The species flocks of cichlid fish in the three great East African Lak
es, Victoria, Malawi, and Tanganyika, have arisen in each lake by expl
osive adaptive radiation. Various questions concerning their phylogeny
have not yet been answered. In particular, the identity of the ancest
ral founder species and the monophyletic origin of the haplochromine c
ichlids from the East African lakes have not been established conclusi
vely. In the present study, we used the anonymous nuclear DNA marker D
XTU1 as a step towards answering these questions. A 280 bp-fragment of
the DXTU1 locus was amplified by the polymerase chain reaction from E
ast African lacustrine species, the East African riverine cichlid spec
ies Haplochromis bloyeti, H. burtoni and H. sparsidens, and other Afri
can cichlids. Sequencing revealed several indels and substitutions tha
t were used as cladistically informative markers to support a phylogen
etic tree constructed by the neighbor-joining method. The topology, al
though not supported by high bootstrap values, corresponds well to the
geographical distribution and previous classification of the cichlids
. Markers could be defined that: (i) differentiate East African from W
est African cichlids; (ii) distinguish the riverine and Lake Victoria/
Malawi haplochromines from Lake Tanganyika cichlids; and (iii) indicat
e the existence of a monophyletic Lake Victoria cichlid superflock whi
ch includes haplochromines from satellite lakes and East African river
s. In order to resolve further the relationship of East African riveri
ne and lacustrine species, mtDNA cytochrome b and control region segme
nts were sequenced. The mtDNB-based trees support the notion of the mo
nophyly of the Lake Victoria superflock but are ambigious with respect
to the phylogenetic position of the Lake Malawi flock.