title: Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba.
abstract: A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation.
  
  
  
  In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods. Extremely small effective population size (Ne) was inferred in populations from both eastern and western Malay Peninsula (44 and 396, respectively), mirroring the fragility of mangrove plants and their paucity of robustness against future climate perturbations and human activity. Two major genetic lineages of high divergence were identified in the two mangrove biodiversity centres: the Indo-Malesia and Australasia regions. The estimated splitting time between these two lineages was 3.153 million year ago (MYA), suggesting a role for pre-Pleistocene events in shaping the major diversity patterns of mangrove species. Within the Indo-Malesia region, a subdivision was implicated between the South China Sea (SCS) and the remaining area with a divergence time of 1.874 MYA, corresponding to glacial vicariance when the emerged Sunda Shelf halted genetic exchange between the western and eastern coasts of the Malay Peninsula during Pleistocene sea-level drops. Notably, genetic admixture was observed in populations at the boundary regions, especially in the two populations near the Malacca Strait, indicating secondary contact between divergent lineages during interglacial periods. These interregional genetic exchanges provided ample opportunity for the re-use of standing genetic variation, which could facilitate mangrove establishment and adaptation in new habitats, especially in the context of global climate changes.
  
  
  
  Phylogeogrpahic analysis in this study reveal that Pleistocene sea-level fluctuations had profound influence on population differentiation of the mangrove tree S. alba. Our study highlights the fragility of mangrove plants and offers a guide for the conservation of coastal mangrove communities experiencing ongoing changes in sea-level.
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
authors.forename: Yuchen
authors.initials: Y
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
authors.forename: Jianfang
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
authors.forename: Shuhuan
authors.initials: S
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
authors.forename: Xinnian
authors.initials: X
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Fang
authors.affiliation: Hainan Dongzhai Harbor National Nature Reserve, Haikou, 571129, China.
authors.forename: Cairong
authors.initials: C
authors.lastname: Zhong
authors.affiliation: Trop WATER, James Cook University, Townsville, Quennsland, Australia.
authors.forename: Norman C
authors.initials: NC
authors.lastname: Duke
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China. zhrench@mail.sysu.edu.cn.
authors.forename: Renchao
authors.initials: R
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China. lssssh@mail.sysu.edu.cn.
authors.forename: Suhua
authors.initials: S
authors.lastname: Shi
mesh_terms: D016000:Cluster Analysis; D051456:Gene Flow; D014644:Genetic Variation; D005843:Geography; D016013:Likelihood Functions; D009711:Nucleotides / Q000235:genetics; D009792:Oceans and Seas; D010802:Phylogeny; D011157:Population Dynamics; D011336:Probability; D043982:Rhizophoraceae / Q000254:growth & development*; D013997:Time Factors
chemical_list: D009711:Nucleotides
keywords: Gene flow; Genetic diversity; Indo-West Pacific; Mangroves; Pleistocene glaciations