Abstract
The cichlid fishes of the Great East African Lakes are, along with Darwin finches, a classical example of adaptive radiation. They underwent an extremely rapid speciation process that resulted in the generation of hundreds of new species. The genes of the Major Histocompatibility Complex (Mhc) constitute a suitable molecular marker for the elucidation of the phylogenetic relationships among these closely related, but yet different species, due to their extensive polymorphism and transpecific mode of evolution. Even though Mhc class II B DNA sequences had previously been described and shown to be highly polymorphic in cichlids from Lakes Malawi, Victoria and Tanganyika, no information was available about the locus/allele relationships between these genes. Here, we used a combination of two different approaches: (a) sorting of single sperm cells, and (b) generation of andro/gynogenetic offspring, to produce hemizygous and homozygous genomes, respectively. Mhc typing of the samples produced in this way, shows that in cichlids, class II B genes are linked and arranged in haplotypes that may vary in their number of loci. The 12 loci here identified constitute a linkage group, not linked to class I genes. Characterization of cDNA sequences in several individuals reveals that all genomic sequences identified are transcribed, and their products probably functional.In addition, we studied DNA sequence polymorphism at eight Mhc class II B loci and mitochondrial (mt) DNA variation in Oreochromis alcalicus, a cichlid that lives at temperatures of up to 40$\sp\circ$C and pH 10.5 in the small alkaline lakes Natron and Magadi, on the Great Rift Valley of East Africa. Adaptation to these conditions occurred rapidly 9-12,000 yr BP. Our data show that the Mhc genes of O. alcalicus are as highly polymorphic as those of a freshwater cichlict from Lake Victoria, implying that the size of its founding population remained large during and after this rapid adaptation process. In addition, the sharing of Mhc and mt DNA polymorphisms between the reproductively isolated populations of the two lakes confirms their recent common origin. Dating of the O. alcalicus (mt) DNA haplotypes indicates that Lakes Natron and Magadi were continuously populated for the last 800,000 years.