DNAbarcoding of economically important freshwater fish species from north‐central Nigeria uncovers cryptic diversity

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.

Patterns of ichthyofaunal diversity and distribution across Jebba Hydro-Electric Power (HEP) dam, Jebba, north-central Nigeria

“…Vouchers were fixed with 4% formalin and kept in 70% ethanol for long-term storage. Procedures for DNA barcoding for species identification followed the methodology described by Iyiola et al (2018).…”

DNA Barcoding Silver Butter Catfish (Schilbe intermedius) Reveals Patterns of Mitochondrial Genetic Diversity Across African River Systems

“…This could be attributed to morphometric characteristic changes associated with ontogenetic development and/or species' local adaptation to its environment 1 . As such, the use of morphometric and meristic characters in taxonomy, particularly for species with extremely similar external features and high levels of phenotypic plasticity, could hinder the discovery and identification of cryptic intraspecific diversity [1][2][3][4][5] . While morphology-based taxonomy might possibly overlook such diversity, DNA barcoding, involving mitochondrial cytochrome c oxidase subunit I (COI), has been recommended as a complementary taxonomic tool for species identification and unravelling cryptic diversity 6 .…”

“…While morphology-based taxonomy might possibly overlook such diversity, DNA barcoding, involving mitochondrial cytochrome c oxidase subunit I (COI), has been recommended as a complementary taxonomic tool for species identification and unravelling cryptic diversity 6 . The COI barcoding has proven successful in the identification of fish species [1][2][3][4][5]7 and the discovery of cryptic diversities 2,[8][9][10][11] . Several examples of deep COI sequence divergences within fish species have been attributed to cryptic speciation 2,3,[8][9][10][11] .…”

“…These organisms are important and often underappreciated component of African biodiversity. Additionally, these fishes are significant economic and food resources for residents of African river watersheds 2 . Given their importance to humans, the ability to accurately identify species and other evolutionary distinct units are prerequisites for sustainable management of fish genetic resources and improving our knowledge of the diversity of African riverine fish diversity [2][3][4][5] .…”

“…Several molecular phylogenetic studies based on DNA barcode data have explored the mitochondrial diversity of S. intermedius 2,3,11 , though the results of these studies were equivocal. For instance, while Van der Bank et al 11 recovered three distinct matrilines across African river systems (South Africa, East Africa, and West Africa), Iyiola et al 2 revealed the presence of four geographically structured matrilines with two restricted to West Africa (Nigeria) and the other two to East and Central Africa. Nonetheless, these studies strongly suggest that the genetic diversity of S. intermedius remain under-estimated.…”