Abstract
This study examines the utility of morphology and DNA barcoding in species identification of freshwater fishes from north‐central Nigeria. We compared molecular data (mitochondrial cytochrome c oxidase subunit I (COI) sequences) of 136 de novo samples from 53 morphologically identified species alongside others in GenBank and BOLD databases. Using DNA sequence similarity‐based (≥97% cutoff) identification technique, 50 (94.30%) and 24 (45.30%) species were identified to species level using GenBank and BOLD databases, respectively. Furthermore, we identified cases of taxonomic problems in 26 (49.00%) morphologically identified species. There were also four (7.10%) cases of mismatch in DNA barcoding in which our query sequence in GenBank and BOLD showed a sequence match with different species names. Using DNA barcode reference data, we also identified four unknown fish samples collected from fishermen to species level. Our Neighbor‐joining (NJ) tree analysis recovers several intraspecific species clusters with strong bootstrap support (≥95%). Analysis uncovers two well‐supported lineages within Schilbe intermedius. The Bayesian phylogenetic analyses of Nigerian S. intermedius with others from GenBank recover four lineages. Evidence of genetic structuring is consistent with geographic regions of sub‐Saharan Africa. Thus, cryptic lineage diversity may illustrate species’ adaptive responses to local environmental conditions. Finally, our study underscores the importance of incorporating morphology and DNA barcoding in species identification. Although developing a complete DNA barcode reference library for Nigerian ichthyofauna will facilitate species identification and diversity studies, taxonomic revisions of DNA sequences submitted in databases alongside voucher specimens are necessary for a reliable taxonomic and diversity inventory.
Highlights
Nigerian freshwater bodies include reservoirs, lakes, rivers, ponds, and perennial swamps which constitute about 12% of Nigeria’s total surface area (Ita, Sado, Balogun, Pandogori, & Ibitoye, 1985)
Our study demonstrates the usefulness of DNA barcoding for the identification of fish species in north-central Nigeria and uncovering lineage diversity
This study contributes to the construction of DNA reference barcode data for Nigerian fish fauna
Summary
Nigerian freshwater bodies include reservoirs, lakes, rivers, ponds, and perennial swamps which constitute about 12% of Nigeria’s total surface area (Ita, Sado, Balogun, Pandogori, & Ibitoye, 1985) They are richly endowed with fishery resources of more than 268 species of freshwater fishes (Froese & Pauly, 2017; Olaosebikan & Bankole, 2005; Olaosebikan & Raji, 1998). The challenges of the use of morphology lie in the discrimination of closely related organisms (Rasmussen, Morrissey, & Hebert, 2009) This has paved way for the development of improved molecular approaches for identification of fish species (Abdullah & Rehbein, 2017; Nazarov et al, 2012; Nwani, Eyo, & Udoh, 2016; Ratnasingham & Hebert, 2007). We examined the usefulness of DNA barcode reference data in uncovering cryptic lineage diversity in fish species from north-central Nigeria
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