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Over the past century, grassland and forest ecosystems globally have been heavily influenced by land-use changes driven by diverse socioeconomic activities. Ski resorts are a modern land-use type associated with biodiversity loss in mountain ecosystems worldwide. Below the treeline, by contrast, some ski slopes have been shown to provide suboptimal semi-natural habitats for native grassland plants and animals, depending on specific construction and management practices. We compared environmental factors and grassland vegetation between two types of ski slopes in central Japan with different land-use histories: slopes constructed on old pastures (pasture slopes) and slopes constructed by clearing secondary forests or larch plantations established on abandoned pastures during the 1940s-1990s (forest slopes). We examined the effects of land-use history and machine grading as well as other environmental factors on ski slope vegetation, including total species richness and the richness of native, endangered, and exotic plants, using a total of 108 plots of 2 m × 10 m. Compared to pasture slopes, forest slopes exhibited significantly lower richness of native grassland species, including endangered species. Forest slopes were more graded than pasture slopes, resulting in lower native and higher exotic grassland species richness. A significantly lower duration of direct sunlight on forest slopes than on pasture slopes likely decreased endangered species richness. The lower species richness on forest slopes may be also caused by seed dispersal limitations. Our findings demonstrate that ski slopes have good potential to support numerous native grassland plant species, including endangered species, but this potential is significantly and negatively affected by forest use history and concomitant environmental changes. The conservation of semi-natural conditions on pasture slopes as habitats for native grassland species can be promoted through the maintenance of annual mowing practices, avoidance of machine grading, and wider ski courses., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Atushi Ushimaru reports equipment, drugs, or supplies and travel were provided by Japan Society for the Promotion of Science. Tanaka Kenta reports equipment, drugs, or supplies was provided by Japan Society for the Promotion of Science. Yuki A. Yaida reports financial support, equipment, drugs, or supplies, and travel were provided by Japan Society for the Promotion of Science. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Past forest use often has a long-term negative impact on the recovery of the original plant composition of semi-natural grasslands, which is known as a legacy effect. This study investigates the impact of seed dispersal limitations on the restoration of grassland plant diversity on ski slopes with past forest use, highlighting the negative legacy effect on biodiversity recovery. Focusing on ski areas, our research contrasts the vegetation on ski slopes originally created on semi-natural grasslands such as pasture (pasture slopes) and constructed by clearing secondary forests or conifer plantations (forest slopes). We examined species richness and diversity, considering seed dispersal modes, grassland management history, and seed source proximity. We reveal that the proximity to species-rich grassland sources is pivotal for the restoration of native grassland vegetation. Particularly, wind-dispersed species show significant recovery on slopes with sustained management for more than 70 years and those with neighboring species-rich grasslands, suggesting that both the duration of management and the proximity to seed sources are critical for overcoming the legacy effects of past forest use. Meanwhile, gravity-dispersed species failed to recover their richness and diversity regardless of both the duration of management and the proximity to seed source grasslands, which their diversity recovered where seed sources neighbored. Our findings emphasize the importance of considering seed dispersal limitation and management history in the restoration and conservation of grasslands and their biodiversity, particularly in landscapes experiencing past human intervention., Competing Interests: The authors declare no conflict of interest., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software that extracts leaf color by detecting plant individuals automatically. As a case study, we applied PlantServation to examine environmental and genotypic effects on the pigment anthocyanin content estimated from leaf color. We processed >4 million images of small individuals of four Arabidopsis species in the field, where the plant shape, color, and background vary over months. Past radiation, coldness, and precipitation significantly affected the anthocyanin content. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation facilitates the study of plant responses to complex environments termed "in natura"., (© 2023. Springer Nature Limited.)

