UNIVERSITY PARK – Beginning this week, scientists and nonscientists now have easy access to information about when living species and their ancestors originated, information that previously was difficult to find or inaccessible.
Free access to the information is part of the new Timetree of Life initiative developed by Blair Hedges, a professor of biology at Penn State University, and Sudhir Kumar, a professor of life sciences at Arizona State University. The Timetree of Life project debuted this week with the simultaneous release of a major online resource called “TimeTreeWeb“, and a book titled “The Timetree of Life” (Oxford University Press), which is written by a consortium of 105 experts on specific groups of organisms and is edited by Hedges and Kumar. Nobel laureate James D. Watson, co-discoverer of the structure of DNA, comments in his foreword to the book, “I look in wonder at The Timetree of Life, at the breadth of life that it covers, and the extraordinary data presented in it.”
“The ultimate goal of the Timetree of Life initiative is to chart the timescale of life — to discover when each species and all their ancestors originated, all the way back to the origin of life some four billion years ago,” Hedges said. Many researchers long have studied the times of origin of individual species in order to piece together a Tree of Life, but now the Timetree of Life project provides a synthesis of the time-calibrated Tree of Life, in addition to adding much new information from previously unpublished scientific studies.
“The TimeTreeWeb tool belongs to a new genre of resources that lets anyone easily mine knowledge previously locked up in technical research articles, without needing to know the jargon of the field,” said Kumar. “For example, if you type in ‘cat’ and ‘dog,'” Hedges said, “the program will navigate through the timetree of life to the point where the cat and dog species split, and it will find all the studies bearing on that divergence. Within a few seconds, you will learn that your pet cat and dog diverged in evolutionary time about 50 to 60 million years ago.”
“Timetrees are having broad impact in biology and in other fields such as geology, and even in human health, where researchers need to track the evolution and spread of disease-causing organisms,” said Hedges. At the other end of the timescale, astrobiologists, who study the origin and development of life in the universe, need to know which organisms were responsible for changes in the chemistry of rocks on Earth that are billions of years old. A timetree could rule out species that had not yet evolved at the time the rock formed, while implicating other species that have deep evolutionary branches. “The variety of uses of a timetree really drives home its power as an interdisciplinary tool,” said Hedges, himself an astrobiologist.
One fifth of “The Timetree of Life” book contains new data, published for the first time, which fill many gaps in the family tree of life down to the taxonomic level of “family” (groups of species). For example, the book’s chapter on stingrays and sharks is the first published timetree analysis of the existing molecular data about these animals. Almost all of the previously published data reviewed in the book became known only recently, in the hundreds of scientific articles published during the past five or ten years.
Commenting on the Timetree of Life initiative, James Collins, assistant director for biological sciences at the National Science Foundation, said “The origin of life is a grand-challenge problem in biology that is as compelling as the origin of the universe in the physical sciences. Hedges and Kumar take us closer to solving this mystery. Their synthesis volume on the history of life on earth is an invaluable contribution to researchers and educators alike.
TimeTreeWeb is an innovative on-line resource for scientists and non-scientists to explore the full timescale of life, down to the level of individual species. With this Web resource, “finding the time when two species last shared a common ancestor is as simple as giving their names to TimeTreeWeb and pressing the search button,” says Kumar. TimeTreeWeb then translates common and scientific names into appropriate search terms and uses a unique “tree-climbing” system to produce a time of divergence after searching through all published studies, including those in “The Timetree of Life” book. Over 800 studies currently are searchable in the TimeTreeWeb, with more being added continuously.
As part of the output of TimeTreeWeb, users get the time estimate from “The Timetree of Life” book, where an expert has applied a quality judgment, as well as the absolute average of the estimates from all the studies. “The Timetree of Life initiative is an example of how a book and a Web resource can be integrated, to the benefit of both,” Hedges said.
To collect the genes of most or all the species living on Earth, scientists must first find the species. “Discovering the tree or timetree of life requires field work — going to remote parts of the world and collecting species for scientific study,” Hedges said. This adventure is something Hedges knows well, having spent years exploring islands in the Caribbean where he has discovered, with collaborators, more than 100 new species, including the world’s smallest frog, smallest lizard, and smallest snake.
Each chapter of “The Timetree of Life” book is a review of the evolutionary history of the families within a particular group of organisms, such as mosses, ferns, fungi, beetles, sea urchins, frogs and toads, turtles, owls, primates, and many others. The chapters each contain a photograph of a representative organism, a color-coded timetree showing how the families are related and when they split from their closest relative, and a table with divergence times. Each chapter of the book was subjected to a rigorous scientific review by other experts in the respective field.
As an ongoing service to the scientific community, Hedges and Kumar plan to continue adding new data to TimeTreeWeb from future peer-reviewed studies. They also will develop programs that will make it easier to access the information and to explore the timetree of life, and easier for scientists to deposit new data in TimeTreeWeb. Once deposited, each data set first will be reviewed by members of a board of experts before it can be integrated into TimeTreeWeb. “One of our goals is to have a rigorous system that is nearly self-perpetuating and is run largely by the scientific community,” Kumar said.
Support for developing TimeTreeWeb has come from the U. S. National Science Foundation, the Astrobiology Institute of the U. S. National Aeronautics and Space Administration, the Science Foundation of Arizona, and the Biodesign Institute of ASU.