May 31, 2016

by Jonathon Berlin

The Field Museum has more than a half-million fossils in its collection comprising all manner of plants and animals. It includes fossils from 430 million-year-old trilobites from Chicagoland's Silurian reef to 195 million-year-old dinosaurs from Antarctica to 7,000-year-old humans from Iran, Iraq and Turkey.

Those relics alone offer clues as to how animals and plants once lived, but an ongoing effort by researchers seeks more: a digital database of fossils that aims to help understand evolution. The idea was hatched at the Field Museum and combines the very old -- fossils, some as old as 500 million years -- and the very new, open-access science on the Web.

In 2008 at the Field Musuem, evolutionary biologist Jim Parham was studying biodiversity on a project with the goal to fill out the tree of life, a diagram of all living things over time and how they relate to each other. "I was realizing that there was a major disconnect between the people who looked at the timing of the tree of life using fossils, and those that looked at it using DNA," Parham said. Scientists who use DNA to study evolution were not able to easily access information from fossils that could help them, and when they did, Parham said, they were doing it incorrectly.

How to address the disconnect? Bring paleontologists, molecular biologists, computer programmers and others together in a completely new way. Here is how it happened.

The tree of life

Imagine every type of plant and animal that ever lived, organized as a big tree. When new species emerge, new branches are formed. When a species goes extinct, a branch ends. The database of fossils helps determine when the splits and ends of the branches happen.

"What we are trying to do is reconstruct the timing of evolutionary events," said Daniel Ksepka, who helped lead the effort and edits the database. "What we do is use fossils to calibrate the (evolutionary) clock," he said. Ksepka is a curator at the Bruce Museum in Greenwich, Ct., and was a research associate at the Field Museum.

Kenneth Angielczyk, associate curator of paleomammalogy at the Field, said molecular clock dating has become a key technique in evolutionary biology. "The method considers the rate at which DNA sequences change over time. Once that rate is known it is possible to estimate when two species last shared a common ancestor by comparing the degree to which their DNA sequences have diverged," he said.

Angielczyk said the dates help scientists estimate important events in the history of life and to study the rates at which evolutionary changes occur for different forms of life in different circumstances. "Scientists use fossils to make these calibrations," he said.

The lessons can go deeper, understanding evolution to learn about what might happen in the future. "The time that animals and plants split is widely variable," said Adam Smith, who until last year was a postdoctoral fellow at the Field and now is curator of the Bob Campbell Geology Museum at Clemson University in South Carolina. "Correlating diversity and extinction with paleontological events, we can learn about how response might be now."

Using a fossil to determine a creature's place in the tree of life, known as calibration, often was inconsistent and sometimes incorrect. There were no common standards or a central place to log the information.

"As it stood, molecular biologists were using fossil data but did not have the understanding to use it properly," said Parham, now a paleontology and conservation biologist at California State University at Fullerton. "Consequently, they often got it wrong and used the wrong fossils or assigned the wrong dates."

The database, part of the electronic journal "Palaeontologia Electronica", puts all of that information in one place in a searchable format, with all fossils calibrated to the same standards.

The final product, which launched last year, is a tool for scientists that also happens to be available to all on the Internet. The database currently has 144 entries.

paleontologist, discovered

fossils of flowered plants

outside Richmond, Va.

One of those fossils, a microscopic piece of a 107.7 million-year old laurales, stored at the Field Museum, turned out to be significant: It represents a key moment in the evolution in the group of plants that include avocado, cinnamon and bay laurels.

For that reason — because it represents a branching out of the evolutionary tree — the tiny sample is included in the fossil calibration database.

When a fossil is part of the database, here is what it includes:

Its lineage

Its age

Identifying details about the specific fossil

Its significance in terms of evolution

And a diagram of where it fits on the tree of life, relative to its closest relatives.

paleontologist, discovered

fossils of flowered plants

outside Richmond, Va.

One of those fossils, a microscopic piece of a 107.7 million-year old laurales, stored at the Field Museum, turned out to be significant: It represents a key moment in the evolution in the group of plants that include avocado, cinnamon and bay laurels.

For that reason — because it represents a branching out of the evolutionary tree — the tiny sample is included in the fossil calibration database.

When a fossil is part of the database, here is what it includes:

Its lineage

Its age

Identifying details about the specific fossil

Its significance in terms of evolution

And a diagram of where it fits on the tree of life, relative to its closest relatives.
Building the database

Each fossil entry into the database must first pass a rigorous process, Ksepka said, a process that nails down how old it is, where it was found and how it fits on the evolutionary tree. Publishing the calibration online also gives paleontologists a place where their work is published and can be cited.
How a fossil is verified

"Any fossil that is used as a calibration point must have a well-constrained age and position of the tree of life," Angielczyk said.
Specimen: Each fossil is first based on an individual museum specimen or set of specimens; that makes sure the fossil in question is something that can be found. Physical characteristics: Demonstrate that anatomical characteristics support the placement of the fossil in the evolutionary tree. DNA vs. archeology: Reconcile any differences between evolutionary trees based on anatomical data and DNA. Location: Identify the physical location from which the fossil was collected and tie it to a specific level in a rock formation. Age: Translate that geological placement into a numerical age.

As the idea to create a fossil database grew, it led to grants and gatherings of experts from the worlds of paleontology, molecular biology and computer programming. The support of the National Evolutionary Synthesis Center in North Carolina, now the Triangle Center for Evolutionary Medicine and other organizations was key to the effort. Over the course of the meetings from 2009 to 2014 there were nearly 40 people who attended, including 19 paleontologists, 13 molecular biologists, five computer scientists and one editor.

The mix paid off. "All of the different perspectives were extremely rewarding," Ksepka said.

The next steps? Keep adding fossils to the database and fill in more branches of the tree. "We are hoping to grow the database," Parham said. "Whereas we have good coverage of the basic branches of the tree of life, we need to fill it more."

How does the tree get filled out? Parham said mainly through word of mouth, social media and speaking at conferences. "The project is open-ended, and since there are lots of branches to the tree of life that have fossils, I think we can definitely expect to get hundreds more, if not thousands eventually."

The team is consistently hearing of new fossils to be entered and new scientists interesting in contributing.

"And that's the really exciting thing, to realize that there will always be a need to know what is the oldest physical record of a lineage and so the database will always serve a purpose and continue to grow," Parham said.
How old are the fossils: Timeline of what is in the database

The timeline below shows the fossils that are part of the database through 2015, along with significant evolutionary markers for context.

Sources: Palaeontolgia Electronica Fossil Calibration Database, The Field Museum, "The Illustrated Timeline of the History of the World" by Roshen Dalal, University of California Museum of Paleontology, National Center for Science Education, Tribune reporting

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