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