Naofumi Nomura

Research Institute for Humanity and Nature, Kioto, Kyōto, Japan

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Publications (9)20 Total impact

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    ABSTRACT: The invasion of natural ecosystems by exotic species is a major threat to biodiversity on a local, regional, and global scale. Endemic island flora are particularly vulnerable to invasive species. Bidens pilosa var. radiata is a common invasive weed of roadsides, which are subject to clipping, on Japanese subtropical islands. To assess compensation by the weed to damage by clipping, a pot experiment was conducted under common garden conditions. The above-ground parts were clipped with pruning shears at various frequencies, ranging from no clipping (the control) to clipping at 4–16 week intervals for 32 weeks in summer. The clipped individuals regenerated new branches from the axillary buds and flowered for ≤12 weeks after the clipping. The regeneration after the clipping gave rise to secondary reproduction, whereas minimal regeneration occurred in the unclipped individuals after the maturation of the fruit. Consequently, the total flower head mass, represented by the dry weight of the inflorescences throughout the experiment, was higher on the individuals that were clipped at 12 and 16 week intervals than on the unclipped individuals, suggesting overcompensation in fecundity. At the higher frequencies of above-ground clipping, the flower head mass was suppressed at 8 week clipping intervals, while both the flower head mass and the productive biomass were suppressed at 4 week clipping intervals. This indicates that clipping at intervals of ≤8 weeks is required to prevent the reproduction of this weed.
    Weed Biology and Management 09/2011; 11(3). · 0.60 Impact Factor
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    ABSTRACT: Farfugium japonicum (L.f.) Kitam., a facultative rheophyte occupying both dryland and riparian habitats within the species range, exhibits various shapes of leaves ranging from stenophyllous to round. The present study assesses variability in leaf morphology (five leaf characters) and genetics (305 AFLP markers) for populations from dryland and riparian habitats on Yaeyama Islands, Japan. Results from the two datasets produced somewhat different patterns indicating that selection for habitat type is effective on leaf shape attributes, while lack of differentiation was observed for neutral markers caused by extensive gene flow. Leaf-shape attributes were clustered into three groups: shade (round), sun (round), and narrow (stenophyllous) leaves. Narrow leaves were only found in riparian populations, indicating that flood intensity acts as a selective agent for this attribute. Although high within-population variation was demonstrated by AMOVA, the populations were distinct enough to be classified in separate groups irrespective of habitat type. However, Nei’s genetic diversity index (H) was low; suggesting lack of barriers to gene flow among individuals and selection for narrow leaves may act on the survivorship of young seedling.
    Canadian Journal of Botany 03/2011; 85(7):637-643. · 1.40 Impact Factor
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    ABSTRACT: Understanding the role of habitat-associated adaptation in reducing gene flow resulting in population differentiation and speciation is a major issue in evolutionary biology. We demonstrate a significant role for habitat divergence in species isolation between two naturally hybridizing riparian and nonriparian plants, Ainsliaea faurieana and A. apiculata (Asteraceae), on Yakushima Island, Japan. By analyzing the fine-scale population structure at six sympatric sites, we found that variations in leaf shape, geography, light conditions, and genotype were strongly correlated across riverbank-forest transitions. No evidence of effective gene flow was found between the two species across the majority of the transition zones, although the NewHybrid clustering analysis confirmed interspecific hybridization. However, a relatively high level of gene flow was observed across one zone with a more diffuse ecotone and intermediate flooding and light conditions, possibly generated by human disturbances. These results suggest that the barriers to gene flow between the riparian and forest species are primarily ecological. Additional common garden experiments indicated that the two species are adaptively differentiated to contrasting flooding and light environments. Overall, our study suggests that adaptations to different habitats can lead to the formation of reproductive isolating barriers and the maintenance of distinct species boundaries.
    Evolution 02/2011; 65(2):335-49. · 4.66 Impact Factor
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    ABSTRACT: Farfugium (Asteraceae) is a small genus that contains the two species F. japonicum and F. hiberniflorum and is distributed along a long archipelago in east Asia. The common taxon, F. japonicum, includes three varieties associated with a wide range of habitats, including forest understorey (sciophytes), coastal crag (heliophytes) and riverbed (rheophytes). Leaf shape is an important taxonomic character within this genus and is associated with the habitat. Twenty populations that included all Farfugium taxa were collected throughout its range. Leaf morphology was measured to determine differences amongst the taxa. Phylogenetic analyses based on sequences of the internal transcribed spacer of nuclear rDNA and four plastid DNA regions (matK, trnL-trnF, trnH-psbA and rpl20-rps12) were conducted separately. Leaf morphology was significantly different amongst taxa, but morphological variations were partly explained by adaptation to certain environmental conditions that each population inhabited. Molecular phylogenies for the nDNA internal transcribed spacer and cpDNA were consistent in classifying F. hiberniflorum and the Taiwanese var. formosanum, whilst suggesting polyphyletic origins for the rheophyte, sciophyte and heliophyte taxa. All samples from the southern Ryukyus (Japan) and Taiwan clustered into a monophyletic group, which corroborates the land configuration theory involving Quaternary land-bridge formation and subsequent fragmentation into islands. The incongruence between the two DNA datasets may imply traces of introgressive hybridization and/or incomplete lineage sorting. The occurrence of rheophyte, sciophyte and heliophyte plants within Farfugium may be attributable to their isolation on islands and subsequent adaptation to the riparian, coastal crag and forest understorey environments, following their migration over the Quaternary land-bridge formation along their distribution range. Nearly identical DNA sequences coupled with highly divergent morphologies amongst these taxa suggest that diversification was rapid.
