A team of researchers from universities and colleges across the United States—including Smith's biological sciences professor Laura Katz—is working with the National Science Foundation to lay out a complete evolutionary tree that brings together every single known organism on Earth and, more important, shows how all living things are related.
/ Published December 12, 2012
First, there was one demure cell, a single, primordial speck of life that quietly took form on Earth eons ago.
Now, more than three billion years later, an unruly throng of some 2.5 million known species exists on a planet that, in its incomplete summation, is undoubtedly teeming with biodiversity.
In short, life used to be so simple. Now it’s not.
And that is precisely why a new initiative developed by the U.S. National Science Foundation (NSF) is putting money toward a project that will visualize, design and assemble a complete online “tree of life” to represent all life forms on Earth and their evolutionary history. Creating such a comprehensive tree presents huge challenges, but the project nonetheless aims to integrate everything scientists know about how all living things are related: from the amoeba in local Massachusetts bogs to Darwin’s finches in the Galápagos and the tallest trees in Africa.
Launched in June 2012, the $13 million, three-year project called the Open Tree of Life has a $5.7 million grant going to the team of scientists who are currently at work on the Assembling, Visualizing and Analyzing a Tree of All Life aspect of the program.
Laura Katz, the Elsie Damon Simonds Professor of Biological Sciences at Smith, is among the team of 11 principal investigators chosen for the project. The rest of the team is made up of researchers from universities and research centers across the country: the National Evolutionary Synthesis Center at Duke University; Texas A&M University; the Universities of Kansas, Florida, and Michigan; Michigan State University; Clark University; Brigham Young University; and the Field Museum of Natural History.
The team is working now to provide the infrastructure and computational tools to create the project as well as to develop the analytical and visualization techniques to build the evolutionary tree online. By August 2013, they hope to produce a first rough draft of the tree. The final goal is to create a model that will be accessible through an interactive website that synthesizes the molecular data of every single known organism while assembling that information into tree branches to illustrate the connections between all species of animals, plants, fungi and microbes.
“This is the first real attempt to synthesize available information and create both a public and scientific resource for the tree of life. Our project involves no data collection; we want to take what’s already out there, figure out how the millions of species on Earth are related to one another and assemble it into the tree,” says Katz. “We are actually starting with a taxonomy of life with a complex list of 1.9 million species of the 2.5 million known species on Earth.”
Katz, the only microbiologist on the project, jokingly asserts that for her part she has multiple roles and, literally, a very small focus: “microbes, microbes, microbes.”
“Microbes dominate the planet in terms of biodiversity, biomass and biological innovation,” she says. “For example there are more bacteria in your intestines than there have ever been people alive on earth. In fact, there are 10 bacteria in/on your body for every one of your own cells.”
But microbes pose unique challenges. “Most biodiversity on Earth is microbial,” says Katz. “But we still know very little about microbial life, with the bulk of microbial diversity as yet unsampled by modern (i.e., molecular) methods.”
Likewise, the microbes pass their genes to their descendants “both vertically, parents to offspring, and laterally, as in the sharing of genes between species (such as the sharing of antibiotic resistance genes among lineages). Hence, microbes, and to some extent macrobes, have created a web of life that lies on top of the branches of the tree of life. So it’s not always going to look very treelike.”
Since Charles Darwin first penciled into a notebook in 1837 a drawing of a small tree with a few branches representing how he thought the species were related, biologists have sketched out their own evolutionary trees to try to understand the many important details about living organisms and how they are connected to one another.
What makes this project different from previous efforts with evolutionary trees, Katz says, is its scope.
“Our goal is to show there has been only a single origin of life on Earth and then to outline the major domains of life: bacteria, eukaryotes (cells with nuclei of humans) and archaea.”
Katz says she and her colleagues will collect the raw data from thousands of other evolutionary trees already archived online and then finesse the data into a single-file database before grafting the information together into one single tree.
“It’s a super daunting task. We have molecular data now for only 10 percent—about 250,000 species—and there is not yet a single resource that puts all named species into a reasonable taxonomic framework,” says Katz. “But in addition to the 11 researchers, we have a really exciting group of support personnel working on it now, including undergraduates and graduate students. Among them is my research assistant and grad student Jessica Grant, who is using computer programming to merge information from a variety of sources, including the Catalogue of Life and the Global Names Initiative, to help us build the taxonomy.”
When this phase of the project is complete, Katz hopes two resources will be available for exploring the tree: both “a nerdy science tree” for researchers and an accessible version for the general public. Katz is also helping to develop an undergraduate course on the tree of life that would involve college students across the country in the ongoing process of keeping the tree up to date.
What would Darwin say about the Open Tree of Life project?
“This tree will look profoundly different from his sketch. But I think Darwin would be struck by how much biodiversity is on Earth. And I hope he would appreciate the clumsiness of our efforts while appreciating that biodiversity doesn’t have clean edges and connections, and some of it is almost unknowable,” Katz says.
“But he would like this work. And he would like all this complication,” she says smiling.
Katz promises the tree will continue to grow. “We plan to release a draft of the ongoing tree every year. There will always be new species being discovered, new relationships suspected and explored.”
In fact, the tree will never be done. “In some ways, the tree of life is unknowable. We will never be able to sample all biodiversity on Earth, particularly given both the microbial nature of the build of diversity and the rapid human-driven extinction that we are living through. Key species may disappear without our ever having known about them.”