Brown tree snakes on Guam reveal hidden genetic diversity

Following the Second World War, a small number of brown tree snakes arrived on the Pacific island of Guam, probably hidden in cargo. Genetic estimates suggest there were no more than 10.

A population founded by so few individuals would normally become inbred rapidly, with inbreeding expected to reduce the genetic diversity a species requires to adapt. Yet these snakes have done the opposite.

They colonised Guam, consumed the island’s native forest birds and drove several species to local extinction. There are now thought to be about 2 million brown tree snakes across Guam.

Such explosive success has been difficult to explain given the species’ exceptionally limited ancestry on the island.

A new genome study by the University at Buffalo (UB) offers an explanation that earlier sequencing methods were unable to reveal.

Scientists from the U.S. Geological Survey (USGS) collaborated on the research.

Advanced technology reveals new clues

Much of scientists’ understanding of genetic diversity in a species comes from identifying single-letter DNA errors: one base replacing another, such as an A appearing where a G was previously found.

These errors were straightforward to count because early sequencing technologies read DNA in short sections.

However, larger alterations were often missed, including instances where an entire stretch of DNA is deleted, duplicated or relocated elsewhere on a chromosome.

More recent long-read sequencing technology can track far longer DNA sequences at once. It can therefore detect these larger alterations, known as structural variants, which are defined as changes involving at least 50 base pairs.

Levi Gray is a postdoctoral researcher in the UB laboratory that led the analysis.

“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,” said Gray.

“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.”

Thousands of DNA variants

The researchers began by assembling a high-quality genome using one female snake caught on Cocos Island, a barrier islet roughly 1.9 km south of Guam.

They then resequenced eight more snakes from Guam’s main island: three females and five males.

The team identified and confirmed almost 19,000 structural variants, with deletions and insertions making up most of them.

That represents considerable variation in a snake whose single-letter genetic diversity appears limited.

The scale of the difference was particularly notable. Structural variants affected almost eight times as much of the genome as single-letter changes.

When researchers considered only differences between an animal’s two copies of each chromosome, structural variants changed around 10 times more DNA than single-letter changes.

Until now, this source of variation had been almost completely overlooked.

Brown tree snake diversity clusters in immunity and smell

The variants were not randomly distributed. Their greatest density occurred in gene promoters, short DNA regions that determine when nearby genes are activated, at around 17.58 per megabase.

They were also concentrated, beyond what chance would predict, in two specific groups of genes: those involved in the immune system and those responsible for smell.

The immune-related genes included the major histocompatibility complex (MHC), a group used by the body to identify invading microbes.

Genetic diversity in these genes often persists through inbreeding more successfully than diversity in other regions, because a varied immune toolkit can help an animal resist a wider range of pathogens.

Trevor Krabbenhoft is an associate professor of biological sciences at UB and the study’s corresponding author.

“The brown tree snake is maybe not wildly diverse, but it has important sources of genetic diversity that have been underappreciated,” said Krabbenhoft.

A heightened sense of smell

The smell-related genes may suggest a mechanism through which immune diversity continues to be replenished. Many animals use scent to identify mates with immune genes unlike their own, enabling their offspring to inherit a more varied set.

Brown tree snakes rely heavily on smell when hunting, sampling the air with their forked tongues. That same sensory ability may also influence their interactions with other snakes on Guam.

Within their native range, these snakes are known to eat other snakes, but there is little evidence of such behaviour on 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 said.

Severe level of inbreeding

By conventional measures, Guam’s brown tree snake population has experienced a severe genetic bottleneck.

On average, 49.2 percent of each snake’s genome lies in long regions containing almost no variation, which is a marker of close inbreeding.

The historical decline was extreme. Models estimate that the number of effective breeders during the invasion was below 1,000, despite the millions of snakes now living on the island.

This degree of inbreeding is comparable to that of the eastern massasauga rattlesnake, a threatened species reduced to several small populations and considered vulnerable because of its declining gene pool.

The two snakes carry a similar genetic burden, yet brown tree snakes continue to flourish.

Did the diversity come before Guam?

The study cannot establish when this variation developed. Large genomic alterations generally accumulate over many generations, although a severe bottleneck may accelerate their emergence.

“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 noted.

The authors also identify further limitations. Although their approach detects complex rearrangements effectively, it can fail to find certain large insertions.

Regions containing many repeats, such as the immune gene cluster, are difficult to assemble. A complete map of these genes would therefore be required to verify the observed pattern.

Hope beyond the invasion

The results add complexity to decades of work to control brown tree snakes on Guam. At the same time, they raise the possibility that endangered species may contain more concealed genetic diversity than scientists previously recognised.

Wildlife managers commonly assess a population’s genetic health using single-letter diversity alone.

A species that appears genetically depleted by that measure may still possess a store of structural variation that such counts do not detect.

The study’s first author, Christopher Osborne, is a former doctoral student in Krabbenhoft’s laboratory and is now an aquatic biologist at the State University of New York at Oswego.

“It’s possible that endangered species may have more flexibility in their genes than we realize,” said Osborne.

“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.”

The research was funded by laboratory start-up funding provided to Krabbenhoft by UB, and the authors reported no competing interests.