode and minibarcode identification of freshwater fishes from Cerrado headwater streams in Central Brazil

Abstract

The extraordinary species diversity of the Neotropical freshwater fish fauna is world renown. Yet, despite rich species diversity, taxonomic and genetic resources for its Cerrado ichthyofauna remain poorly developed. We provide a reference library of 149 DNA barcodes for 39 species/lineages of Cerrado headwater stream fishes from the Brazilian Distrito Federal and nearby areas and test the utility of distance‐based criteria, tree‐based criteria and minibarcodes for specimen identification. Mean Kimura 2‐parameter genetic distances within species to orders ranged 1·8–12·1%. However, mean intraspecific v. congeneric‐interspecific distances (0·9–1·3%) overlapped extensively and distance‐based barcoding failed to achieve correct identifications due to c. 4–12·1% error rates and 19·5% ambiguous identifications related to the presence of singletons. Overlap was reduced and best‐match success rates improved drastically to 83·5% when Characidium barcodes representing potential misidentifications or undescribed species were removed. Tree‐based monophyly criteria generally performed similarly to distance methods, correctly differentiating up to c. 85% of species/lineages despite neighbour‐joining and Bayesian tree errors (random lineage‐branching events, long‐branch attraction). Five clusters (Ancistrus aguaboensis, Characidium spp., Eigenmannia trilineata, Hasemania hanseni and Hypostomus sp. 2) exhibited deep intraspecific divergences or para−/polyphyly and multiple Barcode Index Number assignments indicative of putative candidate species needing taxonomic re‐examination. Sliding‐window analyses also indicated that a 200 bp minibarcode region performed just as well at specimen identification as the entire barcode gene. Future DNA barcoding studies of Distrito Federal–Cerrado freshwater fishes will benefit from increased sampling coverage, as well as consideration of minibarcode targets for degraded samples and next‐generation sequencing.

Using ddRAD-seq phylogeography to test for genetic effects of headwater river capture in suckermouth armored catfish (Loricariidae:Hypostomus) from the central Brazilian Shield

“…The main goal of this study was to use ddRAD-seq phylogeography to test for predicted spatial-genetic effects of river capture in the Paraná–Tocantins–São Francisco headwater river system in central Brazil (Table 1; Figure 1), derived from two main hypotheses advanced in a previous phylogenetic community ecology study of freshwater fishes in this system (Aquino and Colli, 2017). We focused on a distinct lineage or species complex (Bagley et al, 2019) of suckermouth armored catfish, Hypostomus sp. 2 (Aquino et al, 2009), that is endemic to and distributed across this region, and was included in Aquino and Colli’s (2017) study.…”

“…1’, which is the sister species to Hypostomus sp. 2 (Aquino et al, 2009; Aquino, 2013; Bagley et al, 2019), as outgroups. Our final dataset encompassed 40 Hypostomus sp.…”

“…2 is a genetically diverse lineage or species complex containing multiple Barcode Index Numbers, or operational taxonomic units (OTUs), that is sister to a distinct candidate species ‘ Hypostomus sp. 1’ forming a single OTU (BOLD:ADR4025; Bagley et al, 2019). Aquino and Colli (2017) conducted a phylogenetic community ecology study testing whether species richness and phylogenetic alpha and beta diversity in the Paraná–Tocantins–São Francisco headwater river system were consistent with the direction and frequency of river capture predicted from the geological setting, including higher relative richness in the capturing Tocantins basin.…”

Two new species of Hypostomus suckermouth‐armoured catfishes (Teleostei: Loricariidae) from central Brazil

“…The practice of accurately and rigorously describing new species through alpha‐taxonomy is critical for improving biodiversity accounting in the context of the current biodiversity crisis and also provides a basis for using organisms as model systems in various disciplines of the biological sciences (Drew, 2011; Wheeler, 2004; Wilson, 1985). The authors of this study set out to test the hypothesis that populations of Hypostomus from central Brazil that were identified as phylogenetically distinct, and therefore in need of taxonomic reassessment, in recent molecular studies (Bagley et al ., 2019; Bagley et al ., 2021) represent new species. Apparently, H. cafuringa was found only in the headwaters of the Maranhão River, in the Federal District region.…”

Contribution to a reference library of DNA barcodes of Colombian freshwater fishes

“…An alternative to perform a rapid identification of species relies on the DNA barcoding approach, based on the sequencing of the mitochondrial gene cytochrome c oxidase subunit I (COX1) and its contrast to previously sequenced specimens with morphological identification and resolved taxonomy (Hebert et al 2003, Kress andErickson 2012). The efficacy in the discrimination of fish species, in different stages of development, using COX1 has previously been demonstrated (Ward et al 2005, Frantine-Silva et al 2015, Bagley et al 2019) and the method can be very useful to document the diversity of fishes in megadiverse countries such as Colombia and potentially validate further species still to be described (DoNascimiento et al 2017).…”