Lineage divergence across geographic distribution
Four lineages were identified with phylogenetic, Bayesian clustering
approaches and PCA based on nuclear SNPs and chloroplast genomes: the NE
lineage included A. viridiflora and A. kamelinii , the EL
lineage included A. viridiflora and A. hebeica , and the CN
and NW lineages only included A. hebeica and A.
viridiflra , respectively, which is different from taxonomic recognition
species (Figure 1). The moderate genetic divergence (both
FST and DXY) among different lineages
may be explained by two nonmutually exclusive factors,
isolation-by-distance
and gene flow. While a strong pattern of isolation-by-distance (IBD) was
observed across all of the study populations and could explain the
variance in genetic differentiation (Figure 4B), gene flow after lineage
differentiation may be decrease the level of genetic differentiation. We
took advantage of the whole-genome dataset of the A. viridifloracomplex to infer the amount of gene flow of the recovered lineages,
revealing that a higher level of recent gene flow than ancient was shown
to have occurred. Hybrids with two or three lineages mixed in the
contact zone existed because of the absence of strong biogeographical
barriers. Chloroplast capture might result in the chloroplast genome of
populations in the contact zone exhibiting inconsistent clustering with
nuclear SNPs, which also supported recent hybridization occurring in the
contact zone. In particular, gene flow between pairs of lineages with
close geographic distribution ranges was relatively large, indicating
that geographic isolation might shape the present range and phylogeny of
the recovered lineages. Although no recent gene flow was detected
between NW and the other three lineages (Figure 3A-B), hybrids which
formed by NE, CN and NW lineage mixing still arose, which resulted from
the ancient gene flow not only between the ancestral clade of NE and EL
lineages and NW lineage, but also between the ancestral clade of NE and
EL lineages and the ancestral clade of CN and NW lineages. Additionally,
the level of divergence between the CN and NW lineages was higher than
that between the other two lineages according to the FSTvalue. DXY was also evaluated the divergence between
pairs of lineages and was consistent with the FST value
(Figure 3C). Therefore, the incipient lineage divergence of the A.
viridiflora complex could be largely explained by geographic isolation
and the decrease of gene flow caused by the increase of divergence time.
These
results are in line with recent studies suggesting that gene flow may
have occurred between currently geographically isolated East Asia and
played a major role in other plant radiations (Hu et al.; Xiao et al.,
2020; L. L. Xu et al., 2021).