Open-source ‘Tree of Life’ includes all known life on Earth

Combing through records spanning over 3.5 billion years, scientists 11 institutions have complied a ‘tree of life’ that includes the approximately 2.3 million known species of animals, plants, fungi, and microbes.

Many other, smaller, trees of life have been constructed over the years but those only contain about 100,000 species of select branches of life forms. This new tree aims to include all life on Earth.

“This is the first real attempt to connect the dots and put it all together,” said principal investigator Karen Cranston of Duke University. “Think of it as Version 1.0.”

The team pieced together the known trees, using them to form branches and stems that shoot off of the main trunk of the ‘supertree’. The project took over three years to complete.

“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,” said Cody Hinchliff, of the University of Idaho.

The website for the tree,, functions as a digital resource for any interested parties to contribute to or edit- something like a Wikipedia for evolution.

The project cost $5.76 million and was funded by the US National Science Foundation. Such knowledge is crucial to helping researchers discover new drugs, increase yields, and trace the origins of diseases.

“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,” said Stephen Smith of the University of Michigan. “To complete this project, we had to code our own solutions. There was nothing out of the box that we could use.”

The team hoped to build a collection of software tools that could enable viewers to search the tree with ease. Indeed, underlying data and source codes are open to the public.

“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,” said Smith. “For comparison, other state-of-the-art methods we tried would have taken hundreds of years to finish on that kind of hardware.”

None of the scientists admit to being finished with the project. Science only knows about five percent of the DNA data for the millions of species 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 Douglas Soltis, of the University of Florida.

The researchers hope that others will log on and update or revise the tree with new data so that it can be as complete and accurate as possible.

“This is just the beginning,” said Smith. “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.”

“Twenty five years ago, people said this goal of huge trees was impossible,” said Soltis. “The Open Tree of Life is an important starting point that other investigators can now refine and improve for decades to come.”

A paper that summarizes the findings was published in the Proceedings of the National Academy of Sciences.



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