No abstract

(2011) Deep barcode divergence in Brazilian freshwater fishes: the case of the São Francisco River basin, Mitochondrial DNA, 22:sup1, 80-86, DOI: 10.3109/19401736.2011.588214 To link to this article: https://doi.org/10. 3109/19401736.2011.588214 View supplementary material Abstract Background and aims. The application of DNA barcoding as a global standard for fish identification is probing diverse worldwide realms (Nearctic, Australian and the Neotropics) and environments (e.g. marine and freshwater). Comparing the patterns of sequence divergence among conspecific and congeneric taxa between realms can provide valuable information on recent evolutionary histories of lineages as barcode data accumulates. Materials and methods. Herein, we have analyzed over 100 species (around 50%) of the Neotropical fish fauna from the São Francisco River, in southeast Brazil. Our aims were to test the performance of DNA barcoding in this biodiversity-rich region, and to compare patterns of genetic divergence with previous studies. Results. The mean Kimura two-parameter distances within species, genera, families, orders, and classes were 0.5, 10.6, 21.0, 22.7, and 24.4%, respectively, with 100% of the species examined successfully differentiated by barcoding. With the exception of Astyanax bimaculatus lacustris, Piabina argentea, and Bryconamericus stramineus, all other species yield a single, cohesive cluster of barcode sequences. The average 'nearest-neighbor distance' was 11.12%, 21-fold higher than the mean within species distance of around 0.54%. In a few instances, deep lineage divergences among conspecifics (up to 10%) and congenerics (up to 22.9%) taxa were revealed. Conclusions. Reflecting possible cases of cryptic speciation and the deeper phylogeographic history of São Francisco fish fauna, with some higher clades extending back into the late Cretaceous and Cenozoic (90 mya), when much of the diversification of the Neotropical region apparently took place. In addition, barcodes also highlighted misidentifications and helped to document range extensions for known species.

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Environmental DNA (eDNA) has rapidly emerged as a promising biodiversity monitoring technique, proving to be a sensitive and cost‐effective method for species detection. Despite the increasing popularity of eDNA, several questions regarding its limitations remain to be addressed. We investigated the effect of sampling medium and time, and preservation methods, on fish detection performance based on eDNA metabarcoding of neotropical freshwater samples. Water and sediment samples were collected from 11 sites along the Jequitinhonha River, Southeastern Brazil; sediment samples were stored in ethanol, while the same amounts of water per sample (3 L) were stored in a cool box with ice, as well as by adding the cationic surfactant benzalkonium chloride (BAC). Sediment and water samples yielded a similar amount of fish MOTUs (237 vs. 239 in the first sampling event, and 153 vs. 142 in the second sampling event). Water stored in ice provided better results than those preserved in BAC (239 and 142 vs. 194 and 71 MOTUs). While documenting the effectiveness of eDNA surveys as practical tools for fish biodiversity monitoring in poorly accessible areas, we showed that keeping water samples cooled results in greater eDNA recovery and taxon detection than by adding cationic surfactants (BAC) as sample preservatives. Furthermore, by comparing two sets of samples collected from the same locations at a 3‐week interval, we highlight the importance of conducting multiple sampling events when attempting to recover a realistic picture of fish assemblages in lotic systems.