A population genetic study on dispersed repeated sequences in the genome

在高等真核生物基因组中，广泛存在着具有大量拷贝的分散重复序列，如SINE和LINES。了解这些序列是如何进化的以及它们具有哪些生物学功能是非常有意义的。在本研究中，建立了这类重复序列的群体遗传模型并进行了分析。首先，计算在不同方案下采样的基因组中在特定位置找到元件的概率。根据这些概率，发展了估计扩增周期和计算推断错误系统发育关系的概率的方法。这些结果被应用于人类Alu序列数据。其次，考虑了序列差异。开发了统计方法和计算机程序来分析包含Jurka编制的3000多个序列的人类Alu的大型数据库。尽管分析尚未完成，但数据表明，扩增不太可能是由于很少的母拷贝。此外，根据这些数据估计了扩增周期和扩增速率。我们需要完成分析，并使用本研究开发的方法将分析扩展到其他逆转录病毒家族。此外，包含选择的种群遗传模型在未来值得考虑。然后，我们将能够通过比较模型和数据的预期来推断这些重复序列的重要性。

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.