Daniela Arenas-ViverosTeresa TarifaMarisol Hidalgo-CossioOmar F. OscoXimena Velez–LiendoJorge Salazar‐Bravo2026-03-222026-03-22202510.21203/rs.3.rs-6513653/v1https://doi.org/10.21203/rs.3.rs-6513653/v1https://andeanlibrary.org/handle/123456789/84440<title>Abstract</title> Studies on conservation genetics of endangered species have the ability to identify which populations should be the focus of management plans. The Bolivian chinchilla rat, <italic>Abrocoma boliviensis</italic>, is currently threatened by its rarity, paucity of information about its natural history, and landscape transformation driven by anthropogenic activities. Given the conservation status and limited distribution of <italic>A. boliviensis</italic>, understanding how its genetic diversity is apportioned is crucial to inform any potential conservation efforts. In this study, we assessed the genetic diversity and population structure of <italic>A. boliviensis</italic> as a first approximation to a comprehensive evaluation of the species. Mitochondrial data from 11 individuals of <italic>A. boliviensis</italic> reveal high levels of genetic distance, nucleotide diversity and polymorphisms, all of which indicate the existence of three separate clades. This is further supported by reduced representation genomic data that shows little to no admixture between these clades, suggesting that these lineages have been on separate evolutionary pathways and should be identified, at minimum, as separate evolutionary significant units. Our contribution highlights the urgency with which survey efforts must become the first order of action, and how new population-level data will provide a better understanding of the species, the evolutionary trajectory of its lineages, and the steps to take towards its conservation.enEndangered speciesChinchillaBiologyPopulationPopulation structureLineage (genetic)Conservation geneticsPopulation geneticsZoologyGeographypreprint