Decomposition of plant organic matter plays a key role in the terrestrial biogeochemical cycles. Sunlight has recently been identified as an important contributor to carbon [C] turnover through photodegradation, accelerating decomposition even in forest ecosystems where understorey solar irradiance remains relatively low. However, it is uncertain how C and nutrients dynamics respond to fluctuations in solar spectral irradiance caused by canopy structure (understorey vs. gaps) and season (open vs. closed canopy phenology). Spectral-attenuation treatments were used to compare litter decomposition over eight months, covering canopy phenology, in a temperate deciduous forest and an adjacent gap. Exposure to the full spectrum of sunlight increased the loss of litter C and lignin by 75% and 64% in the forest gap, and blue light was responsible for respectively 27% and 42% of that loss. Whereas in the understorey, C and lignin loss were similar among spectral-attenuation treatments over the experimental period, except prior to and during spring canopy flush when exposure to the full spectrum of sunlight promoted C loss by 15% overall, 80% of which was attributable to ultraviolet-B (UV-B) radiation. Nitrogen [N] was immobilized in the understorey during canopy flush before the canopy completely closed but N was swiftly released during canopy leaf-fall. Our study suggests that blue-driven photodegradation plays an important role in lignin decomposition and N dynamics in canopy gaps, whereas seasonal canopy phenology affecting sunlight reaching the forest floor drastically changes patterns of C and N in litter during decomposition. Hence, including sunlight dynamics driven by canopy structure and phenology would improve estimates of biogeochemical cycling in forests responding to changes in climate and land-use., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Premise: Relict species provide valuable insights into the origin and formation of extant vegetation. Here, we aimed to elucidate the genetic structure and diversity of a riparian relic, Acer miyabei, in Japan. Once widely distributed, it now occurs in three isolated regions. The most northern regional group is located at low elevation on Hokkaido Island, whereas the southernmost group in central Honshu Island is at high elevation in a mountainous landscape. This contrastive distribution enables us to examine the effects of climate oscillations on genetic diversity in relation to topographic variation., Methods: We collected 604 individuals of A. miyabei from 43 sites. Their genetic structure and diversity were analyzed using 12 microsatellite markers and cpDNA sequences., Results: According to structure analyses, ∆K was lowest at K = 2; the clustering essentially separated many of the individuals in the most northern regional group from the others. In contrast, the two southern groups were not clearly differentiated from each other, despite their geographic discontinuity. The proportion of private alleles was high in populations from the mountain terrain in the southern group although the number of extant populations is limited., Conclusions: Genetic clustering of A. miyabei is not perfectly congruent with the current patterns of geographic distribution. We infer that disjunction of the two southern groups occurred more recently than that between these groups and the northern group. The mountainous landscape in the most southern region likely provided multiple refugia and contributed to the retention of distinctive genetic variation., (© 2022 Botanical Society of America.)

Litter decomposition determines carbon (C) backflow to the atmosphere and ecosystem nutrient cycling. Although sunlight provides the indispensable energy for terrestrial biogeochemical processes, the role of photodegradation in decomposition has been relatively neglected in productive mesic ecosystems. To quantify the effects of this variation, we conducted a factorial experiment in the understorey of a temperate deciduous forest and an adjacent gap, using spectral-attenuation-filter treatments. Exposure to the full spectrum of sunlight increased decay rates by nearly 120% and the effect of blue light contributed 75% of this increase. Scaled-up to the whole forest ecosystem, this translates to 13% loss of leaf-litter C through photodegradation over the year of our study for a scenario of 20% gap. Irrespective of the spectral composition, herbaceous and shrub litter lost mass faster than tree litter, with photodegradation contributing the most to surface litter decomposition in forest canopy gaps. Across species, the initial litter lignin and polyphenolic contents predicted photodegradation by blue light and ultraviolet B (UV-B) radiation, respectively. We concluded that photodegradation, modulated by litter quality, is an important driver of decomposition, not just in arid areas, but also in mesic ecosystems such as temperate deciduous forests following gap opening., (© 2020 The Authors New Phytologist © 2020 New Phytologist Foundation.)

Empirical evidence is limited on whether allopolyploid species combine or merge parental adaptations to broaden habitats. The allopolyploid Arabidopsis kamchatica is a hybrid of the two diploid parents Arabidopsis halleri and Arabidopsis lyrata . A. halleri is a facultative heavy metal hyperaccumulator, and may be found in cadmium (Cd) and zinc (Zn) contaminated environments, as well as non-contaminated environments. A. lyrata is considered non-tolerant to these metals, but can be found in serpentine habitats. Therefore, the parents have adaptation to different environments. Here, we measured heavy metals in soils from native populations of A. kamchatica. We found that soil Zn concentration of nearly half of the sampled 40 sites was higher than the critical toxicity level. Many of the sites were near human construction, suggesting adaptation of A. kamchatica to artificially contaminated soils. Over half of the A. kamchatica populations had >1,000 μg g -1 Zn in leaf tissues. Using hydroponic treatments, most genotypes accumulated >3,000 μg g -1 Zn, with high variability among them, indicating substantial genetic variation in heavy metal accumulation. Genes involved in heavy metal hyperaccumulation showed an expression bias in the A. halleri -derived homeolog in widely distributed plant genotypes. We also found that two populations were found growing on serpentine soils. These data suggest that A. kamchatica can inhabit a range of both natural and artificial soil environments with high levels of ions that either of the parents specializes and that it can accumulate varying amount of heavy metals. Our field and experimental data provide a compelling example of combining genetic toolkits for soil adaptations to expand the habitat of an allopolyploid species., (Copyright © 2020 Paape, Akiyama, Cereghetti, Onda, Hirao, Kenta and Shimizu.)

