The Open Tree of Life: toward a global synthesis of phylogenetic knowledge

2013 REU Project:

In the field of systematic biology, scientists study species of all kinds to determine how one is related to another by evolutionary descent.  In other words, they are trying to reconstruct the great Tree of Life -- the branching genealogy of all species, traced all the way back to a single common ancestor. (The scientific term for 'Tree of Life' is 'phylogeny'.)

Individual scientists typically have expertise in only one or a few branches on the tree -- for instance, one might study dung beetles, while another studies venus flytraps. Every year, experts like these publish thousands of scientific papers describing new phylogenetic trees for different group of organisms: clams, birds, mushrooms, and so on. However, these newly discovered trees are generally recorded simply as figures embedded in the pages of scientific journals.

The Open Tree of Life project seeks to extract all these trees from the literature and graft them together by entering them into a common database. This will enable computational analyses that will produce, for the first time, an estimate of the Tree of Life that includes all species ever studied.

Research methods and techniques: interns on this project will learn how to download data sets of DNA sequences, perform phylogenetic analyses, and interpret the results. They will also have the opportunity to learn basic computer programming and Linux shell computing, or advance their current knowledge of these topics. Their contributions will be recorded in a public database for posterity. It is perfect fit for anyone interested in both biology and computers.

Curator/Advisor: Dr. Richard Ree (Curator, Botany)