How much information is there for inferring species trees?

Abstract

AO_SCPLOWBSTRACTC_SCPLOWAs modern phylogenomics datasets become increasingly large, it is useful to develop recommendations for how to subsample datasets for best species tree inference. Here we apply a new measure of phylogenetic information content that estimates the reduction in tree space occupied by a posterior sample of inferred trees relative to a prior sample in order to assess the effects of gene tree parameters on species tree estimation. We find that, consistent with earlier studies, when data are informative, more data result in better species tree inference. However, when data are uninformative, subsampling a dataset to include only the most informative loci may produce a better species tree sample. We perform analyses on a variety of simulated and empirical datasets.