Genomic evidence for genetic erosion and strong population subdivision in Amomum hainanense (Zingiberaceae), an endangered island endemic plant from Hainan, China

Abstract Amomum hainanense is an endangered understorey herb narrowly distributed in tropical montane forests of Hainan Island, China, but its evolutionary history and conservation status remain poorly understood because genomic information is scarce. Here, we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to assess genetic diversity, population structure and demographic history in Amomum hainanense, and assembled complete chloroplast genomes from low-coverage whole-genome sequencing reads to clarify its phylogenetic placement. Genome-wide single nucleotide polymorphisms (SNPs) revealed exceptionally low nucleotide diversity (π = 0.7–1.7 × 10−4 among the five well-sampled populations; mean = 1.2 × 10−4), substantially lower than values reported for cultivated source taxa of Amomi Fructus (4.1–10.4 × 10−4). Pronounced population structure and high, statistically significant pairwise genetic differentiation (FST = 0.280–0.621) were consistent with restricted connectivity among populations. Stairway Plot 2 based on both pooled and PCA-defined group-level folded SFSs recovered a broadly consistent long-term decline in effective population size over the last ca. 10,000 years. Chloroplast genomes showed very low intraspecific diversity (π ≈ 0.2 × 10−4) and recovered A. hainanense as a strongly supported monophyletic lineage. Phylogenetic analysis of three plastid loci further identified A. repoeense as the closest sampled relative. Together, these results indicate severe genetic erosion coupled with strong population subdivision in A. hainanense. We recommend prioritising in situ protection of the highest-diversity populations (XL and MLD) and establishing population-stratified ex situ germplasm collections that represent all major genetic groups.