February 10, 2009
Biologists Work Towards Documenting The Tree Of Life
Biologists all over the world are working on an effort to determine how all the estimated 500,000 species of plants are related to one another.
According to the New York Times, researchers have been able to sequence DNA from thousands of species from jungles, tundras and museum drawers, using supercomputers to crunch all of the genetic data.
Biologists may figure out how the millions of species on Earth are related to one another over the next few decades. But for people to actually see that tree of life, the tree itself will have to evolve along with technology that could make such a massive collection of data easier to catalog and study.
Companies like Google and Adobe are aiding biologists by enlisting the help of computer scientists and software designers to find a new way of looking at evolution. Their goal is to create a program that allows scientists and nonscientists alike to search through evolutionary trees.
"Just like Google Earth changed the way people look at geography, a sophisticated tree of life browser could really change the way we look at the life around us," said Mark W. Westneat, the director of the Biodiversity Synthesis Center at the Field Museum in Chicago.
In the late 1900s, the science of tree-building took a significant step forward, as biologists set up standard rules for comparing species and figuring out which species were most closely related to others. It became possible to compare not just the skeleton or color patterns of species, but also their proteins and genes.
However, experts believe simply comparing every single tree would be impossible. But now, mathematicians have developed statistical methods for searching quickly through potential trees to find the ones that do the best job of explaining all the evidence.
For biologists, computers can do millions of calculations and store a growing database of information on Web sites. Tree data grew hundreds of new branches, then thousands.
Scientific literature is now taking note of trees with thousands of branches, sometimes called "supertrees" or "megatrees". Their branches reveal patterns in evolution that were missed in smaller studies.
Plants, however, are not just related to one another "” they're also related to humans, animals, fungi, bacteria and all other living things on Earth.
The National Science Foundation has been financing a project for the past seven years called, "Assembling the Tree of Life," with the goal of reconstructing the evolutionary origins of all living things. Researchers are analyzing slices of the tree, while mathematicians and computer scientists work on methods to combine them into a single analysis.
However, biologists have reached the conclusion that they are going to have to find new ways to draw evolutionary trees.
"Our advances in understanding evolution are moving really fast now, but the tools for looking at these big trees are lagging behind," Dr. Westneat said.
Biologists are now working with computer scientists and other visualization experts to bring evolutionary trees up to date. Dr. Westneat has been organizing meetings over the past year to bring the two cultures together. "It has the potential to move us beyond what biologists with a little bit of programming can do," Dr. Westneat said.
However, even with the help of visualization experts, biologists won't be able to fly through the tree of life any time soon. "It's definitely not small potatoes "” it's cutting-edge research," said Dr. Tamara Munzner, a computer scientist at the University of British Columbia.
Munzner is working on a project that will allow biologists to see details of the tree of life without losing sight of its overall shape. One of her programs acts like a fisheye lens, blowing up clusters of branches. It also makes it possible for biologist to stretch some parts of it open and squeeze others down, while handling millions of branches.
Dr. David Hillis, a biologist at the University of Texas, believes drawing the tree of life will become a practical tool, in the same way online databases of DNA have become practical tools for geneticists.
"What I'd really like is the entire tree of life on a small hand-held device," Dr. Hillis told the New York Times.
Such a system would allow biologists to put a tissue sample from a plant, animal or other organism in the machine, which would then scan its DNA and find its place in the tree of life, even if it's a new species. A worldwide database could collect the information so that every biologist's machine would get an updated tree.
"It would be a "Ëtricorder'-like device, able to identify any species on Earth in the field," Dr. Hillis said.
But identifying every species on Earth would be a task of enormous complexity. Experts say lineages do branch as they evolve, and sometimes the branches join back together. Separate plant species sometimes produce hybrids that can no longer interbreed with their parent species"”essentially becoming new species. When biologists draw the relationships of some groups of plant species, their pictures can appear more web-like than tree-like.
Therefore, genes don't have to wait for two species to come together"”they just leap from one branch of life to another. Viruses sometimes infect a new host species, transferring genes from its previous host. Bacteria can also ingest naked DNA or pass it to one another on tiny genetic ringlets.
Peer Bork of the European Molecular Biology Laboratory said each gene has its own evolution. "It's not inherited from mother to daughter; it's inherited from a neighbor," he said.
How this different kind of heredity alters the tree of life is something biologists are just beginning to understand. Some genes can move from one species to another quite often, but it may be rare that they become a permanent part of a new genome.
Tal Dagan, a biologist at the University of Dsseldorf, has estimated their impact by analyzing hundreds of thousands of genes from microbes. "Some 80 percent of the genes in any microbe have been passed from one species to another at some point," she estimated.
However, she said her team couldn't simply publish their results as a table of numbers. "We had to have a new picture of evolution," she said.
Dr. Dagan believes evolution is still shaped like a tree. "Most of the evolution is still going on in the branches," she said.
But thousands of genes have shuttled among the branches over billions of years. Dr. Dagan and her colleagues have drawn a dense filigree of lines between the branches of the tree of life to prove the point.
"You see the tree and you see the thousands of edges, and you know this is how it is," she said.
Experts wonder if these sorts of evolutionary vines could be added to a complete tree of life without letting visitors get lost in the complexity.
"It does make things more complicated," Dr. Munzner said. "But it doesn't mean it's hopeless. My answer is, "ËBring it on.' "
On the Net:
- University of Arizona
- Field Museum, Chicago
- National Science Foundation
- Assembling the Tree of Life
- University of British Columbia
- University of Texas
- European Molecular Biology Laboratory
- University of Dsseldorf