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Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modeling to consider the gene flow between ecotypes. Solidago yokusaianais a rheophyte endemic to the Japanese Archipelago that diverged from Solidago virgaurea. This study examined the parallel origins of S. yokusaianaby distinguishing between multiple and single origins and subsequent gene flow. The haplotypes of noncoding chloroplast DNA and genotypes at 14 nuclear simple sequence repeat (nSSR) loci and single-nucleotide polymorphisms (SNPs) revealed by double-digest restriction-associated DNA sequencing (ddRADseq) were used for phylogeographic analysis; the SNPs were also used to model population demographics. Some chloroplast haplotypes were common to S. yokusaianaand its ancestor S. virgaurea. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modeling supported the multiple origins of S. yokusaianain at least four districts and rejected a single origin with ongoing gene flow between the two species, implying that S. yokusaianaindependently and repeatedly adapted to frequently flooding riversides.

Climate relicts hold considerable importance because they have resulted from numerous historical changes. However, there are major interspecific variations among the ways by which they survived climate changes. Therefore, investigating the factors and timing that affected population demographics can expand our understanding of how climate relicts responded to historical environmental changes. Here, we examined herbaceous hydrangeas of genus Deinanthein East Asia, which show limited distributions and a remarkable disjunction between Japan and central China. Chloroplast genome and restriction site-associated DNA sequencing revealed that speciation event occurred in the late Miocene (ca. 7–9 Mya) in response to global climate change. Two lineages apparently remained not branched until the middle Quaternary, and afterwards started to diverge to regional population groups. The narrow endemic species in central China showed lower genetic diversity (He= 0.082), as its population size rapidly decreased during the Holocene due to isolation in montane refugia. Insular populations in the three Japanese islands (He= 0.137–0.160) showed a genetic structure that was inconsistent with sea barriers, indicating that it was shaped in the glacial period when its range retreated to coastal refugia on the exposed sea floor. Demographic modelling by stairway-plot analysis reconstructed variable responses of Japanese populations: some experienced glacial bottlenecks in refugial isolation, while post-glacial range expansion seemingly exerted founder effects on other populations. Overall, this study demonstrated the involvement of not just one, but multiple factors, such as the interplay between climate changes, geography, and other population-specific factors, that determine the demographics of climate relicts.

ABSTRACTThe phylogenetic origin of endangered species extinct in the wild is not always well understood, as a consequence of limited historical records of the original populations. Magnolia pseudokobus(Magnoliaceae) is one of only a few such woody plants in Japan. This triploid species was described in 1954 on Shikoku Island, but since then, no other individuals have been found in other locations. Currently, the only genet clonally propagated from the original tree can be seen in botanic gardens. In this study, we aimed to phylogenetically position M. pseudokobusby investigating genetic variations in the chloroplast genome, genome-wide SNPs, and microsatellites of focal and related species.Phylogenetic trees based on the chloroplast genome and nuclear single nucleotide polymorphism (SNP) markers consistently showed that M. pseudokobusis well embedded within a clade consisting of M. kobussamples. Microsatellite analysis on a seedling of M. pseudokobus, which was cultivated adjacent to a M. kobustree, showed that it was an interspecific hybrid. The genetic data suggest that M. pseudokobuswas generated recently from M. kobus, allowing for the production of viable seedlings. Considering that the species is triploid and is not agamospermous, and any wild populations of M. kobusare not known from Shikoku Island, M. pseudokobusmay be a ploidy variant of M. kobus, generated by spontaneous triploidization in M. kobusindividual(s), which were possibly introduced by humans as ornamental tree(s). In conclusion, M. pseudokobusappears to be conspecific with M. kobus, and better recognized as M. kobusf. pseudokobus.

ABSTRACTNuclear microsatellite markers were developed for Aphananthe aspera(Thunb.) Planch. (Cannabaceae), a deciduous canopy tree species distributed in East Asia, to evaluate the genetic diversity and genetic structure of A. asperapopulations in remnant forest fragments in urbanized areas of Japan. A total of 94 primer pairs were designed based on genomic sequence data. Of the 25 primer pairs which showed clear microsatellite peaks, 20 pairs showed allelic polymorphisms in 57 individuals collected from two distant populations. The length of PCR products ranged from 120 to 482 bp, and expected heterozygosity for the 20 microsatellite markers ranged from 0.017 to 0.768. These newly developed simple sequence repeat markers will be used in population genetic studies of A. asperato evaluate genetic diversity and the extent of genetic isolation of the fragmented populations in urban areas.

