A whale skeleton from the Galapagos Islands. Photo: University of Pennsylvania
University of Pennsylvania
evolutionary biologists have resolved a long-standing paleontological problem
by reconciling the fossil record of species diversity with modern DNA samples.
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 it can be full of holes or totally
nonexistent, depending on the type of organisms. The only hope in such cases is
to infer historical diversity from modern DNA sequences, but such techniques
have a fatal flaw: the results they provide are demonstrably incorrect.
The Penn team has
developed a new technique for analyzing phylogenies and shown that the results
stand up against the known fossil history of whale species, a gold standard in
terms of fossil records.
“We’ve put contemporary
molecular approaches on equal footing with classical paleontological
approaches,” says Joshua B. Plotkin of the Department of Biology in Penn’s School of Arts
and Sciences and the Department of Computer and Information Science in the School of Engineering and Applied Science.
Plotkin conducted the
research along with postdoctoral fellows Hélène Morlon and Todd Parsons, both
Their work will appear in
the Proceedings of the National Academy
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 to the present, 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 a problem with the approach is now evident.
“When scientists use
these phylogenetic techniques, they always infer patterns of increasing
diversity. In whatever group of species they inspect, they see virtually no
extinctions and a steadily increasing number of species over time,” Plotkin
says. “This molecular inference is problematic because it’s known to be false.
The fossil record clearly shows extinctions and long periods of diversity
The cetaceans, a group of
species that includes whales, dolphins, and porpoises, are ideal for testing
ideas about evolutionary diversification, as their fossil record is especially
clear. Because they are large animals, and the sea floor is well suited to fossilization,
paleontologists are confident that the cetaceans came into existence about 35
million years ago and reached a peak of diversity about 10 million years ago.
The number of cetaceans then crashed from about 150 species to the 89 species
in existence today.
“The problem with
phylogenetic inferences is that you get the opposite view when you apply it to
the cetaceans. You would see the number of whale species increasing over time,
so that the 89 species we have today is the apex. But we know that this is
flat-out wrong because it’s directly contradicted by the boom-then-bust pattern
in the fossil record.”
This realization was a
major blow for the field; if molecular reconstructions can’t be trusted, there
would be no way for scientists to ever learn the history of species that don’t
have good fossil records. The only hope was that phylogenetic methods could be
In their study, Plotkin
and his colleagues added new variables to these methods. The flaw in existing
techniques was the reliance on a static rate of diversification. Because that
variable could never be negative, the number of species inferred necessarily
increased over time.
“What we’ve done is a
fairly modest extension of these techniques, but we allow for changing rates of
speciation and extinction over time and among lineages,” Plotkin says. “Most
importantly, we allow for periods of time during which the extinction rate
exceeds the speciation rate.”
When applied to the DNA
of the 89 whale species that survive today, Plotkin’s molecular method closely
matched the dynamics in the number of whale species during the last 35 million
years as determined through traditional paleontological approaches.
“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.”