Wednesday, March 10, 2010

Resolving the Vertebrate Tree

In a recent paper from BMC Biology, Bob Thomson and Brad Shaffer at the University of Californa - Davis quantify progress toward resovling the vertebrate tree of life. Using a phyloinformatic pipeline and GenBank data from a large sample of vertebrate diversity (100 clades, encompassing about 12,000 species), the authors ask the simple question: "How many nodes in the vertebrate tree do we have some information about?" The brief answer is about a quarter, though this information is highly skewed. Avian and mammalian clades are on average better resolved than the other major vertebrate lineages, and marine clades are on average very poorly resolved. In addition to estimating current 'resolution', Thomson and Shaffer analyze the accumulation of this resolution through time. The superexponential growth curve of sequences in GenBank is now well-known. However, there is little understanding of how this accumulation of data correlates with accumulation of phylogenetic information. These analyses indicate that information is accumulating polynomially and, if current rates continue, we might understand a large majority of the vertebrate tree within a few decades.

Bob has made their data available via a google motion chart, which allows for easy exploration of the studies' results (embedded below):


Neil said...

Amazing. Is there anyway to view this in a separate window? The right side is cropped in my browser.

Glor said...

Trying to fix it now. It's a bit small, but you can see the full size version at Bob's page.

Anonymous said...

Wow- this is really impressive.

slybird said...

That is awesome! How soon can we get interactive graphics like that in publications? :)

Poletarac said...

I'm in a cafe with ten people who don't know anything about biology peering over my shoulder to see the pretty moving bubbles. Maybe I'm wrong, but it looks like someone at Google took to heart Hans Rosling's TED talk, and it's already filtered to biology! Excellent!

Epic Systems said...

I have the pleasure to brief on our Data Visualization software "Trend Compass".

TC is a new concept in viewing statistics and trends in an animated way by displaying 5 axis (X, Y, Time, Bubble size & Bubble color) instead of just the traditional X and Y axis. It could be used in analysis, research, presentation etc. In the banking sector, we have Deutsche Bank New York as our client.

Link on Chile's Earthquake (27/02/2010):

This a link on weather data :

This is a bank link to compare Deposits, Withdrawals and numbers of Customers for different branches over time ( all in 1 Chart) :

Misc Examples :

This is a project we did with Princeton University on US unemployment :

A 3 minutes video presentation of above by Professor Alan Krueger Bendheim Professor of Economics and Public Affairs at Princeton University and currently Chief Economist at the US Treasury using Trend Compass :

Latest financial links on the Central Bank of Egypt:

I hope you could evaluate it and give me your comments. So many ideas are there.

You can download a trial version. It has a feature to export EXE,PPS,HTML and AVI files. The most impressive is the AVI since you can record Audio/Video for the charts you create.

Dan Warren said...

Google actually bought the motion chart technology from Hans Rosling a few years back. I wrote a script to make it possible to build them from Excel spreadsheets and was all set to post it on the Wainwright lab blog, but then Google went ahead and just added it to Google Docs.

Chris said...

Need a youtube movie to explain what it's all about: looks cool though