Can Evolutionary Rate Matrices be Estimated from Allele Frequencies?

Conrad J. Burden

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Paper

Can Evolutionary Rate Matrices be Estimated from Allele Frequencies?

Topics: Biostatistics and Stochastic Models; Sequence Analysis

In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, 183-188, 2015 , Lisbon, Portugal

Author: Conrad J. Burden

Affiliation: Australian National University, Australia

ISBN: 978-989-758-070-3

ISSN: 2184-4305

Keyword(s): Evolutionary Rate, Wright-Fisher Model, Fokker-Plank Equation.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Biostatistics and Stochastic Models ; Sequence Analysis

Abstract: This paper is a work in progress in which aims to combine the principles of population genetics and continuous-time Markovian evolutionary models to estimate evolutionary rate matrices from the current observed state of a single genome. A model is proposed in which sections of the genome which are not susceptible to natural selection are considered to be a statistical ensemble of individual genomic sites. Each site is a representative from a stationary distribution of allele frequencies 0 = ? = 1 within the population. Simulations of this distribution via a finite-state Markov model based on a finite effective population size are compared with the stationary solution to the continuum Fokker-Planck equation. Parameters of the evolutionary rate matrix introduced via mutation rates within the Fokker-Planck equation are estimated for simulated data in a number of exploratory examples.

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Paper citation in several formats:

J. Burden, C. (2015). Can Evolutionary Rate Matrices be Estimated from Allele Frequencies?. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015) ISBN 978-989-758-070-3 ISSN 2184-4305, pages 183-188. DOI: 10.5220/0005253701830188

@conference{bioinformatics15,
author={Conrad {J. Burden}.},
title={Can Evolutionary Rate Matrices be Estimated from Allele Frequencies?},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)},
year={2015},
pages={183-188},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005253701830188},
isbn={978-989-758-070-3},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)
TI - Can Evolutionary Rate Matrices be Estimated from Allele Frequencies?
SN - 978-989-758-070-3
IS - 2184-4305
AU - J. Burden, C.
PY - 2015
SP - 183
EP - 188
DO - 10.5220/0005253701830188