Figure 1 Avicennia marina distribution range and sampling locations. Ranges of the three subspecies are shown in colors as indicated in the legend. Sampling locations are indicated by circles. Location information and population abbreviations are listed in Table 1. Leaf, flower, and fruit morphological differences are presented on the right and summarized in the imbedded table. Imbedded drawings of morphological traits were adapted from Duke (1991).
Figure 2 Genetic divergence and differentiation amongAvicennia marina populations. (a-c): colors indicate subspecies. (a) Multi-dimensional scaling analysis of the FSTand DXY matrices of 16 A. marinapopulations. (b) The neighbor-joining tree on the right was constructed using the DXY matrix. (c) Clustering of theA. marina populations using principal component analysis (PCA). PCA was performed on the SNP frequency matrix. (d) boxplots ofDXY values. “au,” “ma,” and “eu” indicateaustralasica , marina, and eucalyptifoliarespectively. “maWest” and “maEast” refer to the two recognized geographical groups of marina populations west and east of the Malay Peninsula (see the Results section). “BB” refers to the population from Bunbury, Australia.
Figure 3 Different levels of genetic diversity among subspecies. Boxplots of θ computed for each gene in each population and points with line linked indicate mean θ and π values computed by pooling all SNPs in a population.
Figure 4 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 segment are classified to each type of a to f respectively.
Figure 5 evolutionary history of Avicennia marinasubspecies. (a) Simulations reconstructing demographic history ofAvicennia marina populations. Graphical presentation of the eight models of the three subspecies. N stands for effective size and T stands for time of split. (b) Graphical presentation of the four models to investigate the contrast between morphological and genetic characters of the BB population in western Australia. vT0 and vT1 indicate divergence time points and Neu, Nbb, and Nmaindicated effective population size. The constant bi-directional migration rates are denoted by ma and mb. (c) 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 right indicates residual fit from the maximum likelihood tree. Residuals above zero imply candidate admixture events.