University of Texas-Austin Professor Helps Create New 'Tree Of Life'

AUSTIN, TX — An international team of researchers that includes a University of Texas-Austin assistant professor have devised the most comprehensive genomic "tree of life" helping to better illustrate the diversity of life on the planet, officials announced.

The revamped tree of life closely mirrors the arbor metaphor, with branches sprouting off its main trunk to illustrate various genomes represented. Using genetic data collected only in recent years, researchers found a group of bacteria so genetically diverse, that they represent half of all diversity of bacteria in general, university officials detailed.

“The tree of life is our central organizing unit of biology,” said assistant professor Brett Baker from UT's Texas Marine Science Institute, who participated in plotting out the reconfigured tree. “It’s the way we understand relationships amongst all life. Charles Darwin drew trees of what he was seeing in nature, and we now use genetic sequences to draw them.”

Indeed, Darwin was fond of invoking the image of a tree as he sought to explain the origins of species. He likened all life as having emerged from a common tree -- dubbed the tree of life.

"The affinities of all the beings of the same class have sometimes been represented by a great tree," Darwin once said. "I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species."

The newly unveiled, genome-based tree vividly illustrates Darwin's vision. Until just recently, most trees of life depicting the evolution of life forms were based on physical traits of organisms rather than their genes. The new tree of life, however, is intricately detailed -- the breadth of the various genomes utilized creating a tree that dramatically illustrates Darwin's preferred metaphor to explain life in all its forms.

UT officials note that much of microbial diversity utilized to devise the tree of life remained hidden until the so-called "genome revolution" allowed microbiologists to search directly for new microbes in the environment. They do this by analyzing their genomes, rather than culturing them in a lab dish, officials said.

Yet as richly textured as the new tree of life is, it is but the best achievable approximation at representing life. UT officials noted that less than 0.1 percent of microbes in the world can be cultured, which means there are thousands -- maybe even millions -- of microbes yet to be discovered.

Baker likens the new technique of using genomes to discover new microorganisms to the invention of the telescope and the resulting discoveries of planets, stars and galaxies.

"This incredible diversity means that there are a mind boggling number of organisms that we are just beginning to explore the inner workings of, which could change our understanding of biology," Baker said.

To be sure, scientists have created trees of life in the past. But past iterations have focused disproportionately on plants and animals. This newest tree — incorporating 3,083 organisms, one from each genus for which fully or almost fully sequenced genomes were available — more closely represents the full richness of life on the planet, UT officials said.

“This is the first three-domain genome-based tree to incorporate these uncultivable organisms, and it reveals the vast scope of as yet little known lineages,” said research team lead Jill Banfield from the University of California, Berkeley, referring to the three major domains of life: bacteria, Archaea and eukaryotes.

“The new depiction will be of use not only to biologists who study microbial ecology, but also biochemists searching for novel genes and researchers studying evolution and Earth history,” Banfield said.

The new tree, published online April 11 in the journal Nature Microbiology, reinforces the idea that the life we see around us in our immediate environment — plants, animals, fellow humans — represents but a tiny percentage of the world’s biodiversity, officials said.

To illustrate, they point to one part of the new tree they categorize as visually striking: a group of bacteria described as the “candidate phyla radiation” that forms a very major branch. Only recently recognized, it was once thought to comprise bacteria with symbiotic lifestyles.

It is -- as illustrated in the new tree of life -- so much more. The candidate phyla radiation now appears to contain about half of all bacterial evolutionary diversity.

In addition to Baker, the paper's authors are: Laura Hug of the University of Waterloo; Jill Banfield, Karthik Anantharaman, Christopher Brown, Alexander Probst, Cindy Castelle, Cristina Butterfield, Brian Thomas, Alex Hernsdorf, Ronald Amundson and Kari Finstad of the University of California, Berkeley; Yuki Amano and Kotaro Ise of the Japan Atomic Energy Agency; Yohey Suzuki of the University of Tokyo; Natasha Dudek of the University of California, Santa Cruz; and David Relman of Stanford University.

The research was supported primarily by the Department of Energy (DOE) through Lawrence Berkeley National Laboratory, with metagenomic sequencing by DOE’s Joint Genome Institute in Walnut Creek, California.

>>> Illustration courtesy of the University of Texas at Austin