Spatial genetic structure of the nomadic Vanilla trigonocarpa populations in Costa Rica reveals clonality and effective gene flow

Vanilla trigonocarpa, a climbing and partially clonal orchid, occurs in contiguous and disjunct populations in Costa Rica. Using high-quality single-nucleotide polymorphisms (SNPs) generated via Restriction-Site Associated DNA sequencing (RADseq), we analysed individuals from five sampling sites in Costa Rica (separated by 1 to 217 km apart) to investigate population genetic diversity, differentiation, and the influence of the reproductive system on these patterns. From 279 sampled individuals, 20 0 49 690 SNPs were initially identified in the reference-based assembly, followed by post-assembly filtering, analyses of population genetic structure and clonal relationships among individual samples. Vanilla trigonocarpa appeared to have guerrilla-type clonal growth. Heterozygosity excess and negative inbreeding coefficients were probably linked to clonality. The fine-scale genetic structure pattern we detected suggested the combined effects of clonality, sexual reproduction, along with pollen and seed dispersal. However, no significant Isolation-By-Distance (with low genetic differentiation) was observed among the five sampling sites. This suggested ongoing pollen- and seed-mediated gene flow and the possible expansion of the local microrefugia of the relict plant communities. The genomic data in this study represent a valuable resource for Vanilla, supporting future research on the reproductive strategies of this species and other orchids with similar life-history traits, and have implications for evolutionary and conservation studies.