In the last two years, several studies have used whole genomes to infer the phylogeny of animals. With the exception of one paper published a few days ago, they have consistently found that comb jellies (Ctenophora) are sister group of all remaining animals, including sponges. Since these four studies have similar datasets and analyzed them in different ways, it seems a great opportunity to discuss the various choices that go into using data from whole genomes in phylogenetics and their potential consequences.
Instead of having everyone reading a single paper as usual, this week the idea is to contrast four recent papers on the animal phylogeny during our discussion. For those that intend to attend Journal Club this week, we ask to choose at least one of the four papers below to read. To make sure every paper will be read by at least 1-2 people , we have also prepared a sign-up sheet where you can let others know which paper you will be reading.
You can find the sign-up sheet at https://docs.google.com/spreadsheets/d/1nWGGVGFHZICiDknMfDGYEWXoSF5tTtqCvWmcOhsUG9Q/edit?usp=sharing and the paper pdfs below.
- Borowiec, M.L., Lee, E.K., Chiu, J.C. & Plachetzki, D.C. 2015. Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC Genomics 16: 987. doi: 10.1186/s12864-015-2146-4
- 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. Proc. Natl. Acad. Sci. 201518127. doi: 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: 1242592. doi: 10.1126/science.1242592
- Whelan, N. V., Kocot, K.M., Moroz, L.L. & Halanych, K.M. 2015. Error, signal, and the placement of Ctenophora sister to all other animals. Proc. Natl. Acad. Sci. 112: 5773–5778.
We will be meeting at Friday December 11 at 11am in the MCZ labs 4th floor seminar room. Snacks and coffee will be provided!
borowiec_et_al._2015_bmc_genomics_extracting_phylogenetic_signal_and_accounting_for_bias_in_whole-genome_data_sets_supports_the_ctenopho.pdf |
pisani_et_al._2015_proceedings_of_the_national_academy_of_sciences_genomic_data_do_not_support_comb_jellies_as_the_sister_group_to_all_o.pdf |
ryan_et_al._2013_science_the_genome_of_the_ctenophore_mnemiopsis_leidyi_and_its_implications_for_cell_type_evolution.pdf |
whelan_et_al._2015_pnas_error__signal__and_the_placement_of_ctenophora_sister_to_all_other_animals.pdf |