Figure 1 Avicennia marina distribution range and sampling locations. Ranges of the three varieties are shown in colors as indicated in the legend. Sampling locations are indicated by black circles with numbers. Location name and population abbreviation are as follows: 1, Meed Creek, maMC; 2, Laemson, MaLS; 3, Penang, maPN; 4, Thongnian, maTN; 5, Samut Sakon, maSS; 6, Ban Kunsha, maBK; 7, Sanya, maSY; 8, Wenchang, maWC; 9, Cebu, maCB; 10, Sabah, maSB; 11, Bali, maBL, 12, Bunbury, maBB; 13, Darwin, euDW; 14, Cairns, euCA; 15, Brisbane, auBS; 16, Auckland, auAK. Detailed information for these sampling locations is in Table 1. Morphological differences between the three subspecies in leaf, flower and fruit are presented on the right.
Figure 2 Genetic divergence and differentiation amongAvicennia marina populations. (a) Clustering of the A.marina populations using principal component analysis (PCA). PCA was performed on the SNP frequency matrix. Colors indicate subspecies. (b) Multi-dimensional scaling analysis of the FSTand DXY matrices of 16 A. marinapopulations. (e-d) boxplots of DXY andFST values. “au”, “ma” and “eu” indicateA. m. australasica , A. m. marina and A. m. eucalyptifolia respectively. “maWest” and “maEast” refer to the two recognized groups of A. m. marina populations west and east of the Malay Peninsula (see the Results section). “BB” refers to the maBB population from Bunbury, Australia.
Figure 3 The subspecies evolved independently. a) Boxplots of θ computed for each gene in each population (upper graph) and barplots of mean θ and π values computed by pooling all SNPs in a population (lower graph). (b) Simulations reconstructing demographic history ofAvicennia marina populations. Graphical presentation of the ten models of the three subspecies. N stands for effective size and T stands for time of split. Black arrows in models 8-10 indicate gene flow.
Figure 4 Gene flow between subspecies. (a) Graphical presentation of the four models to investigate the contrast between morphological and genetic characters of the maBB population in western Australia. vT0 and vT1 indicate divergence time points and Neu, Nbb, and Nma indicated effective population size. The constant bi-directional migration rates are denoted by ma and mb. (b) TreeMix to capture gene flow events on a population splitting graph. On the Maximum likelihood tree, each yellow line indicates a gene flow event between branches it links, with color indicating migration weight. Horizontal branch lengths of the tree are proportional to the amount of genetic drift that has occurred on the branch. The triangle matrix on the top-right indicates residual fit from the maximum likelihood tree. Residuals above zero imply candidate admixture events.
Figure 5 Networks and geographical distribution of haplotypes inferred in eight Avicennia marina populations. Haplotypes are indicated by different colours. Lines linking haplotypes reflect mutations, with mutations exceeding a single step marked. The geographic distribution of haplotypes is also indicated. The presented a to f cases are six typical ones to represent six types of haplotype networks. Among the 231 segments, 134, 66, 14, 11, 5 and 1 segments are classified to each type of a to f respectively.