Phylogenetic position of Ctenophora. A follow-up.

In a previous post I nagged about a paper reporting a genome of a ctenophore Mnemiopsis leidyi (Ryan et al. 2013), where it was suggested that ctenophores are the sister group to all other animals. Now another genome from this animal phylum, that of Pleurobrachia bachei, has been sequenced along with transcriptomes of additional 10 ctenophore species (Moroz et al. 2014)! Regarding the phylogenetic position of Ctenophora, the analysis by Moroz et al. are even less convincing than those by Ryan et al. (2013). Apparently only maximum likelihood analyses with RAxML were done (or at least reported), which either support Ctenophora as sister group to other animals or are inconclusive. But this is not the main point of the article. Moroz et al. suggest that nervous system and possibly muscles of ctenophores evolved independently from other animals (Cnidaria and Bilateria). They showed not only that ctenophores lack many Cnidaria+Bilateria specific genes associated with muscles, nervous system etc, but that ctenophores have recruited for those purposes nearly entirely different set of genes. So it seems unlikely that Ctenophora lost muscles and nervous system specified by genetic toolkit found in Cnidaria and Bilateria and then invented everything from scratch once again. More likely, Ctenophora and Cnidaria+Bilateria evolved phenotypic complexity independently from simpler ancestors. However, this does not mean that Ctenophora has to be a sister group to other animals, but a phylogenetic arrangement where Ctenophora is sister to Cnidaria and these together (called Coelenterata) form a sister group of Bilateria (as found by Philippe et al. 2009), seems less likely now, because it might exactly mean the loss and re-evolution of nerves and muscles in Ctenophora. Then again, compared to Bilateria, Cnidaria, and Porifera, contemporary ctenophores are genetically very closely related to each other (see Podar et al. 2001 and Extended Data Figure 3d in Moroz et al. 2014), meaning that they diverged from each other relatively recently, leaving a long stem going probably back to Precambrian. A lot can happen along this long stem, so who knows...

Regardless of the deepest phylogenetic relationships between animals, independent evolution of muscles and nervous system in ctenophores seems quite likely based on the results by Moroz et al. 2014. This led me to a realization that maybe the phylogenetic relationships between Porifera, Placozoa, Ctenophora, Cnidaria, and Bilateria actually do not matter much. These relationships tend to vary from study to study and the internal branches uniting these groups in different combinations tend to be very short. As short branches suggest little amount of evolution, maybe nothing remarkable happened along those branches anyway and most of the possible relationships between those main animal lineages are more or less equivalent? Then again, considering that these lineages diverged from each other more than 540 million years ago, difficulties in reconstructing their relationships can be expected. Too early to give up. More sophisticated analyses might help to figure out what are the likely causes for conflicting results (systematic errors or true lack of phylogenetic signal).

References

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

Podar M, Haddock SH, Sogin ML, Harbison GR (2001) A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes. Molecular phylogenetics and evolution 21: 218–230. doi: 10.1006/mpev.2001.1036

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. doi: 10.1126/science.1242592