The red-tailed snake has become one of the world’s best-known examples of invasive species.
The snake, which is native to Australia and the South Pacific, probably reached Guam sometime after World War II, perhaps hiding on a military cargo plane. Its arrival had devastating consequences. The black-throated snake has locally wiped out many bird species in Guam’s forests, and causes hundreds of power outages each year by climbing utility poles and electrical equipment.
In some areas of the U.S. territory, snake numbers can reach as many as 30,000 snakes per square mile.
The unexpected invasion of snakes
This invasion has long puzzled biologists, as Guam’s population is thought to have started with a small number of snakes.
Such limited founding populations typically create severe genetic bottlenecks. Because there is less genetic variation available, inbreeding typically reduces the adaptive capacity of a species and reduces the likelihood of rapid population growth.
A new study led by the University at Buffalo was published on July 24th. scientific progresssuggests that brown tree snakes have far more genetic variation than scientists previously realized.
Researchers from UB and the United States Geological Survey (USGS) used advanced long-read sequencing to examine large portions of the snake’s genome. They discovered thousands of structural mutations, including duplicated, deleted, or rearranged DNA segments.
Many of these mutations were concentrated in genes related to immunity and smell.
This hidden genetic diversity may help explain how a population formed by just a handful of snakes survived intense inbreeding, adapted to Guam, and expanded so dramatically.
“Although red-tailed snakes may not be very diverse, they have an important source of genetic diversity that has been underappreciated,” says study lead author Trevor Kravenhoft, Ph.D., associate professor in UB’s School of Biological Sciences.
Findings that impact beyond Guam
The discovery may be a disappointment to government agencies that have spent decades trying to contain Guam’s red-tailed snake population. Increased genetic flexibility may make invasive species more resilient than previously assumed.
At the same time, the results may offer hope for endangered species with small populations or highly inbred strains.
“Endangered species may have more genetic flexibility than we realize,” said lead author Dr. Christopher Osborne. He is a former doctoral student in Krabenhoft’s lab and currently an aquatic biologist at the State University of New York at Oswego. “We now have a better understanding of previously unappreciated sources of genetic diversity, which may explain how some inbred species are able to respond to their environments.”
Long-read sequencing reveals hidden DNA changes
Much of what scientists know about genetic diversity comes from studying changes in individual DNA base pairs, such as an A changing to a G or a T changing to a C.
Early DNA sequencing tools were designed primarily to detect these small changes. It was much less effective at identifying major differences involving longer DNA.
Long-read sequencing allows researchers to examine larger, contiguous parts of the genome. This makes it possible to detect structural variations that affect more than 50 base pairs.
Collectively, structural mutations alter the genome nearly eight times more than changes involving single base pairs.
“It’s like looking at parts of two books letter by letter with a magnifying glass and thinking they’re the same, but not realizing that whole paragraphs have been moved or duplicated. Older sequencing techniques couldn’t easily confirm that one person’s DNA could be in a completely different place on the chromosome than another person’s DNA,” says Dr. Levi Gray, a postdoctoral researcher in Krabbenhoft’s lab. “How we define genetic diversity and how we actually measure it is largely shaped by the technology of the time.”
Gray previously studied Guam’s red-tailed snake problem while working for the USGS. Through this collaboration, researchers obtained DNA from the USGS Brown Tree Snake Rapid Response Team (RRT), which works to prevent the spread of invasive species to other parts of the United States and its territories.
Over 19,000 structural variants
When the research team analyzed the samples in Krabbenhoft’s lab, they identified more than 19,000 structural variations in the python’s genome.
In other words, the researchers discovered that there are approximately 19,000 different places where parts of the DNA have been duplicated, deleted, or rearranged.
These mutations are not randomly distributed throughout the genome. Instead, they appeared particularly frequently in genes involved in immune function and olfaction, or the sense of smell.
Black-bellied snakes rely heavily on scent to navigate and hunt. By flicking their forked tongue, they collect chemical signals from the air that help them locate potential prey.
The unusual diversity found in their olfactory genes may also help explain behavioral mysteries. Although black-throated snakes are known to eat other snakes within their range, there is little evidence that they frequently prey on each other on Guam.
“Snakes’ enhanced sense of smell may enable them to perceive each other as more like siblings than as prey, especially in situations of high inbreeding,” Gray said.
Has genetic diversity emerged on Guam?
Scientists still don’t know whether the structural variation was already present before the snakes arrived on Guam, or whether it appeared after the invasion began.
Large genomic changes typically accumulate over many generations. However, some studies suggest that severe population bottlenecks can accelerate the occurrence of structural variation.
To determine when these changes appeared, comparisons need to be made with native red-tailed snakes.
“Is it possible that some of this diversity emerged after the invasion? Yes, but we need to sequence snakes from native populations to know for sure,” Gray said.
Other co-authors include USGS scientists Dr. M. Renee Bellinger and Dr. Melia Nafus, UB research scientist Brian Foote, postdoctoral researcher Dr. Steven Fleck, and doctoral students Sarah Chang and Hannah Waterman.
