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Modeling neutral evolution of Alu elements using a branching process.

Kimmel M, Mathaes M - BMC Genomics (2010)

Bottom Line: Our proposed theoretical neutral model follows a discrete-time branching process described by Griffiths and Pakes.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.This observation suggests that Alu sequences do not evolve neutrally and might be under selection.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Statistics, Rice University, Houston, TX 77005, USA. kimmel@rice.edu

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.

Show MeSH
AluYa1 data-based class frequencies against the theoretical {Ψk} in log scale. Fitted by Griffiths-Pakes process with linear-fractional distribution, with b = 0.016, p = 0.983.
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Figure 1: AluYa1 data-based class frequencies against the theoretical {Ψk} in log scale. Fitted by Griffiths-Pakes process with linear-fractional distribution, with b = 0.016, p = 0.983.

Mentions: Figures 1, 2, 3, 4 depict the maximum-likelihood fits of the model to the data from AluYa1, AluYa5, AluYb8 and AluYc1 subfamilies, respectively. They are presented in the semi-logarithmic scale, to amplify the tail probabilities. The graphical comparison demonstrates that the data fit relatively well for allele classes 1 and 3 - 7. Notably, the allele class 2 shows the worst fit among the first seven allele classes. These seven classes account for at least 0.99 cumulative class frequency observed in the data.


Modeling neutral evolution of Alu elements using a branching process.

Kimmel M, Mathaes M - BMC Genomics (2010)

AluYa1 data-based class frequencies against the theoretical {Ψk} in log scale. Fitted by Griffiths-Pakes process with linear-fractional distribution, with b = 0.016, p = 0.983.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2822525&req=5

Figure 1: AluYa1 data-based class frequencies against the theoretical {Ψk} in log scale. Fitted by Griffiths-Pakes process with linear-fractional distribution, with b = 0.016, p = 0.983.
Mentions: Figures 1, 2, 3, 4 depict the maximum-likelihood fits of the model to the data from AluYa1, AluYa5, AluYb8 and AluYc1 subfamilies, respectively. They are presented in the semi-logarithmic scale, to amplify the tail probabilities. The graphical comparison demonstrates that the data fit relatively well for allele classes 1 and 3 - 7. Notably, the allele class 2 shows the worst fit among the first seven allele classes. These seven classes account for at least 0.99 cumulative class frequency observed in the data.

Bottom Line: Our proposed theoretical neutral model follows a discrete-time branching process described by Griffiths and Pakes.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.This observation suggests that Alu sequences do not evolve neutrally and might be under selection.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Statistics, Rice University, Houston, TX 77005, USA. kimmel@rice.edu

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.

Show MeSH