Posts tagged “Arbor

Mapping the Tree of Life: the ARBOR Project

arbor

Open Tree of Life met with ARBOR, a program funded by the National Science Foundation, to talk about what changes have been made featuring the synthetic tree of life. We spoke with Dr. Luke Harmon, an associate professor at the University of Idaho’s department of Biology.  Dr. Harmon has been using comparative biology to determine what the tree of life can tell us about evolution over long time scales.

What has ARBOR been working on right now?

 Comparative Biology is at the heart of the ARBOR project. Using the evolutionary relationships among species, we can learn something about trait evolution and the formation of new species. For example, there really is no basic ‘ladder of life’ stemming from simpler organisms to more complex; instead, evolution varies among groups and through time in complex and interesting ways. It’s hard to do what we do with traditional tools. Instead, we have to use new tools to analyze how species have diversified to generate the tree of life

How have phylogeny studies changed over time?

A lot of progress has been made in the last twenty years regarding our understanding of the relationships among different species. We now know a lot more about how species are related to one another and how they evolved from their common ancestors. The Open Tree of Life is the best possible example of this sort of synthesis – it’s almost like the human genome project in that it is generating a very good map that will connect all organisms on earth in a single phylogenetic tree. One problem, though, is that there is just so much information contained in large phylogenetic trees, and we don’t always know how to extract information about how organisms evolve. ARBOR is developing tools to read the stories of evolution from these phylogenies.

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Online publication to follow the three AVAToL projects

PLOS Currents: Tree of Life

PLOSPeer-reviewed articles about the Open Tree of Life as well as two related projects, Arbor and Phenomics, will be available on PLOS Currents: Tree of Life. The online publication allows the researchers to document their progress in developing software and other tools.

The three research endeavors were developed during an Ideas Lab last year as part of the National Science Foundation’s (NSF) Assembling, Visualizing, and Analyzing the Tree of Life (AVAToL) program. The Open Tree of Life project strives to produce the first draft of a comprehensive tree of life and provides tools for community enhancement and annotation. The Arbor project is developing comparative methods with utility across large sections and the entire tree of life. Finally, the Phenomics project is developing approaches for exploring and documenting phenotypic diversity across the tree of life.

“It’s meant to be a quick outlet for solid phylogenetic studies”

PLOS Currents websites encourage researchers to share their findings with a minimal delay to their peers. The Tree of Life section is focused on rapid publication of phylogenetic and systematic studies with novel data and/or analyses. According to Keith Crandall, one of the three editors of the journal and an investigator of the Open Tree of Life, “it’s meant to be a quick outlet for solid phylogenetic studies to get them and their data into the public domain.” (more…)