I gave a phyloseminar last week, on the problem of dealing with patter-heterogeneity across sites in phylogenetic inference. I find this idea of phyloseminars really neat. Many thanks (and kudos) to Erick Matsen, for organizing all this. There is now quite a rich collection of phyloseminars given by many people and on many subjects in evolutionary sciences, which represents a such a valuable resource on the web. Here is the link:
To put things in context, I have been caught in the middle of a controversy about the phylogeny of animals — more specifically, but not only, concerning the phylogenetic position of ctenophores (comb jellies). As you may know, ctenophores have been recently proposed as being the sister-group to all other animals, including sponges (Moroz et al, 2014, Ryan et al, 2014). This ctenophore-sister hypothesis is not supported, however, when you use more sophisticated models accounting for variation across sites in the amino-acid replacement process (the CAT and CAT-GTR models, implemented in PhyloBayes). Instead, these two models give sponges sister to all other animals, as is more traditionally believed (although never with really strong support, and in a way that depends on the exact choice for the outgroup). A detailed analysis is given in Pisani et al (2015).
My interpretation of all this (which is also the interpretation suggested in Pisani et al, 2015) is that ctenophore-sister is fundamentally a long-branch attraction artifact caused by the use of inadequate models of sequence evolution. But then, not everyone agree with this interpretation (e.g. Halanych et al, 2016). And progressively, this controversy about ctenophores is becoming a question about which models — and which software programs — should be used in the context of large-scale phylogenetic reconstructions. The phyloseminar I gave last week is in fact the last of a series of three (the other two were given by Andrew Roger and Nathan Whelan), series which can be seen as organizing a debate about the role of site-heterogeneity in phylogenetic inference.
In any case, all this raises very important questions about the current situation in the field of phylogenetic studies. Are current models and methods adequate, in particular, for reconstrcuting ‘deep’ phylogenies (over deep evolutionary times)? Where do we stand today, and what can we hope, in terms of methodological progress, for the next years on this front?
In the next posts I will publish on this blog, I will come back to some of those questions. So, bear with me!..
Halanych, K. M., Whelan, N. V., Kocot, K. M., Kohn, A. B., & Moroz, L. L. (2016). Miscues misplace sponges. Proceedings of the National Academy of Sciences, 113(8), E946–7. http://doi.org/10.1073/pnas.1525332113
Moroz, L. L., Kocot, K. M., Citarella, M. R., Dosung, S., Norekian, T. P., Povolotskaya, I. S., et al. (2014). The ctenophore genome and the evolutionary origins of neural systems. Nature, 510(7503), 109–114. http://doi.org/10.1038/nature13400
Pisani, D., Pett, W., Dohrmann, M., Feuda, R., Rota-Stabelli, O., Philippe, H., et al. (2015). Genomic data do not support comb jellies as the sister group to all other animals. Proceedings of the National Academy of Sciences, 112(50), 15402–15407. http://doi.org/10.1073/pnas.1518127112
Ryan, J. F., Pang, K., Schnitzler, C. E., Nguyen, A.-D., Moreland, R. T., Simmons, D. K., et al. (2013). The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science, 342(6164), 1242592. http://doi.org/10.1126/science.1242592