    Annals of Botany 09/2010; 106(3):467-82. · 3.45 Impact Factor
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    ABSTRACT: Tricyrtis ishiiana is a relic endemic plant taxon of the Convallariaceae that inhabits two nearby gorges in Kanagawa Prefecture, Japan. The distribution range and number of populations are thought to have been reduced to the present refugial populations during the Quaternary climatic oscillations. Because of its showy flowers, this plant has faced illegal removal from its natural habitats for horticultural use and has been designated a critically endangered species (class IA). In this study, we analyzed the genetic structure of the relict populations of T. ishiiana in order to contribute to the conservation strategies of the prefectural government. Our analyses of nine nuclear microsatellite loci detected high genetic diversity (H E=0.704 and H O=0.541) for the two populations. The two populations were slightly differentiated (R ST=0.032), accompanied by faint substructure across the populations (K=3). In addition, each population exhibited spatial genetic structuring. The relatively low inbreeding coefficient for both populations together (F IS=0.233) and each population separately (F IS=0.217–0.246) may be attributable to crossing among descendants within a population along with occasional gene flow between the populations. These results suggested that the extant populations have not experienced a severe bottleneck. The two extant populations were genetically differentiated at a very low level, accompanied by occasional pollen flow via pollinators and/or seed dispersal by gravity in the mountainous environment. Occasional gene exchange between the populations has allowed T. ishiiana to harbor high genetic diversity despite being a relic plant confined to two small refugial populations. KeywordsConvallariaceae–Gene flow–Microsatellite–Refugia– Tricyrtis ishiiana
    Conservation Genetics 04/2010; 12(2):491-501. · 1.85 Impact Factor
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    ABSTRACT: Eight microsatellite loci of Calystegia soldanella useful for comparisons of the genetic structure of isolated populations in the ancient Lake Biwa and coastal populations in Japan were isolated and characterised. The number of alleles ranged from 2 to 5. The expected (H E) and observed (H O) heterozygosities were 0.097-0.583 and 0.000-0.380, respectively, from 100 individuals from Lake Biwa and coastal populations. Seven of the eight loci exhibited significantly fewer heterozygotes than expected based on the Hardy-Weinberg equilibrium (P < 0.05). These primers amplifying microsatellites in C. soldanella may provide a population genetics tool useful in the establishment of a conservation strategy.
    Conservation Genetics 01/2009; · 1.85 Impact Factor
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    ABSTRACT: Eight microsatellite loci for the perennial herb Farfugium japonicum, including the rheophytic variety luchuense endemic to riparian areas of the Ryukyu Islands, Japan, were isolated and characterised. The number of alleles ranged from 5 to 14. The expected (H E) and observed (H O) heterozygosities were 0.344–0.885 and 0.121–0.754, respectively, from 69 individuals in one population. Six loci exhibited significantly fewer heterozygotes than expected under Hardy–Weinberg equilibrium (P<0.05). The primers amplifying microsatellite sequences in F. japonicum may provide a population genetics tool useful in the establishment of a conservation strategy.
    Conservation Genetics 01/2009; 10(4):1093-1095. · 1.85 Impact Factor
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    ABSTRACT: Nine microsatellite loci were isolated and characterized for the endangered and tertiary relict perennial herb, Tricyrtis ishiiana. The number of alleles ranged from 2 to 33. The expected (H E) and observed (H O) heterozygosities were 0.207–0.944 and 0.215–0.813, respectively, from 96 individuals on one population. Five loci exhibited significantly fewer heterozygotes than expected under Hardy–Weinberg equilibrium (P<0.05). These primers amplifying microsatellites in this species may provide a useful tool for population genetics to establish conservation strategy.
    Conservation Genetics 01/2009; 10(3):705-707. · 1.85 Impact Factor
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    ABSTRACT: We investigated the anatomical and physiological characteristics of stenophyllous leaves of a rheophyte, Farfugium japonicum var. luchuence, and sun and shade leaves of a non-rheophyte, F. japonicum, comparing three different populations from coastal, forest floor, and riparian habitats. Light adaptation resulted in smaller leaves, and riparian adaptation resulted in narrower leaves (stenophylly). The light-saturated rate of photosynthesis (P (max)) per unit leaf area corresponded to the light availability of the habitat. Irrespective of leaf size, the P (max) per unit leaf mass was similar for sun and shade leaves. However, the P (max) per mass of stenophyllous leaves was significantly lower than that of sun and shade leaves. This was because the number and size of mesophyll cells were greater than that required for intercellular CO(2) diffusion, which resulted in a larger leaf mass per unit leaf area. Higher cell density increases contact between mesophyll cells and enhances leaf toughness. Stenophyllous leaves of the rheophyte are frequently exposed to a strong water flow when the water level rises, suggesting a mechanical constraint caused by physical stress.
    Journal of Plant Research 12/2006; 119(6):645-56. · 2.51 Impact Factor

Publication Stats

32 Citations
20.00 Total Impact Points


  • 2009–2011
    • Research Institute for Humanity and Nature
      Kioto, Kyōto, Japan
  • 2006–2010
    • Kyoto University
      • • Graduate School of Human and Environmental Studies
      • • Division of Natural Sciences
      Kioto, Kyōto, Japan