Ctenophora is not a sister group to other animals after all

Since 2008 there have been a debate whether the phylum Ctenophora is a phylogenetic sister group to other animals or not (Dunn et al. 2008; Philippe et al. 2009). There were some who claimed to have resolved the debate (that Ctenophora really is a sister group to other animals: Ryan et al. 2013), but the presented evidence was not at all convincing, as I discussed some time ago. Recently, another paper (Whelan et al. 2015) came out that favoured Ctenophora as the sister group to other animals (hereafter referred to as Ctenophora-basal tree), but this time the results were much more convincing and I was prepared to believe the Ctenophora-basal tree.

But not so fast. It turns out I was fooled. Only half a year after the Whelan et al. (2015) publication, Pisani et al. (2015) showed that the analyses by Whelan et al., as well as all previous analyses favouring Ctenophora-basal tree, were still plagued by systematic errors. Pisani et al. (2015) found that the sponges (Porifera) are probably the sister group to other animals (as is usually assumed) after all, although exact position of Ctenophora relative to the remaining animals still needs additional research. For me, one of the most striking results from Pisani et al. (2015) was the re-analysis of genome content data (presence/absence of protein coding genes) from Ryan et al. (2013). The genome content tree that Ryan et al. (2013) recovered, contained several phylogenetic relationships that are highly suspect (e.g. non-monophyly of Annelida and a group containing a mollusc, an annelid and a chordate Branchiostoma). Remarkably, when Pisani et al. (2015) used a less biased model of gene content evolution, which does not underestimate gene losses as much as did the model used by Ryan et al. (2013), they recovered an animal tree of life that fully agreed with independent phylogenomic analyses based gene sequences. There was not a single nonsense clade left. And in that tree, Porifera replaced Ctenophora as the sister group to other animals.

As for the Whelan et al. (2015) study that fooled me, the main issue comes down to the choice of an out-group. Whelan et al. (2015) analysed some of their datasets also with more realistic, but computationally more demanding CAT model, but recovered nevertheless Ctenophora-basal tree. It turns out, though, that when more distant out-groups to animals (Fungi or Fungi plus non-choanoflagllate members of Holozoa) are excluded from the analysis (retaining only the members of Holozoa or only the choanoflagllates), Whelan et al. (2015) datasets do not support Ctenophora-basal tree anymore or even favour Porifera-basal tree. Whelan et al. (2015) actually did analyse their datasets also with alternative out-group compositions, but only with simpler evolutionary models and therefore it was not possible to discover that different out-group compositions affect results when using more complex CAT model! Such a simple trick which the authors could have done to test their results...

Another recent study also found Ctenophora-basal tree (Chang et al. 2015) using the CAT model. Although Chang et al. (2015) analyses did not include Fungi, it was not tested if excluding more distant non-choanoflagllate Holozoa taxa could affect the results. But this Ctenophora question was not the topic of this paper (it was about Myxozoa, highly reduced parasitic Cnidaria), although one of the co-authors was (Hervé Philippe) also a co-author in Pisani et al. (2015) paper, which studied the effect of out-group composition.

Still, it is disconcerting that depending on the composition of the out-group, even if the closest relatives are included, the results can change that dramatically: using CAT model and including Fungi, the Ctenophora-basal tree can be recovered with maximal statistical support, but using CAT model and excluding all out-groups except choanoflagllates (the closest relatives of animals), Porifera-basal tree can be recovered with maximal support instead. I would have thought that as long as the closest out-groups are also included (choanoflagllates) in the analyses, the more distant out-groups (Fungi) should not influence the results that much. This tells me again (as I discussed before) that whatever phylogenetic signal there is for the relationships between Porifera, Ctenophora, Placozoa, Cnidaria, and Bilateria, it is quite tiny. These groups separated from each other in the Precambrian (>540 Ma) probably rather rapidly, perhaps within a few tens of millions of years or even within a shorter time period. Because it starts to look like the nervous systems and perhaps muscles might have evolved independently even three times in Ctenophora, Cnidaria, and Bilateria (Liebeskind et al. 2015; Moroz et al. 2014), it seems to be of less importance what are the exact phylogenetic relationships between Porifera, Ctenophora, Placozoa, Cnidaria, and Bilateria. Ctenophora, Cnidaria, and Bilateria might have evolved their morphological complexity independently from Porifera or Placozoa-like ancestors.


