Climate change threatens to shrink the habitat of Japan’s giant living fossil

The Japanese giant salamander is a creature that seems to have slipped through time. Growing up to 1.8 metres long, retaining larval traits into adulthood, breathing largely through its skin and relying on external fertilisation guarded by devoted males, Andrias japonicus is one of the world’s largest amphibians and a keystone predator in the mountain streams of western Japan. But a new study published in Frontiers of Biogeography suggests that this living fossil may be running out of time in a very modern way: climate change is projected to strip away more than half of the geographic area currently suitable for the species, with losses intensifying through 2090 under both optimistic and pessimistic emissions scenarios.

The research team, led by scientists at the University of Liège, set out to answer two questions that have long frustrated conservationists. First, which environmental conditions actually determine where Japanese giant salamanders can live? Second, how will those conditions shift as the planet warms? To do this, they deployed species distribution models, a cornerstone tool of modern macroecology, over an area of 282,916 square kilometres covering the entirety of Honshu, Shikoku and Kyushu islands. The models compared 477 high-resolution occurrence records, gathered from field surveys and published studies dating back to 1970, against seven remote-sensing environmental predictors spanning climate, topography and land use.

The occurrence data required careful preparation. The team collected 1,228 presence records in total, but to avoid spatial autocorrelation and overfitting, they thinned the dataset so that no two points fell within one kilometre of each other, a distance chosen because it matches the grid scale of the environmental data and the typical migratory range of the species. The result was a robust set of 477 presence points on which to train the models. Environmental predictors were selected based on the salamander’s ecology: four bioclimatic variables from the WorldClim dataset, including mean temperature of the wettest and warmest quarters and precipitation of the warmest and coldest quarters, alongside mean slope, agricultural area and urban area, all at a one-square-kilometre resolution.

The modelling itself used MaxEnt, a presence-background method that compares the environmental conditions at species locations with those available across the landscape. To ensure the model captured conditions specific to the salamander’s actual range, the team restricted the background to the known distribution during training, then projected the model across all of Japan to explore potential suitability beyond it. They corrected for sampling bias using a bias grid built from a minimum convex polygon around occurrence points buffered by 50 kilometres, and partitioned the data spatially into four folds to improve transferability across space and time. Model calibration tested 36 parameter combinations of feature classes and regularisation multipliers, with the optimal model selected using corrected Akaike Information Criteria and validated against null models built from 100 iterations.

The findings are striking. Climatic variables dominated the distribution model, contributing 76.21 percent of the total, with precipitation of the warmest quarter alone accounting for 36.73 percent. The salamanders favour areas with moderate precipitation during cold and wet seasons and mild summer temperatures, with the highest probability of presence at average air temperatures around 20 to 24 degrees Celsius. Excessive precipitation proved detrimental, with suitability dropping sharply above 500 millimetres in the wettest quarter, likely because strong currents and prolonged flooding threaten larvae and disrupt the submerged nests that males guard. Slope also mattered, with suitability rising up to a mean of 17 percent before declining in steeper terrain, while land-use variables contributed relatively little.

Perhaps the most unexpected result concerns geography. The current habitat suitability map reveals highly suitable areas both within and beyond the species’ known range. In the northern part of Honshu Island, far from any confirmed salamander populations, the model identified 42,508 square kilometres of high-suitability habitat. Yet the salamanders cannot reach them. The Japanese Alps, a mountain chain bisecting Honshu, form an impassable natural barrier for a fully aquatic species that cannot climb terrestrial environments outside of riverine areas. The team’s analysis suggests that climatic differences between northern and southern Japan do not explain the species’ absence in the north; rather, it is the biogeography of the Alps that has confined the salamander to the south-western regions of the island.

Within the current distribution range, which covers 59,193 square kilometres, the picture is already mixed. Thirty percent of the area was identified as unsuitable, 37 percent as low suitability, 22 percent as moderate and just 11 percent as high suitability. The projections for the future are more alarming. Considering the extent of the current range, more than 50 percent of the geographic area is expected to lose habitat suitability at any point between 2050 and 2090, under both the optimistic SSP126 scenario and the pessimistic SSP370 scenario. The most severe loss, affecting 64.5 percent of the area, is predicted for 2090 under the pessimistic scenario. Gains in suitability do occur, reaching 14.5 percent of the area in 2070 under the optimistic scenario, but they are insufficient to offset the losses.

The mechanisms behind these projected losses are rooted in the salamander’s physiology. Japanese giant salamanders prefer relatively cold mountainous streams with high levels of dissolved oxygen, which promotes cutaneous respiration. Rising air temperatures raise water temperatures and reduce dissolved oxygen concentrations, a critical parameter for survival. Heavy and sustained rainfall is also expected to increase across Japan, raising the frequency of flooding events that particularly affect larval stages and nesting sites. A study on the North American giant salamander, or hellbender, showed that a two-degree increase in water temperature decreased immune function and growth rate while increasing physiological stress, offering a sobering parallel for what warming may mean for the Japanese species.

The conservation implications are complex. The species was reassessed from Near Threatened to Vulnerable on the 2022 IUCN Red List, but many populations are declining and the salamander’s long life expectancy makes the true status of populations difficult to assess. Habitat fragmentation from dams, built for agriculture and flood control, blocks movement along waterways and reduces breeding microhabitat availability. Without connectivity between habitats, even the suitable areas identified by the models would be inaccessible to the salamanders. Interestingly, the declining human population in rural Japan may offer some relief, as unmaintained agricultural dams eventually burst and restore connectivity, though new flood-control infrastructure linked to climate change threatens many habitats.

The study calls for new surveys based on the projected maps, particularly on Shikoku and Kyushu islands where distribution data remain sparse, and for fine-scale research on disturbances to aquatic habitats. Environmental DNA surveys could identify previously unknown populations, followed by visual confirmation at positive sites. Because giant salamanders act as top predators structuring aquatic communities, protecting their habitat may benefit other species relying on the same streams, an umbrella effect that amplifies the conservation value of every stream saved. As climate change tightens its grip on the cold, clear waters these ancient creatures depend upon, the race is on to understand and preserve what remains of their world before the living fossil becomes a fossil in fact.

Subject of Research: Projected climate-driven loss of habitat suitability and distribution range of the endangered Japanese giant salamander

Article Title: Loss of habitat suitability and distribution range of the endangered Japanese giant salamander under climate change

Article References: Duret, C., Bartet, T., Hambuckers, A., Kishida, O., Okada, S., Taguchi, Y., Takahashi, M. K., & Denoël, M. (2025). Loss of habitat suitability and distribution range of the endangered Japanese giant salamander under climate change. Frontiers of Biogeography, 18, Article e133105. https://doi.org/10.21425/fob.18.133105

Image Credits: AI Generated

DOI: 10.21425/fob.18.133105

Keywords: Japanese giant salamander, Andrias japonicus, climate change, species distribution models, MaxEnt, habitat suitability, amphibian conservation, biogeography, Japanese Alps, habitat fragmentation, Frontiers of Biogeography, freshwater megafauna