BUFFALO, N.Y. — If you look up invasive species in a textbook, there’s a good chance you’ll find a picture of a brown tree snake.
Native to Australia and the South Pacific, the brown tree snake arrived on Guam sometime after World War II, possibly by stowing aboard cargo planes. Since then, the snakes have driven many of the island’s native forest birds to local extinction and trigger hundreds of power outages each year by climbing electrical poles. In some areas of the U.S. territory, they reach densities as high as 30,000 per square mile.
The scale of the invasion has befuddled biologists given that only a small number of tree snakes were initially introduced. Inbreeding should have limited their ability to adapt to a new environment and slowed the population’s growth.
But it turns out that brown tree snakes have more genetic diversity than meets the eye, according to a new University at Buffalo-led study published Friday (July 24) in Science Advances .
Researchers from UB and the U.S. Geological Survey (USGS) used advanced long-read sequencing technology to reveal thousands of structural variants in the species’ genome. These variants — including duplications, deletions and rearrangements of DNA — are heavily concentrated in genes involved in immunity and smell.
This previously unseen genetic diversity may help explain how a population founded by only a handful of snakes was able to thrive despite a severe genetic bottleneck.
“The brown tree snake is maybe not wildly diverse, but it has important sources of genetic diversity that have been underappreciated,” says the study’s corresponding author, Trevor Krabbenhoft, PhD, associate professor in the UB Department of Biological Sciences.
The findings may be unwelcome news for agencies that have spent decades trying to control the brown tree snake population on Guam, but they could offer an encouraging message for conservation efforts.
“It’s possible that endangered species may have more flexibility in their genes than we realize,” says first author Christopher Osborne, PhD, a former PhD student in Krabbenhoft’s lab and now an aquatic biologist with State University of New York Oswego. “We're now getting a better understanding of unappreciated sources of genetic diversity that may explain how some inbred species can still respond to their environment.”
Long-read sequencing allows genome to be read cover to cover
Much of our understanding of genetic diversity comes from analyzing changes to single base pairs of DNA — like flipping an A to a G, or T to a C. That’s because that’s all initial DNA sequencing technology could reveal.
But long-read sequencing can characterize much longer pieces of DNA, revealing structural variants that can each affect 50 base pairs or more. In fact, structural variants affect nearly eight times more of the genome overall than single base-pair changes.
“It’s like looking at portions of two books letter by letter with a magnifying glass and thinking they’re the same, but not realizing entire paragraphs have been moved around or duplicated. Older sequencing technology didn’t allow us to easily see that DNA in one individual might be in a completely different place on the chromosome than in another,” says Levi Gray, PhD, a postdoctoral researcher in Krabbenhoft’s lab. “How we define genetic diversity and how we actually measure it is shaped largely by the technology of the day.”
Gray previously studied the brown tree snake problem in Guam while working for the USGS. It was through that collaboration that the researchers received DNA from the USGS Brown Tree snake Rapid Response Team (RRT), which aims to prevent the spread of the species in the U.S. and its territories.
Analyzing the DNA in Krabbenhoft’s lab, the team found that the brown tree snake genome has over 19,000 structural variants — or roughly 19,000 locations in the genome where segments of DNA differ due to duplications, deletions, or rearrangements.
These variants were not randomly distributed, but enriched in genes involved in immunity and olfaction, or sense of smell.
Brown tree snakes rely heavily on smell — using their forked tongues to taste chemical cues in the air and locate prey. Their enriched diversity in olfactory genes could help explain why brown tree snakes are known to eat other snakes in their native habitats but there’s little evidence of them doing so in Guam.
“The snakes’ heightened sense of smell may allow them to recognize one another as something more like siblings — especially given the high levels of inbreeding — than as prey,” Gray says.
It remains unclear whether the snakes’ structural variants arose before or after their introduction to Guam. Large-scale genomic changes typically accumulate over many generations, but some studies suggest that severe population bottlenecks can accelerate the formation of structural variants.
“Is it possible some of this diversity emerged after the invasion? It is, but we would have to sequence snakes from the native populations to know for sure,” Gray says.
Other co-authors include USGS scientists M. Renee Bellinger, PhD, and Melia Nafus, PhD, as well as UB research scientist Brian Foote, postdoctoral researcher Steven Fleck, PhD, as well as PhD students Sarah Chang and Hannah Waterman.
Science Advances
Data/statistical analysis
Animals
Genomic Structural Variation Rescues a Classic Biological Invader from a Population Bottleneck