Cataloging the diversity of life on Earth is challenging enough, but when scientists attempt to draw a phylogeny — the branching family tree of a group of species over their evolutionary history — the challenge goes from merely difficult to potentially impossible.

The fossil record is the only direct evidence scientists have about the history of species diversity. But depending on the type of organisms, the fossil record can be full of holes or totally nonexistent. The only hope in such cases is to infer historical diversity from modern DNA sequences. But those techniques have a fatal flaw: the results they provide are demonstrably incorrect.   

To overcome this problem, Penn evolutionary biologists have developed a new technique for analyzing phylogenies—a technique that applies new variables for tracing the history of species using modern DNA.

 “We’ve put contemporary molecular approaches on equal footing with classical paleontological approaches,” says one of the researchers, Joshua B. Plotkin, an associate professor of biology in the School of Arts and Sciences and the Department of Computer and Information Science in the School of Engineering and Applied Science.

The limitations of the fossil record, and the lack of good alternatives, represent a longstanding problem in paleontology. Some species, due to the makeup of their bodies, or the geology of the areas where they lived, don’t leave fossils. If they leave any legacy, it must be inferred from the DNA of their modern descendants, or from the descendents of their relatives.

For a few decades, scientists have compared the DNA of modern species, making mathematical inferences about the history of species diversity in a group going back to their most recent common ancestor.

This reconstructive technique held much promise for the field. But when it is checked against a group of species that do have a good fossil record, a glaring problem emerges: it cannot account for extinctions.

In their study, Plotkin and colleagues added new variables to this technique and tested it against whale fossils, considered the gold standard of fossil records.

Traditional paleontological approaches suggest that, over the last 35 million years, the number of whale species grew to as many as 150, but that number has since dwindled to 89. When applied to the DNA of current whale species, Plotkin’s reconstruction closely matched that boom-and-bust dynamic.

“It’s almost miraculous that we can inspect the DNA sequences of organisms living today and figure out how many such species were present millions of years ago,” Plotkin says. “We’re studying some of the largest species to have ever existed, and we are deciphering their evolutionary history based on information encoded in microscopic DNA molecules.”