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.