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The archipelago comprises areas of the biogeographic regions Sunda and Wallacea, separated by Wallace's line. Here, we used the true mangrove species <jats:italic>Lumnitzera littorea<\/jats:italic> and <jats:italic>Lumnitzera racemosa<\/jats:italic> as a study case for understanding the effects of phylogeographic history, sea surface currents, and geographical distance on genetic diversity and genetic structure. We sampled 14 populations of <jats:italic>L. littorea<\/jats:italic> (<jats:italic>N<\/jats:italic>\u2009=\u2009106) and 21 populations of <jats:italic>L. racemosa<\/jats:italic> (<jats:italic>N<\/jats:italic>\u2009=\u2009152) from Indonesia and used 3122 and 3048 SNP loci, respectively, genotyped using the ddRADseq approach. We assessed genetic diversity, genetic structure, and effective dispersal of the populations and related them to geographical distance and sea surface currents. Our study revealed low levels of genetic variation at the population level in <jats:italic>Lumnitzera<\/jats:italic>. Pronounced genetic differentiation between populations indicated two phylogroups in both species. While in <jats:italic>L. littorea<\/jats:italic> the two phylogroups were largely separated by Wallace's line, <jats:italic>L. racemosa<\/jats:italic> showed a northwest vs. southeast pattern with strong mixture in Wallacea. Our findings provide novel insights into the phylogeography of the mangrove genus <jats:italic>Lumnitzera<\/jats:italic> and the role of sea surface currents in the Indonesian Archipelago.<\/jats:p>","DOI":"10.1111\/jse.12923","type":"journal-article","created":{"date-parts":[[2022,10,17]],"date-time":"2022-10-17T17:00:05Z","timestamp":1666026005000},"page":"299-314","update-policy":"http:\/\/dx.doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Deep phylogeographic splits and limited mixing by sea surface currents govern genetic population structure in the mangrove genus <i>Lumnitzera<\/i> (Combretaceae) across the Indonesian Archipelago"],"prefix":"10.1111","volume":"61","author":[{"ORCID":"http:\/\/orcid.org\/0000-0003-3406-0960","authenticated-orcid":false,"given":"Jeprianto","family":"Manurung","sequence":"first","affiliation":[{"name":"Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology Leipzig University Johannisallee 21\u201023 Leipzig D\u201004103 Germany"},{"name":"German Centre for Integrative Biodiversity Research (iDiv) Halle\u2010Jena\u2010Leipzig Puschstrasse 4 Leipzig D\u201004103 Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-7164-1313","authenticated-orcid":false,"given":"Blanca M.","family":"Rojas Andr\u00e9s","sequence":"additional","affiliation":[{"name":"Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology Leipzig University Johannisallee 21\u201023 Leipzig D\u201004103 Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-3267-8855","authenticated-orcid":false,"given":"Christopher D.","family":"Barratt","sequence":"additional","affiliation":[{"name":"German Centre for Integrative Biodiversity Research (iDiv) Halle\u2010Jena\u2010Leipzig Puschstrasse 4 Leipzig D\u201004103 Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-0843-4503","authenticated-orcid":false,"given":"Jan","family":"Schnitzler","sequence":"additional","affiliation":[{"name":"Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology Leipzig University Johannisallee 21\u201023 Leipzig D\u201004103 Germany"},{"name":"German Centre for Integrative Biodiversity Research (iDiv) Halle\u2010Jena\u2010Leipzig Puschstrasse 4 Leipzig D\u201004103 Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-9580-3129","authenticated-orcid":false,"given":"Bror F.","family":"J\u00f6nsson","sequence":"additional","affiliation":[{"name":"Plymouth Marine Laboratory Prospect Place Plymouth PL1 3DH UK"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-0342-2906","authenticated-orcid":false,"given":"Ruliyana","family":"Susanti","sequence":"additional","affiliation":[{"name":"Research Center for Biology National Research and Innovation Agency Jl. 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