Contrasting clonal and population genetic structure in two endangered Costa Rican Vanilla species of commercial interest

Wild relatives of the commercially grown Vanilla planifolia, such as Vanilla odorata and V. pompona, are understudied despite their ecological and agricultural importance. Both species are listed as endangered by the IUCN, but limited research on their genetic diversity hinders effective management. While Vanilla species reproduce extensively by cloning, wild populations may retain significant genetic diversity valuable for crop improvement and conservation. To evaluate genetic diversity and structure, we analyzed 146 individuals from 10 V. pompona populations and 75 individuals from six V. odorata populations in Costa Rica, using 11 and 10 microsatellites, respectively. Vanilla odorata showed higher clonality than V. pompona (63% vs. 35%). Both species exhibited low to moderate genetic diversity (V. odorata: H_O = 0.47, H_E = 0.29; V. pompona: H_O = 0.43, H_E = 0.41). Vanilla odorata populations revealed greater genetic differentiation than V. pompona populations (Nei's G_ST = 0.51 vs. 0.091), with V. odorata also exhibiting isolation by distance (R² = 0.704, p < 0.05). Both species showed fine-scale genetic structure, with higher levels linked to clonality. Gene flow in V. pompona benefits from broad distribution and sexual reproduction, while V. odorata experiences limited gene flow due to its high clonality and restricted range. Protecting habitats and promoting outcrossing may aid V. odorata viability while V. pompona serves as an important resource for increasing genetic diversity in cultivated vanilla.