Abstract
Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.
Highlights
584 c oxidase subunit I (COI) sequences of the African Cyprinidae specimens were retrieved from the Barcode of Life Database (BOLD; www.boldsystems.org) and GenBank/EBI
The interspecific genetic distances (K2P) ranged from 0 to 0.30 and are larger than the intraspecific genetic distances. This is indicative of a barcode gap in the COI dataset of the studied Cyprinidae
We found the optimised distance d = 0.015 suitable for species discrimination in the studied African Cyprinidae (Figure 3)
Summary
Cyprinidae is the most diverse family of freshwater fishes (Nelson et al 2006; Imoto et al 2013) with 377 genera and over 3000 described species (Eschmeyer and Fong 2015; Froese and Pauly 2017). There are key morphological features that distinguish the males from the females, including a brighter breeding colour, longer fins and presence of the tubercles on the body and head in some African genera (Skelton 2001). Morphological features such as the presence/absence of barbels, the number of barbels, as well as barbel type, pattern of innervation, and barbel position have been used to differentiate species within and between genera of the subfamilies Cyprininae sensu lato and Danioninae sensu lato (Howes 1991; Skelton 2001)
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