Twelve different genomic regions were used in the study.
Branch lengths were estimated for these tests under the Hasegawa-Kishino-Yano (HKY) mutation model (Hasegawa, Kishino, and Yano 1985).
Portions of 12 nuclear loci were sequenced in nine rock-dwelling species (mbuna) and three representatives of pelagic nonmbuna species.
In contrast to the pattern of variation at mitochondrial genes, which do provide phylogenetic resolution at the level of mbuna versus nonmbuna, and among some genera, the nuclear loci were virtually devoid of phylogenetic signal.
Nuclear genes also differed from the mitochondria in having nearly twice the amount of divergence from The cichlid fishes (Teleostei: Cichlidae) of the East African Rift Valley lakes Malawi, Tanganyika, and Victoria and their satellites offer spectacular examples of rapid radiation (Fryer and Iles 1972; Echelle and Kornfield 1984). 2004) that makes up a large subset of the tribe Haplochromini (Eccles and Trewavas 1989; Salzburger et al. All Malawi haplochromine types fall into one of the two widely used, albeit informal, taxa: the mbuna (from the local name for rock-dwelling types) and the nonmbuna.
For Lake Malawi, over 600 species have been described (including formal and informal descriptions) (Konings 2001). All the mbuna are similar small forms that dwell in rocky shallow regions of the lake.