Woolly-Mammoth Gene Study Changes Extinction Theory

Penn State University genomicists Webb Miller and Stephan C. Schuster, in front of the Roche/454 Life Sciences Genome Sequencer 20 System that was used to sequence mammoth mitochondrial DNA from the hair of woolly mammoths. Credit: Penn State

A large genetic study of the extinct woolly mammoth has revealed that the species was not one large homogeneous group, as scientists previously had assumed, and that it did not have much genetic diversity. "The population was split into two groups, then one of the groups died out 45,000 years ago, long before the first humans began to appear in the region," said Stephan C. Schuster, associate professor of biochemistry and molecular biology at Penn State University and a leader of the research team. "This discovery is particularly interesting because it rules out human hunting as a contributing factor, leaving climate change and disease as the most probable causes of extinction." The discovery will be published later this week in the early online edition of the Proceedings of the National Academy of Sciences (PNAS).

The research marks the first time scientists have dissected the structure of an entire population of extinct mammal by using the complete mitochondrial genome — all the DNA that makes up all the genes found in the mitochondria structures within cells. Data from this study will enable testing of the new hypothesis presented by the team, that there were two groups of woolly mammoth — a concept that previously had not been recognized from studies of the fossil record.

The scientists analyzed the genes in hair obtained from individual woolly mammoths — an extinct species of elephant adapted to living in the cold environment of the northern hemisphere. The bodies of these mammoths were found throughout a wide swathe of northern Siberia. Their dates of death span roughly 47,000 years, ranging from about 13,000 years ago to about 60,000 years ago.

Schuster and Webb Miller, professor of biology and computer science and engineering at Penn State, led the international research team, which includes Thomas Gilbert at the University of Copenhagen in Denmark and other scientists in Australia, Belgium, France, Italy, Russia, Spain, Sweden, the United Kingdom, and the United States. The team includes experts in the fields of genome evolution, ancient DNA, and mammoth paleontology, as well as curators from various natural-history museums.

Life-size model mammoths at the Ice Age Museum in Moscow. Credit: Ice Age Museum, Moscow/Fyodor Shidlovskiy

Another important finding for understanding the extinction processes is that the individuals in each of the two woolly-mammoth groups were related very closely to one another. "This low genetic divergence is surprising because the woolly mammoth had an extraordinarily wide range: from Western Europe, to the Bering Strait in Siberia, to Northern America," Miller said. "The low genetic divergence of mammoth, which we discovered, may have degraded the biological fitness of these animals in a time of changing environments and other challenges."

Our study suggests a genetic divergence of the two woolly-mammoth groups more than 1-million years ago, which is one quarter the genetic distance that separates Indian and African elephants and woolly mammoths," Miller said. The research indicates that the diversity of the two woolly-mammoth populations was as low centuries ago as it is now in the very small populations of Asian elephants living in southern India. "The low genetic divergence of the elephants in southern Indian has been suggested as contributing to the problems of maintaining this group as a thriving population," Schuster said. Intriguingly, the mitochondrial genomes revealed by the researchers are several times more complete than those known for the modern Indian and African Elephants combined.

Whereas studies before this research had analyzed only short segments of the DNA of extinct species, this new study generated and compared 18 complete genomes of the extinct woolly mammoth using mitochondrial DNA, an important material for studying ancient genes. This achievement is based on an earlier discovery of the team led by Miller, Schuster, and co-author Thomas Gilbert, which was published last year and that revealed ancient DNA survives much better in hair than in any other tissue investigated so far. This discovery makes hair, when it is available, a more powerful and efficient source of DNA for studying the genome sequences of extinct animals. Moreover, mammoth hair is found in copious quantities in cold environments and it is not regarded as fossil material of enormous value like bone or muscle, which also carries anatomical information.

Ball of permafrost-preserved mammoth hair containing thick outer-coat and thin under-coat hairs. Credit: Stephan Schuster lab, Penn State

"We also discovered that the DNA in hair shafts is remarkably enriched for mitochondrial DNA, the special type of DNA frequently used to measure the genetic diversity of a population," Miller said. The team's earlier study also showed that hair is superior for use in molecular-genetic analysis because it is much easier than bone to decontaminate. Not only is hair easily cleaned of external contamination such as bacteria and fungi, its structure also protects it from degradation, preventing internal penetration by microorganisms in the environment.

An important aspect of the new study is that the hair samples it used had been stored in various museums for many years before being analyzed by the researchers, yet the scientists were able to obtain lots of useful DNA from them. "One of our samples originates from the famous Adams mammoth, which was found in 1799 and has been stored at room temperatures for the last 200 years," Schuster said. This research technique opens the door for future projects to target interesting specimens that were collected a long time ago and are no longer available from modern species, the scientists said. Even the molecular analysis of entire collections seems now possible, an effort that the team calls "Museomics."

"We plan to continue using our techniques to untangle the secrets of populations that lived long ago and to learn what it might have taken for them to survive," Schuster said. "Many of us also have a personal interest in learning as much as we can about how any species of large mammal can go extinct."

The research was supported, in large part, by Penn State University, Roche Applied Sciences, and a private sponsor. Additional support was provided by the National Human Genome Research Institute, Marie Curie Actions, the Australian Research Council, the Russian Foundation for Basic Research, and the Pennsylvania Department of Health.

CONTACTS

— Stephan Schuster: (+1)814-863-9278 or (+1)814-441-3513, scs@bx.psu.edu, Penn State Center for Comparative Genomics and Bioinformatics

— Webb Miller: (+1)814 865-4551, webb@bx.psu.edu, Penn State Center for Comparative Genomics and Bioinformatics

— Barbara Kennedy (PIO): 814-863-4682, science@psu.edu

BACKGROUND INFORMATION:

Woolly mammoths, descended from ancestors in Africa, were widespread in northern Europe, Asia, and North America during the last Ice Age. However, by 11,000 years ago, they all had died out, except for tiny isolated populations that held out for another few thousand years.

Ball of permafrost-preserved mammoth hair. Credit: Andrei Sher/Fyodor Shidlovskiy

Copenhagen Ancient DNA Laboratory, where the ancient samples are processed prior to sequencing. Credit: Stephan Schuster, Penn State

Mammoth hair samples being digested in the Copenhagen ancient DNA Laboratory. Credit: Stephan Schuster, Penn State

Drawing of a woolly mammoth

For comparison, a drawing of a contemporary elephant

Partially frozen mammoth remains, containing preserved muscle tissue and hair. Credit: Mammuthus lab Khatanga/Tom Gilbert