Posts tagged “evolutionary trees

You don’t want to build a new tree from scratch?

‘Let the computer do the work’

Creating a phylogenetic tree is no easy task. It usually involves a complex synthesis of multiple datasets, but it leads to much satisfaction when all work is done—until new data come in.

Then, the process typically starts all over again: building a new tree from scratch.

Mark Holder, a professor of statistical phylogenetics at Kansas University and one of the investigators of the Open Tree of Life project, maintains that there is a real need for scientists to have access to digital tools that save them from doing quite a few labor-intensive procedures.

“In the past, researchers combined information from different trees and then analyzed the data. But they never made good computer systems that allowed for continuous updating. They would not be able to see how an entire tree would look like when they added more data or another individual tree. In that case, they had to start over.”

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Puzzling:

Connecting millions of pieces

Creating the entire tree of life is like completing a jigsaw puzzle with more than two million pieces. And to make it even harder; the illustration of how the solved puzzle would look like is missing.

No one knows precisely how all pieces are related.

This disparity is unmistakably demonstrated by disagreements between evolutionary biologists about how certain species and branches are linked together. Throughout the years they have created a large variety of trees with specific groups of species that contradict each other. For example, one researcher maintains that species A is the closest living relative of species B, but another scientist thinks that species C is actually most closely related to B. (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.

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