Two cichlid species, the haplochromine Aulonocara hansbaenschi and the tilapiine
Oreochromis niloticus, were used to study the major histocompatibility complex (Mhc)
class II A variation within this group. Multiple class II A sequences were recovered from
A. hansbaenschi and O. niloticus cDNA libraries and three sequence families,
DAA, DBA, and DCA, were identified. Sets of O. niloticus haploid embryo families were
used to determine the linkage relationships of these genes. Two independently asserting
linkage groups were detected, DAA and DBA/DCA, neither of which is linked to the previously
described Mhc class I gene cluster. Three DCA genes and up to four DBA genes were found to
segregate in different haplotypes, whereas DAA occurred as a single locus. Four DBA haplotypes,
DBA*H1-H4, were identified and shown to co-segregate with the previously described class
II B haplotypes. Four DCA haplotypes, DCA*H1- H4, were found at a distance of 37 cM from
the DBA/class II B cluster; in one DCA haplotype, DCA*H5, the genes were tightly linked to
the DBA/class II B clusters. Transcripts of DAA and DBA genes were found in O. niloticus
hepatopancreas and spleen; transcripts of DCA genes were detected in the A. hansbaenschi
cDNA library, but not in O. niloticus. These findings provide a basis for using class
II haplotypes as markers in the study of adaptive radiation in the cichlid species flocks of
the East African Great Lakes.