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DNA barcoding the Lake Edward basin: high taxonomic coverage of a tropical freshwater ichthyofauna

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Abstract

We present an extensive DNA barcoding study of the fish species of the Lake Edward system, including information on intraspecific variation. The DNA barcode gene, cytochrome c oxidase I (COI), failed to discriminate the 35 species of the genus Haplochromis analysed. For the non-Haplochromis species, the reference library had a near complete coverage of 91.2%, with 31 out of the 34 known species of the system sequenced. With the recent morphology-based review of the ichthyofauna of the system as a backbone, the DNA barcoding library proved to be very effective for future species identifications. High identification successes were obtained based on Best Match (98.2%), Best Close Match (97.9%), and All Species Barcode (95.0%) criteria. Surprisingly, Laciris pelagicus and Micropanchax vitschumbaensis, two morphologically distinct species, had very similar and even identical COI haplotypes, whilst in Enteromius the existence of possible cryptic species was revealed. Few species occurring in the Lake Edward system were already represented in the global database Genbank. For some widespread species, regional genetic differences were found, highlighting the value of basin-specific information in reference databases. The provided reference library of DNA barcodes is a valuable tool for future conservation actions, which is certainly relevant in a system where the fisheries are under pressure.

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Data availability

The COI sequences used for this study are openly available in Genbank, GenBank accessions MT523142 – MT52383; MT250998—MT251134 (published in Maetens et al., 2020), and MZ081460-MZ081545 (published in Diederickx et al., 2021).DNA sequence assemblies: upon request. A BOLD project, i.e. a library consisting of voucher ID, collection numbers, photographs, and sequence data, is available for the data within this article [HIPEB]. Morphological identifications and sampling localities are available in Supplementary Information.

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Acknowledgements

This publication is the output of work done under the Belspo-funded BRAIN-be projects ‘HIPE’ (Human impacts on ecosystem health and resources of Lake Edward) and ‘KEAFish’ (The biodiversity, biogeography and evolutionary history of the northern basins of the Great African Lakes: the enigmatic fish faunas of Lakes Kivu, Edward and Albert revisited). The fieldwork by NV, MVS, and ED was supported by the FWO and fieldwork by MVS by the King Leopold III Fund for Nature Exploration and Conservation. We are very grateful to M. Mbalassa (Université Officielle de Bukavu), L. Wasswa (Ugandan Fisheries Department), and M. Bifamengo (NaFIRRI, Uganda) for their indispensable help during the fieldwork and to W. Okello (NaFFIRI) for the major logistic support during the multidisciplinary field trips. We thank P. Bragança (SAIAB) for help in identifying the killifish and M. Parrent (RMCA) for the collection management.

Funding

The expeditions to the Lake Edward system took place under the Belspo-funded BRAIN-be project ‘HIPE’ (Human impacts on ecosystem health and resources of Lake Edward). The fieldwork by NV, MVS, and ED was supported by the FWO and fieldwork by MVS by the King Leopold III Fund for Nature Exploration and Conservation.

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Authors and Affiliations

  1. Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium

    Eva Decru, Nathan Vranken, Heleen Maetens, Amber Mertens De Vry, Jos Snoeks & Maarten Van Steenberge

  2. Royal Museum for Central Africa, Section Vertebrates, Ichthyology, Leuvensesteenweg 13, 3080, Tervuren, Belgium

    Eva Decru, Nathan Vranken, Heleen Maetens, Annelies Kayenbergh & Jos Snoeks

  3. Department of Wildlife, Fish and Environmental Studies, Molecular Ecology Research Group, Swedish University of Agricultural Sciences, Umeå, Sweden

    Amber Mertens De Vry

  4. Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000, Brussels, Belgium

    Maarten Van Steenberge

  5. Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic

    Maarten Van Steenberge

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  1. Eva Decru
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  2. Nathan Vranken
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  5. Annelies Kayenbergh
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  6. Jos Snoeks
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Contributions

ED, HM, AM, AK, and MVS performed the DNA work in the lab. Maarten Van Steenberge, Nathan Vranken, Jos Snoeks, and Eva Decru collected samples during the field work. Heleen Maetens constructed the sequence data files, Eva Decru did the DNA analyses. Eva Decru and Maarten Van Steenberge wrote the manuscript, with input from all authors. Final editing was done by Jos Snoeks and Maarten Van Steenberge. All authors read and approved the manuscript.

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Correspondence to Eva Decru.

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Decru, E., Vranken, N., Maetens, H. et al. DNA barcoding the Lake Edward basin: high taxonomic coverage of a tropical freshwater ichthyofauna. Hydrobiologia 849, 1743–1762 (2022). https://doi.org/10.1007/s10750-022-04812-0

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