New technique fills gaps in fossil record

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 on earth is challenging enough, but when scientists attempt to draw a — the branching family tree of a group of species over their evolutionary history — the challenge goes from merely difficult to potentially impossible. The is the only direct evidence scientists have about the history of , 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," said 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 Helene Morlon and Todd Parsons, both of Biology.

Their work will appear in the journal Proceedings of the National Academy of Sciences.

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 said. "This molecular inference is problematic because it's known to be false. The fossil record clearly shows extinctions and long periods of diversity loss."

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 refined.

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 said. "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 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 said. "We're studying some of the largest to have ever existed, and we are deciphering their evolutionary history based on information encoded in microscopic DNA molecules."

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Sep 19, 2011
But we know that this is flat-out wrong because it's directly contradicted by the boom-then-bust pattern in the fossil record.

So what happens when this particular boom-then-bust pattern has itself also been been inferred incorrectly? One can study certain things that happened in the past and no matter how meticulous one has been, one can STILL come up with the wrong conclusion. And others can follow suit.
It might well be the case here - and I'm not saying this to support any phylogeny, just pointing out that people can and do make mistakes.

Sep 19, 2011
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.

Here again one needs to be especially careful not to want to reach the conclusion one is looking for, in spite of the evidence at hand, simply because it supports a certain way of thinking about the origin of fossils and hence species.

Sep 20, 2011
Since the booms and busts of diversification and extinction will be unknown without fossil evidence then presumably researchers using this technique will need to plug in a range of parameters for historical diversification rates and extinction rates (shouldn't they be two distinct parameters by the way - can't you have high diversification AND high extinction at the same time?) and then produce a range of phylogenetic trees - (a bit like the way weather researchers calculate a range of predictions - in their case using slightly different initial conditions).

Done this way, one can see a bigger picture - and see areas of parameter sets where the trees are relativly unaffected.

Sep 20, 2011
I have serious doubts that anything can be learned about rates of extinction when you are only looking at the genetic of the survivors. It seems to be a complete logical disconnect involved here.

Kind of like Kevin and the Great Flood.


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