ABSTRACTSeries Sakawanum(genus Asarum, Aristolochiaceae) comprises four taxa of forest understory herbaceous plants, which exhibits a geographical cline of calyx lobe length across taxonomic units. To understand the formation process of this series, it is necessary to investigate the evolutionary history based on maternally inherited seed-mediated plastid markers. Using pyrosequencing technique, nearly complete chloroplast genomes of two species (A. minamitanianumand A. costatum) were obtained. Furthermore, nine polymorphic chloroplast single nucleotide polymorphisms (SNPs) and 11 simple sequence repeat (SSR) markers were developed. Most of these markers showed interspecific variations and all markers showed transferability to other Asarumspecies, while most of markers showed little intra-population variations. These chloroplast genomes and markers can be applied in future studies investigating the contributions of the maternal lineage in shaping the population genetic structure of series Sakawanumand the evolutionary processes underlying their morphological diversification including the characteristic calyx lobe length variation. Moreover, this study showed the applicability of comparative chloroplast genome analysis to develop the chloroplast markers for species group for which it is difficult to obtain polymorphism data using the universal primers.

ABSTRACTBased on organelle DNA phylogeographic analyses and ecological niche modeling (ENM), we investigated the range-shift history of the Japanese wingnut (Pterocarya rhoifolia) during the Quaternary climatic oscillations with particular emphasis on the Last Glacial Maximum (LGM). Phylogeographic patterns of this species were determined using 376 individuals from 53 populations for chloroplast DNA sequencing of three spacers. Spatial analysis of molecular variance revealed that the current phylogeographic structure would be sculptured by multiple range shifts from each glacial refugium, which would have been repeated several times during the Quaternary climatic oscillations. High haplotype diversity and private haplotypes were detected in southwestern Japan, where wingnut is currently infrequent and found mainly in high mountains, whereas in northernmost Japan, haplotype diversity was low though this plant is quite common at present. According to ENM approach, during the LGM, the climatically suitable distribution areas were not recovered in northeastern Japan but in lowlands of southwestern Japan. Our combined results suggest that Japanese wingnut primarily persisted in the lowlands of southwestern Japan and coastlines below 36.5°N latitude during the LGM, having led to the postglacial range expansion from the refugia in each area of southwestern and lower latitudinal northeastern Japan, and to the wide-range recolonization from the southerly refugium/refugia to the north in northernmost Japan. The southwestern and coastal refugia have played a role in shaping the current haplotype diversity and phylogeographic structure, whereas some rear edge populations, harboring unique haplotypes, have been also maintained.

The mode of chloroplast inheritance was investigated in the four Australian conifer species; Callitriscolumellaris, C. intratropica, C. gracilisand C. verrucosa(Callitroideae, Cupressaceae), as a basis for future use of chloroplast genetic markers for the genus. Open-pollinated seeds and the foliage tissue of the mother trees were collected from one population per species, in which two distinct chloroplast haplotypes at the trnL (UAA) 5′ exon–trnF (GAA) region were co-distributed. In total, the DNA sequences of the chloroplast fragments in 255 samples were determined, and the haplotypes of the germinated seedlings and the mother trees were compared. Among the 16 mother trees examined across all species, 12 trees were shown to have produced at least one offspring with a different haplotype from the mother, indicating the occurrence of paternal inheritance of chloroplast in the fertilization processes. In binomial GLMM analyses, the haplotype of mother trees in C. columellaris, C. gracilis, and C. verrucosadid not significantly affect those of their offspring, and the predicted frequency of seedlings’ haplotypes was compatible with the observed frequency in adult canopy trees. These findings provide a genetic support that paternal inheritance of chloroplast DNA via pollen dispersal would be dominant in the Callitrisspecies.

