Young-Jong Jang1P, Eun-Kyeong Han2, Jung-Hyun Lee2

1Department of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, Korea; 2Department of Biology Education, Chonnam National University, Gwangju, Korea

Sporophytic apomixis is a distinctive reproductive mode in which clonally and sexually derived embryos coexist within a single seed. In such reproductive systems, population genetic features are expected to reflect the relative success of clonal versus sexual offspring, yet the determinants of these patterns remain poorly understood. Here, we investigate reproductive mode, population genetic structure, and polyploid origins in the warm-temperate evergreen shrubs Damnacanthus indicus and D. major. Micro-CT and flow cytometric seed screening show that tetraploid populations of both taxa reproduce via sporophytic apomixis. Microsatellite analyses reveal strikingly contrasting clonal structures: D. indicus comprises 26 multilocus clonal lineages (MLLs), whereas D. major is dominated by a single MLL across its range. Phylogenetic analysis of the low-copy nuclear gene ABCI15 indicates contrasting polyploid origins, with D. indicus derived from allopolyploidization between closely related diploids (AABB) and D. major from hybridization between two allotetraploids sharing a B subgenome (BBA′C′). We propose that the extreme predominance of a single MLL in D. major reflects strong purifying selection against maladapted recombinant genotypes, likely associated with its asymmetric composite subgenomic architecture, whereas D. indicus, with a more stable subgenomic composition, maintains diverse recombinant genotypes. Together, these results indicate that subgenomic composition, rather than ecological factors, underlies population genetic features in sporophytic apomictic systems.