Deep barcode divergence in Brazilian freshwater fishes: the case of the São Francisco River basin

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.

Keywords::

• neotropical
• fishes
• phylogeography
• cytochrome oxidase c subunit I
• São Francisco River
• cryptic species

Acknowledgements

The authors are grateful to José Vanderval Melo Junior, Arno Soares Seerig, Danilo Pimenta, Bernardo Lage, Ivo, Francisco Andrade, and Lucas Vilea Pires for helping with the collection of fish; to all personnel of the Biology Institute of Ontario and of the Laboratory of Animal Genetics at UFMG Veterinary College, for their assistance; to Luciano Beheregaray for comments on the manuscript; and to Heather Braid for assistance with formatting. The present study was supported by CNPq/FAPEMIG (INCT 573899/2008-8), the Canadian Barcode of Life Network via the Natural Sciences and Engineering Research Council of Canada, the Consortium of Barcode of Life, Instituto Estadual de Florestas and other sponsors listed at www.BOLNET.ca. D.C.C. is also grateful to CNPq for the PDJ fellowship (process number 150420/2009-9).

Declaration of interest: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.