Colonization by Distinct Lineages, the Sundaland Barrier, and Historical Bottlenecks Shape the East–West Population Structure of Avicennia Mangroves Across the Indo-Pacific Interface

The emergence of Sundaland during the Pleistocene glaciation has played a crucial role, as the Indo-Pacific Barrier (IPB), in shaping the genetic structure of marine taxa and coastal flora, specifically mangroves. This study investigated the genetic diversity, population structure, demographic history and phylogeography of <i>Avicennia marina</i> and two other Indo-West Pacific (IWP) <i>Avicennia</i> species, <i>Avicennia alba</i> and <i>Avicennia officinalis</i>, across the Andaman Sea (Indian Ocean) and the Gulf of Thailand (Pacific Ocean). Using Restriction-site-Associated DNA sequencing (RADseq), we generated thousands of genome-wide SNPs for 362 <i>Avicennia</i> individuals and revealed a pronounced East-West genetic divergence, separating the Andaman and Gulf of Thailand populations. Phylogeographic and demographic analyses suggest that colonization events by distinct ancestral lineages (Indian and West Pacific Ocean lineages), the Indo-Pacific Barrier (Sundaland), and Pleistocene sea-level fluctuations shaped the population structure and contributed to low genetic diversity (<i>H</i>_o = 0.073-0.083) and high inbreeding coefficients (<i>F</i>_IS = 0.169-0.501). This study highlights the importance of Thailand, as part of the Indo-Pacific interface, in harboring genetic resources from both Indian and West Pacific Ocean lineages, as exemplified in <i>A. marina</i>. Consequently, Andaman and Thai Gulf populations should be managed as distinct evolutionarily significant units (ESUs).