Phylogeny digitisation

I was hunting around for further research on phylogeny image digitisation to see whether any advances had been made since I last published on the topic and to keep my previous post up-to-date. The main reason behind all of this is to see whether there would be a faster way to digitise a bunch of images that are accumulating on my hard drive. I thought it would be cool to do something with the ripped phylogenies for the iEvoBio Challenge but my current set of trees only has a total of 2,000 leaves and I need 10,000.
Anyway, I came across PHYLODIGM in my searches which looks promising. Thomas Laubach has also done some further work on TreeSnatcher Plus including using the benchmarking dataset from TreeRipper and a number of tree files found via Google searches. Additionally, he has released the source code under the GNU General Public License.
This all looks promising!!!

The phyloscape changes quickly, we need to build a better way to keep track of it

Since Hennig's 1969 major publication on the phylogeny of hexapod orders (Insecta + Entognatha), I have found more than 60 publications of phylogenies on the ordinal relationships within the group. Some may be re-analyses of the same data but it is still quite a large number of studies. Thirty-seven of these have been published in the last decade and this rapid change in the phylogenetic landscape of this group (and this is probably the case for many other lineages) is increasingly becoming hard to keep track of. Sure, you could do a regular Pubmed or WoS search for phylogen* + insecta but you then need to extract the phylogeny and put it in the context of previously published studies. Sure there are databases like TreeBase and PhyLoTa that provide ready-made phylogenetic reconstructions but the former has limited content and the latter has limited resolution at many nodes of interest.

It is important to have an up-to-date and complete image of the phylogenetic landscape of the groups we work on, even if the overall picture is blurry. This would provide a better idea of areas that require further taxonomic sampling and/or a larger number of characters to resolve the relationships of interest, it would also provide a valuable resource for comparative studies. For this to work, information needs to be integrated between different databases like PhyLoTA, TreeBASE, GenBank, Treefam etc. in an automated fashion as well as defrosting phylogenetic reconstructions from previously published studies (see my previous post). Perhaps a simple repository of third-party phylogenetic reconstructions would help: submitter - publication reference - figure number - phylogeny (newick, nexus, phyloxml, nexml ....). Although would anybody submit data? Perhaps I need to think of a way to reward those that do/

Reference

Hennig, W. 1969. Die Stammesgeschichte der Insekten. Frankfurt am Main, Germany: Kramer.

Comparing the different hypotheses for Strepsiptera

Image via Wikipedia
I have been comparing the different phylogenetic hypotheses for the Strepsiptera. As always, it has been hell to get the trees from images back into a suitable format for topology comparison. I have used the program METATREE for comparing multiple trees. The tree of trees essentially shows the two main hypotheses "Strepsiptera sister to Diptera" supported by the studies of Whiting and Wheeler using 18S and 28S rDNA, and at the other end of the metatree the "Strepsiptera sister to Coleoptera" supported by morphological studies and recent molecular studies using nuclear genes. Other differences in the Holometabola topologies are also illustrated in the metatree such as the variable position of the Hymenoptera. Anyway, to me, it looks like the research community is reaching a consensus on the "Strepsiptera problem": Strepsiptera sister to Coleoptera. What do you think?