Shrinkage Effect in Ancestral Maximum Likelihood

arXiv0802.0914MaRDI QIDQ6208328FDOQ6208328

Sebastien Roch, Elchanan Mossel, Mike Steel

Publication date: 7 February 2008

Abstract: Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral sequences maximize the probability of observing the given data under a Markov model of sequence evolution, in which branch lengths are also optimized but constrained to take the same value on any edge across all sequence sites. AML differs from the more usual form of maximum likelihood (ML) in phylogenetics because ML averages over all possible ancestral sequences. ML has long been known to be statistically consistent -- that is, it converges on the correct tree with probability approaching 1 as the sequence length grows. However, the statistical consistency of AML has not been formally determined, despite informal remarks in a literature that dates back 20 years. In this short note we prove a general result that implies that AML is statistically inconsistent. In particular we show that AML can `shrink' short edges in a tree, resulting in a tree that has no internal resolution as the sequence length grows. Our results apply to any number of taxa.

This page was built for publication: Shrinkage Effect in Ancestral Maximum Likelihood

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q6208328)