Ancestral state reconstruction with large numbers of sequences and edge-length estimation

Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and edge lengths are known. In some scenarios the tree topology might be reasonably well known for the taxa under study. When sequence length is much smaller than the number of species, however, edge lengths are not likely to be accurately estimated. We study the consistency of the maximum likelihood and empirical Bayes estimators of the ancestral state of discrete traits in such settings under a star tree. We prove that the likelihood-based reconstruction is consistent under symmetric models but can be inconsistent under non-symmetric models. We show, however, that a simple consistent estimator for the ancestral states is available under non-symmetric models. The results illustrate that likelihood methods can unexpectedly have undesirable properties as the number of sequences considered gets very large. Broader implications of the results are discussed.