Abstract
M.Sc. (Zoology)
Species identification and delineation are very important in studies such as biodiversity, conservation biology, ecology and evolutionary biology. Cichlids are the common model group of fishes which are used to explicate the mechanisms of adaptation, speciation and diversification. Application of combined molecular genes (such as 16S, Cytochrome oxidase subunit I (COI), histone H3 & recombination activating gene two TMO4C4) on the phylogeny of cichlids has played an important role in cichlid phylogenetic studies. Here, identification of cichlids were assessed using DNA barcoding and phylogenetic tree reconstruction. All analyses were based on a single mitochondrial gene COI. Sequences of Alcolapia grahami and Thoracochromis albolabris were generated for the first time along with mined sequences from Barcode Of Life Data base systems (BOLDsystems). BRONX (Barcode Recognition Obtained with Nucleotide eXposés) was also used to confirm unique sequences representing each species. The performance of COI gene was tested based on three identification metrics namely best close match (bcm), near neighbour (nn) and BOLD identification criteria (BOLD id) using SPIDER in R. Next, occurrence of barcode gap was established on the difference of furthest intraspecific distance among its own species and the closest, non-conspecific distance (nonConDist – maxInDist). A maximum parsimony and a Bayesian inference (bi) tree were reconstructed to further investigate species delimitation among cichlid fishes. Both nn and bcm showed 89% true and 87% correct identification respectively in the dataset whereas BOLD id gave a lower correct identification (54%). There were well-supported values at each node of bi tree reconstruction, indicating evolutionary divergence among cichlids. COI gene performed well in the identification of Alcolapia and Thoracochromis (nn and bcm = 100%). It also performed well in the phylogenetic positions of Alcolapia and Thoracochromis (support values of 92% and 100% respectively). However, populations of Alcolapia grahami were not fully resolved by COI gene. The COI barcoding gene is viewed as an efficient tool for enhancing species identification and delimitation. Morphological data and nuclear genes or microsatellites should be added to resolve the ambiguity in the problematic specimens.