A first draft of the “tree of life” for the roughly 2.3 mil­lion named species of ani­mals, plants, fungi and microbes — from platy­puses to puff­balls — has been released. This large, open-​access resource aims to be “Wikipedia” for evo­lu­tion­ary history.

A col­lab­o­ra­tive effort among eleven insti­tu­tions, the tree depicts the rela­tion­ships among liv­ing things as they diverged from one another over time, trac­ing back to the begin­ning of life on Earth more than 3.5 bil­lion years ago. Tens of thou­sands of smaller trees have been pub­lished over the years for select branches of the tree of life — some con­tain­ing upwards of 100,000 species — but this is the first time those results have been com­bined into a sin­gle tree that encom­passes all of life. The end result is a dig­i­tal resource that avail­able free online for any­one to use or edit, much like a “Wikipedia” for evo­lu­tion­ary trees.

This cir­cu­lar fam­ily tree of Earth’s life­forms is con­sid­ered a first draft of the 3.5-billion-year his­tory of how life evolved and diverged. Image credit: Stephen Smith.

“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 cur­rent ver­sion of the tree, along with the under­ly­ing data and source code, is avail­able to browse and down­load. It is also described in an arti­cle pub­lished 18 Sep­tem­ber in the Pro­ceed­ings of the National Acad­emy of Sciences.

Evo­lu­tion­ary trees, branch­ing dia­grams that often look like a cross between a can­de­labra and a sub­way map, aren’t just for fig­ur­ing out whether aard­varks are more closely related to moles or man­a­tees, or pin­point­ing a slime mold’s clos­est cousins. Under­stand­ing how the mil­lions of species on Earth are related to one another helps sci­en­tists dis­cover new drugs, increase crop and live­stock yields, and trace the ori­gins and spread of infec­tious dis­eases such as HIV, Ebola and influenza.

Rather than build the tree of life from scratch, the researchers pieced it together by com­pil­ing thou­sands of smaller chunks that had already been pub­lished online and merg­ing them together into a gigan­tic “supertree” that encom­passes all named species. The ini­tial draft is based on nearly 500 smaller trees from pre­vi­ously pub­lished stud­ies. To map trees from dif­fer­ent sources to the branches and twigs of a sin­gle supertree, one of the biggest chal­lenges was sim­ply account­ing for the name changes, alter­nate names, com­mon mis­spellings and abbre­vi­a­tions for each species. The east­ern red bat, for exam­ple, is often listed under two sci­en­tific names, Lasi­u­rus bore­alis and Nyc­teris bore­alis. Spiny anteaters once shared their sci­en­tific name with a group of moray eels.

“Although a mas­sive under­tak­ing in its own right, this draft tree of life rep­re­sents only a first step,” the researchers wrote. For one, only a tiny frac­tion of pub­lished trees are dig­i­tally avail­able. A sur­vey of more than 7,500 phy­lo­ge­netic stud­ies pub­lished between 2000 and 2012 in more than 100 jour­nals found that only one out of six stud­ies had deposited their data in a dig­i­tal, down­load­able for­mat that the researchers could use. The vast major­ity of evo­lu­tion­ary trees are pub­lished as PDFs and other image files that are impos­si­ble to enter into a data­base or merge 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.

As a result, the rela­tion­ships depicted in some parts of the tree, such as the branches rep­re­sent­ing the pea and sun­flower fam­i­lies, don’t always agree with expert opin­ion. Other parts of the tree, par­tic­u­larly insects and microbes, remain elu­sive. That’s because even the most pop­u­lar online archive of raw genetic sequences — from which many evo­lu­tion­ary trees are built — con­tains DNA data for less than five per­cent of the tens of mil­lions 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.

To help fill in the gaps, the team is also devel­op­ing soft­ware that will enable researchers to log on and update and revise the tree as new data come in for the mil­lions of species still being named or dis­cov­ered. “It’s by no means fin­ished,” Cranston said. “It’s crit­i­cally impor­tant to share data for already-​published and newly-​published work if we want to improve the tree.”
“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.”

(Source: Duke Uni­ver­sity news release, 18.09.2015)