A recent phylogenetic study based only on chloroplast DNA (cpDNA) variation revealed that populations of an Isodon species are frequently embedded paraphyletically among other Isodon species. This phylogenetic discrepancy between species taxonomy and molecular phylogeny was considered to have resulted from chloroplast DNA captures and/or incomplete lineage sorting. To elucidate which of these factors was mainly responsible for the observed phylogenetic pattern, we performed phylogenetic analyses of multiple populations of Isodon species in Japan using cpDNA variation, three single‐copy nuclear genes, and double‐digest restriction‐site‐associated DNA sequencing (ddRAD‐seq). Although a species often shared chlorotypes with other species, our phylogenetical analyses based on variation in the three single‐copy nuclear genes and the ddRAD‐seq data showed that most populations belonging to the same species were monophyletic at the species level, suggesting that chloroplast capture may have frequently occurred between Isodon species. Some populations of an intraspecific taxon were embedded paraphyletically within the species, regardless of the large amount of phylogenetic information in nuclear DNA; this incongruity may have resulted from incomplete lineage sorting.
Adaptation to local pollination regimes and secondary contact of allopatrically differentiated populations with respect to pollination ecology may result in geographical variation in floral traits. We examined the contributions of these two processes in Isodon shikokianus, which showed remarkable geographical variation in corolla tube length in western Japan. Corolla tube length varied among 17 study populations located within a relatively narrow area, and covaried with altitude and distribution of two bumblebee pollinators with different tongue lengths: the longer corolla was found at lower altitudes where the long‐tongued pollinator was more abundant, and vice versa. Additionally, bumblebee species preferentially visited flowers that fit their tongue lengths. Population genetic analysis based on 11 microsatellite loci revealed that populations with long and short corolla tubes constituted genetically distinct groups. Migration rates were low between the groups, but high within each group. These results indicate that two genetically differentiated groups made secondary contact and hybridized, and gene flow between the groups was limited. Thus, the geographical variation in corolla tube length in I. shikokianus may be a result of past allopatric differentiation and subsequent secondary contact of populations with different corolla tube lengths. The variation in corolla tube length within a narrow area may be maintained by selection owing to the altitudinally structured pollinator assemblages. Altitudinal differences in relative abundance of two pollinators and their assortative visitation with respect to corolla tube length may contribute to reproductive isolation between the two groups.
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