Two Giant Flying Squirrels, One Island, Two Very Different Genetic Journeys

High in the forests of Taiwan, two species of giant flying squirrels glide through the same island’s treetops, eat similar foods, and lead strikingly similar lives. Yet according to a new genomic study published in the journal Heredity, these close relatives carry within their DNA profoundly different stories of how they came to be distributed across the island, stories shaped not primarily by the environment they inhabit, but by the sheer geography of Taiwan itself and by the demographic twists of fate each lineage experienced through the ice ages.

The study, led by Carina Lee Terry of National Taiwan University together with colleagues including senior authors Hurng-Yi Wang and Cheng-Ruei Lee, set out to answer a deceptively simple question: when two closely related species share the same island, do they show the same patterns of genetic structure within their populations? Geographic isolation and environmental differences are both well-known drivers of genetic differentiation, and decades of research have examined their relative importance in individual species. But comparing closely related species living side by side on the same landmass offers a rare natural experiment, because it holds much of the shared history constant while allowing differences in ecology, in this case elevational range, to reveal their influence.

The two subjects of the investigation were Petaurista lena and Petaurista grandis, two giant flying squirrels endemic to Taiwan. Although they have similar life histories, the species occupy different elevational bands in the island’s mountainous terrain, which rises steeply from coastal plains to peaks approaching four thousand meters. Taiwan’s dramatic topography, sculpted by tectonic uplift and carved by Pleistocene glaciations, has long been recognized as a cradle of endemism, and small mammals on the island have repeatedly shown phylogeographic breaks that hint at past isolation. The researchers wanted to know whether these two squirrels, gliding through different altitude zones, had responded to that shared landscape in the same way.

To find out, the team turned to population genomics. They generated genome-wide single nucleotide polymorphism data from tissue samples, which came from the Taiwan Biodiversity Research Institute, the National Museum of Natural Science, and lawfully harvested animals provided by Truku Indigenous hunters in the Hualien region under permits issued by Taiwan’s Forestry Bureau. With thousands of genetic markers in hand, they applied a battery of analytical tools: ADMIXTURE and principal coordinates analyses to visualize population structure, spatial genetic analyses to detect how relatedness decays with distance, and a framework for disentangling the effects of geographic distance from those of environmental variables on genetic differentiation.

The first major result was a striking parallel. Both species showed a clear north-south genetic split, with individuals from the northern part of their ranges genetically distinct from those in the south. This shared pattern suggests that the fundamental geography of Taiwan, its elongated north-south axis and the mountain ridges that run down its spine, has imposed a common signature of isolation on both squirrels. When the researchers statistically accounted for neutral factors such as geographic distance, they found little association between genetic variation and environmental characteristics. In other words, the climate and habitat differences across the island did not appear to be sculpting the squirrels’ genomes in any strong, detectable way; the landscape’s shape was doing most of the work.

But beneath that shared surface pattern, the demographic histories of the two species diverged dramatically, and this is where the study delivers its most surprising findings. Using fastsimcoal2, a coalescent-based program that models complex evolutionary scenarios and estimates the demographic parameters that best explain observed genetic data, the team reconstructed each species’ past. Petaurista lena, the species associated with higher elevational ranges, experienced an early north-south divergence dated to roughly 163 thousand years ago, deep in the Pleistocene. After that split, gene flow between the northern and southern populations remained comparatively high, and the species maintained a larger overall population size with correspondingly higher genetic variation.

Petaurista grandis told a very different story. Its north-south differentiation is far more recent, dated to approximately 46 thousand years ago, and its population size is smaller. Most dramatically, the northern population of P. grandis appears to have passed through a strong bottleneck, a severe reduction in numbers that would have stripped away genetic diversity and left the surviving population with a compressed, less varied gene pool. The team corroborated their coalescent modeling with Stairway Plot v2, an complementary method that infers changes in population size through time from the folded SNP frequency spectrum, and plotted the inferred trajectories against historical temperature records to see how the squirrels’ fortunes tracked the climate’s swings.

Why would two species with such similar ecologies end up with such different demographic pasts? The researchers turned to niche suitability modeling with Maxent, which uses occurrence records and climate layers to estimate where conditions favorable to each species existed in the past. The answer that emerged is elegantly simple: area. Across historical climate scenarios, the suitable habitat for P. lena was generally larger than that available to P. grandis. A species with more room to live can sustain larger populations, retain more genetic variation, and maintain enough connectivity between regions to soften the effects of any single isolation event. P. lena’s earlier divergence with sustained gene flow fits that picture of a species with a broad, stable footprint across the island through the Pleistocene.

P. grandis, by contrast, appears to have been squeezed into a smaller historical suitable area, which would have kept its numbers lower and made its populations more vulnerable to the climate oscillations of the ice ages. The authors suggest that its relatively recent north-south divergence and reduced genetic variation may be tied to that constrained historical range. They also raise the possibility of competitive exclusion between the two species as a contributing factor, a reminder that the demographic history written in a genome reflects not just climate and geography but also the ecological push and pull among species that share a landscape. The elevational ranges that separate the two squirrels today may thus be both a cause and a consequence of their divergent histories.

The broader lesson of the study resonates far beyond Taiwan’s forests. Species with similar life histories on the same island can indeed converge on similar patterns of within-species divergence, in this case a north-south split that mirrors the island’s geometry. But the depth of that divergence, the amount of gene flow, and the size and resilience of populations can differ enormously depending on each species’ elevational range, its response to past climate change, and its interactions with close relatives. For conservation, the implications are concrete: the northern population of P. grandis, with its bottlenecked, low-diversity gene pool, may warrant particular attention as the island’s climate continues to change. And for evolutionary biologists, the two squirrels of Taiwan offer a vivid demonstration that the same island can tell two species very different stories, and that genomes remember which story each one lived.

Subject of Research: Comparative population genomics and demographic history of two sympatric giant flying squirrel species with different elevational ranges in Taiwan

Article Title: Distinct demographic histories associated with elevational ranges of two giant flying squirrel species in Taiwan

Article References: Terry, C. L., Chang, S.-W., Pei, K. J.-C., Chen, H.-W., Chen, Y.-J., Wang, H.-Y., & Lee, C.-R. (2026). Distinct demographic histories associated with elevational ranges of two giant flying squirrel species in Taiwan. Heredity. https://doi.org/10.1038/s41437-026-00891-0

Image Credits: AI Generated

DOI: 10.1038/s41437-026-00891-0

Keywords: giant flying squirrels, Petaurista, Taiwan, population genomics, phylogeography, demographic history, elevational range, Pleistocene climate, niche modeling, genetic divergence, bottleneck, island biogeography