Morphological characters can strongly influence early animal relationships inferred from phylogenomic data sets

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: The sister to all other Metazoa (SOM). Here we use published phylogenomic datasets (∼45,000-400,000 characters in size with ∼15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological datasets (∼15-275 characters). We additionally use small exemplar datasets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, i.e. likelihood models and their \"equivalent\" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, i.e., that genomic-scale datasets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10× in both likelihood and parsimony can in some cases \"flip\"...