title: Pronounced genetic differentiation and recent secondary contact in the mangrove tree Lumnitzera racemosa revealed by population genomic analyses.
abstract: Systematically investigating the impacts of Pleistocene sea-level fluctuations on mangrove plants may provide a better understanding of their demographic history and useful information for their conservation. Therefore, we conducted population genomic analyses of 88 nuclear genes to explore the population dynamics of a mangrove tree Lumnitzera racemosa across the Indo-West Pacific region. Our results revealed pronounced genetic differentiation in this species between the populations from the Indian Ocean and the Pacific Ocean, which may be attributable to the long-term isolation between the western and eastern coasts of the Malay Peninsula during sea-level drops in the Pleistocene glacial periods. The mixing of haplotypes from the two highly divergent groups was identified in a Cambodian population at almost all 88 nuclear genes, suggesting genetic admixture of the two lineages at the boundary region. Similar genetic admixture was also found in other populations from Southeast Asia based on the Bayesian clustering analysis of six nuclear genes, which suggests extensive and recent secondary contact of the two divergent lineages in Southeast Asia. Computer simulations indicated substantial migration from the Indian Ocean towards the South China Sea, which likely results in the genetic admixture in Southeast Asia.
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: 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: Qipian
authors.initials: Q
authors.lastname: Chen
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: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Ziwen
authors.initials: Z
authors.lastname: He
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Wuxia
authors.initials: W
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Sitan
authors.initials: S
authors.lastname: Qiao
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Zhengzhen
authors.initials: Z
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Miaomiao
authors.initials: M
authors.lastname: Guo
authors.affiliation: Hainan Dongzhai Harbour National Nature Reserve, Haikou 571129, China.
authors.forename: Cairong
authors.initials: C
authors.lastname: Zhong
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
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.
authors.forename: Suhua
authors.initials: S
authors.lastname: Shi
mesh_terms: D001499:Bayes Theorem; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D040961:Genetic Drift; D008040:Genetic Linkage; D005828:Genetics, Population; D005843:Geography; D057232:Global Warming; D006239:Haplotypes; D019156:Indian Ocean; D019684:Magnoliopsida / Q000235:genetics*; D010140:Pacific Ocean; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011157:Population Dynamics
chemical_list: D004272:DNA, Mitochondrial