U-M biologist plays key role in effort to create first comprehensive tree of life
ANN ARBOR—Since Darwin, assembling an evolutionary tree that shows the relationships between all known species of life has been one of the grandest and most daunting challenges facing biologists.
Despite 150 years of effort, there’s still no comprehensive tree of life, no single diagram that displays the links between all of the 1.8 million or so named species of animals, plants and microorganisms.
Now, with $5.76 million from the U.S. National Science Foundation, a group of scientists from across the country will attempt to complete the first rough draft of the entire tree of life in the first year of a three-year project called the Open Tree of Life.
This tree is expected to be a powerful tool that will enable scientists to interpret the patterns and processes of evolution and to predict the responses of life to rapid environmental change. NSF announced the award of first-year funding for the project last week.
The Open Tree of Life project is led by Karen Cranston of Duke University and has several sub-groups. University of Michigan computational evolutionary biologist Stephen Smith heads the group that will tackle the nitty-gritty details of piecing together all the existing branches, stems and twigs of life’s tree into a single diagram.
Smith joined the U-M faculty in January as an assistant professor of ecology and evolutionary biology, his first university faculty position.
“This is a very complicated beast, and I’m really looking forward to the challenge,” Smith said of the draft tree. “I really like taking on a problem that somebody, at some point, in a room that I’ve been sitting in, has said is not possible to do. And this is one of those instances.”
Originally trained as a botanist, Smith began building evolutionary trees, also call phylogenetic trees or simply phylogenies, in 2003 as a Ph.D. student at Yale. When confronted by the fact that the computer software needed to build very large trees did not exist, Smith—who began studying programming when he was 12—began writing his own.
Since then, Smith’s written countless programs that have enabled him and his colleagues to create some of the largest “mega-phylogenies” in existence, including one that displays 56,000 species of flowering plants.
The self-described computer geek and ex-punk rocker was dubbed the “botanist hacker” by The Scientist magazine in 2010. Both Smith’s computer savvy and his knowledge of evolutionary biology will be essential to the Open Tree of Life project, which will require the use of computer programs that don’t yet exist.
“We’ll be taking advantage of the efforts of the many other researchers who’ve built smaller trees, and finding new ways to combine that published data to help give us a look at the first draft of the full tree of life,” Smith said. “To do this, we’ll have to code our own solutions. There’s nothing out of the box that we can use.”
The Open Tree of Life project is part of a larger NSF-funded effort called Assembling, Visualizing and Analyzing the Tree of Life. In addition to the University of Michigan and the National Evolutionary Synthesis Center at Duke University, the Open Tree of Life project includes scientists from Texas A&M University, the University of Kansas, the University of Florida, Brigham Young University, the Field Museum of Natural History and Michigan State University.
Smith said previous efforts to build a complete tree of life fell short due to a lack of both phylogenetic data and computer power. But over the last decade, computer power has increased substantially, and the ability to build enormous phylogenies has emerged.
“Thanks largely to previous tree-of-life funding from the National Science Foundation, researchers have been able to piece together the backbone of the tree, which helped us understand, for example, the early branches of the animal and plant trees of life,” Smith said. “So we are poised now to use the data that’s been generated over the last 10 years to construct the full tree of life.”
Just as the Human Genome Project provided numerous, largely unanticipated new insights about the genetic underpinnings of life, constructing the full phylogenetic tree of life is expected to fuel fundamental research on the nature of biological diversity and its relationship to human well-being, AVAToL scientists stated in their proposal to NSF.
The new information is expected to help enhance agriculture, identify and combat diseases (of humans and crops), conserve biodiversity, and predict responses to global climate change and to biological invasions.
The information will be available on a publicly accessible website where users can browse, search and contribute new information. Scientists will be encouraged to share their phylogenetic trees to the constantly-updating project. As an incentive, the AVAToL team will offer various computer tools that will enable researchers to better understand the evolutionary relationships between the organisms they study.
Smith’s lab will receive about $900,000 over the next three years for the tree project. He plans to hire two postdoctoral researchers and will include several graduate students.
“This is similar to when astronauts went to the moon and looked back at the Earth for the first time,” Smith said. “It will be our first opportunity to see all of the organisms that we know on Earth. This is our moon shot.”
- Department of Ecology and Evolutionary Biology: http://www.lsa.umich.edu/eeb
- “Stephen Smith: The Botanist Hacker,” an article in The Scientist: http://classic.the-scientist.com/blog/print/57180
- Interested in doing a profile on this University of Michigan scientist? Watch him play the banjo: http://www.youtube.com/watch?v=KrzdoigLmbY