Genomic insights into endangerment and conservation of Euryodendron excelsum, a critically endangered plant

Strengthening the protection of biodiversity has become a focus of attention in the field of evolutionary biology. Euryodendron excelsum H. T. Chang is a critically endangered plant with small and fragmented populations. However, the effects of gene flow, adaptive genes, environmental factors, and anthropogenic interference, all considered as significant factors affecting the survival and adaptation of endangered plants, on the adaptation of E. excelsum populations have not been fully explored. In this study, the population genomic analysis of 70 E. excelsum individuals was conducted using restriction-site associated DNA sequencing approach. High genetic diversity (π = 0.268–0.320), moderate genetic differentiation (FST = 0.065–0.193), clear genetic structure, and accumulation of deleterious mutations were found in E. excelsum populations. Historical bottleneck events, limited gene flow, anthropogenic disturbance, and intrinsic biological characteristics have led to the formation of small and fragmented populations of E. excelsum. Soil composition, temperature, precipitation, leaf area index, and coverage of arbor layer were considered as candidate factors promoting population adaptation. Candidate genes with adaptive signals were found to be involved in functions related to binding, metabolism, stress response, cellular components, and transcriptional regulation. Furthermore, ecological niche modeling predicted that the suitable niche range of E. excelsum occurred contraction during the glacial periods and appeared range expansion in the future. Our research elucidates potential factors contributing to the formation of small and fragmented populations in E. excelsum, identifies candidate SNP loci associated with environmental adaptation, and projects the dynamics of its ecological niche under climate change. Based on these findings, we propose a differentiated conservation strategy, including in situ protection for genetically diverse populations (e.g., HLGW and CD) and ex situ conservation for those with high genetic load (e.g., SM and ZT), while emphasizing that genetic rescue should only follow experimental validation to mitigate outbreeding depression. Additionally, we recommend recognizing the genetically distinct QJ population as an independent conservation unit and exploring predicted suitable but unoccupied regions (e.g., Hainan, Fujian) for assisted translocation. The population genomic analysis of E. excelsum provides effective genetic resources for its conservation efforts.