Ancient fossils, an Internet database and evolution: An idea hatched at the Field Museum

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.”

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.

The scientists

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.