Phylogeographic and demographic modelling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana

<p>Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modelling to consider the gene flow between ecotypes. <i>Solidago yokusaiana</i> is a rheophyte endemic to the Japanese Archipelago that diverged from <i>Solidago virgaurea</i>. This study examined the parallel origins of <i>S. yokusaiana</i> by distinguishing between multiple and single origins and subsequent gene flow. The haplotypes of non-coding chloroplast DNA and genotypes at 14 nuclear simple sequence repeat (nSSR) loci and single nucleotide polymorphisms (SNPs) revealed by double-digest restriction-associated DNA sequencing (ddRADseq) were used for phylogeographic analysis; the SNPs were also used to model population demographics. Some chloroplast haplotypes were common to <i>S. yokusaiana</i> and its ancestor <i>S. virgaurea</i>. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modelling supported the multiple origins of <i>S. yokusaiana</i> in at least four districts and rejected a single origin with ongoing gene flow between the two species, implying that <i>S. yokusaiana</i> independently and repeatedly adapted to frequently flooding riversides.</p>