Papers by Yoshihisa Suyama
The taxonomy of Quercus langbianensis and its relatives in Vietnam and Cambodia have been revised... more The taxonomy of Quercus langbianensis and its relatives in Vietnam and Cambodia have been revised based on evidence obtained from field observations, morphological comparison of herbarium specimens and molecular analyses using both classic and next generation DNA markers. Based on Bayesian inference using rbcL, matK and ITS regions and Neighbour-joining tree using genome-wide sequences amplified with multiplexed inter-simple sequence repeat (ISSR) primers (MIG-seq), the authors recognised ten species in the complex in Vietnam and Cambodia, three of which are newly described in this paper: Q. baolamensis sp. nov., Q. bidoupensis sp. nov. and Q. honbaensis sp. nov. These new species are all phenotypically similar to Q. langbianensis s. str. in having lanceolate to oblanceolate leaf shape, upper 4-5/6-serrated leaf margin, acute or acuminate leaf apex and bracts of cupule arranged in 5-9 rings but distinguished both morphologically and phylogenetically. In molecular phylogenetic reconstructions, Q. bidoupensis is not close to any other species. In the Bayesian tree, Q. honbaensis is sister to both Q. blaoensis and Q. camusiae
trnL sequences and taxonomic assignments NG
The taxonomy of Quercus langbianensis and its relatives in Vietnam and Cambodia have been revised... more The taxonomy of Quercus langbianensis and its relatives in Vietnam and Cambodia have been revised based on evidence obtained from field observations, morphological comparison of herbarium specimens and molecular analyses using both classic and next generation DNA markers. Based on Bayesian inference using rbcL, matK and ITS regions and Neighbour-joining tree using genome-wide sequences amplified with multiplexed inter-simple sequence repeat (ISSR) primers (MIG-seq), the authors recognised ten species in the complex in Vietnam and Cambodia, three of which are newly described in this paper: Q. baolamensis sp. nov., Q. bidoupensis sp. nov. and Q. honbaensis sp. nov. These new species are all phenotypically similar to Q. langbianensis s. str. in having lanceolate to oblanceolate leaf shape, upper 4-5/6-serrated leaf margin, acute or acuminate leaf apex and bracts of cupule arranged in 5-9 rings but distinguished both morphologically and phylogenetically. In molecular phylogenetic reconstructions, Q. bidoupensis is not close to any other species. In the Bayesian tree, Q. honbaensis is sister to both Q. blaoensis and Q. camusiae
Myrmecological News, 2020
Multiplexed inter-simple sequence repeat genotyping by sequencing – MIG-seq – is an effective PCR... more Multiplexed inter-simple sequence repeat genotyping by sequencing – MIG-seq – is an effective PCR-based method for genome-wide SNP detection using the Next-Generation Sequencing platform, and it provides a potential solution to a central problem in museomics – the difficulties of obtaining useful sequence data from aged specimens with often degraded and / or low yields of DNA. We demonstrate and validate the cost effectiveness and utility of the MIG-seq workflow in obtaining useful and robust sequence data from aged museum specimens. We applied the MIG-seq approach to 55 aged (10 23 years old) millimeter-sized dry-mounted specimens of the hyper-diverse ant genus Pheidole. A total of 50,782,736 reads were generated from the 55 samples (259,902 3,693,375 reads per sample). The reads corresponded to 36,862 SNPs from 4,849 polymorphic loci; the SNP dataset was then used to construct a Bayesian phylogenetic tree. The topology of the phylogenetic tree was highly compatible with existing k...
