Among-group genetic divergence
We obtained 76 to 87 kb of DNA sequence covering 88 to 94 genes from
each population (Table 1). By mapping short reads to reference
sequences, we identified 74 to 1657 segregating sites (Table 1). We
calculated among-population pairwise DXY values
to assess genetic divergence and used the resulting distance matrix to
construct a neighbor-joining tree (Supplementary Figure 1). TheDXY matrix showed clear divergence between the
three varietal groups previously designated as subspecies (Figure 2b),
the maBB is an outlier discussed below. The largestDXY values were observed between the A. m.
australasica populations and the other two subspecies, ranging from 7.7
to 9.9/kb (Supplementary Table 4). Relatively lower divergence was
observed between A. m. eucalyptifolia and A. m.marina populations, with DXY values
between 6.5 and 7.4/kb. By pooling populations within putative
subspecies, we estimated the DXY to be 8.2/kb
between A. m. eucalyptifolia and A. m. australasica ,
6.7/kb between A. m. marina and A. m. eucalyptifolia and
9.1/kb between A. m. marina and A. m. australasica .
Genetic divergences were generally lower among populations than among
subspecies. The two A. m. australasica populations diverged
little from each other (DXY =2.2/kb), while theA. m. eucalyptifolia pair diverged more but still less than
differentiation among subspecies (DXY = 5.48/kb).
Within A. m. marina , we see two major groups, one containing
maMC, maLS, and maPN (west of the Malay Peninsula), the other maTN,
maBK, maSS, maSY, maWC, maSB, maCB, and maBL (east of the Malay
Peninsula, Supplementary Figure 2). DXY per kb
ranges from 1.27 to 3.75 within the first and from 0.94 to 4.69 within
the second group. Between the two groups, DXYranges from 4.32 to 5.69, still lower than between subspecies. The maBB
population is an outlier and has diverged far from other A. m.
marina populations (DXY = 7.76-8.43/kb), to a
level comparable with among subspecies differentiation.
Genetic divergences can also be observed by comparing the polymorphism
frequencies within populations. By plotting principal components of the
allele frequency matrix, we again see clear differences among the three
subspecies. The two A. m. eucalyptifolia populations also
show obviously different polymorphism frequency patterns (Figure 2a).DXY quantifies the absolute divergence between
groups, while FST reflects how much genetic
divergence is fixed in each subspecies (Cruickshank & Hahn, 2014). The
120 values of pairwise FST calculated for the 16
populations are generally high, with the average value of 0.61 (first
and third quartiles are 0.50 and 0.76 respectively).FST values among five A. m. marinapopulations from the South China Sea, i.e. maTN, maBK, maSS, maSY and
maWC cluster at the bottom of the distribution. If we exclude the ten
values or pairs of these five populations, the average of remaining 110
pairs is elevated to 0.66 (first and third quartiles 0.54 and 0.77).
Notably, the FST values among populations fromA. m eucalyptifolia and A. m. australasica are 0.19 and
0.42 respectively. The prevalence of such highFST value indicates that genetic polymorphisms
are fixed to a large extent between subspecies as well as between some
populations within A. m. marina .
Both the nucleotide diversity (π) and Watterson’s estimator of
nucleotide polymorphism (θ) identified different levels of
within-population genetic variation. The two A. m.eucalyptifolia populations have the highest genetic diversity,
with average θ (across segments) = 2.82 and 3.94/kb and average π = 3.41
and 4.06/kb (Figure 3a). In contrast, A. m. marina populations
are low in genetic diversity, with average θ ranging from 0.21 to
0.91/kb and average π ranging from 0.15 to 1.39/kb (Table1, Figure 3a).
The two A. m. australasica populations have very different levels
of genetic diversity (Table1, Figure 3a). The very low level of
diversity in the auAK population is likely due to its marginal location.
Marginal populations of A. m. marina such as maWC and maSY are
also very monomorphic. The auBS population of A. m. australasicahas an intermediate level of genetic diversity, higher than A. m.
marina but lower than A. m. eucalyptifolia .