Genetic structure and demographic decline in the endangered short-tailed chinchilla (Chinchilla chinchilla) of the Atacama Region

The short-tailed chinchilla ( Chinchilla chinchilla ) was historically subjected to intense exploitation for the fur trade and currently faces multiple threats, yet knowledge of its genetic structure and demographic history remains limited. Here, we analysed genetic variation in populations from the Atacama Region (Chile) using single-nucleotide polymorphism (SNP) and microsatellite markers. Genetic diversity was relatively homogeneous among sampling localities, which exhibited moderate to high genetic differentiation without a pattern of isolation by distance, indicating that geographic proximity is not the primary driver of population structure. Demographic reconstructions indicated relative stability during the late Pleistocene, followed by a sustained decline in effective population size throughout the Holocene and a possible accentuation during the last century. This trajectory broadly coincides with post- Last Glacial Maximum (LGM) environmental changes, including the progressive aridification of the Atacama Desert, while more recent anthropogenic pressures have further contributed to the decline. Taken together, our findings are consistent with a regional metapopulation system composed of genetically differentiated local populations with restricted connectivity and provide a basis for conservation strategies that consider both reduced effective population sizes and the need to preserve distinct genetic units.