Assembling, Visualizing, and Analyzing the Tree of Life

Posts tagged “nsf

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.


Teamwork:

Across disciplinary boundaries

The interdisciplinary team of the Open Tree of Life project

What do a fungal evolutionary biologist and a computer scientist have in common?

It is usually easier to name a long list of differences, but that does not mean that those scholars are investigating different issues all the time. They may be very much interested in the same problems, yet apply different perspectives and methods in search for answers.

Those scientists could continuously work on their individual research projects for may years. However, in some cases only an interdisciplinary collaboration leads to a solution. The investigators of the Open Tree of Life project hope this will be the case for them as well. Their goal: creating a tree of life that includes all 1.9 million known species. (more…)


Help!

Wanted: All your favorite trees

With eleven investigators, the Open Tree of Life project is already a large-scale research endeavor. But that does not mean that they can add all 1.9 million known species to a database by themselves. In fact, they are looking for help.

A lot of help.

The main goal of the project is to merge all existing phylogenetic trees in one overarching tree of life. In the past few months, the researchers have been working on software applications to make it possible to store all known species and, more important, to specify how they are all linked to each other in evolutionary terms.

(more…)


Quiz time!

Dear Colleagues,

Put on your quiz hats! We need some good questions!

As our team works to build an Open Tree of Life for professionals we are also working on a educational version of the tree for the everyone else, meaning educators, students, and the public in general.This public site will have a FUN QUIZ to test people’s knowledge of evolution, and we need questions for it!

SUBMIT YOUR QUESTIONS HERE

SAMPLE QUESTIONS:
Easy:
• Sponges fall within which major group on the tree of life? (animal, plant, bacteria)
• Which are mushrooms more closely related to: (animals, red algae or plants?)
• How many origins of life were there on Earth? (1, 2, 3)
Medium:
• Which organisms represent the greatest biomass on Earth?
(bacteria and archaea, mammals, fish)
• How many major groups of organisms are represented in a ham sandwich? (1, 2, 3)
• Genes (i.e. portions of genomes) yield the same estimate for the ToL? (Yes, No, Sometimes)
Expert:
• The top 10 infectious agents on earth appear where on the tree? (bacteria only, in both bacteria and eukaryotes, in both bacterial and archaea)
• Each gene sequenced and analyzed yields the very same answer for the ToL? (Yes, No, Sometimes)You can submit up to three questions with this form, but feel free to submit more by starting a new one!

What data should we collect about the input trees for the tree of life?

The absence of a formal reporting standard for phylogenetic analyses is a major impediment for digital access and reuse of published gene trees and species trees.  Efforts are underway to develop a standard for Minimal Information About Phylogenetic Analyses (MIAPA).  An important part of this process is community input on metadata – what is important for use and evaluation, and what is reasonable to expect from producers of trees?

Results from this survey will inform two efforts: the collection of digital phylogenetic data for Open Tree of Life and the development of a minimum information standard for reporting phylogenetic analyses (MIAPA, http://www.evoio.org/wiki/MIAPA).  If you have any questions, please contact Karen Cranston, National Evolutionary Synthesis Center (karen.cranston@nescent.org).

Please add your opinion here


What are your favorite species?

Dear Colleagues,

We need your help creating a list of exemplar species from across the tree of life for our public tree!

As our team works to build an open tree of life for the systematics community, we are also working on a educational version of the tree for the public . Our goal is to depict about 200 better-known (i.e. phylogenetically or otherwise important in some way (pathogen, food source, etc.) species from all three domains of life. The intended audience of this effort includes educators, students, and the public in general.

Please click this link to vote for your 5 best exemplars.

And please join the OpenTree conversation through our websiteemail, and Twitter (opentreeoflife).Thank you!


NSF’s press release on the Open Tree of Life

Press Release 12-106 (original article)
Assembling, Visualizing and Analyzing a Tree of All Life

National Science Foundation grants will bring together what’s known about how species are related

The “Open Tree of Life” is one of three major new scientific projects funded by the NSF.

June 4, 2012

A new initiative aims to build a comprehensive tree of life that brings together everything scientists know about how all species are related, from the tiniest bacteria to the tallest tree.

Researchers are working to provide the infrastructure and computational tools to enable automatic updating of the tree of life, as well as develop the analytical and visualization tools to study it.

Scientists have been building evolutionary trees for more than 150 years, since Charles Darwin drew the first sketches in his notebook.

Darwin’s theory of evolution explained that millions of species are related and gave biologists and paleontologists the enormous challenge of discovering the branching pattern of the tree of life.

But despite significant progress in fleshing out the major branches of the tree of life, today there is still no central place where researchers can go to visualize and analyze the entire tree.

Now, thanks to grants totaling $13 million from the National Science Foundation’s (NSF) Assembling, Visualizing, and Analyzing the Tree of Life (AVAToL) program, three teams of scientists plan to make that a reality.

(more…)


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