Preliminary phylogenetic insights into Japanese willows (Salix L.) using low-copy nuclear genes, with emphasis on endemic species

In this study, we aimed to reveal the phylogenetic relationships of Salix species in Japan, with particular emphasis on the speciation process of endemic species. We performed molecular phylogenetic analyses of all available native species using multilocus datasets of low-copy nuclear genes and chloroplast sequences. Although gene-tree incongruence and basal reticulation were evident—implying the need for future genome-scale analyses— our analyses still provided sufficient resolution to clarify the phylogenetic structure of the Japanese Salix flora and to offer meaningful insights into its diversification. The integrated analyses identified three major lineages within the Japanese subg. Vetrix, revealed the polyphyly of the subg. Chamaetia, and clarified the phylogenetic context of several key endemic species. For example, S. hukaoana of the monotypic section Hukaoana and S. futura were inferred to be relicts of ancient lineages that diverged during the Mid to Late Miocene, whereas the species of sect. Hastatae (i.e., S. rupifraga, S. shiraii, and S. japonica) were suggested to be neoendemics derived from S. vulpina. Moreover, intraspecific taxa such as S. miyabeana and S. nakamurana showed signs of hybridization, suggesting that interspecific hybridization and introgression may contribute in lineage differentiation.