Beth Shapiro: Creatures Great and Small

By Victoria Stern Beth Shapiro: Creatures Great and Small Courtesy of the John D. & Catherine T. MacArthur Foundation In 2001, while scanning a river bank in northern Alaska for fossils, Oxford PhD student Beth Shapiro saw her advisor Alan Cooper, a pioneer in the field of ancient DNA, tugging on something big embedded in the frozen earth. When Shapiro got closer, she saw that Cooper had uncovered a late Pleistocene-era woolly mammoth

Victoria Stern
Nov 30, 2009

Beth Shapiro: Creatures Great and Small

Courtesy of the John D. & Catherine T. MacArthur Foundation

In 2001, while scanning a river bank in northern Alaska for fossils, Oxford PhD student Beth Shapiro saw her advisor Alan Cooper, a pioneer in the field of ancient DNA, tugging on something big embedded in the frozen earth. When Shapiro got closer, she saw that Cooper had uncovered a late Pleistocene-era woolly mammoth femur, which was likely more than 21,000 years old.

“It was the first time I’d seen such a big bone,” says Shapiro. “It was almost as tall as I am, and I’m about five foot.”

Once they removed the femur from the ice, Shapiro and her colleagues extracted and sequenced some of the mammoth’s DNA and published one of the first woolly mammoth genome sequences 5 years later.1

After the success of her Alaskan trip, expeditions to cold locations in search of preserved DNA became routine for Shapiro. She trekked to the frozen tundra of the Yukon to reconstruct the evolutionary history of an extinct species of bison,2 and she’s been to Siberia in search of the ancient DNA of extinct wild horses. Recently, she’s turned her attention to polar bears, pursuing her theme of determining how genetic diversity in mammal populations changes in response to environmental shifts and human contact.

“As the data are increasing, it seems that climate is a really important force driving genetic changes in populations of large mammals,” says Shapiro.

But Shapiro hasn’t just focused on charismatic macrofauna. Now head of her own lab at Pennsylvania State University, Shapiro splits her time between hunting for ancient DNA and trying to understand viral evolution. She’s applied the molecular techniques she honed studying ancient DNA to map the evolution of RNA viruses. “We use the same statistical techniques—sampling genetic sequences through time—to reconstruct the dynamics of viruses and DNA.”

Although the interactions between viruses and their hosts are very complicated, she says, RNA viruses mutate much more rapidly than DNA, making it possible to analyze genetic changes over 10 years instead of thousands. Shapiro is currently looking at HIV3 and influenza evolution to better understand the strategies these viruses use to infect hosts.

Since her Oxford days, Shapiro has published over 40 papers in journals such as Science, PLoS Biology, Current Biology, and PNAS and has become a reviewer for almost 20 peer-reviewed journals as well.

“She is so full of ideas. It’s exciting to be around the research projects she’s involved in,” says Tara Fulton, a postdoc who started working in Shapiro’s Penn State lab about a year ago. “She’s also a really good role model and a great mentor.”

Fulton is helping Shapiro with her polar bear studies in the Yukon, and the two are using volcanic ash layers to pinpoint the age of polar bear DNA that’s more than 50,000 years old.

“Beth is fantastic to work with,” says Marc Suchard, a biomathematician at the David Geffen School of Medicine at UCLA who develops quantitative tools to help Shapiro analyze her varied biological samples. “She’s my most dynamic colleague and is constantly surprising me.”

Title: Assistant Professor, Department of Biology, The Pennsylvania State University
Age: 33
Representative publications:

1. H. Poinar et al., “Metagenomics to paleogenomics: Large-scale sequencing of mammoth DNA,” Science, 311:392–94, 2006. (Cited in 121 papers)
2. B. Shapiro et al., “Rise and fall of the Beringian steppe bison,” Science, 306:1561–62, 2004. (Cited in 128 papers)
3. P. Lemey et al., “Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics,” PLoS Comp Bio, 3:282–92, 2007. (Cited in 22 papers)