The brown tree snake, Boiga irregularis
Photo: USGS
Photo: USGS
Biological invasions present evolutionary biologists with an apparent paradox. A newly established population may begin with only a handful of individuals and therefore contain only a small sample of the genetic variation present in its parent population. The resulting population bottleneck should increase inbreeding, reduce its capacity to adapt and expose harmful recessive mutations to natural selection. In extreme cases, the population should succumb to what population geneticists call an “extinction vortex”, in which declining genetic diversity and declining population size reinforce one another.
And yet some introduced species do precisely the opposite. They survive, proliferate and overwhelm the ecosystems into which they have been introduced. Few examples are more spectacular—or more ecologically destructive—than the brown tree snake, Boiga irregularis, on the Pacific island of Guam.
Native to Australia, Papua New Guinea and other parts of the western Pacific, brown tree snakes probably reached Guam as accidental stowaways in military cargo sometime after the Second World War. The invading population is believed to have been founded by only a handful of snakes. Nevertheless, their descendants multiplied until, in some parts of the island, densities reached an extraordinary 30,000 snakes per square mile.
The consequences for Guam’s wildlife have been catastrophic. As nocturnal, generalist predators encountering abundant prey that had evolved without such a snake, they devastated the island’s native birds, causing several species to disappear from the wild on Guam. They have also disrupted food webs, preyed upon reptiles and small mammals and caused hundreds of power cuts by climbing electricity infrastructure.
But how did a population founded by so few individuals avoid collapsing under the burden of inbreeding?
A new paper in Science Advances by Christopher A. Osborne of the University at Buffalo and colleagues from Buffalo and the US Geological Survey suggests that the answer lies partly in a form of genetic variation that earlier sequencing methods tended to miss.
The snakes did not, in fact, avoid the bottleneck. Their genomes retain compelling evidence of it. The researchers found that roughly half of each snake’s genome consisted of long “runs of homozygosity”—regions in which the copies inherited from the mother and father were almost identical. This is a genomic signature of intense inbreeding, comparable with that seen in some endangered species of conservation concern.
However, genetic diversity is not confined to changes in individual DNA letters. Using long-read sequencing, which can detect much larger differences, the researchers found nearly 19,000 structural variants. These included sections of DNA that had been duplicated, deleted, inserted or rearranged. Together, these structural variants affected almost eight times as much of the genome as the single-nucleotide variants upon which conventional estimates of genetic diversity have largely relied.
More importantly, the surviving variation was not distributed randomly. Structural variants were especially abundant around gene promoters and in genes associated with adaptive immunity and olfaction. Variation in immune genes could help the snakes respond to pathogens, while variation affecting their highly developed sense of smell could influence their ability to recognise prey, exploit different foods and distinguish closely related snakes from potential prey. In other words, a population can be genetically impoverished overall while retaining disproportionately important variation in precisely those parts of its genome that influence survival and adaptability.
Additioanlly, if an introduced species has effectivey pre-adapted to the new environment, hence their ability to invade it and establish breeding populations in the first place, the new environment will select for those variants and any new ones, which increase success within it. This has been likened to an invasive species riding a wave of increasing success as it advances into its new range.
This does not mean that structural variation alone caused the invasion’s success. Guam also offered abundant, evolutionarily naïve prey and few effective predators or competitors. Nor have the researchers yet established whether these structural variants were carried to Guam by the founders, arose during the subsequent population expansion, or represent a mixture of both. Answering that question will require long-read genomic comparisons with brown tree snakes from their native range. The study identifies a plausible supply of evolutionary raw material, rather than demonstrating the adaptive effect of every variant.
The Guam invasion nevertheless provides an unusually clear natural experiment in the early stages of allopatric evolution. A tiny founder population became geographically isolated from its source population by hundreds of kilometres of ocean, effectively ending gene flow between them. From that point onwards, founder effects and genetic drift altered allele frequencies, while mutation, recombination and structural genomic change continued to produce variation upon which natural selection could act in a radically different environment.
There is no evidence that the Guam snakes have already become a new species; seven or eight decades is a very short evolutionary interval. What the population shows is how allopatric divergence begins. Isolation does not halt evolution or freeze a population in the form of its founders. It creates an independent evolutionary experiment in which inherited variation, new genomic changes, chance and natural selection can send an isolated population along a trajectory increasingly different from that of its ancestors.
Far from supporting the creationist caricature that a population deprived of genetic diversity must either remain unchanged or deteriorate inexorably, the Guam snakes show that genomes contain more variation—and evolution has more material with which to work—than a simple count of point mutations can reveal. The bottleneck was real, the inbreeding was severe, and yet natural evolutionary processes provided sufficient flexibility for a few accidental stowaways to become one of the most destructive invasive populations on Earth.
Other Species That Beat a Founder Bottleneck. The brown tree snake is not the only species to have prospered after colonisation by a remarkably small number of founders. Several recent genomic studies have examined similarly successful populations, illustrating the different ways in which organisms can retain enough evolutionary potential to survive a severe bottleneck.
Asian honeybee — northern Australia The northern Australian population of the Asian honeybee, Apis cerana, appears to have originated in about 2007 from a single swarm, possibly containing only one multiply-mated queen. Within little more than a decade, its descendants had produced more than 10,000 colonies occupying approximately 10,000 square kilometres.
A 2024 genomic study found that natural selection had acted on genetic variants already carried by the founders rather than waiting for useful new mutations. The founding queen’s stored sperm also represented contributions from several males, while balancing selection helped preserve diversity at the vital sex-determining locus. Nevertheless, a second 2024 study found reduced brood viability at the advancing margins of the population, showing that the bottleneck still imposes a cost even though it has not stopped the invasion.
