substitution will be discussed in the context of genetic diversity. Patterns of genetic diversity provide insight into the population genetic processes that act on different regions of the genome and thus uncover the evolutionary forces that act on genomes. We focus on maize throughout the paper but also generalize to other species when appropriate.
The first hints of the complex organization of the maize genome came from cytological studies. Although maize is diploid, early studies by McClintock (McClintock 1930, 1933) demonstrated the association of nonhomologous chromosomes during meiosis. Later studies documented the formation of bivalents and multivalents in maize haploids (Snope, 1967; Ting, 1966). Altogether, cytological observations suggested that the maize genome contains extensive regions of homology, probably reflecting chromosomal duplications.
Evidence for chromosomal duplication also came from linkage information. In 1951, Rhoades (1951, 1955) noted that some regions of link-