Incorporating DNA barcodes into a multi-year inventory of the fishes of the hyperdiverse Lower Congo River, with a multi-gene performance assessment of the genus Labeo as a case study

Abstract

Background and aims: Here we describe preliminary efforts to integrate DNA barcoding into an ongoing inventory of the Lower Congo River (LCR) ichthyofauna. The 350 km stretch of the LCR from Pool Malebo to Boma includes the world's largest river rapids. The LCR ichthyofauna is hyperdiverse and rich in endemism due to high habitat heterogeneity, numerous dispersal barriers, and its downstream location in the basin.

Materials and methods: We have documented 328 species from the LCR, 25% of which are thought to be endemic. In addition to detailing progress made to generate a reference sequence library of DNA barcodes for these fishes, we ask how DNA can be used at the current stage of the Fish Barcode of Life initiative, as a work in progress currently of limited utility to a wide audience. Two possibilities that we explore are the potential for DNA barcodes to generate discrete diagnostic characters for species, and to help resolve problematic taxa lacking clear morphologically diagnostic characters such as many species of the cyprinid genus Labeo, which we use as a case study.

Results: Our molecular analysis helped to clarify the validity of some species that were the subject of historical debate, and we were able to construct a molecular key for all monophyletic and morphologically recognizable species. Several species sampled from across the Congo Basin and widely distributed throughout Central and West Africa were recovered as paraphyletic based on our molecular data.

Conclusion: Our study underscores the importance of generating reference barcodes for specimens collected from, or in close proximity to, type localities, particularly where species are poorly understood taxonomically and the extent of their geographical distributions have yet to be established.

Keywords::

• Africa
• fish
• DNA barcoding
• Congo
• cytochrome c oxidase subunit I
• RAG1

Acknowledgements

We are extremely grateful to Sinaseli M. Tshibwabwa for his identification of the Labeo specimens used in this study. His efforts are greatly appreciated, and while he is in disagreement with some of the conclusions presented here, without his help we could not have carried out this study. The authors also thank H. Escobar, V. Mamonekene, J.J. Mbimbi, R. Monsembula, R. Schelly, and J. Schwarzer for field assistance, U. Schliewen (ZSM) for generously providing tissues, and WWF-Kinshasa for logistical support in the field. This manuscript benefited immensely from comments by S.O. Kolokotronis and an anonymous reviewer.

Declarations of interest: Funding for field research, collecting, and student training was provided by the National Science Foundation, through Biotic Surveys and Inventories award to M. L. J. S. (DEB Grant No. 0542540); the Axelrod Curatorship at AMNH (conferred on M. L. J. S.) provided additional funding to support S. M. T. on three study visits to examine Labeo specimens at the AMNH Ichthyology Collections. J. H. L. received funding from Columbia University's Department of Ecology, Evolution, and Environmental Biology, as well as a NSF Graduate Research Fellowship, in addition to support by the AMNH Axelrod Curatorship (conferred on M. L. J. S.). The authors acknowledge the International Barcode of Life Project (funded by Genome Canada via the Ontario Genomics Institute) and the Canadian Barcode of Life Network funded by the Natural Sciences and Engineering Research Council of Canada for informatics and sequencing support.