Ecotypic divergence in tree taxa often occurs in sub-alpine habitats, where environmental conditions are more stressful than those in lower elevations. In the mountain oak species in Japan, Quercus crispula (Qc), the sub-alpine shrubby variety, Q. crispula var. horikawae (Qch), has been recognized in central and northern Honshu. Although Qch has different phenotypes from Qc, genetic divergence between Qc and Qch has not been examined yet. Pairs of Qc and Qch populations in eight locations and additional Qc and Qch populations around these locations were investigated. Leaf size of Qch was smaller than that of Qc. Chloroplast DNA haplotypes were shared between the Qc and Qch populations. In genotypes at 29 nuclear microsatellite loci, genetic diversity did not differ between the Qc and Qch populations. Principal component analysis and a neighbor-joining tree of populations based on microsatellite genotypes demonstrated that 13 Qc populations and eight Qch populations were grouped separately, except for three Qch populations that were grouped to Qc. Climatic conditions in the eight Qch populations were characterized by lower temperature and heavier snowfall than those in the 16 populations of the genetic group of Qc. These results suggest the genetic divergence between Qc and Qch associated with sub-alpine climatic conditions, irrespective of leaf size. The origin of the sub-alpine Qch lineage and the history of ecotypic divergence should be investigated in future genomic studies.

Adaptive introgression has been proposed in oaks (genus Quercus). In northern Japan, Q. mongolica var. crispula (Qc) is common in inland habitats, and Q. dentata (Qd) occurs in coastal habitats. At the northern distributional limit of Qd, Q. × angustilepidota (Qa), a hybrid taxon between Qc and Qd, occurs in coastal habitats. The three taxa, Qc, Qa, and Qd, were transplanted to inland and coastal common gardens (sites). Genotypes at 27495 loci, phenotypes of eight traits of leaves and shoots, and 30-year-old tree size were measured for 224 individuals in both sites. Genotypic variation revealed a hybrid zone between Qc and Qd, including both northern-edge Qd admixed with Qc and coastal Qa backcrossed to Qc. Phenotypes of Qa trees were intermediate between those of Qc and Qd trees. Size of Qa and Qd trees was smaller than that of Qc trees in the inland site but was larger in the coastal site, suggesting adaptation of Qa and Qd to coastal environment. Local ancestry was estimated from phased genotypes of admixed trees using reference genotypes of 47 Qc and 25 Qd trees, indicating heterogeneous ancestry along chromosomes. Association mapping of genotypes and admixture mapping of ancestry suggested that some loci potentially associated with four traits were related to stress response and were located at introgressed genomic regions. Further studies are necessary to show the genetic basis of adaptive introgression resulting in Qd-like phenotypes of Qa in coastal habitats.