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Squirrels' Evolutionary Family Tree Reveals Influence of Climate, Geology

Duke evolutionary biologists used DNA and fossil records to trace back the genealogies of all but one of today's groupings of squirrel species


The first-ever genetic delineation of nearly all existing squirrel groups suggests not only some surprising branchings in the squirrels' family tree. The study also reveals strong evidence that geological and climatic change influenced how their ancestors evolved and spread over 36 million years from just one part of ancient North America to nearly all of today's world.

"By modifying habitats and creating bridges and barriers between land masses, climate change and tectonic events [land mass movements] are believed to have important consequences for diversification of terrestrial organisms," wrote two Duke University evolutionary biologists in a paper posted on the Feb. 20, 2003, edition of Science Express, the on-line version of the journal Science.

"Such consequences should be most evident in the phylogenetic histories of groups that are ancient, widespread and diverse. The squirrel family is one of the very few mammalian families endemic to Eurasia, Africa, North America and South America, and is ideal for examining these issues," continued John M. Mercer, a Duke assistant professor of the practice of biology, and V. Louise Roth, a Duke associate professor of biology and biological anthropology and anatomy.

In research supported by the National Science Foundation and Duke, Mercer and Roth analyzed DNA differences among 50 of the 51 present-day squirrel genera to deduce their interrelationships, leaving out only one Indian flying squirrel that is too rare to study.

They determined squirrel family ties by statistically analyzing representative DNA sequences extracted from live animals or preserved museum specimens. To deduce how long ago and where various lineages lived, they also used fossil dating records and "molecular clock" analyses, which predict how DNA sequences change over time.

Comparing their findings with geological evidence, they noted "an interesting interplay between global change and the way this particular group of animals diversified," Mercer said in an interview. "Just from looking at modern day taxa and where they're distributed, you wouldn't deduce that the earliest squirrel was in North America," added Roth.

The earliest fossil evidence for squirrels was found in western North America and dated to about 36 million years ago, the authors wrote. Based on the Duke scientists' evidence, during the 5 million years that followed "there appears to have been a very rapid divergence of squirrels into five major branches," Roth said.

"That also corresponds in timing with the biggest climatic deterioration in the past 55 million years. There's an abrupt cooling and climatic fluctuation, and also a lot of extinctions in other animal groups. Big things were happening environmentally."

The first evidence for squirrels in Europe dates to about 30 million years ago, though the researchers are not sure how they got there, she said. However fossil evidence provides a clue. For much of the period in which squirrels have existed, "there was easy passage between Eurasia and North America," she added.

According to fossil records, the first squirrels arrived in Africa shortly after that former island continent collided with Eurasia about 18-20 million years ago, the Duke researchers said. And their DNA evidence shows the first branchings in the lineages of modern African ground and tree squirrels date to shortly after that. "So squirrels seem to have arrived in Africa and begun their diversification shortly after land animals first had access," Roth said.

At about 11 million years ago, their research points to what Roth called "an explosive diversification of genera of squirrels" that now inhabit the islands and continental land masses of Southeast Asia. That divergence coincided with extremely low local sea levels, perhaps caused by geological changes in the ocean floor or perhaps by the final formation of the Antarctic ice sheet, Mercer said.

The sea level drop could have exposed now-submerged land between islands along a geological feature called the Sunda Shelf. The authors hypothesized that squirrels could have proliferated across the shelf, with individual populations then diversifying through evolution when the islands were again isolated.

Before about 7 million years ago a forested land connection existed between what is now Alaska and Siberia, according to the Science Express article. And the authors' evidence suggests that both tree and flying squirrel lineages crossed between the two continents there at a time when the land bridge was open and the environment properly leafy.

Evidence for the Asia-North America migration of certain ground squirrel lineages, however, appears to come after a subsequent period when rising sea levels cut off that passage, the Duke scientists said. When seas next subsided, the reemerging land bridge would have been treeless and the climate colder. "Ground squirrels can live in treeless habitats like arctic meadows," Mercer added.

Before about 3 million years ago, South America was an isolated island continent with no fossil records of squirrels, Roth said. Then complex geological shifts created a land bridge at what is now the Isthmus of Panama. The Duke biologists' evidence suggests that all but one squirrel group now in South America descended from a common ancestor that crossed when the isthmus formed.

The exception among South American tree squirrels is a pygmy variety that the researchers' evidence suggests diverged from other squirrels as long as 35 million years ago, when South America was still presumably isolated. "The intriguing question is: where were its ancestors during that very long time since its divergence from other squirrels?" Roth asked.

Other surprises include new questions about the evolutionary branching off of flying squirrels. "Our results argue against the long-standing practice of segregating all tree and ground squirrels into a group distinct from flying squirrels," the authors wrote.

"We think of 'squirrels' as those that invade trash cans on campus," Roth said. "But they have a great diversity of body types and habits. Most are not common, even in regions where you find them. Most are not habituated to humans.

"There is a giant wooly flying squirrel that lives in caves in the mountains of Kashmir," she continued. "Until 1994, it was believed to be extinct. We were actually able to analyze its tissues. There are anteating squirrels in Southeast Asia. There's a mouse-sized pygmy squirrel in Gabon; we ended up using museum specimens to get its DNA."

To obtain their DNA samples, the researchers relied on "colleagues who do field work in various places," Mercer said. Other key help came from natural history museums that agreed to let the researchers try extracting DNA from preserved remains. "Some of these squirrels are really rare," he added. "They're not only difficult to find in their natural settings. They're rare in museums."

Sensitive to the possibility that museum specimens' DNA might be degraded or contaminated, Mercer said they sought "multiple samples wherever possible from different collectors from different museums." They also ruled out contamination from sources other than squirrels by comparing their DNA data with that available in established genetic data bases.

"We worked hard to try and be sure that when we made a claim it was well-substantiated," Mercer said.