Hybridisation between exotic species and closely related native species has become a problem in various taxa, and management of the resulting hybrids is urgently needed. However, by the time their existence has been confirmed, hybrids have often already increased in number and spread over wide areas, such that assessing their current status is a top priority. This study estimated temporal changes in giant salamander populations in the Kamo River in Kyoto, Japan to obtain basic knowledge necessary for the management of non-native species and hybrids. The native Japanese giant salamander (Andrias japonicus) is threatened by environmental degradation, habitat fragmentation, and population decline and loss of genetic uniqueness due to hybridisation with the non-native Chinese giant salamander (Andrias davidianus). Hybridisation is ongoing in the Kamo River, which was surveyed 134 times between 2005 and 2021. This study constructed a Bayesian state-space model based on these survey data to estimate the populations of Japanese individuals, non-native individuals, first-generation hybrids, and unknown hybrids. The results indicated that unknown hybrids currently constitute the main population in the Kamo River, while the numbers of native and pure non-native individuals are quite limited. At the beginning of the survey period, the population of first-generation hybrids was the largest, but unknown hybrids subsequently dominated, suggesting that most individuals deemed unknown hybrids were second-generation or later hybrids. The detection rate of individuals per survey was less than 0.1%, indicating that the current survey method is ineffective for population control. Furthermore, the survival rates of native, non-native, and first-generation hybrid individuals declined during the survey period, suggesting that they are aging. These results indicate that the management of non-native and hybrid giant salamanders requires limiting target areas and adopting more efficient control methods.
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