Vista scientist helps unlock genome for threatened tortoise
A scientist from Vista was part of the team that unlocked the genome for the threatened desert tortoise, a feat that could guide conservation of the animal and advance understanding of reptile genetics.
Brian Henen, the base ecologist for the U.S. Marine Corps at Twentynine Palms and a graduate of Vista High School, worked with a team of researchers from California, Arizona and Canada to unravel the DNA of the long-lived animal. They published their findings in the online science journal PLOS One on May 31.
It’s the first time scientists have sequenced the entire genome of a tortoise, and one of only about eight projects in which they have deciphered the genome of a reptile. A genome is the complete set of genes in an organism, and guides its development and function. It also makes up a library of information about the organism’s evolution, physiology and relationship to other species.
“The genome is a tremendous resource to identify the ability of the tortoise to persist,” Henen said. “The species have both preexisting traits and things from other species that help it survive in the Mojave Desert, such as disease resistance or the ability to survive the arid climate…. Almost all of those have a genetic basis.”
Plodding through the desert with a rounded shell and stumpy legs, a desert tortoise can live an estimated 50 to 80 years. It’s native to parts of California, Arizona , Nevada , Utah and Baja, Mexico, and specializes in digging long burrows where it spends most of its time.
The species has existed for 15 to 20 million years, according to the National Park Service. But loss of habitat and disease have wiped out parts of its population, and the desert tortoise is now listed as “threatened” under the Endangered Species Act, and ranked as “vulnerable” by the International Union for Conservation of Nature. Genetic analysis has become an increasingly important resource in scientists’ toolkit for studying and reversing that decline.
To sequence the tortoise genome, researchers took tissue samples of muscle, lung, brain and blood, the paper reported. They processed them in a machine that matches a complete set of base pairs, the chemical building blocks of DNA, Henen said, and then placed those in sequence. Then they compared that to genomes of other species to identify specific genes that control particular traits. Some of those are similar to humans, he said, and some may be found among tortoises, crocodiles and birds.
By tracing common genes, they can better map out the lineage of desert tortoises in relation to other species, he said. And they can investigate genes that control key traits — such as the tortoises’ heat tolerance or immune response. An infection called upper respiratory tract disease syndrome has been linked to the species’ decline and was a factor in its threatened listing, Henen said. Other conditions such as metabolic bone disease and shell disease, which cause deterioration of the skeleton and shell, are also threats.
Researchers will mine the genome to see how some of the animals ward off those conditions, and why others don’t.
“The formation of those tissues has genetic basis,” Henen said. “Those things may help us understand if there are some individuals or populations that are more susceptible because they don’t have the best genetic makeup.”
That could help researchers develop treatments for disease among the animals, and enable them to focus conservation efforts on tortoise populations that are most at risk, he said.
“We will be able to direct our efforts to areas to protect genetic diversity,” Henen said. “If there are certain populations that are small and vulnerable we may need to protect them more. We may have to spend more effort to protect that population from predators or invasive plant species, or climate change.”
About 100,000 of the tortoises remain including 5,000 to 10,000 on the Marine base at Twentynine Palms, said Henen, who supervises efforts to protect and restore the species.
“The (desert tortoise) species continues to decline, and because of that we need to understand what are the critical factors,” that affect its survival, he said. “And having this as a reference is a tremendous step in that direction.”