Modernizing the Tree of Life

I am in the process of reading papers & articles on the topic of Phylogenetics to acquire domain knowledge. I started with a topic I am familiar with: the Tree of Life.

Modernizing the Tree of Life
Elizabeth Pennisi, et al.
Science 300 1692 (2003);
DOI: 10.1126/science.300.5626.1692

I am not sure how most biologists & systematists feel today, but I am guessing the idea suggested here was something big in 2003. What idea? That all of life could be "barcoded" using one mitochondrial gene (cytochrome oxidase I). The article, in general, talks a bit about the field and how larger projects are going to radically change the landscape (this article was published the same year that CIPRES started). And this effort, barcoding organisms, could help move us toward a time when all of life could be easier & quickly identified with a small, Star Trek-like "bio-coder" device (something also suggested in David Hillis' Discovering Life on Earth talk to Villanova University). I doubt the relevance of this concept now having seen my former supervisor/mentor, David Maddison, practice a talk refuting that a specific group of beetles (descendents of Bembidion, which he studies) were not easily classified using any gene - let alone the mitochondrial gene suggested. I do find it interesting that there is an effort to strive for a unique identifier for organisms. Given that some researchers estimate there are 10 million undescribed species out there, it would seem that a hashing approach might be more feasible. Take, say, 5 or 10 genes - create a hashcode from them and then chose your favorite way to resolve collisions (or do nothing - just add them to a list). That is just a wild & naive guess - but it seems like barcoding is a pipedream.

The article still helped give me the mood of the community and an idea of the debates that exist. They also made an important point - researchers agree more than they disagree. So even if it seems there are numerous hotly debated arguments raging, there exists a large set of facts that they agree on.

For me, the sidebar on the construction of the Tree of Life for plants was probably the highlight. I had heard some mention of Deep Green - but was not really clear on the project or the purpose of it. So now I can queue up another article to read (Science, 13 August 1999) and a project to research. I thought the view of the plant science community was also interesting to see:

"...plant people have a good handle on all sorts of data, almost to the point of being truly comprehensive,” says John Gittleman, an evolutionary biologist at the University of Virginia,Charlottesville.

Having good data is one thing, but sharing it with the rest of the community is really the goal. You see that with efforts like NESCent's Hackathon on Database Interopability. It's good to know the data is there; it sounds like Deep Green, Deep Gene, Deep Time, and Deepest Green have the community in a good position. I can see why the push for a cyberinfrastructure would follow those advancements.

Another good piece of insight was that supertrees are not all that useful. I have a bit of a background with phylogenies (having worked on the Tree of Life Web Project). But I thought supertrees would be helpful to researchers:

“Supertrees don’t have much value,” says Ward Wheeler

He said that they're just 'summaries of summaries.' Supertrees are easier to build, but if they have no value then they're pointless to construct.