New Branches (of Knowledge) Help Grow the Tree of Life

Wednesday, July 18 2012

By Amanda Cairo

MOSCOW, Idaho – It’s a revolutionary time in biology and resulting data are piling up. Luke Harmon, University of Idaho associate professor of biological sciences, and his peers are hoping to add to a global research corps of knowledge focused on evolution, with the help of a three-year, $4 million National Science Foundation grant.

“As we’re sequencing whole genomes of a wide variety of species, we’re swamped with information,” said Harmon. “It’s important to use this information to understand evolution, and to know where we come from.”

The grant will use information from the growing Tree of Life – a diagram showing how all species are related – to learn more about evolution.

Harmon is the principal investigator for the project, entitled "Arbor: Comparative Analysis Workflows for the Tree of Life.” He is joined by co-investigators Robert Thacker, University of Alabama-Birmingham; Chelsea Specht, University of California-Berkeley; Curtis Lisle, chief executive officer of Knowledge Vis; Jorge Soberon, University of Kansas; Wes Turner, technical leader at Kitware and Charles Hughes, University of Central Florida. In addition, at least 8-9 graduate and post-doctoral students and a handful of computer programmers will be involved in the project.

“It’s an exciting time in evolutionary studies, and Luke and his team are leading the charge to make sure data are being collected in a central, manageable space with the appropriate tools that will allow researchers to use it effectively,” said Jack McIver, University of Idaho vice president of research and economic development. “The University of Idaho is dedicated to the stewardship of data so that it can be used to generate new knowledge and to address the problems of the future.”

While there are computer programs that aid researchers in making evolutionary links between species, Harmon said those can be cumbersome and require someone deeply entrenched in computer programming. With the software Harmon and the team will be creating, researchers will readily be able to access information and make faster deductions and links in their research.

“Right now, we still don’t know how many species are on the planet, it could be 10 million, 100 million or more,” said Harmon. “That’s a lot of data and connections that we’re bringing into one tree.”

Once the data come together, researchers can better see how species interact, how their traits evolve, the nature of their geographic relationships, and their emergence and extinction patterns all based on where those species are on the tree.

“You can do a lot with this,” said Harmon. “People will be able to do things that we haven’t even imagined yet. I look forward to what that might be.”

In addition, the program developed by Harmon’s research team can be used to map branches on a smaller scale to look at specific groups of species. For example, one could study the evolution of a particular group of bacteria from a common ancestor – and figure out how some became harmful and others benign, and how to treat associated illnesses.

Harmon said the tree could even help in court cases. In one famous case an evolutionary tree was used to show how HIV was transmitted from a dentist to patients.

The project came out of an NSF ideas lab, a gathering that drew scientists from around the country into a think tank retreat. Harmon connected with like-minded researchers from across the country to create this Tree of Life project concept.
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