Fighting over a comb MAXIMILIAN J. TELFORD T he Ctenophora, also known as comb jellies or sea gooseberries, are a phylum of beautiful marine animals. Several molecular phylogenetic studies 2–4 have made the extra- ordinary claim that Ctenophora, despite sharing ‘advanced’ characteristics — such as muscles, nerves and epithelial tissues — with Bilateria and Cnidaria, are more distantly related to these groups than are the simple Porifera, which lack these features. In contrast to the conventional ‘Porifera- sister’ hypothesis, the Ctenophora-sister tree, in which the Ctenophora are the sister group of all other animals, implies either that muscles, nerves and epithelia evolved independently in two animal lineages (in Ctenophora and in the ancestor of Bilateria and Cnidaria), or that these characteristics are ancient and have been lost by sponges (Fig. 1). Considering these surprising implications, it was inevitable that the Ctenophora-sister idea would be highly controversial 5–7 .  Critics of the original studies suggest that they were affected by errors in tree reconstruc- tion caused by the use of inadequate phylo- genetic models. Pisani et al. 1 investigate this possibility by reanalysing several published data sets comprising concatenated alignments of many genes 2–5 , and a data matrix recording the presence or absence of more than 23,000 genes in different animal species 3 . The authors present three lines of evidence to suggest that the Ctenophora-sister trees are an artefact. First, recognizing that tree-reconstruction errors can stem from a poor fit between an evolutionary model and real data, they use the statistical technique of cross-validation to show that a ‘site-heterogeneous’ model 8 best fits the data. These CAT models (named for modelling multiple categories of site) avoid the assumption of a homogeneous process of amino-acid substitution across sites within genes, and they have repeatedly been shown to outperform site-homogeneous models. The CAT model provided the best fit to the pub- lished data and supported the Porifera-sister hypothesis; less-well-fitting models better suit a Ctenophora-sister situation. The authors’ second approach considers the common artefact of long-branch attraction (LBA), which could cause the long ctenophore branch to be attracted downwards towards the long branch leading to the non-animal species that form the root of the tree 9 — these groups are referred to as outgroups. The authors rea- son that, the longer the branch leading to the outgroups, the higher the likelihood of LBA. Removing the most distant outgroups shifts support from the Ctenophora-sister to the Porifera-sister picture, suggesting that the Ctenophora-sister result is an effect of LBA. Third, the authors show that previous analyses of the gene presence-or-absence matrix, cited as an independent source of evi- dence supporting the Ctenophora-sister tree 3 , were affected by an unintentional bias: genes present in only one species were not recorded in the original matrix, and the prior existence of genes that have been lost in all sampled species was ignored. These exclusions lead to a systematic underestimation of the likelihood of a gene being lost in any given species. The effect is that missing genes (such as those absent from ctenophores) are more likely to be interpreted as never having existed than as having been lost during evolution — effectively pushing species that have lost many genes towards the root of the tree. When this known problem with pres- ence–absence data 10 is corrected, the result is a much more credible tree (the previous work had several odd features), and independent support for the Porifera-sister hypothesis. The position of Ctenophora has proved so difficult to determine because it involves three confounding circumstances: the main animal groups separated more than 540 million years ago during the Precambrian period, meaning that the phylogenetic signal supporting any clade is faint; Ctenophora was a fast-evolving taxon that seems to have lost features along the way; and there is a lack of informative interme- diates on a long branch leading to the recent radiation of modern ctenophore species. Care- ful use of models designed to avoid the worst effects of these problems, and experiments designed to detect these issues, are essential for us to understand the true affinities of this phy- lum. The analyses that fit these requirements support the Porifera-sister camp, providing a parsimonious interpretation of morphological evolution. Maximilian J. Telford is in the Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. e-mail: m.telford@ucl.ac.uk Methodological misconceptions LEONID L. MOROZ & KENNETH M. HALANYCH E ach new analysis of early animal phylogeny fuels debate about animal origins and the parallel evolution of animal complexity. Pisani et al. 1 have used phylogenetic methods that we FORUM Evolution A sisterly dispute Which phylum first branched off from the animal phylogenetic tree is a contested issue. A new analysis challenges the proposal that comb jellies are the sister group to all other animals, and emphasizes a ‘sponges-first’ view. Three evolutionary biologists weigh up the evidence. THE PAPER IN BRIEF ● ● There are five major branches of animals: Porifera (sponges), Cnidaria (jellyfishes, corals and related species), Ctenophora (comb jellies), Placozoa (Trichoplax) and Bilateria (all other animal phyla). ● ● Writing in Proceedings of the National Academy of Sciences, Pisani et al. 1 reanalyse some existing data and support the case that Porifera are the sister group to all other animals. ● ● The authors propose that this conclusion fits with the fact that sponges lack features present in the other phyla, such as a nervous system and muscles. ● ● However, other recent genomic analyses have suggested that the more complex Ctenophora are the sister group. 286 | NATURE | VOL 529 | 21 JANUARY 2016 NEWS & VIEWS For News & Views online, go to nature.com/newsandviews © 2016 Macmillan Publishers Limited. All rights reserved