ddRAD sequences of the mangroves Lumnitzera littorea and Lumnitzera racemosa from the Indonesian Archipelago

The Indonesian Archipelago accommodates the largest mangrove area in Southeast Asia and possesses the world's most diverse set of mangrove species. We use the mangrove species Lumnitzera littorea and L. racemosa as a study case for understanding the effects of sea surface currents and geographical distance on population level genetic diversity and genetic structure. We sampled 14 populations of L. littorea (N = 106) and 21 populations of L. racemosa (N = 152) from Indonesia. We used the ddRADseq approach with EcoRI and MspI restriction enzymes for SNP genotyping. We assessed genetic diversity, genetic structure, and effective dispersal of the populations and related them to geographical distance and sea surface currents. We observed low genetic diversity and strong genetic differentiation among populations in both species. Bayesian cluster analysis indicated K = 3 groups in L. littorea, with populations distributed in the northern and southern part of the Sunda region and the eastern part of Indonesia. In L. racemosa, a more complex pattern was found (K = 5). Two groups were found in the Malacca Strait and Ternate Island, while the other three admixed groups occurred in Wallacea. Sea surface currents and isolation by distance may have contributed to the two species' dispersal dynamics, genetic diversity, and genetic structure. Our finding provides novel insights into the role of sea currents in shaping the evolution and contemporary distribution of Lumnitzera in Indonesia.