Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular
example of adaptive radiation. To clarify the phylogenetic relationships among these fish, we
examined the presence and absence of SINEs (short interspersed repetitive elements) at
orthologous loci. 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. The relationships were in good agreement with those deduced in
previous studies with various different markers, demonstrating that the SINE method is useful
for the elucidation of phylogenetic relationships among cichlids in Lake Malawi. 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.