Population dynamics and evolutionary history of an endemic Sambucus africana Standl. (Viburnaceae): Evidence from complete plastomes and ecological niche analysis

Evolution and demographic history of plant populations are primarily influenced by climatic and geological events. However, evolutionary population dynamics of endemic herbaceous plants in East Africa remains unexplored. In this study, we integrated chloroplast genomes, environmental variables, and geographical distribution datasets to assess the evolutionary relationships and population dynamics of Sambucus africana Standl., an endemic medicinal herb in East African highlands. The findings showed that S. africana genomes exhibited typical quadripartite structures and contained 129 unique genes, including 88 protein-coding, 33 tRNAs, and 8 rRNAs. Population genomics revealed significant degree of intraspecific variations within isolated African-limit populations. The phylogenetic relationship of Dipsacales yielded significantly supported topologies (ML ≥ 83, BI ≥ 0.4) which strongly supported the monophyly of Sambucus. Major lineages of Viburnaceae were estimated to have diverged from the Late Cretaceous 80.89 Mya (95 % PHD = 68.90–91.99 Mya), while within-genus diversification was dated to Eocene and later. Ancestral area reconstruction revealed that the most probable ancestral area for Sambucus is Asia, with a secondary ancestral presence in North America, followed by diversification to other regions. Species distribution modeling indicated that under Shared Socio-Economic Pathway 585 (SSP585), the potentially suitable habitats for S. africana would significantly decline around Mt. Elgon parts of Uganda (western) and Kenya (central parts of Mt. Kenya) and southwestern parts of Ngorongoro conservation area relative to SSP126. Therefore, conservation units of western and eastern Mt. Elgon groups in Uganda, among other distributional regions in Kenya and Tanzania should be established for this endemic medicinal herb. • We present the first phylogenomic study of an endemic S. africana species with morphological and geographical support. • Phylogenetic analysis confirms close relationships between S. africana and S. ebulus species. • •Nucleotide diversity analysis identifies polymorphic sites of chloroplast genomes. • Ecological niche modeling was employed to predict the suitable distribution areas of S. africana . • Climate changes could have substantial impacts on the distribution of S. africana .