Clonality, management and geography shape genetic structure in a perennial species with restricted distribution

BACKGROUND AND AIMS: Genetic information is essential for understanding evolutionary processes across different temporal scales, particularly those occurring over contemporary or recent generations influenced by management, and for guiding conservation actions. These components are now explicitly incorporated into the Kunming-Montreal Global Biodiversity Framework (GBF), which emphasizes metrics such as the effective population size as key indicators for monitoring and management. However, the genetic context of partly clonal and economically important systems remains insufficiently explored. Agave karwinskii, a mezcal-producing species with a restricted distribution in southern Mexico, which occurs along a gradient of management intensity dominated by clonal propagation, provides an excellent model for informing conservation strategies in these understudied systems. METHODS: We generated genomic data using restriction site-associated DNA sequencing and conducted population-level analyses, integrating the biological and management context of the species to understand its genetic patterns and delineate conservation units. We also evaluated GBF-relevant indicators to assess genetic diversity and support management planning. KEY RESULTS: Agave karwinskii exhibited high genetic diversity (Hs = 0.25) and moderate population differentiation (FST = 0.19), shaped by geographical, ecological and, particularly, management factors. We identified 173 single nucleotide polymorphisms as candidate loci potentially associated with local adaptation to environmental variation, including 15 robust single nucleotide polymorphisms consistently detected by four complementary approaches and associated with defence responses, adaptation to environmental stressors, growth and metabolic regulation. Two evolutionarily significant units and seven management units were delineated. The effective population size declined sharply in clonal and semi-cultivated systems, with most units falling below the GBF threshold (Ne > 500), despite large census sizes. Traditional mixed management helps to maintain diversity by promoting gene flow and reducing inbreeding, acting as a form of in situ conservation. CONCLUSIONS: This study provides a population genetic framework for understanding evolutionary processes influenced by management and guiding conservation strategies in A. karwinskii, offering insights applicable to other perennial, partly clonal and semi-domesticated plant species.