Moleculer Phylogenetic Study of Cichlid Fishes in Africa

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Lake Tanganyika harbors numerous endemic species of extremely diverse cichlid fish that have been classified into twelve major taxonomic groups known as tribes. Analysis of SINE insertion data has been acknowledged as a powerful tool for the elucidation of phylogenetic relationships, and we applied this method in an attempt to clarify such relationships among these cichlids. We studied insertion patterns of 38 SINEs in total, 24 of which supported the monophyly of three clades. The other 14 loci revealed extensive incongruence in terms of the patterns of SINE insertions. These incongruence most likely stems from period of adaptive radiation. One possible explanation for this phenomenon in the extensive incomplete lineage sorting of alleles for the presence or absence of a SINE during successive speciation events during this period which took place about 5-10 million years ago.Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation. We identified six loci at which a SINE sequence had apparently been specifically inserted by retroposition in the common ancestor of all the investigated species of endemic cichlids in Lake Malawi. At another locus, unique sharing of a SINE sequence was evident among all the investigated species of endemic non-Mbuna cichlids with the exception of Rhamphochromis sp. We also characterized a locus that exhibited transspecies polymorphism with respect to the presence or absence of the SINE sequence among non-Mbuna species. This result suggests that incomplete lineage sorting and/or interspecific hybridization might have occurred or be occurring among the species in this group, which might potentially cause misinterpretation of phylogenetic data, in particular when a single-locus marker, such as a sequence in the mitochondrial DNA, is used for analysis.