95% CI indicates the 95% confidence intervals.
Nerepresents the number of diploid individuals in the population.
T0 represents the time the “Indo-Malayan” lineage and the ancestor of the “Australasia” and “s-SCS” lineages diverged. The unit of time is million years.
T1 represents the time the “s-SCS” lineage diverged from the “Australasia” lineage. The unit of time is million years.
T2 represents the time the Ne of the “s-SCS” lineage increased. The unit of time is million years.
m1, m2, m3, and m4 represent the gene flow from the “Indo-Malayan” to the “s-SCS” populations, from the “s-SCS” to the “Indo-Malayan” populations, from the “s-SCS” to the “Australasia” populations, and from the “Australasia” to the “s-SCS” populations, respectively.
bottleneck represents the proportion of Ne reduced.
Figure 1. Population genetic diversity of Aegiceras corniculatum . (a) Distribution of π and θ across 18 populations (per kb). The height of the rectangle is proportional to the levels of π and θ. Blue is π, and red is θ. Dark red/blue bar indicate value obtained from Illumina data while light red/blue ones indicate values obtained from Sanger data. (b) Boxplots of the π of each gene across 11 Illumina-sequenced populations (per kb). (c) Boxplots of the θ of each gene across 11 Illumina-sequenced populations (per kb). Boxes of the same colour indicate populations in the same geographical area. “s-SCS”, “n-SCS”, “Gulf of Bengal” and “Australasia” indicate geographical regions. “Total” indicates the genetic divergence ofAegiceras corniculatum at the species level.
Figure 2. Genetic differentiation and structure ofAegiceras corniculatum populations. (a) Heatmap of the pairwiseFST values of the 18 populations estimated from the six Sanger-sequenced genes. (b) Plot of the first and second axes of a principal component analysis based on the frequency of single nucleotide polymorphisms within each population of 82 deep sequencing genes. The letters are the site ID of the sampled populations. The populations in different clusters are indicated by different colours. (c) Bayesian clustering with STRUCTURE split the 18 populations ofAegiceras corniculatum into two groups, and each group was further clustered into 3 (4) or 2 subgroups. Each thin vertical bar represents an individual, and each bold vertical bar separated by a black line represents a population. The population names are listed below the plot.
Figure 3. Geographical distribution patterns of the haplotypes inferred in the 6 Sanger-sequenced genes. The corresponding haplotype networks are drawn in the lower left corners of the maps; the colours corresponded to the haplotypes. In the haplotype network, the circle size is approximately proportional to the number of individuals of each haplotype. The number beside the lines indicates the mutation steps. The representative gene segment ID of each pattern is written to its upper right.
Figure 4. Six different geographical distribution patterns of the haplotypes inferred from the 41 Illumina-sequenced genes. The corresponding haplotype network is drawn in the upper right corner of each map; the colours correspond to the haplotypes. In the haplotype network, the circle size is approximately proportional to the number of individuals of each haplotype. The small black nodes on the lines are the median vectors, indicating the hypothesized (often ancestral) sequences required to connect the existing sequences within the network with maximum parsimony. The number beside the lines indicates the mutation steps. The representative gene segment ID of each pattern is written to its lower left.
Figure 5. Geographical factors underlying the genetic structure of Aegiceras corniculatum revealed by BARRIER inference and Mantel test. (a) Results of the barrier analysis (Manni et al., 2004) based on deep-sequencing data, showing the spatial separation ofA. corniculatum populations. The detected barriers (thick coloured lines) separate 11 populations into five groups. Green, blue, orange and purple lines correspond to the first, second, third and fourth barriers. The thickness of a coloured line indicates the number of FST matrices (black number adjacent to the line) that support the corresponding barrier. (b) Mantel test based on the FST matrices of six Sanger-sequenced genes. Different types of population pairs were indicated with different marks and colours.
Figure 6. Twelve models simulating demographic history. Blue indicates Lineage 1, which includes Kuching and Chai-ya. Orange indicates Lineage 2, which includes U-Daintree, Darwin, and Sorong. Green indicates Lineage 3, which includes Sanya, Wenchang, Yalong, La-un, Ngao and Bali. The double-sided arrow indicates migration. T0-T2 indicate the time points of historic events and m1-m4 indicate gene flows.