Selfing species has greater genetic diversity and less structure than related outcrossing species due to seed dispersal and population history in Roscoea (Zingiberaceae)

Abstract Mating system is a crucial factor shaping the amount of genetic diversity and the fine-scale spatial genetic structure (FSGS), with selfing species usually having less diversity and stronger FSGS than outcrossing species. Such general conclusions resulted from comparisons among distant species, often neglecting consideration of co-effects of the population history, microhabitat and seed dispersal in different habitats. This study is based on two species of the genus Roscoea (Zingiberaceae) with contrasting mating systems to explore the FSGS. Using thousands of single nucleotide polymorphisms (SNPs) found in outcrossing Roscoea cautleoides (RC) and selfing R. schneideriana (RS) located in different habitats from same region, we compared genetic diversity, FSGS and historical population dynamics using outlier (non-neutral) SNPs and neural SNPs, integrating with field observation of seed dispersal distance. Roscoea cautleoides has lower genetic diversity and showed stronger FSGS than RS, which conflicted with the general expectations. Outlier SNPs exhibited significantly larger genetic diversity and genetic differentiations among individuals within population suggested adaptive divergence to different microhabitats. Both RC and RS experienced bottlenecks that are consistent with the Last Glacial Maximum (~21 kyrs) and the last second Glacial Maximum (~150 kyrs), respectively. Field investigation indicated seeds of RS were transported from stock plants by ant significantly further than seeds of RC. Our results indicate that seed dispersal, different historical population dynamics, and environmental heterogeneity can over-ride the initial impact of mating systems. This study remind us that collection of plant germplasm resources and ex-situ conservation should consider environmental heterogeneity within a population.