Estimating Common Ancestors

Abstract

The fifth chapter explains three ways to infer ancestral sequences from sequence data. After explaining a heuristic approach to build the intuition of the readers, the chapter explains maximum likelihood estimation and Bayesian estimation with some simplifications to keep the formulas minimal. To adjust the results for uncertainty not quantified in the models, the previous chapter’s method of uncertainty quantification is adapted. Exercises provided at the end of the chapter give readers practical experience with estimating ancestral sequences and intuition about the uncertainty involved.

Notions of significance tests, confidence intervals, posterior intervals and all the formal apparatus of inference are valuable tools to be used as guides, but not in a mechanical way; they indicate the uncertainty that would apply under somewhat idealized, may be [sic] very idealized, conditions and as such are often lower bounds to real uncertainty.

– Sir David Cox¹