Population genomics reveals a representation gap in the conservation of Ardisia gigantifolia (Primulaceae), an endangered species endemic to China

Ardisia gigantifolia Stapf is a critically endangered medicinal plant endemic to China that is characterized by a narrow distribution range and small population sizes. Ex situ conservation is an important complementary strategy for in situ, protecting wild plant species from loss of genetic diversity and possible extinction in the wild. However, the extent to which ex situ collections genetically represent their wild populations remains poorly understood. In this study, we analyzed the genetic diversity and structure of 67 individuals using double digest restriction-site-associated DNA sequencing (ddRAD). The sampled populations included three wild populations from Hekou Town (HK), Gulinqing Town (GLQ), and Nanxi Town (NX), Yunnan Province, as well as one ex situ conservation population originating from Mahuangbao Farm (MHB), Yunnan Province and cultivated at the South China Botanical Garden (SCBG). The results revealed comparatively low genetic diversity across wild populations, with observed heterozygosity of 0.1441–0.1767 and expected heterozygosity of 0.1575–0.2255. Lower genetic diversity was detected in the HK population with small population size and the GLQ population located in severe shading compared to that in the NX population. Notably, the SCBG ex situ population retained a level of genetic diversity comparable to the best-preserved wild population (NX). The genetic structure analysis demonstrated significant differentiation among wild populations. The SCBG ex situ population formed a distinct genetic cluster, showing moderate-to-high differentiation from all extant wild populations. These findings revealed a critical “representation gap”: while the collection preserves unique genetic variation from an extinct source population, it fails to capture the extant genetic diversity partitioned among the surviving wild populations. Collectively, our findings provide a genomic baseline and strategic insights for the future ex situ conservation and management of A. gigantifolia .