Phylogenetic analysis of a retrotransposon with implications for strong evolutionary constraints on reverse transcriptase.

This study examines the evolutionary dynamics of a retrotransposon in a group of parasitoid wasps. A region containing the reverse transcriptase (RT) domain was sequenced for 43 elements from the genomes of nine different wasp species. Phylogenetic analysis of the elements revealed concordance with taxonomic classification of the host species, and the pattern was consistent with that expected for vertical transmission of a multicopy element during differentiation of the species. Twenty-three of the 43 elements had comparable intact open reading frames in the amplified region, and these were used in an analysis of evolutionary constraint on the amino acid sequence. As previously documented for retroelements, closely related elements exhibited nearly equal substitution rates at nonsynonymous and synonymous sites, but relative nonsynonymous substitution rates decreased as increasingly divergent elements were compared. A statistical test indicated that the decrease was not due to saturation of weakly selected sites. The pattern is most likely caused by a "pseudogene effect." Individual elements are not subject to purifying selection, and therefore, synonymous and nonsynonymous substitutions accumulate at equal rates. Comparisons among closely related elements are influenced strongly by this pseudogene evolution, whereas comparisons among distantly related elements reveal selection on the actively replicating lineages connecting the elements. These distant comparisons more accurately reflect the constraints on the amino acid sequence, and the comparisons among elements in this study indicated strong constraints on RT.