Modeling Neutral Evolution of Alu Elements Using a Branching Process

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2010 Feb 18

PMID 20158868

Citations 4

Authors

Marek Kimmel

Matthias Mathaes

Affiliations

Soon will be listed here.

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.

Citing Articles

Patterns of piRNA Regulation in Drosophila Revealed through Transposable Element Clade Inference.

Said I, McGurk M, Clark A, Barbash D Mol Biol Evol. 2021; 39(1).

PMID: 34921315 PMC: 8788220. DOI: 10.1093/molbev/msab336.

Dynamics of Transposable Element Invasions with piRNA Clusters.

Kofler R Mol Biol Evol. 2019; 36(7):1457-1472.

PMID: 30968135 PMC: 6573471. DOI: 10.1093/molbev/msz079.

Stochastic Hypothesis of Transition from Inborn Neutropenia to AML: Interactions of Cell Population Dynamics and Population Genetics.

Kimmel M, Corey S Front Oncol. 2013; 3:89.

PMID: 23641360 PMC: 3638131. DOI: 10.3389/fonc.2013.00089.

Modeling neutral evolution of Alu elements using a branching process.

Kimmel M, Mathaes M BMC Genomics. 2010; 11 Suppl 1:S11.

PMID: 20158868 PMC: 2822525. DOI: 10.1186/1471-2164-11-S1-S11.

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