Integrating phenotypic and genetic diversity, and species distribution modeling to set long-term conservation strategies for the endangered Afzelia africana in Benin (West Africa)

• Afzelia africana is a widespread and endangered species in Benin (West Africa). • Intraspecific variation of phenotypic and genetic diversity traits was detected in Afzelia africana populations in Benin. • Climate change threatens genetic and phenotypic diversity in Afzelia Africana. • The regional models into SDMs has increased their predictive capacity. Afzelia africana is one of the most threatened multipurpose species in sub-Saharan Africa. Understanding its potentially suitable habitats, coupled with its phenotypic and genetic diversity is valuable for establishing sustainable and efficient conservation strategies for the species. This study combines phenotypic and genetic data with best-fit habitat models to identify conservation opportunities for A. africana across Benin. Natural populations were sampled for phenotypic and genetic diversity. Occurrence data were collected in the field and supplemented with available data from GBIF. Current and future climate data under two Shared Socioeconomic Pathways (SSP2-4.5 and SSP5-8.5) were used to model the current and potential future distribution of the species using MaxEnt. The results showed a large natural variation in phenotypic diversity, with populations from the Sudano–Guinean zone exhibiting intermediate diversity ( H’ = 0.45), while those from the Guinean and Sudanian zones exhibited high levels of diversity ( H’ > 0.60). Currently, 55.40 % of the country was predicted to be potentially suitable for the conservation of A. africana . Under the SSP5-8.5 and SSP2-4.5 scenarios, a significant increase respective of 70.27 % and 68.85 % in suitable habitat is predicted by 2041–2060. Nevertheless which will negatively affect both phenotypic and genetic diversity. However, individuals from the Sudano–Guinean subgroup are the most vulnerable to future climate conditions. This integrated approach not only helps to identify potential conservation areas but also reveals a crucial interplay in the phenotypic diversity and genetic dynamics of the species.