A population genetic study on dispersed repeated sequences in the genome

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Dispersed repeated sequences with a large number of copies such as SINEs and LINEs are abundantly found in higher eukaryotic genomes. It is of great interest to know how these sequences are evolving and what biological functions they have. In the present study, population genetic models for this type of repeated sequences were developed and analyzed. Firstly, the probabilities of finding an element at a specific site in genomes sampled in various schemes are computed. From these probabilities, methods to estimate the period of the amplification and to calculate the probability of inferring an incorrect phylogenetic relationship were developed. These results were applied to the human Alu sequence data. Secondly, the sequence divergences were considered. Statistical methods and computer programs are developed to analyze the large database of human Alu which contains more than 3000 sequences compiled by Jurka. Although the analyzes have not been completed yet, the data suggest that the amplification is unlikely to be due to a very few master copies. Furthermore, the amplification periods and rates were estimated from these data. We need to complete the analysis and extend the analyzes to other families of retroposons using the methods developed in the present study. Furthermore, population genetic models incorporating selection are worthwhile considering in the future. Then, we would be able to infer the significance of these repeated sequences by comparing the expectation of the models and the data.