Assembling, Visualizing, and Analyzing the Tree of Life

Posts tagged “science

Karen Cranston talks about open licensing and Dryad

Making scientific data available

 

In case you haven’t seen the video yet, Open Tree of Life investigator Karen Cranston talked about sharing research data in open access data repositories during the Creative Commons 10-year celebration in Raleigh, North Carolina, last December. She mainly focused on the use of CC0 for Dryad, which is a curated general-purpose repository that makes the data underlying scientific publications discoverable and freely reusable. Cranston also mentioned that data availability leads to more citations, which is highly valued in the academic community. You can access the presentation slides as well (link).


“We need a sense of ownership of phylogenetic trees”

Where are the fungi datasets?

FungiA couple thousand fungi phylogeny studies have been published in the past twelve years. Clark University postdoc researcher Romina Gazis has gone through all of them. Now she is working on a bigger challenge: finding all the trees and datasets that were the foundation of those studies.

Ideally, all scientists who publish a phylogenetic tree would also deposit the datasets they used to create such trees at a publicly available online database. That allow other researchers to synthesize data from different sources to advance the knowledge about relationships between certain species and their evolutionary history.

Unfortunately, most of those datasets are not publicly available. Gazis only found datasets for about a quarter of the two-thousand fungi articles she surveyed. “Around 600 studies had tree files available, but not necessarily complete,” she concluded. “Some scientists deposited one but not all the trees.” (more…)


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.”

(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…)


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).

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