Haplotype network variation across the genome
Despite clear genomic and morphological differences among A.
marina subspecies, we found evidence of gene flow. Thus, the genomes of
these groups are expected to be mosaic, with regions of high divergence
interspersed among undifferentiated loci subject to exchange of genetic
material among subspecies. To verify this, we inferred haplotype
networks across the close to 100 loci we sequenced on the genome. Using
an expectation-maximization method to infer the linkage of the SNPs
detected from these loci, we split these regions into 454 linked
segments (Supplementary Table 3). Segments with missing data and with
length less than 100bp were discarded and 231 segments were retained for
haplotype network reconstruction, with A. alba as the outgroup
(Figure 5).
Among these segments, 134 (58.0%) were not genetically distinguishable
among groups with only one or a few haplotypes identified and all
haplotypes closely related to each other and shared among the three
subspecies. The other 66 segments (28.6%) reliably distinguishedA. m. australasica from the other two subspecies. Among these 66
segments, the maBB population shared haplotypes with A. m.
australasica rather than A. m. marina in seven loci. The third
type of segments, which was 14 in total (6.1%), delimited A. m.
marina from the other two subspecies. Five segments (2.2%) distinguishA. m. eucalyptifolia , but maBB shared haplotypes with A. m.
eucalyptifolia in all cases. Most importantly, 11 segments (4.8%)
allow clear delimitation of all three subspecies, with haplotypes split
into three groups and each subspecies containing haplotypes from a
single group. However, in eight of the 11 segments, maBB shared
haplotypes with A. m. eucalyptifolia . Finally, one segment
(0.4%) separated A. m. marina and A. m. australasica, butA. m. eucalyptifolia contained haplotypes from both subspecies.