per site (Ananiev et al., 1998a). Their structure and dispersed occurrence further suggest that they are transposable (Ananiev et al., 1998a, b; Buckler et al., 1999). The combination of transposability and preferential transmission of chromosomes with expanded knobs thus provides an additional mechanism for genome expansion.
Are there genetic mechanisms that contract genomes? Careful analysis of the relative deletion frequency and length in drosophilid non-LTR retrotransposons supports the inference that there are more deletions per point mutation in Drosophila than in mammals and that the average deletion size is almost eight times larger (Petrov and Hartl, 1998). Thus mechanisms that contract genomes by preferential deletion may exist, as well. Bennetzen and Kellogg have argued that despite ample evidence for the operation of mechanisms that expand genomes in plants, there is little evidence that plant genomes contract (Bennetzen and Kellogg, 1997). The maize intergenic regions that have been analyzed, for example, comprise predominantly intact retrotransposons, rather than solo LTRs, which can arise by unequal crossovers between the repeats at retrotransposon ends and are common in other genomes (Bennetzen and Kellogg, 1997). However, it also is known that both the Ac and Spm transposons of maize frequently give rise to internally deleted elements, and Ac ends are very much more abundant in the maize genome than are full-length elements, suggesting deletional decay of transposon sequences (Fedoroff et al., 1983, 1984; Schwarz-Sommer et al., 1985b; Masson et al., 1987). So it would not be surprising to find mechanisms that preferentially eliminate sequences. And indeed, preferential loss of nonredundant sequences early after polyploidization has been detected in wheat (Feldman et al., 1997).
Despite our growing awareness of the abundance of plant transposable elements and the role they have played in shaping contemporary chromosome organization, the fact is they eluded discovery for the first half century of intensive genetic analysis. Thus what is perhaps the most striking observation about transposable elements is not their instability, but precisely the opposite: their stability. Not only are insertion mutations in genes infrequent, but retrotransposition events are so widely separated that the time interval between insertions in a particular region of the genome can be counted in hundreds of thousands to millions of years (SanMiguel et al., 1998). Chromosomes containing many hundreds of