Genetic structure and conservation status of sympatric Polylepis incana and Polylepis racemosa (Rosaceae) populations in Paluguillo, Pichincha, Ecuador

Background and Aims: Polylepis forests occur at high elevations and provide essential ecosystem services, including water regulation and soil protection. In Ecuador, reforestation programs have introduced the Peruvian species Polylepis racemosa without prior evaluation of potential gene flow or hybridisation risks with native congeners, which could compromise the genetic integrity of native P. incana populations. This study aims to characterise the genetic structure of sympatric populations of P. incana and P. racemosa in the Paluguillo area, Pichincha, Ecuador.Methods: The genetic structure of P. incana and P. racemosa was analysed using inter-simple sequence repeat (ISSR) markers in 60 adult individuals from six populations (three per species, ten adults per population). Genetic diversity parameters, including the proportion of polymorphic loci and expected heterozygosity, were calculated based on ISSR data. Population structure was evaluated through analysis of molecular variance (AMOVA), UPGMA clustering and Bayesian assignment analysis. Seedlings were not sampled because none were present during the survey period; therefore, all genetic inferences refer to adult cohorts.Key results: ISSR data revealed low genetic diversity in both species and evidence of gene flow between them. Despite this exchange, the species remained moderately differentiated, with 59% of genetic variation occurring within populations. Conclusions: Polylepis incana and P. racemosa populations exhibit low genetic diversity but clear genetic differentiation. Gene flow between species suggests potential long-term risks to the genetic integrity of native P. incana. These results provide a molecular baseline for monitoring and managing genetic integrity in Andean reforestation programs, emphasising the priority use of native species.