The phylogenetic utility of the 16S gene in cichlids is assessed. Eighty-six (86) partial sequences belonging to 37 genera of cichlids from the Genbank was analyzed. The alignment had four hundred and sixty three (463) basepairs with 337 conserved sites and 126 variable sites. Base compositional bias is similar to that found in higher organism with Adenine having the highest average of 30.3%, followed by cytosine, guanine and thiamine with the average values of 26.1, 21.9 and 21.7% respectively. The most suitable evolutionary model is the K2+G+I model as this had the lowest Bayesian Information Criterion. There were 4 major indels at basepair positions 328 which is unique to the Heterotilapia buttikoferi, position 369 unique to Gramatoria lemarii, position 396 which is shared by Tilapia sparrmanii, T. guinasana and T. zilli. The indel at position 373 was found in all tested species except the Oreochromis mossambicus. The Tilapine general is the basal group in Cichlids. The 16S gene separates the Tilapia genera without any ambiguity but there were phylogenetic overlaps in the Sarotherodon and Oreochromis. More finite molecular and statistical methodology may be needed to distinguish the Sarotherodon and Oreochromis. The diversity of cichlids is generally very low due to a common ancestry with little differentiation genetically. The grouping of the Oreochromis and Sarotherodon genera together in the same clade is not unconnected with the preservation of genetic beacons that the group retained as it evolved.
Key words: Cichlids, 16S gene, phylogeny, evolutionary model, monophyletic, conserved segment, speciose, indels
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