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Ancestral Sequence Reconstruction$
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David A Liberles

Print publication date: 2007

Print ISBN-13: 9780199299188

Published to Oxford Scholarship Online: September 2008

DOI: 10.1093/acprof:oso/9780199299188.001.0001

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PRINTED FROM OXFORD SCHOLARSHIP ONLINE (oxford.universitypressscholarship.com). (c) Copyright Oxford University Press, 2021. All Rights Reserved. An individual user may print out a PDF of a single chapter of a monograph in OSO for personal use. date: 06 March 2021

Estimating the history of mutations on a phylogeny

Estimating the history of mutations on a phylogeny

(p.69) CHAPTER 6 Estimating the history of mutations on a phylogeny
Ancestral Sequence Reconstruction

Jonathan P. Bollback

Paul P. Gardner

Rasmus Nielsen

Oxford University Press

Evolution has left its signature on the molecules and morphology of living organisms. Ancestral reconstruction offers an excellent tool for understanding the process of evolution using comparative information. Methods for ancestral reconstruction have generally focused on reconstructing the ancestral states at the internal nodes of a phylogeny. Often, we are not interested in particular nodes of the phylogeny but the whole history of a character. This chapter focuses on a Bayesian method for estimating these histories, or mutational paths, on phylogenies. Mutational path methods differ most notably from other approaches in their ability to estimate not only the ancestral states at the internal nodes of a phylogeny, but also the order and timing of mutational changes across the phylogeny. The chapter provides a concise introduction to the statistical tools needed for sampling mutational paths on a phylogeny.

Keywords:   mutational path, character history, Bayesian, likelihood, predictive, inference, phylogeny

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