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

Abstract 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 effective population size (Ne) as key indicators for monitoring and management. However, the genetic context of partially clonal and economically important systems remains insufficiently explored. Agave karwinskii, a mezcal-producing species with a restricted distribution in southern Mexico that 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 RADseq and conducted population-level analyses following the framework proposed by Funk et al., (2012), integrating the species’ biological and management context to understand its genetics patterns and delineate conservation units. We additionally 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 by management factors. We identified 173 SNPs as candidate loci potentially associated with local adaptation to environmental variation, including 15 robust SNPs 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. Ne 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 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, partially clonal, and semi-domesticated plant species.