Molecular population genetic studies on the evolution of retroposons

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In order to elucidate evolutionary mechanisms of retroposons, Drosophila I elements were cloned from Drosophila melanogaster and its sibling species and their sequences were determined. Analysis of them showed that I elements invaded populations of D.melanogaster at least twice, before and after the diversification of D.melanogaster and D.simulans and the second invasion occurred recently. We extended the survey to include I-homologous elements in other species groups of Drosophila and silk moth and determined their sequences and distribution on the chromosome. They were diverged from those of D.melanogaster but sometimes have gag^- and revesetranscriptase-like sequnces with TAA repeats. Generally, I elements are found both on chromosome arms and chromocenters but more likely to be on the latter. Because they were found in a wide range of species, their origin is considered to be fairly old.To understand the dynamics of retroposon evolution, a transient population genetic model of SINE evolution assuming the master copy model was theoretically inverstigated. Means and variances of consensus frequency, nucleotide homozygosity, and the number of shared differences which are considered to have been caused by mutations occurring in the master copy lineages are computed. All quantities investigated are shown to be monotone functions of the duration of the expansion period. Using the theoretical results, the Sb subfamily of fuman Alu sequences is analyzed. The expansion period is estimated to be short compared to the time since the end of the expansion of the subfamily. However, the observed number of the shared differences is about one half of that expected under the master copy model with the estimated expansion period suggesting the presence of multiple master copy loci in the Sb subfamily.