Co-evolution is incompatible with the markov assumption in phylogenetics

Tamir Tuller; Elchanan Mossel

doi:https://doi.org/10.1109/TCBB.2010.124

Co-evolution is incompatible with the markov assumption in phylogenetics

Tamir Tuller, Elchanan Mossel

Weizmann Institute of Science

Research output: Contribution to journal › Article › peer-review

Abstract

Markov models are extensively used in the analysis of molecular evolution. A recent line of research suggests that pairs of proteins with functional and physical interactions co-evolve with each other. Here, by analyzing hundreds of orthologous sets of three fungi and their co-evolutionary relations, we demonstrate that co-evolutionary assumption may violate the Markov assumption. Our results encourage developing alternative probabilistic models for the cases of extreme co-evolution.

Original language	English
Article number	5654502
Pages (from-to)	1667-1670
Number of pages	4
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume	8
Issue number	6
DOIs	https://doi.org/10.1109/TCBB.2010.124
State	Published - Nov 2011

Keywords

Markov models
Phylogenetic reconstruction
co-evolution
models of molecular evolution

All Science Journal Classification (ASJC) codes

Biotechnology
Genetics
Applied Mathematics

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Cite this

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title = "Co-evolution is incompatible with the markov assumption in phylogenetics",

abstract = "Markov models are extensively used in the analysis of molecular evolution. A recent line of research suggests that pairs of proteins with functional and physical interactions co-evolve with each other. Here, by analyzing hundreds of orthologous sets of three fungi and their co-evolutionary relations, we demonstrate that co-evolutionary assumption may violate the Markov assumption. Our results encourage developing alternative probabilistic models for the cases of extreme co-evolution.",

keywords = "Markov models, Phylogenetic reconstruction, co-evolution, models of molecular evolution",

author = "Tamir Tuller and Elchanan Mossel",

note = "Funding Information: The authors thank Prof. Martin Kupiec and Prof. Eytan Ruppin for helpful discussions. We also want to thank the two anonymous reviewers and the editor, Prof. Mike Steel, for their helpful comments. Tamir Tuller is a Koshland Scholar at Weizmann Institute of Science and is supported by a travel fellowship from EU grant PIRG04-GA-2008-239317. Elchanan Mossel was supported by US National Science Foundation (NSF) DMS 0548249 (CAREER) award, by Israel Science Foundation grant 1300/08, and by EU grant PIRG04-GA-2008-239317.",

year = "2011",

month = nov,

doi = "https://doi.org/10.1109/TCBB.2010.124",

language = "الإنجليزيّة",

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pages = "1667--1670",

journal = "IEEE/ACM Transactions on Computational Biology and Bioinformatics",

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AU - Mossel, Elchanan

N1 - Funding Information: The authors thank Prof. Martin Kupiec and Prof. Eytan Ruppin for helpful discussions. We also want to thank the two anonymous reviewers and the editor, Prof. Mike Steel, for their helpful comments. Tamir Tuller is a Koshland Scholar at Weizmann Institute of Science and is supported by a travel fellowship from EU grant PIRG04-GA-2008-239317. Elchanan Mossel was supported by US National Science Foundation (NSF) DMS 0548249 (CAREER) award, by Israel Science Foundation grant 1300/08, and by EU grant PIRG04-GA-2008-239317.

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N2 - Markov models are extensively used in the analysis of molecular evolution. A recent line of research suggests that pairs of proteins with functional and physical interactions co-evolve with each other. Here, by analyzing hundreds of orthologous sets of three fungi and their co-evolutionary relations, we demonstrate that co-evolutionary assumption may violate the Markov assumption. Our results encourage developing alternative probabilistic models for the cases of extreme co-evolution.

AB - Markov models are extensively used in the analysis of molecular evolution. A recent line of research suggests that pairs of proteins with functional and physical interactions co-evolve with each other. Here, by analyzing hundreds of orthologous sets of three fungi and their co-evolutionary relations, we demonstrate that co-evolutionary assumption may violate the Markov assumption. Our results encourage developing alternative probabilistic models for the cases of extreme co-evolution.

KW - Markov models

KW - Phylogenetic reconstruction

KW - co-evolution

KW - models of molecular evolution

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M3 - مقالة

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JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics

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ER -

Co-evolution is incompatible with the markov assumption in phylogenetics

Abstract

Keywords

All Science Journal Classification (ASJC) codes

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