Wednesday, June 08, 2011

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.

5 comments:

Ross Mounce said...

easy solution: GenBank-style mandatory data submission to an archive (e.g. TreeBASE) to be enforced by journals. 

Why did this not happen years ago? [seriously]

We're in such an irrecoverable mess now with trees spread far and wide across 1000+ journals and +40k articles... So much has been lost, and won't ever be re-extracted from images of pdfs... *sighs*

bljog said...

Never say never.

Victoria Plesskott said...

Hey, at first: I loooove your blog! Congrats.
I have made a new blog and I think we should talk about it because we kind of share the same interest and I have got some ideas. Would you like to hear them?:) Leave me a comment if you're interested. Peace!

Victoria Plesskott said...

Hey, at first: I loooove your blog! Congrats.
I have made a new blog and I think we should talk about it because we kind of share the same interest and I have got some ideas. Would you like to hear them?:) Leave me a comment if you're interested. Peace!

Panic Attacks said...

I agree with Ross. This should have happened years ago. So much lost, so much time wasted... 

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