Tanaka Kenta

Variation in pollen dispersal between years with different pollination conditions in a tropical emergent tree

We examined differences in pollen dispersal efficiency between 2 years in terms of both spatial dispersal range and genetic relatedness of pollen in a tropical emergent tree, Dipterocarpus tempehes. The species was pollinated by the giant honeybee (Apis dorsata) in a year of intensive community‐level mass‐flowering or general flowering (1996), but by several species of moths in a year of less‐intensive general flowering (1998). We carried out paternity analysis based on six DNA microsatellite markers on a total of 277 mature trees forming four spatially distinct subpopulations in a 70 ha area, and 147 and 188 2‐year‐old seedlings originating from seeds produced in 1996 and 1998 (cohorts 96 and 98, respectively). Outcrossing rates (0.93 and 0.96 for cohorts 96 and 98, respectively) did not differ between years. Mean dispersal distances (222 and 192 m) were not significantly different between the 2 years but marginally more biased to long distance in 1996. The mean relatedness among cross‐pollinated seedlings sharing the same mothers in cohort 96 was lower than that in cohort 98. This can be attributed to the two facts that the proportion of intersubpopulations pollen flow among cross‐pollination events was marginally higher in cohort 96 (44%) than in cohort 98 (33%), and that mature trees within the same subpopulations are genetically more related to each other than those between different subpopulations. We conclude that D. tempehes maintained effective pollen dispersal in terms of outcrossing rate and pollen dispersal distance in spite of the large difference in foraging characteristics between two types of pollinators. In terms of pollen relatedness, however, a slight difference was suggested between years in the level of biparental inbreeding.

Mass flowering of the tropical tree Shorea beccariana was preceded by expression changes in flowering and drought‐responsive genes

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.

Multiple factors contribute to outcrossing in a tropical emergent Dipterocarpus tempehes, including a new pollen-tube guidance mechanism for self-incompatibility

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.

Resource allocation to reproductive organs during masting in the tropical emergent tree, Dipterocarpus tempehes

Some tree species exhibit large year-to-year variation in seed production, a phenomenon known as masting (Kelly 1994, Kelly & Sork 2002). Even in tropical rain forests, in which the climate is suitable for plant growth all year round with little seasonal variation (Whitmore 1998), there are many reports of masting (Appanah 1993, Hart 1995, Newbery et al . 1998, Newstrom et al . 1994, Wheelwright 1986). In particular, Dipterocarpaceae, the dominant family in lowland mixed dipterocarp forests in South-East Asia, undergo mast fruiting following mass-flowering with strong interspecific synchronization in aseasonal western Malesia (Appanah 1985, 1993; Ashton 1989, Ashton et al . 1988, Curran et al . 1999, Janzen 1974, Medway 1972, Sakai et al . 1999, Whitmore 1998, Wood 1956). In mixed-dipterocarp forests, dipterocarp species contribute more than 70% of the canopy biomass (Bruenig 1996, Curran & Leighton 2000). Masting of dipterocarp species is therefore likely to have a major impact on animal populations, and also on the nutrient cycle in such forest ecosystems by causing fluctuations in the availability of resources (Sakai 2002).

Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica

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.

Clinal Variation in Flowering Time and Vernalisation Requirement across a 3000-M Altitudinal Range in Perennial Arabidopsis kamchatica Ssp.Kamchatica and Annual Lowland Subspecies Kawasakiana

Clines in ecologically important traits across environmental gradients provide evidence of historical natural selection. Among the many adaptive traits that are relevant in natural habitats, flowering timing is a primary determinant of a plant’s lifetime fitness. In a laboratory experiment, we studied the divergence in flowering time and vernalisation requirement among 38 populations of two Arabidopsis subspecies: perennial A. kamchatica ssp. kamchatica across an altitudinal gradient from 30 to nearly 3000 m in the Japanese Alps, and its annual lowland subspecies, kawasakiana. Flowering time with vernalisation was not different and flowering time without vernalisation was slightly different between the subspecies; however, the altitude of the source populations was the dominant determinant of the variation in these traits for the species as a whole. The flowering time increased linearly and the effect of vernalisation to shorten the flowering time increased non-linearly with increasing altitude of the source population. Low-altitude populations of ssp. kamchatica from laboratory-collected seeds showed a stronger response to vernalisation than field-collected seeds, suggesting an effect of the maternal environment. By replicating the altitudinal gradient and explicitly accounting for the maternal effect, our results clearly suggest the existence of genetically based clinal patterns that provide signs of adaptive evolution. Early flowering is probably advantageous to completing reproduction before the hot summer at low altitudes. In ssp. kamchatica, which is perennial and can reproduce even if it does not flower in its first year, the strong vernalisation requirement may delay the first reproduction at high altitudes, where the growing season is short.

Effects of Population Size, Forest Fragmentation, and Urbanization on Seed Production and Gene Flow in an Endangered Maple (Acer miyabei)

Abstract Forest fragmentation threatens the reproduction of tree species, for which habitats overlap with urban and rural areas. An endangered maple, Acer miyabei f. miyabei, is such a species in northern Japan. We examined the effects of forest fragmentation on seed production and mate diversity and assessed gene flow within and between fragmented forests. We measured the density, viability, and kinship of seeds dispersed around 82 target trees in 21 fragmented forests in rural and urban areas. The dispersed seed density decreased as the size of the target trees and the number of adult trees in each forest decreased. The viable seed proportion also decreased as the number of adult trees in each forest decreased. We did not find any effects on the kinship co-efficient among seeds dispersed around each target tree. The regression line of the pairwise kinship co-efficient of the seeds against the distance had a higher intercept and a more gently declining slope between the forests than within the forests, indicating forest fragmentation altered gene flow patterns. The results suggest reduced seed production due to pollen limitation and changes in the genetic structure of regenerating populations of A. miyabei in fragmented forests.

Development and Evaluation of Microsatellite Markers for Acer miyabei (Sapindaceae), a Threatened Maple Species in East Asia

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.

The effects of vegetation types and microhabitats on carabid beetle community composition in cool temperate Japan

Abstract The effects of vegetation types and environmental factors on carabid beetle (Coleoptera: Carabidae) communities were studied. Carabid beetles were collected using pitfall traps (total 2844 trapping days) and seven microenvironmental factors were measured in four vegetation types: grassland, natural evergreen coniferous forest (Pinus densiflora), deciduous broad-leaved natural forest (Quercus crispula, Betula platyphylla, Alnus japonica, or Fagus crenata), and deciduous coniferous plantation (Larix kaempferi) in cool temperate Japan. These four vegetation types provided a novel comparison between natural forests and plantations because the vast majority of related studies have investigated only deciduous broad-leaved natural forests and evergreen coniferous plantations. PERMANOVA indicated that vegetation types affected carabid community composition. Ordination plots showed that community composition differed greatly between grassland and forest vegetation types, but that community composition in the plantation forest overlapped with that of natural forest types. Characteristics differentiating the grassland included a high proportion of winged species and a low mean carabid body weight. Among the examined environmental factors, litter depth, soil water content, and depth of the soil A-horizon had large effects on carabid communities. These results suggest that the effect of afforestation on carabid communities in cool temperate Japan might be insignificant compared with the effects of cover types (deciduous vs. evergreen) and microenvironmental factors.

Factors influencing leaf- and root-associated communities of bacteria and fungi across 33 plant orders in a grassland

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 138 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.