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The statistical estimation of phylogenies is always associated withuncertainty, and accommodating this uncertainty is an important component ofmodern phylogenetic comparative analysis. The birth-death polytomy resolver isa method of accounting for phylogenetic uncertainty that places missing(unsampled) taxa onto phylogenetic trees, using taxonomic information alone.Recent studies of birds and mammals have used this approach to generatepseudo-posterior distributions of phylogenetic trees that are complete at thespecies level, even in the absence of genetic data for many species. Manyresearchers have used these distributions of phylogenies for downstreamevolutionary analyses that involve inferences on phenotypic evolution,geography, and community assembly. I demonstrate that the use of phylogeniesconstructed in this fashion is inappropriate for many questions involvingtraits. Because species are placed on trees at random with respect to traitvalues, the birth-death polytomy resolver breaks down natural patterns of traitphylogenetic structure. Inferences based on these trees are predictably andoften drastically biased in a direction that depends on the underlying (true)pattern of phylogenetic structure in traits. I illustrate the severity of thephenomenon for both continuous and discrete traits using examples from a globalbird phylogeny.

No substitute for real data: phylogenies from birth-death polytomy resolvers should not be used for many downstream comparative analyses