Open Tree of Life

SciWorks Radio is a production of 88.5 WFDD and SciWorks, the Science Center and Environmental Park of Forsyth County, located in Winston-Salem. Follow Shawn on Twitter @SCIFitz.

What do you, an ankylosaur, and a shiitake mushroom have in common? Every animal, plant, fungus, or microorganism - in other words, all life on earth - can be traced back roughly four billion years to a single-celled common ancestor in Earth's early oceans. How do you keep track of that kind of family history? To find out, I spoke with computational phylogeneticist Dr. Karen Cranston from Duke University. She is one of eleven principal investigators for the Open Tree of Life project, in a collaboration involving ten institutions. (official Duke University press release here)

The goal of Open Tree of Life was to try and create a draft of the evolutionary history of all species, and to make that something that was available on the internet in a way that we could continue to update it as new data is published and made available. Even though there was millions and millions and millions of years, a billion years, between that first life and you or me or your dog or my cat, there's still this shared history. You had DNA in those original organisms. It duplicated, it changed, it mutated over time, and even over all that period of time, we still have enough signal to do the kind of research we're doing now. If we look at DNA of extant, or modern organisms that live right now, we can reconstruct that history that goes back down to the root of the tree.

A tree of life connects species to one another the way a family tree shows how you're related to great uncle Sherman. Tens of thousands of trees have been put together over the years, though this project combines the 500 or so that were available in a compatible digital format. Even with 2.3 million named species, which constitute only the tips of the tree branches, this is considered a first draft.

We know there are far more than 2.3 million species on the planet, so that's part of what we're trying to do here is to say, what can we build a tree of right now, and where do we still need to do more work? The tree is not complete in the sense that it doesn't include what we think is the true extent of biodiversity on the planet. We're still discovering new organisms. In the microbial world, the rate of discovery is just enormous right now. The other thing that will undoubtedly happen as we add new data and revise the methods is that the actual tree itself for those species will change. So over time we revise our hypothesis about evolutionary history and things that we thought were more closely related move further apart on the tree, or we find unlikely connections between species.

And that's the catch with this massive project: it is set up so that researchers worldwide, from now into the future, can contribute their work, giving it a life of its own.

So the name of the project, the Open Tree of Life, what we're talking about is this movement of open science; trying to be as open as possible with our software, trying to make the data as available and easily accessible as possible, trying to keep our conversation and documentation online in public places. All of our software is open source, and we're using the same sort of tools they would use to manage open source software for our primary database of trees. So it makes it really easy for other people to access that data, and it will allow other people to build interfaces to actually deposit into that data store without us actually owning it or controlling it in the way that if we were hosting it on our own servers. The movement of open science is about trying to be as transparent as possible about what we're doing and to make it easy for other projects to build upon what you're doing. It's something that I am really excited about.

This Time Round, the theme music for SciWorks Radio, appears as a generous contribution by the band Storyman and courtesy of UFOmusic.com.