The earliest forms of life were primitive: microbial organisms swimming in the Earth's oceans, somewhere between 3.9 billion and 2.5 billion years ago. In the following mega-annums, life exploded. Today, some 2.3 million species have been identified and named, with more being discovered all the time.
For the first time, a collaborative effort from 11 institutions around the US have compiled the most comprehensive tree of life called the Open Tree of Life. It encompasses every life form known and named, from fungi to shale fossils to our very own homo sapiens, illustrating the relationships as life diverged from a single point.
Tens of thousands of trees of life have been made in the past. Usually, though, they concentrate on specific branches. This is the first time a group has attempted to put every organism, past and present, in the one family tree.
"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 tree is based on almost 500 previously published, smaller trees, which made it a much less complicated proposition than compiling and sorting all the data from scratch. Even so, it took the team of researchers three years to complete, collating the information from the smaller trees into what they call a "supertree" of life.
There were several challenges involved. First, only a small fraction of evolutionary studies are published online. Of over 7,500 studies published between 2000 and 2012, only 1 in 6 was available in a digital format that the researchers could actually use. Most are published as PDFs or other image file types, the content of which can't be digitally scraped to merge with other files.
There are therefore some gaps in parts of the tree, which don't necessarily agree with expert opinion.
"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 explained.
Another challenge was accounting for name changes, misspellings, abbreviations and alternate species names. Yet another is the sheer scope of insect life. It's estimated that there are tens of millions of insect species on Earth. Less than five percent of these are available in online genetic archives.
"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.
Because of these gaps, the tree is still very much a work in progress. While it will possibly never be finished (due to those pesky new discoveries), filling in the gaps is still desirable. Understanding relationships between the species can help prevent the spread of disease, develop new drugs, increase crop and livestock production, and even help develop biologically inspired technology.
To this end, the team is developing software tools that will allow ongoing maintenance and updates on the tree, much like a phylogenetic Wikipedia.
"Twenty five years ago people said this goal of huge trees was impossible," Soltis said. "The Open Tree of Life is an important starting point that other investigators can now refine and improve for decades to come."
The tree is currently available online to browse and download, along with the data that went into it and the source code.
Study co-authors include Cody Hinchliff and Stephen Smith of the University of Michigan; James Allman of Interrobang Corporation; Gordon Burleigh, Ruchi Chaudhary and Jiabin Deng of the University of Florida; Lyndon Coghill, Peter Midford and Richard Ree of the Field Museum of Natural History; Keith Crandall and Christopher Owen 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.