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).