Chang ES, Neuhof M, Rubinstein ND, Diamant A, Philippe H, Huchon D, Cartwright P (2015) Genomic insights into the evolutionary origin of Myxozoa within Cnidaria. Proceedings of the National Academy of Sciences 112: 14912–14917. doi: 10.1073/pnas.1511468112
Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith S a, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen M V, Haddock SHD, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745–749. doi: 10.1038/nature06614
Liebeskind BJ, Hillis DM, Zakon HH (2015) Convergence of ion channel genome content in early animal evolution. Proceedings of the National Academy of Sciences 112: E846–E851. doi: 10.1073/pnas.1501195112
Moroz LL, Kocot KM, Citarella MR, Dosung S, Norekian TP, Povolotskaya IS, Grigorenko AP, Dailey C, Berezikov E, Buckley KM, Ptitsyn A, Reshetov D, Mukherjee K, Moroz TP, Bobkova Y, Yu F, Kapitonov V V, Jurka J, Bobkov Y V, Swore JJ, Girardo DO, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills CE, Rast JP, Derelle R, Solovyev V V, Kondrashov F a, Swalla BJ, Sweedler J V, Rogaev EI, Halanych KM, Kohn AB (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510: 109–114. doi: 10.1038/nature13400
Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, Quéinnec E, Da Silva C, Wincker P, Le Guyader H, Leys S, Jackson DJ, Schreiber F, Erpenbeck D, Morgenstern B, Wörheide G, Manuel M (2009) Phylogenomics revives traditional views on deep animal relationships. Current Biology 19: 706–712. doi: 10.1016/j.cub.2009.02.052
Pisani D, Pett W, Dohrmann M, Feuda R, Rota-Stabelli O, Philippe H, Lartillot N, Wörheide G (2015) Genomic data do not support comb jellies as the sister group to all other animals. Proceedings of the National Academy of Sciences 112: 15402–15407. doi: 10.1073/pnas.1518127112
Ryan JF, Pang K, Schnitzler CE, Nguyen A-D, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P, Smith S a, Putnam NH, Haddock SHD, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD (2013) The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution. Science 342: 1242592–1242592. doi: 10.1126/science.1242592
Whelan N V., Kocot KM, Moroz LL, Halanych KM (2015) Error, signal, and the placement of Ctenophora sister to all other animals. Proceedings of the National Academy of Sciences 112: 5773–5778. doi: 10.1073/pnas.1503453112


Root of the Eukaryotic Tree of Life

While it has become quite clear that the last eukaryotic common ancestor (LECA) was a bikont, i.e. had two anterior cilia to move around (as I wrote previously), it now seems that the LECA wasn't only a bikont, but also an excavate. Excavates are one of the five main groups of eukaryotes (Adl et al.2012) having ancestrally two cilia and a ventral feeding groove. Excavates include for example Trichomonas (Parabasalia), Giardia (Fornicata), Euglenozoa (e.g. Euglena, Trypanosoma), Heterolobosea, Jakobida (latter three belonging to Discoba), and Malawimonas, but it has turned out that they might not form a monophyletic group that seemed quite likely in 2009 (Hampl et al. 2009). In my previous post I treated excavates as monophyletic and avoided discussing them, although I was aware of some problems. Particularly, Malawimonas, which is structurally a typical excavate (possessing two cilia with a characteristic ciliary apparatus and a ventral feeding groove; Simpson, 2003) did not want to group very well with other excavates in phylogenomic analyses (Rodríguez-Ezpeletaet al. 2007; Derelle & Lang, 2012; Zhao et al. 2013; Brown et al. 2013). I thought perhaps the data was incomplete to make a big deal about this. Now it looks pretty clear (Cavalier-Smith et al. 2014; 2015; Derelle et al. 2015) that Malawimonas is more closely related to unikont/Opimoda branch (amoebae, animals, fungi and others; Fig. 1) than to (most) other excavates. Interestingly, phylogenomic analyses by Cavalier-Smith et al. (2014; 2015) reveal that excavate groups Parabasalia, Fornicata, and Preaxostyla might also be more closely related to unikonts than to Discoba (Euglenozoa, Heterolobosoa, and Jakobida). Parabasalia, Fornicata, and Preaxostyla are classified under Metamonada, who are all anaerobic or microaerophilic and lack typical respiratory mitochondria. Many of them are parasites or symbionts of animals. Unfortunately most of them are fast evolving, making it difficult to place them in phylogenetic analyses, particularly Trichomonas and Giardia for which full genomes are available. It would be necessary to obtain additional genome scale data for more slowly evolving free-living species from groups like Dysnectes and Carpediemonas (Takishita et al. 2012) to place representatives of Metamonada among eukaryotes more reliably.

Figure 1. Phylogeny of eukaryotes updated from my previous post mainly on the basis of Cavalier-Smith et al. (20142015) and Derelle et al. (2015) papers. Although since 2010, Cavalier-Smith prefers to root the tree between Euglenozoa (member of Discoba) and other eukaryotes, the rooting found by Derelle et al. (2015) is more reliable, because it is based on large number of mitochondrial and other bacterial genes for which there are closer out-groups available than for genes of archaeal origin (see for example the rooting found by Lasek-Nesselquist& Gogarten, 2013 which fits Cavalier-Smith's scenario). Cavalier-Smith (20102013) lists some genomic characters that appear to be ancestral (i.e. shared with prokaryotes) in Euglenozoa but derived in other eukaryotes. The problem is that full genome sequences are available only for few fast evolving and mostly parasitic Euglenozoa and other excavates, which makes these kinds of lists highly speculative.

If the rooting of the eukoryote tree (Fig. 1) is correct, then it really seems that the LECA might have been quite similar to a typical excavate like Malawimonas or a jakobid (e.g. Jakoba, Reclinomonas, Andalucia). This scenario finds support also from some alveolates (e.g. Colponema) that are structurally quite similar to excavates (Tikhonenkov et al. 2014; Cavalier-Smith et al. 2014). Apparently, Colponema, Acavomonas and many other similar undescribed groups (Janouškovecet al. 2013; Tikhonenkov et al. 2014) are phylogenetically diverse bunch that are variously related to, but clearly outside of the three main groups of alveolates (ciliates, apicomplexans, and dinoflagellates).

Adl SM, Simpson AGB, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Gall L le, Lynn DH, McManus H, Mitchell E a D, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick L, Schoch CL, Smirnov A, Spiegel FW (2012) The revised classification of eukaryotes. The Journal of eukaryotic microbiology 59 (5): 429–514. doi: 10.1111/j.1550-7408.2012.00644.x
Brown MW, Sharpe SC, Silberman JD, Heiss AA, Lang BF, Simpson AGB, Roger AJ (2013) Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proceedings. Biological sciences / The Royal Society 280 (1769): 20131755. doi: 10.1098/rspb.2013.1755
Cavalier-Smith T (2010) Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree. Biology letters 6: 342–345. doi: 10.1098/rsbl.2009.0948
Cavalier-Smith T (2013) Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa. European journal of protistology 49 (2): 115–178. doi: 10.1016/j.ejop.2012.06.001
Cavalier-Smith T, Chao EE, Snell E a, Berney C, Fiore-Donno AM, Lewis R (2014) Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa. Molecular phylogenetics and evolution 81: 71–85. doi: 10.1016/j.ympev.2014.08.012
Cavalier-Smith T, Chao EE, Lewis R (2015) Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista. Molecular phylogenetics and evolution. doi: 10.1016/j.ympev.2015.07.004
Derelle R, Lang BF (2012) Rooting the Eukaryotic Tree with Mitochondrial and Bacterial Proteins. Molecular biology and evolution 29: 1277–1289. doi: 10.1093/molbev/msr295
Derelle R, Torruella G, Klimeš V, Brinkmann H, Kim E, Vlček Č, Lang BF, Eliáš M (2015) Bacterial proteins pinpoint a single eukaryotic root. Proceedings of the National Academy of Sciences 112: E693–E699. doi: 10.1073/pnas.1420657112
Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AGB, Roger AJ (2009) Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proceedings of the National Academy of Sciences of the United States of America 106: 3859–3864. doi: 10.1073/pnas.0807880106
Janouškovec J, Tikhonenkov D V, Mikhailov K V, Simdyanov TG, Aleoshin V V, Mylnikov AP, Keeling PJ (2013) Colponemids represent multiple ancient alveolate lineages. Current biology 23: 2546–2552. doi: 10.1016/j.cub.2013.10.062
Lasek-Nesselquist E, Gogarten JP (2013) The effects of model choice and mitigating bias on the ribosomal tree of life. Molecular phylogenetics and evolution 69: 17–38. doi: 10.1016/j.ympev.2013.05.006
Rodríguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H, Lang BF (2007) Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Current Biology 17: 1420–1425. doi: 10.1016/j.cub.2007.07.036
Simpson AGB (2003) Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). International Journal of Systematic and Evolutionary Microbiology 53: 1759–1777. doi: 10.1099/ijs.0.02578-0
Takishita K, Kolisko M, Komatsuzaki H, Yabuki A, Inagaki Y, Cepicka I, Smejkalová P, Silberman JD, Hashimoto T, Roger AJ, Simpson AGB (2012) Multigene Phylogenies of Diverse Carpediemonas-like Organisms Identify the Closest Relatives of ‘Amitochondriate’ Diplomonads and Retortamonads. Protist 163: 344–355. doi: 10.1016/j.protis.2011.12.007
Tikhonenkov DV, Janouškovec J, Mylnikov AP, Mikhailov KV, Simdyanov TG, Aleoshin VV, Keeling PJ (2014) Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., Two New Alveolate Phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and Their Contributions to Reconstructing the Ancestral State of Alveolates and Eukaryotes. PloS one 9: e95467. doi: 10.1371/journal.pone.0095467
Zhao S, Shalchian-Tabrizi K, Klaveness D (2013) Sulcozoa revealed as a paraphyletic group in mitochondrial phylogenomics. Molecular phylogenetics and evolution 69 (3): 462–468. doi: 10.1016/j.ympev.2013.08.005