Genomic data do not support comb jellies as the sister group to all other animals

Abstract

Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the "Ctenophora-sister" hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.

Keywords: Ctenophora; Metazoa; Porifera; evolution; phylogenomics.

Fig. 1.

(A) Phylogeny inferred from Ryan-Choano (4) using the site-heterogeneous CAT model. (B) Phylogeny inferred from Whelan-D16-Choano (6) using the site-heterogeneous CAT-GTR model. For both analyses, we used the site-heterogeneous model implemented by the original study and limited the outgroups to include only choanoflagellates (the closest living relatives of animals) (details and justifications are provided in Addressing Biases in Phylogenetic Reconstruction and Methods). Major groups are summarized, and full phylogenies illustrated are in Figs. S1 and S4C. Nodes with maximal statistical support are marked with a circle. Most silhouettes from organisms are from Phylopic (phylopic.org/).

Fig. S1.

Bayesian phylogenies inferred from the datasets of Ryan et al. (4) under CAT and CAT-GTR. Nodes are labeled with posterior probabilities distinguishable from 1.0. (Scale bars, expected number of substitutions per site.) (A) Phylogeny inferred from Ryan-Opistho under CAT. Sampled points = 39,362, burnin = 15,000, bpcomp maxdiff = 0.062, tracecomp minimum effsize = 80, maximum rel_diff = 0.19. (B) Phylogeny inferred from Ryan-Holo under CAT. Sampled points = 58,543, burnin = 25,000, bpcomp maxdiff = 0.096, tracecomp minimum effsize = 90, maximum rel_diff = 0.25. (C) Phylogeny inferred from Ryan-Choano under CAT. Sampled points = 53,617, burnin = 22,000, bpcomp maxdiff = 0.077, tracecomp minimum effsize = 116, maximum rel_diff = 0.22. (D) Phylogeny inferred from Ryan-Choano under CAT-GTR. Sampled points = 15,231, burnin = 5,000, bpcomp maxdiff = 0.24, tracecomp minimum effsize = 8, maximum rel_diff = 0.7. This analysis did not reach convergence.

Fig. S2.

(A) Maximum likelihood phylogeny inferred from Moroz-3D (5) under LG. Final log-likelihood score = −502135. The log-likelihood score under WAG was −505012 and recovered the same topology as Moroz et al. (5). (Scale bar, expected number of substitutions per site.) Nodes are labeled with bootstrap support values less than 100%. (B) Phylogeny inferred from Moroz-3D under CAT-GTR. Sampled points = 14,140, burnin = 7,000, bpcomp maxdiff = 0.24, tracecomp minimum effsize = 17, maximum rel_diff = 0.73. This analysis did not reach convergence. (Scale bar, expected number of substitutions per site.) Nodes are labeled with posterior probabilities distinguishable from 1.0.

Fig. 2.

Decreasing support for the Ctenophora-sister hypothesis as distant outgroups are removed from phylogenomic datasets. Statistical support values (posterior probabilities) were obtained from three different datasets using the site-heterogeneous CAT model: Ryan (4) (A), Whelan-6 (6) (B), and Whelan-16 (6) (C). For each dataset, three analyses were conducted, each with a different outgroup sampling scheme: Choanoflagellata = choanoflagellates, Holozoa = nonfungal outgroups, and Opisthokonta = fungal and nonfungal outgroups. Statistical support for Ctenophora-sister and Porifera-sister is indicated in red and green, respectively. Support values are from the trees in Figs. S1, S3, and S4. The Ctenophore silhouette is from Phylopic (phylopic.org/).

Fig. S3.

Bayesian phylogenies inferred from datasets based on Whelan-6 (6) under CAT and CAT-GTR. Nodes are labeled with posterior probabilities distinguishable from 1.0. (Scale bars, expected number of substitutions per site.) (A) Phylogeny inferred from Whelan-6-Opistho under CAT. Sampled points = 66,346, burnin = 20,000, bpcomp maxdiff = 0.038, tracecomp minimum effsize = 152, maximum rel_diff = 0.14. (B) Phylogeny inferred from Whelan-6-Holo under CAT. Sampled points = 18,095, burnin = 2,000, bpcomp maxdiff = 0.097, tracecomp minimum effsize = 50, maximum rel_diff = 0.18. (C) Phylogeny inferred from Whelan-6-Choano under CAT. Sampled points = 11,503, burnin = 3,750, bpcomp maxdiff = 0.073, tracecomp minimum effsize = 50, maximum rel_diff = 0.29. (D) Phylogeny inferred from Whelan-6-Choano under CAT-GTR. Sampled points = 44,405, burnin = 14,000, bpcomp maxdiff = 0.2, tracecomp minimum effsize = 51, maximum rel_diff = 0.45.

Fig. S4.

Bayesian phylogenies inferred from datasets based on Whelan-16 (6) under CAT and CAT-GTR. Nodes are labeled with posterior probabilities distinguishable from 1.0. (Scale bars, expected number of substitutions per site.) (A) Phylogeny inferred from Whelan-16-Opistho under CAT. Sampled points = 35,477, burnin = 15,000, bpcomp maxdiff = 0.1, tracecomp minimum effsize = 61, maximum rel_diff = 0.23. (B) Phylogeny inferred from Whelan-16-Holo under CAT. Sampled points = 12,714, burnin = 5,000, bpcomp maxdiff = 0.07, tracecomp minimum effsize = 63, maximum rel_diff = 0.26. (C) Phylogeny inferred from Whelan-16-Choano under CAT. Sampled points = 9,729, burnin = 3,750, bpcomp maxdiff = 0.08, tracecomp minimum effsize = 84, maximum rel_diff = 0.29. (D) Phylogeny inferred from Whelan-16-Choano under CAT-GTR. Sampled points = 27,929, burnin = 13,965, bpcomp maxdiff = 0.12, tracecomp minimum effsize = 76, maximum rel_diff = 0.3.

Fig. S5.

Bayesian phylogeny inferred from the dataset of Philippe et al. (33) under CAT-GTR after excluding all ribosomal proteins and with only Choanoflagellata as the outgroup. Sampled points = 23,714, burnin = 3,000, bpcomp maxdiff = 0.26, tracecomp minimum effsize = 90, maximum rel_diff = 0.4. (Scale bar, expected number of substitutions per site.) Nodes are labeled with posterior probabilities distinguishable from 1.0.

Fig. 3.

Animal phylogeny obtained after correcting for ascertainment bias in the full-gene content dataset of Ryan et al. (4) (more details are provided in SI Methods). All nodes had maximal statistical support.

Fig. S6.

Bayesian phylogenies inferred from the gene content dataset of Ryan et al. (4) using MrBayes (discussed above and in main text). (Scale bars, expected number of substitutions per site.) Nodes are labeled with posterior probabilities distinguishable from 1.0. (A) Analysis with no ascertainment bias correction. Note that this topology is different from the one obtained by Ryan et al. (4) but gives a higher maximum log-likelihood score in RAxML (−223301 vs. −223502). Sampled points = 1 million, burnin = 250,000, MrBayes maximum SD of split frequencies = 0.017, bpcomp maxdiff = 0.024, tracecomp minimum effsize = 852, maximum rel_diff = 0.049. (B) Analysis using a correction for the absence of parsimony uninformative sites. Note that this correction required the exclusion of 1,615 parsimony uninformative characters before analysis. Sampled points = 1 million; burnin = 250,000, MrBayes maximum SD of split frequencies = 0.0, bpcomp maxdiff = 0.0, tracecomp minimum effsize = 191, maximum rel_diff = 0.17.