Phylogenies constrained by the crossover process as illustrated by human hemoglobins and a thirteen-cycle, eleven-amino-acid repeat in human apolipoprotein A-I.
Examination of human apolipoprotein A-I revealed a segment of eleven amino acids that repeated itself 13 times in succession without any additional intervening amino acids between the beginning of the repeats (amino acid 93) and their end at the carboxyl terminus of the sequence. The segments are not identical, but the pattern of their physical and chemical properties is highly conserved. The pattern is shown to be suitable to the formation of alpha helices with an amphipathic character consistent with the formation of a micellar structure, a process entirely appropriate to the protein's known function in the blood stream as a lipid carrier. The simplest hypothesis to account for repeated segments is a series of unequal crossovers. But such a series implies that some segments are more closely related to each other than they are to others, that is, they have a "phylogenetic" relationship. It is shown that only a small fraction of all possible phylogenies are consistent with a set of segments arising by simple unequal crossing over. Nevertheless, it is shown that the apolipoprotein A-I segments are readily interpretable as the result of simple unequal crossing over. Moreover, the crossover constraint applies with as much force to segments larger than a gene as to segments within a gene, and this is shown to require that the human gamma (Gly) hemoglobin gene lie to the left, rather than to the right, of the other non-alpha human hemoglobin genes, a conclusion for which there is no direct genetic evidence currently available.