The first visual model for the ‘tree of life’ of roughly 2.3 million named species of microbes, fungi, animals and plants has been released.
Whilst this has been a collaborated venture with 11 separate institutions all contributing to the creation of the tree, two biologists from the University of Michigan have done the lion’s share of the work.
Whilst there have been tens of thousands of smaller tree diagrams published, some of which boast over 100,000 species covered by its branches; none can claim to have combined all available data into a single tree that summarises all known life on Earth. Likened to the ‘Wikipedia of evolutionary trees’ this publication has been made free online, as a digital resource that anyone may use or edit.
Keep in mind this tree is not just a vanity project. Understanding the evolutionary connections held by the millions of species on Earth helps scientists with improving agriculture, pharmaceutical discovery and tracing the origins and spread of infectious disease such as HIV, influenza and the Ebola virus.
“This is the first real attempt to connect the dots and put it all together.” says the principal investigator Karen Cranston of Duke university. She encourages everyone to “Think of it as a version 1.0.” An indication that further progress is to be made on the ever-expanding tree. A summary of the findings has been published online in the proceedings of the National Academy of sciences on September the 18th.
University of Michigan biologist Stephen Smith led the group which spearheaded the piecing together of all the current branches of species into a single tree. Ph.D Cody Hinchliff now working at the University of Idaho, was formerly working as a researcher in Smith’s lab where he did much of the hard work on the project. Resultantly he shares the first-author credit with Smith on the P.N.A.S paper.
As opposed to building this monolithic ‘tree of life’ from scratch, the researchers involved compiled thousands of smaller similar projects already published online to create a “supertree” covering all known species.
“Many participants on the project contributed hundreds of hours tracking down and cleaning up thousands of trees from the literature, then selecting 484 of them that were used to generate the draft tree of life,” Hinchliff says.
Smith, assistant professor of the Department of Ecology and Evolutionary Biology at U-M said “Combining the 484 trees was a painstaking process that took three years to complete.”
A knowledge of evolutionary biology alone was not enough on it’s own to complete the project, as many thousands of lines of computer code and a myriad of new software had to be created by the Smith and Hinchliff duo before the projects completion.
“In addition to the process of combining existing trees, much of what was done at the University of Michigan was the development of tools and techniques and the analysis of the tree itself,” Smith said. “To complete this project, we had to code our own solutions. There was nothing out of the box that we could use.”
The aim was to create software tools and algorithms that balanced performance with efficiency when combining large numbers of trees, Hinchliff said.
“Our software, which is called ‘treemachine,’ took a few days to generate the current draft tree of life on a moderately outfitted desktop workstation in Stephen’s office,” he said. “For comparison, other state-of-the-art methods we tried would have taken hundreds of years to finish on that kind of hardware.”
Another problem encountered by the team was that many of the existing data on the trees existed in PDF format and other image files that cannot be entered into a database or merged with other trees.
“There’s a pretty big gap between the sum of what scientists know about how living things are related, and what’s actually available digitally,” Cranston said.
Subsequently, some of the relationships in the tree, such as the branches between the pea and sunflower families contrast with expert opinion.
This is because even the most popular archive of raw genetic sequences -that many of these evolutionary trees are built from- contains DNA data for less than 5% of the millions of species estimated to exist on Earth.
“As important as showing what we do know about relationships, this first tree of life is also important in revealing what we don’t know,” said co-author Douglas Soltis of the University of Florida.
In an effort to fill the gaps in data, the team is developing a program that will allow researchers to update and revise the tree in real-time as new data emerges on the currently unnamed and undiscovered species on Earth.
Smith argues that “While the tree of life is interesting in its own right, our database of thousands of curated trees is an even more useful resource. We hope that this publication will encourage other researchers to contribute their own studies or to enter information from previously published sources.”
As a comment on scientific progress Soltis says “Twenty five years ago, people said this goal of huge trees was impossible,” but with the support of a tree year, $5.76 million grant from the U.S. National Science Foundation including $900,000 to the University of Michigan, this project has not just become a reality, but as Smith says “This is just the beginning,”
Other study co-authors include James Allman of Interrobang Corporation; Gordon Burleigh, Ruchi Chaudhary, Jiabin Deng, Christopher Owen of the University of Florida; Lyndon Coghill, Peter Midford and Richard Ree of the Field Museum of Natural History; Keith Crandall of George Washington University; Bryan Drew of the University of Nebraska-Kearney; Romina Gazis and David Hibbett of Clark University; Karl Gude of Michigan State University; Laura Katz and H. Dail Laughinghouse IV of Smith College; Emily Jane McTavish of the University of Kansas; Jonathan Rees of the National Evolutionary Synthesis Center and Tiffani Williams at Texas A&M University.
The current version of the tree–along with the underlying data and source code–is available to browse and download at https://tree.opentreeoflife.org.