Population Genetic Structure and Colonisation History of the Widely Distributed Mangrove Avicennia marina Across the Western Indian Ocean

ABSTRACT Aim Avicennia marina is a widely distributed mangrove species and a major constituent of Indo‐West Pacific mangroves. To understand spatial patterns of genetic diversity in this species, and the role of ocean currents and historical events in shaping these patterns, we examined population genetic structure, maternal phylogeography, and colonisation history across the species' Western Indian Ocean range. Location Western Indian Ocean, including 34 populations of Kenya, Tanzania, Mozambique, South Africa, Madagascar, Mayotte Island, Europa Island, Aldabra Atoll and Granitic Seychelles; outgroups of the Red Sea and southeast Asia. Taxon Avicennia marina (Forssk.) Vierh. Methods We genotyped 1150 trees using 18 nuclear microsatellites and conducted population genetic analyses, including structure , migrate , barrier and Bayesian origin models. To investigate maternal phylogeography and infer lineage origins from a haplotype network, we analysed chloroplast single nucleotide polymorphisms. Results A. marina exhibited a strong genetic break between island populations (Seychelles, Aldabra, East Madagascar) and African mainland populations, reflecting Pleistocene divergence in nuclear and chloroplast markers. East African populations showed high genetic diversity, aligning with the northward flow of the bifurcated South Equatorial Current carrying limited traces of Late Pleistocene colonisation events. Ocean currents around Madagascar and eddie in the Mozambique Channel Area (MCA) facilitated long‐distance dispersal since the Last Glacial Maximum, connecting islands like Mayotte and Europa. South‐African range‐edge populations showed low genetic diversity, likely due to limited dispersal and bottlenecks after the Late Holocene highstand. Aldabra populations displayed divergent haplotypes, suggesting multiple colonisation events. Main Conclusions Island populations (Seychelles, Aldabra, East Madagascar) experienced multiple Pleistocene colonisations, while mainland African and MCA populations were shaped by Holocene migration reflecting present‐day ocean current patterns. Our findings help in better understanding the spatial patterns of genetic diversity and provide valuable insights for defining evolutionary significant and conservation units in the Western Indian Ocean.