Kapli P and Telford MJ (2020), Topology-dependent asymmetry in systematic erro...

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Sci Adv 2020 Dec 11;650:. doi: 10.1126/sciadv.abc5162.

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Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha.

Kapli P , Telford MJ .

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The evolutionary relationships of two animal phyla, Ctenophora and Xenacoelomorpha, have proved highly contentious. Ctenophora have been proposed as the most distant relatives of all other animals (Ctenophora-first rather than the traditional Porifera-first). Xenacoelomorpha may be primitively simple relatives of all other bilaterally symmetrical animals (Nephrozoa) or simplified relatives of echinoderms and hemichordates (Xenambulacraria). In both cases, one of the alternative topologies must be a result of errors in tree reconstruction. Here, using empirical data and simulations, we show that the Ctenophora-first and Nephrozoa topologies (but not Porifera-first and Ambulacraria topologies) are strongly supported by analyses affected by systematic errors. Accommodating this finding suggests that empirical studies supporting Ctenophora-first and Nephrozoa trees are likely to be explained by systematic error. This would imply that the alternative Porifera-first and Xenambulacraria topologies, which are supported by analyses designed to minimize systematic error, are the most credible current alternatives.

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	Fig. 1. Phylogenetic tree of main animal groups highlighting alternative hypotheses for the positions of the Ctenophora and Xenacoelomorpha.The dotted lines show alternative positions for the Ctenophora and Xenacoelomorpha. The sister group of all other Metazoa could be Ctenophora (Ctenophora-first) or the Porifera (Porifera-first). Xenacoelomorpha could be the sister group of the Ambulacraria (Xenambulacraria hypothesis), or the Xenacoelomorpha could be the sister group of all other Bilateria (Nephrozoa hypothesis). Branch lengths are approximately proportional to the average branch lengths leading to the clades indicated. Long branches leading to Ctenophora and Xenacoelomorpha are evident. The Chordata are shown as a sister group of the Protostomia: a topology supported by the dataset used in our analyses (9).
	Fig. 2. Site-homogeneous models consistently underestimate branch lengths.(A) Tree showing the clades (names) and branches (letters) for which lengths were estimated using Philippe-all data. (B) Estimates of clade and branch lengths using site-heterogeneous model (blue) and site-homogeneous model (brown) based on empirical data. (C) Tree showing the clades and branches for which lengths were estimated using Simion-all data. (D) Estimates of clade and branch lengths using site-heterogeneous (blue) model and site-homogeneous model (brown) based on empirical data. Site-homogeneous models consistently estimate shorter branch lengths.
	Fig. 3. Site-heterogeneous models estimate accurate branch lengths for both site-homogeneous and site-heterogeneous data.(A) The guide tree that was used for simulating the data, showing the clades (names) and branches (letters) used for comparing the estimates across models. (B) Estimates of clade and branch lengths for data simulated under the site-homogeneous model and inferred using the site-heterogeneous model (blue) and site-homogeneous model (brown). Both models give similarly accurate branch lengths for data simulated with the site-homogeneous model; the true branch lengths are shown with the black lines. (C) Equivalent estimates of clade and branch lengths for data simulated under the site-heterogeneous model. Site-heterogeneous models give accurate estimates, whereas site-homogeneous models consistently underestimate the amount of change/branch length.
	Fig. 4. Topology-dependent asymmetry of the ability of model-violating site-homogeneous models to reconstruct the correct tree.(A) A total of 100 datasets were simulated using a site-heterogeneous model for each of the topologies shown (orange/gray boxes). (B) For the datasets based on the whole alignment, site-heterogeneous (top) and site-homogeneous models (bottom) were used to reconstruct a maximum likelihood tree. The proportion of times the orange or black tree was reconstructed is shown in the bar charts. Data simulated under the Nephrozoa and the Ctenophora-first trees always yield the correct topology regardless of the model. Data simulated under the Xenambulacraria and Porifera-first topologies mostly yield the correct topology under the site-heterogeneous model but an incorrect topology under the site-homogeneous model. The incorrect tree is always Nephrozoa and the Ctenophora-first, respectively. (C) The experiments were repeated for the datasets based on the sets of genes best and worst at reconstructing known clades. For the best genes under both models, the inference is improved for data simulated under Xenambulacraria and Porifera-first topologies. A decrease in the performance of both models is observed using the worst data.
	Fig. 5. Topology-dependent asymmetry of tree reconstruction analyses shown using bootstrap.(A) A total of 100 datasets were simulated using a site-heterogeneous model for each of topologies shown in the corresponding box plots (orange/gray boxes). (B) Site-heterogeneous (top) and site-homogeneous models (bottom) were used to reconstruct a maximum likelihood tree, with the bootstrap support measured. The bootstrap support values showing the support of either gray or orange topologies are shown in the bar charts. Data simulated under the Nephrozoa and the Ctenophora-first trees always yield the correct topology regardless of the model with 100% bootstrap support. Data simulated under the Xenambulacraria and Porifera-first topologies mostly yield the correct topology under the site-heterogeneous model but an incorrect topology under the site-homogeneous model. The incorrect tree is always Nephrozoa or Ctenophora-first, respectively.
	Fig. 6. Best genes have short terminal branches and longer internal branches.(A) A tree showing the clades (names) and branches (letters) for which lengths were estimated for the Philippe data. (B) Estimates of clade and branch lengths for empirical data using a site-heterogeneous model for three data samples: best genes (green, highest monophyly scores), all dataset (gray), and worst genes (black, lowest monophyly scores). Best genes have shorter terminal branches within clades than all or worst. Best genes have longer branches separating clades than all or worst. (C) A tree showing the clades (names) and branches (letters) for which lengths were estimated for the Simion data. (D) Estimates of clade and branch lengths for the Simion-best, Simion-all and Simion-worst genes. Best genes have shorter terminal branches within clades than all or worst. For the best genes, most internal branches are the same or longer than for all or worst genes with the exception of the internal branch leading to the Ctenophora clade.

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