Steering clear of unfriendly humans and making do with shrinking habitats, pumas are becoming increasingly isolated—and increasingly inbred. Just how inbred has been hard to gauge, given that genetic studies of puma populations are usually limited to the assessment of DNA markers. A new study, however, has opted for a more comprehensive approach. In addition to DNA markers, the new study has taken in broad swaths of DNA in between DNA markers. Exploiting whole genome sequencing technology, the new study not only estimates the degree of inbreeding in puma populations, it also informs strategies that might be undertaken to enhance the puma’s genetic diversity.

The new study, from scientists based at the University of California, Santa Cruz (UCSC), was led by evolutionary biologist Beth Shapiro, PhD. Shapiro is best known for recovering and sequencing tiny bits of DNA from ancient bones, charting the genetic changes in mammoths and other now-extinct animals that occurred as their numbers shrank. But she also has a keen interest in applying the same techniques to existing creatures, like the North American mountain lion. Shapiro wants to learn more about the genetic roads to extinction—and possibly prevent those creatures from suffering the same fate.

One day, when Shapiro and UCSC wildlife biologist Christopher C. Wilmers, PhD, were discussing the Santa Cruz lion population, the two scientists realized that with up-to-date sequencing technology, it would be possible to assess puma inbreeding, its likely consequences, and potential conservation strategies. Specifically, with whole genomic information, it would be possible to pinpoint puma populations that are in need of an influx of new genes, or to identify the best pumas to move between populations.

Cataloging whole genome sequences could help stop inbreeding in its tracks and keep local populations from going extinct, Shapiro said. To start this work, Shapiro and colleagues assembled a draft puma genome and a geographically broad panel of resequenced individuals. Then the scientists used their findings to assess the long-term efficacy of interpopulation admixture as a way to rescue small and isolated populations from the effects of inbreeding, which include serious abnormalities such as damaged hearts and malformed sperm.

“This is the first time,” Shapiro declared, “that whole genomes have been used in this way.”

Details of the work appeared October 18 in Nature Communications, in an article titled, “Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.” The reference genome cited in the article comes from a puma known as 36m. He had been radio-collared and tagged by Wilmers as part of a long term study of California mountain lions.

“We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity,” the article’s authors wrote. “While translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity.”

Shapiro and colleagues demonstrated that the number and length of the stretches of DNA between DNA markers provide a precise measure of both the extent of inbreeding and how recent it is—and, therefore, how close a population is to falling off a genetic cliff. Inbreeding is not a slow and progressive process, Shapiro explained. Instead, once enough long runs of DNA with identical copies accumulate, the effects of inbreeding kick in suddenly, like turning off a light switch, she said.

In addition to sequencing 36m’s genome, Shapiro and colleagues sequenced the genomes of nine other mountain lions using stored samples—another from the Santa Cruz area, two from the Santa Monica mountains, one from Yellowstone, three from Florida, and one from Brazil.

Comparing these genomes allowed the scientists to confirm what scientists had learned only after years of study—that the translocation of Texas cougars had boosted genetic diversity and health of Florida panthers. The sequences also brought new insights: even after mixing in the Texas DNA, the Florida population remains closer to the genetic brink than previously thought.

“The big takeaway is that translocation worked, but the lights are going to go off because they continue to inbreed,” Shapiro explained.

Similarly, the population in the Santa Cruz Mountains “is not doing as well as we expected,” she said. The 10 genomes also held controversial hints that mountain lions may have existed in North America far longer than previously thought—as many as 300,000 years, instead of fewer than 20,000 years.

More insights will come as scientists ramp up whole genome sequencing. Already, Shapiro’s work is shining a powerful new spotlight on the genetic health of individual mountain lions and populations, pointing the way to more effective conservation strategies. Isolated populations, for example, may benefit from wildlife bridges across major highways, to allow animals to wander more widely.

“Now we can make more informed decisions,” noted Warren E. Johnson, PhD, a molecular ecologist affiliated with the Smithsonian Institution. “In the past, we made decisions based on limited genetic information.” The new approach takes out much of the uncertainty about a population’s genetic heritage, he added. It also offers clues about how to preserve genetic variation and may help populations adapt to change.

Though puma 36m didn’t live to see any of these advances, his genetic legacy will remain. “While 36m was a badass puma by any measure, he might one day come to be the most recognized puma anywhere,” Wilmers wrote in a tribute. “[His] will be the puma genome against which other puma genomes can be compared and used to test all sorts of evolutionary and ecological questions.”

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