Sequence evolution and copy number of Ty1-copia retrotransposons in diverse plant genomes

Sequence evolution of the reverse transcriptase (RT) gene in retrotransposons belonging to the Ty1-copia class was studied in 11 plant species. Phylogenetic reconstruction of the evolutionary history of RT sequences indicated a strong pattern of purifying selection, manifested as high ratios of third to first plus second codon position substitutions, and low ratios of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site, especially in internal portions of the element phylogenies. Evidence of purifying selection was most pronounced in plant species with low estimated copy numbers of Ty1-copia elements. This finding is consistent with the hypothesis that high element turnover rates (e.g., caused by high rates of element loss and selection against high element copy number) favors elements capable of transposition. Simulations of RT sequence evolution were conducted to help verify the logical validity of this conclusion. The results argue that it is incorrect to assume that low copy numbers of transposable elements are the product of reduced levels of element activity.