math_commands Genetic and phenotypic clines in hybrid zones can differ due to various extents of hybridization and selection in heterogeneous environments. Temperate Cerasus leveilleana (Cl) and cool-temperate C. sargentii (Cs) form hybrid zones along elevational gradients. Because their geographic distributional ranges are largely overlapped, the hybrid zones are located across a wide latitudinal range in Japan. We compared variation in genotypes and phenotypes in hybrid zones among the south edge of Cs (south site), the north edge of Cl (north site), and the core of their ranges (central site). Genetic differentiation in nuclear microsatellite genotypes between Cl and Cs was lower, and the proportion of admixed individuals was higher, in the south site than in the central and north sites. Difference in the leaf hair density between Cl and Cs was smaller in the south site than in the central and north sites. Flowering periods at the same elevation were about seven days earlier in Cs than in Cl in the central site, while the periods were about nine days earlier in the south and north sites. These results suggest more admixture in the south site, which may result in introgression in a leaf trait, although staggered flowering is maintained. These findings imply that genetic admixture and phenotypic introgression has been facilitated, except for the latter in traits contributing to reproductive isolation, in the hybrid zone at the south rear edge of either species under the warming trend after the last glacial period.

Climate change and range shift during glacial cycles in the Quaternary resulted in disjunct plant distributions. Geographic genetic structure can imply historical processes that formed disjunct distributions. Betula dahurica Pallas is common in continental northeast Asia but is disjunctly distributed in the Japanese archipelago. To explore the formation process of its disjunct distributions, genome-wide single nucleotide polymorphism (SNP) genotypes, chloroplast (cp) DNA sequences, and leaf morphology were investigated in 10 populations in three regions, Primorsky, Hokkaido, and Honshu. Frequency distributions of the ratio of SNP reads suggested that most individuals in the three regions were octaploid, except for some hexaploid or heptaploid individuals found in Hokkaido and Honshu. SNP genotypes of putative octaploid individuals indicated that Honshu populations were diverged from Primorsky and Hokkaido populations. This genetic divergence was relatively small (0.010 < FST < 0.035) but larger than those between Primorsky and Hokkaido (FST < 0.010) and within regions (FST < 0.008). The effective population size in Honshu was smaller than that in Primorsky and Hokkaido. CpDNA (trnL–trnF) sequences found in Honshu were different from those found in Primorsky and Hokkaido. The variations in leaf size and shape were overlapped among the ploidy levels and among the populations. The findings of geographic genetic structure suggest a plausible process that formed the disjunct distributions, which includes the isolation of persistent populations in Honshu and the post-glacial migration from continental northeast Asia to Hokkaido directly or through Sakhalin.

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.