In Situ Diversity of Native Cherimoya in Southern Ecuador: Phenotypic and Ecological Insights

Cherimoya is a fruit tree native to the Andean regions of South America, also in Central America, prized for its flavor, nutritional properties, and medicinal potential. Despite its economic relevance, in situ assessments of phenotypic diversity are limited, particularly in southern Ecuador, a key center of domestication. This study evaluated the morphological and ecogeographic diversity of 270 native trees across eight cantons in Loja province, Ecuador, using 34 qualitative and quantitative descriptors of leaves, flowers, fruits, and seeds. High phenotypic variability was observed, with coefficients of variation exceeding 40% for key traits, including mature fruit weight (48.15%), pulp weight (55.33%) and pulp-to-seed ratio (64.23%). Principal component analysis revealed three major axes of variation associated with productivity, floral morphology, and organoleptic quality. Cluster analysis identified four groups, with one distinguished by a favorable pulp-to-seed ratio and sugar–acid content. Species distribution modeling, which included bioclimatic and soil variables, showed that Gonzanamá, Quilanga and Espíndola possess the highest ecological suitability for cherimoya. These findings highlight priority areas for in situ conservation and phenotype selection, providing a foundation for sustainable use, genetic improvement, and the preservation of locally adapted germplasm to support climate-resilient agricultural systems.