AbstractThe mode of chloroplast inheritance was investigated in the four Australian conifer species; Callitris columellaris, C. intratropica, C. gracilisand C. verrucosa(Callitroideae, Cupressaceae), as a basis for future use of chloroplast genetic markers for the genus. Open-pollinated seeds and the foliage tissue of the mother trees were collected from one population per species, in which two distinct chloroplast haplotypes at the trnL (UAA) 5′ exon–trnF (GAA) region were co-distributed. In total, the DNA sequences of the chloroplast fragments in 255 samples were determined, and the haplotypes of the germinated seedlings and the mother trees were compared. Among the 16 mother trees examined across all species, 12 trees were shown to have produced at least one offspring with a different haplotype from the mother, indicating the occurrence of paternal inheritance of chloroplast in the fertilization processes. In binomial GLMM analyses, the haplotype of mother trees in C. columellaris, C. gracilis, and C. verrucosadid not significantly affect those of their offspring, and the predicted frequency of seedlings' haplotypes was compatible with the observed frequency in adult canopy trees. These findings provide a genetic support that paternal inheritance of chloroplast DNA via pollen dispersal would be dominant in the Callitrisspecies.

A method for obtaining a relative deer population density index with low cost and effort is urgently needed in wildlife protection areas that need their own deer management guidelines. We recorded the number of deer sighted during our daily trips on forest roads by car in Ashiu Forest at Kyoto University, Japan, beginning in 2006. We used generalized additive mixed models (GAMMs) to estimate among-year trends in the number of deer sighted. We applied models for the total number of deer (TND), number of adults (NA), and number of fawns (NF) sighted, which included both current-year and 1-year-old fawns. Full models included the terms of year (2007, 2008, 2009, and 2010), weather (fine, cloudy, and rain/snow), and nonlinear effects of season (date) and time (time). The optimal GAMMs for TND, NA, and NF did not include the effect of weather but included those of time, date, and year. The detected among-year trends in deer population may be influenced by differences in snow environments among the years. The modeling of road count data using GAMM quantitatively determined among-year variation in the number of deer sighted. This trend was similar to that of the population density estimated using a block count survey conducted in Ashiu Forest.A method for obtaining a relative deer population density index with low cost and effort is urgently needed in wildlife protection areas that need their own deer management guidelines. We recorded the number of deer sighted during our daily trips on forest roads by car in Ashiu Forest at Kyoto University, Japan, beginning in 2006. We used generalized additive mixed models (GAMMs) to estimate among-year trends in the number of deer sighted. We applied models for the total number of deer (TND), number of adults (NA), and number of fawns (NF) sighted, which included both current-year and 1-year-old fawns. Full models included the terms of year (2007, 2008, 2009, and 2010), weather (fine, cloudy, and rain/snow), and nonlinear effects of season (date) and time (time). The optimal GAMMs for TND, NA, and NF did not include the effect of weather but included those of time, date, and year. The detected among-year trends in deer population may be influenced by differences in snow environments among the years. The modeling of road count data using GAMM quantitatively determined among-year variation in the number of deer sighted. This trend was similar to that of the population density estimated using a block count survey conducted in Ashiu Forest.

AbstractA method for obtaining a relative deer population density index with low cost and effort is urgently needed in wildlife protection areas that need their own deer management guidelines. We recorded the number of deer sighted during our daily trips on forest roads by car in Ashiu Forest at Kyoto University, Japan, beginning in 2006. We used generalized additive mixed models (GAMMs) to estimate among-year trends in the number of deer sighted. We applied models for the total number of deer (TND), number of adults (NA), and number of fawns (NF) sighted, which included both current-year and 1-year-old fawns. Full models included the terms of year (2007, 2008, 2009, and 2010), weather (fine, cloudy, and rain/snow), and nonlinear effects of season (date) and time (time). The optimal GAMMs for TND, NA, and NF did not include the effect of weather but included those of time, date, and year. The detected among-year trends in deer population may be influenced by differences in snow environments among the years. The modeling of road count data using GAMM quantitatively determined among-year variation in the number of deer sighted. This trend was similar to that of the population density estimated using a block count survey conducted in Ashiu Forest.