In terrestrial ecosystems, plants interact with diverse taxonomic groups of bacteria and fungi in the phyllosphere and rhizosphere. Although recent studies based on high-throughput DNA sequencing have drastically increased our understanding of plant-associated microbiomes, we still have limited knowledge of how plant species in a species-rich community differ in their leaf and root microbiome compositions. In a cool-temperate semi-natural grassland in Japan, we compared leaf- and root-associated microbiomes across 137 plant species belonging to 33 plant orders. Based on the whole-microbiome inventory data, we analyzed how sampling season as well as the taxonomy, nativeness (native or alien), lifeform (herbaceous or woody), and mycorrhizal type of host plants could contribute to variation in microbiome compositions among co-occurring plant species. The data also allowed us to explore prokaryote and fungal lineages showing preferences for specific host characteristics. The list of microbial taxa showing significant host preferences involved those potentially having some impacts on survival, growth, or environmental resistance of host plants. Overall, this study provides a platform for understanding how plant and microbial communities are linked with each other at the ecosystem level.

While genotype-environment interaction is increasingly receiving attention by ecologists and evolutionary biologists, such studies need genetically homogeneous replicates-a challenging hurdle in outcrossing plants. This could be potentially overcome by using tissue culture techniques. However, plants regenerated from tissue culture may show aberrant phenotypes and "somaclonal" variation. Here, we examined somaclonal variation due to tissue culturing using the response to cold treatment of photosynthetic efficiency (chlorophyll fluorescence measurements for F v /F m , F v '/F m ', and Φ PSII , representing maximum efficiency of photosynthesis for dark- and light-adapted leaves, and the actual electron transport operating efficiency, respectively, which are reliable indicators of photoinhibition and damage to the photosynthetic electron transport system). We compared this to variation among half-sibling seedlings from three different families of Arabidopsis lyrata ssp. petraea Somaclonal variation was limited, and we could detect within-family variation in change in chlorophyll fluorescence due to cold shock successfully with the help of tissue-culture derived replicates. Icelandic and Norwegian families exhibited higher chlorophyll fluorescence, suggesting higher performance after cold shock, than a Swedish family. Although the main effect of tissue culture on F v /F m , F v '/F m ', and Φ PSII was small, there were significant interactions between tissue culture and family, suggesting that the effect of tissue culture is genotype-specific. Tissue-cultured plantlets were less affected by cold treatment than seedlings, but to a different extent in each family. These interactive effects, however, were comparable to, or much smaller than the single effect of family. These results suggest that tissue culture is a useful method for obtaining genetically homogenous replicates for studying genotype-environment interaction related to adaptively-relevant phenotypes, such as cold response, in nonmodel outcrossing plants., (Copyright © 2016 Kenta et al.)

Allopolyploidization combines parental genomes and often confers broader species distribution. However, little is known about parentally transmitted gene expression underlying quantitative traits following allopolyploidization because of the complexity of polyploid genomes. The allopolyploid species Arabidopsis kamchatica is a natural hybrid of the zinc hyperaccumulator Arabidopsis halleri and of the nonaccumulator Arabidopsis lyrata We found that A. kamchatica retained the ability to hyperaccumulate zinc from A. halleri and grows in soils with both low and high metal content. Hyperaccumulation of zinc by A. kamchatica was reduced to about half of A. halleri, but is 10-fold greater than A. lyrata Homeologs derived from A. halleri had significantly higher levels of expression of genes such as HEAVY METAL ATPASE4 (HMA4), METAL TRANSPORTER PROTEIN1 and other metal ion transporters than those derived from A. lyrata, which suggests cis-regulatory differences. A. kamchatica has on average about half the expression of these genes compared with A. halleri due to fixed heterozygosity inherent in allopolyploids. Zinc treatment significantly changed the ratios of expression of 1% of homeologous pairs, including genes putatively involved in metal homeostasis. Resequencing data showed a significant reduction in genetic diversity over a large genomic region (290 kb) surrounding the HMA4 locus derived from the A. halleri parent compared with the syntenic A. lyrata-derived region, which suggests different evolutionary histories. We also estimated that three A. halleri-derived HMA4 copies are present in A. kamchatica Our findings support a transcriptomic model in which environment-related transcriptional patterns of both parents are conserved but attenuated in the allopolyploids., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Premise of the Study: Twelve microsatellite markers were developed and characterized in a threatened maple species, Acer miyabei (Sapindaceae), for use in population genetic analyses., Methods and Results: Using Ion Personal Genome Machine (PGM) sequencing, we developed microsatellite markers with perfect di- and trinucleotide repeats. These markers were tested on a total of 44 individuals from two natural populations of A. miyabei subsp. miyabei f. miyabei in Hokkaido Island, Japan. The number of alleles per locus ranged from two to eight. The observed and expected heterozygosities per locus ranged from 0.05 to 0.75 and from 0.05 to 0.79, respectively. Some of the markers were successfully transferred to the closely related species A. campestre, A. platanoides, and A. pictum., Conclusions: The developed markers will be useful in characterizing the genetic structure and diversity of A. miyabei and will help to understand its spatial genetic variation, levels of inbreeding, and patterns of gene flow, thereby providing a basis for conservation.

