Joint Maximum Likelihood of Phylogeny and Ancestral States Is Not Consistent.

ABSTRACT: Maximum likelihood estimation in phylogenetics requires a means of handling unknown ancestral states. Classical maximum likelihood averages over these unknown intermediate states, leading to provably consistent estimation of the topology and continuous model parameters. Recently, a computationally efficient approach has been proposed to jointly maximize over these unknown states and phylogenetic parameters. Although this method of joint maximum likelihood estimation can obtain estimates more quickly, its properties as an estimator are not yet clear. In this article, we show that this method of jointly estimating phylogenetic parameters along with ancestral states is not consistent in general. We find a sizeable region of parameter space that generates data on a four-taxon tree for which th

SUBMITTER: Shaw DA 

PROVIDER: S-EPMC6759070 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature