Transposable Element- driven Duplications during Hominoid Genome Evolution

p0001 Akin to any large texts in a natural language, hominoid genomes appear as palimpsests ofmorphemes, lexemes and other lexical modules, each with its own structure, distribution and fluctuating copy numbers (Zhou and Mishra, 2004; Thomas et al., 2004). Duplication appears to be one of the main mechanisms in shaping and reshaping this genomic architecture. Duplication occurs at multiple scales, ranging at one end from small local tandem repeats that are the results of polymerase slippage or unequal crossing-over, to the duplication of a whole genome at the other extreme. Segmental duplication (SD)occurs at a scale between small repeats and thewhole genome.Duplications provide the genome with additional and (initially) redundant copies of genes and their regulatory elements, thus initiating gene family expansion and offering the species adequate freedom to explore new functionality and develop more refined regulations (Armengol, 2005; Cheng, 2005) AU:2 . Duplication promotes a faster and more complex dynamics during genome evolution – the duplicated sequences can serve as the homologous region for further recombination events, which can lead to further duplication, deletion and other rearrangement events (Zhou and Mishra, 2004). As was found in the subtelomeric and pericentromeric regions of the mammalian genomes, SDs in such regions generate a complicated pattern of recursively nested events and creates a fertile breeding ground for novel functional elements. Years before the genomic era tools had pinpointed the duplicatedmotifs in genomes, in a surprisingly prescient thesis, SOhno had already suggested a possible reciprocative roles between duplications and selections in the evolutionary dynamics, as he noted that ‘Natural selection merely modified while redundancy created’ (Ohno, 1970) AU:3 .