Italian wall lizard — Pod Mrčaru, Croatia In 1971, researchers transferred only five adult pairs of Italian wall lizards, Podarcis siculus, from Pod Kopište to the nearby islet of Pod Mrčaru. Their descendants multiplied into a dense population and, within about 30 generations, differed markedly from the source population. They ate substantially more plant material and developed larger heads, stronger bites and changes to the digestive tract associated with processing a plant-rich diet.
A 2023 genomic analysis confirmed an extreme founder effect and genetic depletion, yet found clear evidence of population expansion. The results suggest that the rapid changes involved some combination of phenotypic plasticity and selection acting on a small number of variants with relatively large effects.
Common wall lizard — Ohio, USA Cincinnati’s population of the European common wall lizard, Podarcis muralis, reportedly began with fewer than ten animals brought from northern Italy in 1951 or 1952. The population subsequently spread through Cincinnati and founded additional populations elsewhere in Ohio.
A 2026 whole-genome study found evidence of an initial bottleneck and increased inbreeding, but also showed that the population grew so quickly that relatively little genome-wide diversity was lost. The lizards were already well suited to stone walls, gardens and other human-made habitats, so ecological compatibility allowed their numbers to increase before genetic drift could remove much more variation.
Cane toad — Australia Australia’s enormous cane-toad population ultimately derives from only 101 animals brought from Hawai‘i in 1935. These were bred in captivity and thousands of their offspring released, but all carried only the restricted genetic sample present in those original founders. The population has since spread over more than a million square kilometres.
A 2024 mitogenomic study found only a single mitochondrial haplotype in Australia, confirming an exceptionally severe bottleneck; nuclear diversity is also reduced. Despite this, the toads have evolved changes in morphology, physiology, behaviour and dispersal. High fecundity, ecological flexibility, selection on standing variation and the repeated concentration of highly mobile individuals at the invasion front have all contributed to their expansion.
No single solution to the “genetic paradox” These examples show that a bottleneck does not remove every form of useful variation, nor does it necessarily last long enough to prevent population growth. A founder population may succeed because it retains a few important variants, because balancing selection protects essential alleles, because structural variation contains more diversity than single-base comparisons reveal, because phenotypic plasticity allows immediate adjustment, or simply because rapid reproduction shortens the period during which genetic drift is most dangerous.
None of this means that small founder populations usually succeed. Most probably disappear without ever being recorded, while many apparent exceptions are subsequently reinforced by additional introductions. The conspicuous survivors are therefore a highly selected minority. What makes the Guam brown tree snakes especially informative is that long-read sequencing has now revealed another possible route through the bottleneck: extensive variation in large duplicated, deleted and rearranged sections of DNA that conventional sequencing had largely overlooked.
The publication in Science Advances was accompanied by a news release from the University of Buffalo, written by Tom Dinki.
How did inbred brown tree snakes take over Guam? Study suggests hidden genetic diversity
Biologists have long wondered how a small number of the invasive species so successfully colonized the island
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 today (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.
Associate Professor Trevor J. Krabbenhoft, PhD, corresponding author
Department of Biological Sciences
University at Buffalo
Buffalo, NY, USA.
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. 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.
Christopher A. Osborne, PhD, first author.
Department of Biological Sciences
University at Buffalo
Buffalo, NY, USA.
Long-read sequencing allows genome to be read cover to cover
Brown tree snake on a branch.Photo: USGS
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. How we define genetic diversity and how we actually measure it is shaped largely by the technology of the day.
Levi N. Gray, PhD, co-author.
Department of Biological Sciences
University at Buffalo
Buffalo, NY, USA.
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.
Levi N. Gray, PhD.
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.
Levi N. Gray, PhD.
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.
Publication:
The brown tree snakes of Guam therefore provide a particularly instructive example of evolution in an isolated population. A handful of founders became geographically separated from their source population and were exposed to a new combination of prey, competitors, predators and environmental conditions. Genetic drift and inbreeding altered the population, while natural selection acted on the variation that survived the bottleneck. These are precisely the processes expected during the early stages of allopatric divergence.
The population has not necessarily become a new species, and the researchers do not claim that it has. What Guam provides is an opportunity to observe how an isolated founder population can begin following its own evolutionary trajectory. With gene flow from the ancestral population effectively cut off, mutations, structural variants, selection and chance changes in allele frequency can accumulate independently. Given sufficient time and divergence, those are the processes that can eventually produce reproductive isolation and speciation.
The findings also expose the inadequacy of the creationist claim that evolution cannot proceed because a small population lacks sufficient “genetic information”. Genetic variation is not confined to single-letter substitutions in DNA. Duplications, deletions and rearrangements can affect large genomic regions and preserve substantial functional variation even when much of the rest of the genome has become homozygous. Natural selection needs neither unlimited diversity nor foresight; it needs only heritable differences that affect survival or reproduction.
Nor was the snakes’ success evidence of a plan. It resulted from a contingent combination of inherited variation, ecological opportunity, abundant vulnerable prey and the absence of the predators and competitors that constrained the snakes in their native range. Most small founder populations fail; this one happened to possess what was needed to prosper—with catastrophic consequences for Guam’s birds and wider ecosystem.
Far from presenting a problem for evolution, then, Guam’s brown tree snakes demonstrate its opportunistic power. Isolation supplied the evolutionary experiment, structural variation supplied the raw material, and natural selection produced the outcome—without a designer, a plan or a supernatural intervention anywhere in sight.
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