Files changed (1)
The cat analyses of the genome sequence datasets recovered a clade comprised of Ctenophora+Porifera (Table 1, Ryan et al. 2013). The support for this clade was sensitive to outgroup sampling. Here we test whether this novel relationship is incongruent with the gene content analyses using the SOWH test, as implemented by the tool [SOWHAT](https://github.com/josephryan/sowhat). This test strongly reject Ctenophora+Porifera, with a p-value of 0. The test [results](https://bitbucket.org/caseywdunn/mnemiopsis_trees_2014/src/master/tests/sowh_ct_po/ctpo_sowhat.out/sowhat.results) are in the folder `tests/sowh_ct_po/`.
In order to get a sense of the most computationally intensive analyses first, cat+gtr (the most complex model available in phylobayes) was first applied to the EST datasets (the largest matrices). These analyses are in the folder `est_pb_catgtr/`. There are four matrices, which differ in which out groups to Metazoa are included. These matrices are Opisthokonta, Holozoa, Choanimalia, and Animalia. Two chains were run per matrix. Each chain was run for seven days on 40-48 cores.
Ctenophora is recovered as the sister group to all other animals in 100% of the sampled trees. Xenacoelomorpha is polyphyletic.
The cat analyses presented by Ryan et al. of the EST sequence dataset did not converge after months of run time. We therefore created reduced-taxon EST sequence datasets. The following taxa were removed from the EST matrices:
Here we check to see of the clade comprised of Ctenophora+Porifera recovered in the cat analyses of the genome sequence datasets (Table 1, Ryan et al. 2013) is also recovered with the more complex cat+gtr model. These analyses are in the folder `genome_pb_catgtr/`. The Animalia matrix was not analyzed, since it has no outgroup taxa and therefore cannot inform rooting.