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This article is part of the supplement: International Workshop on Computational Systems Biology: Approaches to Analysis of Genome Complexity and Regulatory Gene Networks

Open Access Research

Modeling neutral evolution of Alu elements using a branching process

Marek Kimmel12* and Matthias Mathaes1

Author Affiliations

1 Department of Statistics, Rice University, Houston, TX 77005, USA

2 Systems Engineering Group, Silesian University of Technology, 44-100 Gliwice, Poland

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BMC Genomics 2010, 11(Suppl 1):S11  doi:10.1186/1471-2164-11-S1-S11

Published: 10 February 2010

Abstract

Background

Alu elements occupy about eleven percent of the human genome and are still growing in copy numbers. Since Alu elements substantially impact the shape of our genome, there is a need for modeling the amplification, mutation and selection forces of these elements.

Methods

Our proposed theoretical neutral model follows a discrete-time branching process described by Griffiths and Pakes. From this model, we derive a limit frequency spectrum of the Alu element distribution, which serves as the theoretical, neutral frequency to which real Alu insertion data can be compared through statistical goodness of fit tests. Departures from the neutral frequency spectrum may indicate selection.

Results

A comparison of the Alu sequence data, obtained by courtesy of Dr. Jerzy Jurka, with our model shows that the distributions of Alu sequences in the AluY family systematically deviate from the expected distribution derived from the branching process.

Conclusions

This observation suggests that Alu sequences do not evolve neutrally and might be under selection.