Molecular phylogenetic analyses identify the process of speciation of endemic willow species in the Japanese Archipelago

Abstract Here we examine the evolutionary history of Salix in Japan, and in particular the subg. Vetrix/Chamaetia complex. To do so, we performed molecular phylogenetic analyses covering all available native species, using multilocus datasets of low-copy nuclear genes and chloroplast sequences. Using phylogenetic network analysis and divergence time estimation, we identified three major lineages within Japanese subg. Vetrix , confirmed the polyphyly of subg. Chamaetia , and further resolved the taxonomic status of various taxa at the section to species levels. Moreover, this study also highlighted the speciation processes for many endemic species. These include S. hukaoana , a novel monotypic section of Hukaoana that distinctly shows ancient divergence and not hybrid speciation, and S. miyabeana (sect. Helix ), which shows evidence of genomic and morphological differentiation from subsp. miyabeana via intersectional hybridization and introgression with the sympatric species S. schwerinii (sect. Viminella ). Finally, we also identified local endemics classified into sect. Hastatae (i.e., S. rupifraga , S. shiraii , and S. japonica ) which show evidence of radiative speciation from a single lineage descended from S. vulpina (sect. Cinerella ).