Biodiversity is currently declining at an unprecedented rate worldwide, making it an urgent task to quantify the pace and spatial scale of ongoing extinctions. However, tracking real-time extinctions in natural systems remains challenging, and quantitative assessments are still scarce. This limitation arises from both the lack of historical survey data and the difficulty of defining extinction, particularly at local scales. Freshwater ecosystems are vulnerable to extinction because habitats are constrained within river networks. In this study, we focus on the Japanese crayfish (Cambaroides japonicus), a freshwater species whose habitat is typically limited to stream reaches of only a few hundred meters. As a result, its local populations can be clearly defined, facilitating robust extinction assessments. Therefore, we aimed to quantify the local extinction extent and rate of Japanese crayfish and examine the relationship between environment characteristics and extinction patterns to identify factors driving population decline.
We conducted resurveys at 102 historical occupancy sites across Hokkaido, employing a detection framework that combined traditional hand-capture methods with environmental DNA (eDNA) analysis to account for potential false negatives. We estimated local populations change for two survey periods through comparing capture density of every site. To identify drivers of population loss, we utilized Generalized Linear Models (GLMs) incorporating changes in land use (agricultural, forested, and urban cover) and bioclimatic variables (extreme temperature and precipitation metrics) between the two survey periods.
Our results revealed a significant decline in distribution. While hand-capture confirmed presence at 54 sites, eDNA analysis detected the species at 73 sites, indicating a 27.7% local extinction rate over approximately twenty years (one sample site was excluded from analysis since contamination issue). Furthermore, capture density (CPUE) significantly decreased with the time passed since historical surveys, suggesting a progressive reduction in population density. The GLM identified the change in maximum summer temperature as a primary significant predictor of population loss. These findings suggest that increasing thermal stress, likely driven by extreme weather events, is a critical driver of local extinction for Japanese crayfish. Integrating conventional capture with eDNA reduces false negatives, and comparing this integrated detection signal to historical records enables robust estimation of local extinction. And our results further identify climatic warming as a pivotal threat.