Analysis of major histocompatibility complex haplotypes of t-chromosomes reveals that the majority of diversity is generated by recombination.

t-chromosomes are natural polymorphisms in feral populations of mice that are thought to be descended from a single ancestral chromosome. They carry an inversion of at least 10 cM surrounding the major histocompatibility complex (MHC) that effectively prevents recombination between a t-bearing chromosome and wild type chromosomes. However, on the rare occasion when two different t-chromosomes meet in a wild female, recombination occurs at an apparently normal rate. Since they contain the highly polymorphic MHC, their limited origin and restricted chances for recombination make t-chromosomes a valuable tool for studying the relative contributions of mutation and recombination to the generation of diversity. Using 13 different serological reagents to class I antigens, and studying restriction enzyme polymorphisms detected with three molecular probes for class II genes examined with three endonucleases, we present data indicating that the major factor responsible for the diversity of class I antigens is recombination, but that for class II genes, mutation must play an important role in addition to recombination.