Bird supertree project

Welcome to the bird supertree project! This is Katie Davis's PhD project, under the supervision of Rod Page at the University of Glasgow. These pages provide some results (i.e., the supertree). However, we'd like you to help us make this supertree. We're interested in both getting a better tree, and getting an idea of whether an "open source" approach to large-scale phylogenetics can work.

What is a supertree?

If you are new to supertrees, we suggest looking at this page assembled by Olaf Bininda-Emonds. Olaf has also edited a book on the subject (Phylogenetic supertrees: Combining information to reveal the Tree of Life).

Open source phylogenetics

Katie has assembled 748 source trees (you can view them online). She has built an initial MRP supertree (shown on the results page).

What's in it for us?

In short, it is likely that somebody else has more computational resources than we do, hence we stand to get a better tree.

The other benefit is "with many eyes all bugs are shallow" -- if the data set contains errors (despite our careful checking), then it is likely that the more people look at the data the more likely they will be found.

What's in it for you?

In a word, credit. We will include you in the acknowledgments in the manuscript describing this work if you find a shorter tree than ours, and will offer co-authorship for the person (or persons) that find the best tree.

In addition, if you are interested in bird phylogeny, you get early access to the supertree, with the proviso that it may change if somebody finds a better tree.

How to contribute

Step 1: Grab the data

The source trees (edited to ensure taxonomic names are consistent) are here, and the MRP data matrix is here (in NEXUS format). There is a also a copy in Hennig86 format for programs like TNT. The data set is the same as the one we are using, but some details are not included (such as the source of each tree). This information will be included in the final manuscript.

Step 2: Build supertree

We are using MRP, mainly because it is the only implementation we have available that scales to this problem. If you have alternative methods, we'd also be interested in how that method performs.

Step 3: Upload your results

We provide a form for uploading your supertree (as well as a tool for visualising it online). Your supertree will be visible on the results page.

How to comment on this project

You can send either Katie or Rod an email, or add comments on the blog describing this project.

Bird photos from Flickr Birds of the World