Assembling, Visualizing, and Analyzing the Tree of Life

Posts tagged “research

Tree of Life: Are big changes looming on the horizon?

All species like some gadgets

Photo by PublicDomainPictures (Creative Commons Deed CC0)While movie hero James Bond gets his spy gadgets from his loyal developer Q, almost every other species on Earth has to put a little more effort in armoring themselves. But that does not mean they cannot rely on some good ol’ friends to do so. In fact, the acquisition of genes from two or more species through lateral gene transfer can lead to innovations that at times can be painful—sometimes even deadly—to others.

One of those evolutionary novelties is noticeable for certain types of jellyfish that developed the ability to sting after their ancestors acquired a gene from a bacterium and incorporated that material in their own DNA. This gene transmission helped jellyfish to create an innovative defense tool to fend off other species that could endanger them. The result is quite frightening: more humans get killed by jellyfish than sharks. (more…)


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…)


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…)


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