New sample complexity bounds for phylogenetic inference from multiple loci

Abstract

We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It has been known however that the evolutionary history of individual genes (gene trees) might be topologically distinct from each other and from the underlying species tree, possibly confounding phylogenetic analysis. A further complication in practice is that one has to estimate gene trees from molecular sequences of finite length. We provide the first full data-requirement analysis of a species tree reconstruction method that takes into account estimation errors at the gene level. Under that criterion, we also devise a novel algorithm that provably improves over all previous methods in a regime of interest.