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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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Dealing with uncertainty in ancestral sequence reconstruction: sampling from the posterior distribution

Dealing with uncertainty in ancestral sequence reconstruction: sampling from the posterior distribution

Chapter:
(p.85) CHAPTER 8 Dealing with uncertainty in ancestral sequence reconstruction: sampling from the posterior distribution
Source:
Ancestral Sequence Reconstruction
Author(s):

David D. Pollock

Belinda S.W. Chang

Publisher:
Oxford University Press
DOI:10.1093/acprof:oso/9780199299188.003.0008

The goal of ancestral inference is to have as accurate a picture of ancestral function as possible. Thus, it is worthwhile to try to understand the nature and cause of the sequence and functional bias, and how to overcome this bias. This chapter argues that the bias inherent in in the choice to reconstruct the ancestral sequence with the highest posterior probability, along with the optimization bias due to site-specific model inaccuracy, may have biased the frequencies with which certain amino acids are inferred. Amino acids that tend to have consistently low posterior probabilities are most probably undersampled. A simple strategy to address amino acid sampling bias when reconstructing ancestral proteins in the laboratory is discussed.

Keywords:   amino acids, ancestral function bias, archosaur rhodopsin, sampling

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