Members of the mangrove genus Rhizophora represent the most commonly occurring and highly valued species in the Indo-West Pacific region. However, to date, few studies have been directed towards the understanding of their genetic variation. The levels and patterns of genetic variation at chloroplast and nuclear gene regions were studied in R. apiculata, R. mucronata, and R. stylosa sampled from Southeast Asia and Japan. All three species were characterized by low intraspecific genetic variation and a deficiency of heterozygotes in populations within the region, consistent with findings in studies on other mangrove species. Rhizophora mucronata and R. stylosa were also found to be more closely related than any of them with R. apiculata. During the Last Glacial Maximum, sea levels dropped to 120 m below the current levels, exposing part of the Sunda Shelf that became a barrier that limited gene flow between marine species living in the Pacific and Indian Oceans. Today, the Malay Peninsula is thought to still serve as a barrier to gene flow between populations occurring on its coasts. The pattern of genetic differentiation of R. apiculata supports the hypothesis of the land barrier effect of the Malay Peninsula, but such patterns were not found in R. mucronata and R. stylosa. Our findings suggest that R. apiculata, R. mucronata, and R. stylosa have different demographic histories despite being closely related and having sympatric distributions today. Furthermore, all three species appear to have high levels of inbreeding due to limited pollen and propagule dispersal, and that both these factors contributed to population differentiation.
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