Resolving tricky nodes in the tree of life through amino acid recoding

Genomic data allowed a detailed resolution of the Tree of Life, but tricky nodes such as the root of the animals remain unresolved. Genome-scale datasets are heterogeneous as genes and species are exposed to different pressures, and this can negatively impacts phylogenetic accuracy. We use simulated genomic-scale datasets and show that recoding amino acid data improves accuracy when the model does not account for the compositional heterogeneity of the amino acid alignment. We apply our findings to three datasets addressing the root of the animal tree, where the debate centers on whether sponges (Porifera) or comb jellies (Ctenophora) represent the sister of all other animals. We show that results from empirical data follow predictions from simulations and suggest that, at the least in phylogenies inferred from amino acid sequences, a placement of the ctenophores as sister to all the other animals is best explained as a tree reconstruction artifact.

Automated summary

Genomic data has helped in the understanding of the Tree of Life, but certain nodes remain unresolved. By using simulated datasets, this study found that recoding amino acid data can improve the accuracy of phylogenetic inference. The results suggest that the placement of comb jellies as sister to all other animals in phylogenies inferred from amino acid sequences is likely a tree reconstruction artifact.