Community-level mass flowering, known as general flowering, which occurs in South-East Asia at supra-annual irregular intervals, is considered a particularly spectacular phenomenon in tropical ecology. Recent studies have proposed several proximate factors inducing general flowering, such as drought and falls in minimum temperature. However, limited empirical data on the developmental and physiological processes have been available to test the significance of such factors. To overcome this limitation and test the hypotheses that general flowering is triggered by the proposed factors, we conducted an 'ecological transcriptome' study of a mass flowering species, Shorea beccariana, comparing meteorological data with genome-wide expression patterns obtained using next-generation sequencing. Among the 98 flowering-related genes identified, the homologs of a floral pathway integrator, SbFT, and a floral repressor, SbSVP, showed dramatic transcriptional changes before flowering, and their flowering functions were confirmed using transgenic Arabidopsis thaliana. Expression in drought-responsive and sucrose-induced genes also changed before flowering. All these expression changes occurred when the flowering-inducing level of drought was reached, as estimated using data from the preceding 10 years. These genome-wide expression data support the hypothesis that drought is a trigger for general flowering., (© 2013 Blackwell Publishing Ltd.)

Range margins are spatially complex, with environmental, genetic and phenotypic variations occurring across a range of spatial scales. We examine variation in temperature, genes and metabolomic profiles within and between populations of the subalpine perennial plant Arabidopsis lyrata ssp. petraea from across its northwest European range. Our surveys cover a gradient of fragmentation from largely continuous populations in Iceland, through more fragmented Scandinavian populations, to increasingly widely scattered populations at the range margin in Scotland, Wales and Ireland. Temperature regimes vary substantially within some populations, but within-population variation represents a larger fraction of genetic and especially metabolomic variances. Both physical distance and temperature differences between sites are found to be associated with genetic profiles, but not metabolomic profiles, and no relationship was found between genetic and metabolomic population structures in any region. Genetic similarity between plants within populations is the highest in the fragmented populations at the range margin, but differentiation across space is the highest there as well, suggesting that regional patterns of genetic diversity may be scale dependent.

To understand how a sparsely distributed species can maintain viable populations, and with a particular interest in distance-dependent reproductive success, we investigated the ovule survival and the factors that determine the survival for sparsely distributed Kalopanax pictus (Araliaceae) in a temperate forest landscape around the Ogawa Forest Reserve, central Japan. We found 154 potentially mature trees (>20 cm diameter at breast height) in a 600-ha site. The year 2000 was a mass flowering year for K. pictus; 96.8% of the trees examined flowered in that year; however, this was less than half of the trees that flowered in other years. The flowers of K. pictus include protandrous inflorescences, which bloom on individual tress in midsummer when few other tree species bloom. We conducted pollination experiments with out-crossed, self-pollinated, bagged, and control inflorescences. Results suggest that self-pollination is limited, partially by low self-compatibility and partially by protandry. Ovule survival from the flower to the seed stages was not dependent on the temporal flowering density of conspecific adults. The flowering habit and presence of effective pollinators may allow K. pictus to avoid the negative effects of sparse distribution on pollination efficiency. However, ovule survival during the ovary development stage depended on infection by a species-specific fungus, Mycosphaerella acanthopanacis. The fungus damages leaves, and the infection intensity depends on the distance between conspecific K. pictus adults. Thus, an advantage of sparse distribution in K. pictus is disease avoidance, whereas its disadvantages are overcome by pollination efficiency.

The self-rejection system of Dipterocarpus tempehes (Dipterocarpaceae), an emergent tree of the lowland tropical forests of Borneo, were studied by means of pollination experiments, fluorescence microscopy of pollen tubes, and monitoring of ovary maturation patterns. Fruit set was higher in cross-pollinated flowers than in control and self-pollinated flowers, indicating the existence of pollen limitation and a self-rejection system. Although the adhesion and the germination of self-pollen and the growth of self-pollen tubes were not inhibited, the proportion of cross-pollen tubes that entered the style was 1.7-2.3 times higher than that of self-pollen tubes, indicating a partial self-incompatibility that inhibits self-pollen tubes from entering the style hollow. These results suggest, for the first time, that self-incompatibility is caused by a defect of pollen-tube guidance. We also suggest a threshold effect in number of pollen tubes or late-acting self-incompatibility to fully explain the drastic and uniform selection against self-pollinated flowers before ovary swelling. After that, maternal selection and/or inbreeding depression caused the abortion and delayed maturation of self-pollinated flowers. The advantages of the self-rejection process composed of partial early-acting self-incompatibility and relatively strong delayed abortion is discussed with respect to the general-flowering phenomenon in lowland dipterocarp forests.