of Matzke, Matzke, and colleague (Matzke and Matzke, 1998; Matzke et al., 1999). They argue that polyploid genomes contain duplications of all genes and thus are relatively well buffered against mutations caused by transposon insertion. As a consequence, transposable elements multiply and are maintained in polyploid genomes. For maize, the fact that two major events (polyploidy and retrotransposon multiplication) are located on the same phylogenetic lineage gives credence to the idea that these phenomena are biologically correlated (Fig. 1), but it is not yet known whether this correlation is widely observed.
Genomes are dynamic entities that can be modified extensively by polyploidy and transposon multiplication. However, ongoing evolutionary processes like mutation, recombination, natural selection, and migration also shape the genome. The effect of these extant processes on the genome can be inferred from careful study of genetic diversity.
Diversity throughout the genome is affected strongly by the interplay of recombination and natural selection. In Drosophila, for example, genetic diversity varies along the chromosome as a function of recombination rate (Begun and Aquadro, 1992; Hamblin and Aquadro, 1999). Loci near centromeres tend to have low recombination rates and also tend to have low levels of genetic diversity, but both recombination rate and genetic diversity increase toward the tip of chromosomes. This relationship is not because recombination is mutagenic; rather, it reflects an interdependence between natural selection and recombination (Begun and Aquadro, 1992; Charlesworth et al., 1995). In regions of low recombination, for example, linkage between nucleotide sites ensures that selection for or against a single nucleotide substitution will affect a large region of the genome. In regions of high recombination, nucleotide sites are nearly independent; thus, selection on a single site affects a much smaller region of the genome. The result of the interdependence between selection and recombination is that (i) levels of genetic diversity can be a function of chromosomal position and (ii) large chromosomal regions can be depauperate of genetic diversity.
The correlation between chromosomal position and genetic diversity has been confirmed in plants (Dvorak et al., 1998; Stephan and Langley, 1998), but it is not yet clear whether recombination in maize follows a simple pattern along chromosomes. For example, it has been documented that maize single-copy regions act as recombination hot spots, but recom-