Transposable elements (TEs) generate insertions and cause other mutations i
n the genomic DNA. It is proposed that during co-evolution between TEs and
eukaryotic genomes, an optimal path of the insertion mutagenesis is determi
ned by the surviving TEs. These TEs can become semi-permanently established
, chromatin-regulated 'source' or 'mutator genes', responsible for targetin
g insertion mutations to specific chromosomal regions. Such mutations can m
anifest themselves in non-random distribution patterns of interspersed repe
ats in eukaryotic chromosomes. In this paper we discuss specific models, ex
amples and implications of optimized mutagenesis in eukaryotes.