A new project aims to bring Charles Darwin’s masterclass on evolution into this century. Carl Zimmer of The New York Times reports
In 1837, Charles Darwin opened a notebook and drew a simple tree. Each branch represented aspecies. In that doodle, he captured his newfound realization that species were related, havingevolved from a common ancestor. Across the top of the page he wrote, “I think.”
Two decades later Darwin presented a detailed account of the tree of life in “On the Origin ofSpecies.” And much of evolutionary biology since then has been dedicated to illuminating parts ofthe tree. Using DNA, fossils and other clues, scientists have worked out the relationships of manygroups of organisms, making rough sketches of the entire tree of life.
Scientists want to create a single tree of life out of thousands. An updated model, and Darwin’s effort. Cambridge University Library; Iplant Collaborative,top
Now Dr. Katz and her colleagues are doing somethingnew: they are drawing a tree of life that includes everyknown species – a tree with about two million branches.
“I think it is an amazing step forward for our communityif it can be pulled off,” said Robert P. Guralnick, an expert on evolutionary trees at the University of Colorado who is not part of the project.
Until recently, a complete tree of life would have beeninconceivable. To figure out how species are related,scientists inspect each possible way they could berelated. With each additional species, the total numberof possible trees explodes. There are more possible trees for just 25 species than there are stars.
But scientists have developed computer programs thatfind the most likely relationship among species without considering every possible arrangement. Thosecomputers can now analyze tens of thousands ofspecies at a time.
Yet these studies have thrown spotlights on only smallportions of the tree of life.
“Nobody has tried to put all these results together,” saidthe leader of the new effort, Karen Cranston, a biologistat the National Evolutionary Synthesis Center in Durham, North Carolina.
Last year, Dr. Cranston and other experts came up witha plan for a single tree of life. The National Science Foundation has awarded the team a three-year grant of$5.7 million. The project, the Open Tree of Life, hopes to publish a draft by August 2013. The scientists willgrab tens of thousands of evolutionary trees archived online, then graft the smaller trees into a single big one.
These trees represent just a tiny fraction of all known species. The rest are classified in the oldLinnaean system, in which they are assigned to a genus, a family, a kingdom, and so on. The teamwill use that data too. All the species in a genus, for example, will belong to branches descendingfrom the same common ancestor. The Linnaean system will give the tree only a rough picture ofthe true relationships among species.
“Parts of it will be quite good, and parts will be quite bad,” Dr. Cranston said.
The team will then set up an Internet portal where the entire community of evolutionary scientistscan upload new studies, which can then automatically revise the entire tree.
And the tree will grow. Each year scientists publish descriptions of 17,000 new species. Last yeara team estimated the total number of species to be 8.7 million, although others think it could easilybe 10 times that.
When scientists publish the details of a new species, they typically compare it with known speciesto determine its closest relatives. They will be able to upload this new information into the OpenTree of Life. Scientists who extract DNA from the environment from previously unknown species willbe able to add their information as well.
Animals and plants will take up only a tiny part of the tree. “Most biodiversity on earth is microbial,”said Dr. Katz.
Microbes pose a special challenge. The branches of the tree of life represent how organisms passtheir genes to their descendants. But microbes also transfer genes among one another. Thosetransfers can join branches separated by billions of years of evolution.
“In a lot of the tree of life, it’s not really treelike,” Dr. Cranston said.
She and her colleagues are exploring how they can build their database to include these genetransfers, and how best to visualize them.
“That’s an issue we intend to struggle with for the next three years,” Dr. Katz said.
Luke Harmon, an evolutionary biologist at the University of Idaho who is not involved in the project,looks forward to using the tree to explore the history of life. One major question evolutionarybiologists have long explored is why evolution runs at different speeds in different lineages.
“We can use the tree to identify evolutionary ‘bangs’ and’whimpers’ through the history of life,” said Dr. Harmon said. It may also be possible to see how climate change has driven extinctions, and to make predictions for the future.
Stephen A. Smith, a team member from the University ofMichigan, hopes that the Open Tree of Life will allowscientists to tackle some major questions.
The tree may be able to guide the search for new drugs,for example. Scientists trying to treat infectious bacteria could search for the fungi that makeantibiotics that are effective against it. The relatives of those fungi might make even more effectivedrugs.
“These are questions we can ask now,” Dr. Smith said. “But we don’t have all the data together toanswer them yet.”
Roderic D. M. Page, a professor of taxonomy at the University of Glasgow, called the Open Tree ofLife team “first class,” but added: “Displaying large trees is a hard problem that has so far resistedsolution. We are still waiting for the equivalent of a Google Maps.”
- Open Tree of Life Project Draws In Every Twig and Leaf (nytimes.com)
- Tree of Life Project Aims for Every Twig and Leaf – Carl Zimmer – The New York Times (richarddawkins.net)
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