Pedigree analyses and next-generation sequencing reveal critically low regeneration in extremely threatened Zingiber singapurense (Zingiberaceae)

Molecular tools are crucial in the conservation management of small populations, but they have rarely been used for conservation of threatened plants, especially in the Tropics. Next-generation sequencing allows realistic access to detailed measurements of genetic diversity even in the rarest species. We used 12 170 genomic markers to investigate dynamics in the total population of Zingiber singapurense, one of the rarest well-surveyed herbs in South-East Asia. The markers were used to estimate the population size and to identify pedigrees in the population and introgression with closely related species. This diploid species is strongly clonal with only 13 genetically distinct individuals. The clones included only one probable sibling pair and no observed parent–offspring pairs except for a single hybrid, but the inferred effective population size was 150 individuals. The surviving individuals are ancient relicts without any evidence of recent reproduction. Clonal reproduction, great age and lack of sexual reproduction have protected the species from inbreeding, which is surprising for a small, superficially delicate herb. Similar situations may explain the observed survival of many species in small populations in Singapore. The best conservation interventions are discussed, but more information is needed on the factors that limit reproduction in this species.