Thai Forest Bulletin (Botany), 2020
At present, the genus contains 294 species and is distributed in the Old World tropics and subtro... more At present, the genus contains 294 species and is distributed in the Old World tropics and subtropics, and often cultivated elsewhere (Paton et al., 2019). The genus was first described by Loureiro in 1790 (de Loureiro, 1790). Coleus was either treated as distinct from Plectranthus L'Hér. or merged into Plectranthus by various authors (Paton et al., 2019). Suddee et al. (2004) treated Coleus under Plectranthus in the tribe Ocimeae, subtribe Plectranthinae in a revision of tribe Ocimeae in continental SouthEast Asia (Myanmar, Thailand, Laos, Cambodia and Vietnam); 14 species were recognised under Plectranthus. In a recent study, Paton et al. (2019) treated Coleus as distinct from Plectranthus and a key to the genera of the subtribe Plectranthinae was provided. Several genera were merged into Coleus including
Japanese Journal of Water Treatment Biology, 2016
In this study, soil macrofauna in the beds of a full-scale vertical flow constructed wetland were... more In this study, soil macrofauna in the beds of a full-scale vertical flow constructed wetland were investigated to clarify the effects of vegetation on diversity of soil macrofauna. The investigation was conducted in the vegetative growth stage when plant had a great growth vigor. Because deposits were retained on the surface, macrofauna were investigated only the beds of the first stage. The macrofaunal abundance in vegetated beds was higher than in unvegetated beds, suggesting that vegetation increased macrofaunal diversity. This finding shows that the diversity of vegetation-dependent species generates a different level of diversity in the vegetative growth stage. Though the constructed wetland received rich deposits, i.e. food resources, vegetation affected macrofaunal diversity. Earthworms were most abundant in the 0-10 cm layer of vegetated beds, while their abundance peaked in the 10-20 cm layer of unvegetated beds. These findings may show that importantly, vegetation softens rapid changes in the environment (ex. soil temperature), rather than providing food resources for macrofaunal diversity. It was revealed that plant played an important role on macrofaunal diversity even in the constructed wetland where organic matters were constantly provided from wastewater.
PhytoKeys, 2020
A new species of Lauraceae,Cryptocarya kaengkrachanensisM.Z.Zhang, Yahara & Tagane, from Kaeng Kr... more A new species of Lauraceae,Cryptocarya kaengkrachanensisM.Z.Zhang, Yahara & Tagane, from Kaeng Krachan National Park, Phetchaburi Province, southwestern Thailand, is described and illustrated. This species is morphologically most similar toC. amygdalinain that its leaves are pinnately veined, leathery, and apparently glabrous (but microscopically hairy) abaxially, twigs are yellowish brown hairy, and fruits are 1.36 to 1.85 times longer than width. However,C. kaengkrachanensisis distinguished fromC. amygdalinain having the leaves of ovate and elliptic (vs. oblong-lanceolate) with leaf aspect ratio (length:width) from 1.38 to 2.28 (vs. 2.46–3.43), and ovoid fruits (vs. ellipsoid) with stalk distinctly swollen (vs. not or only slightly swollen). In addition, phylogenetic trees constructed based on internal transcribed spacer sequences (ITS) and genome-wide SNPs using MIG-seq showed thatC. kaengkrachanensisis not sister toC. amygdalinaand is distinct from all the otherCryptocaryaspecie...
Ecology and Evolution, 2018
This is an open access article under the terms of the Creative Commons Attribution License, which... more This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Scientific Reports, 2018
Maintaining the accretion potential and three dimensional structure of coral reefs is a priority ... more Maintaining the accretion potential and three dimensional structure of coral reefs is a priority but reefbuilding scleractinian corals are highly threatened and retreating. Hence future reefs are predicted to be dominated by non-constructional taxa. Since the Late Triassic however, other non-scleractinian anthozoans such as Heliopora have contributed to tropical and subtropical reef-building. Heliopora is an ancient and highly conserved reef building octocoral genus within the monospecific Family Helioporidae, represented by a single extant species-H. coerulea, Pallas, 1766. Here we show integrated morphological, genomic and reproductive evidence to substantiate the existence of a second species within the genus Heliopora. Importantly, some individuals of the new species herein described as Heliopora hiberniana sp. nov. feature a white skeleton indicating that the most diagnostic and conserved Heliopora character (the blue skeleton) can be displaced. The new species is currently known only from offshore areas in north Western Australia, which is a part of the world where coral bleaching events have severely impacted the scleractinian community over the last two decades. Field observations indicate individuals of both H. coerulea and H. hiberniana sp. nov. were intact after the 2016 Scott Reef thermal stress event, and we discuss the possibility that bleaching resistant non-scleractinian reef builders such as Heliopora could provide new ecological opportunities for the reconfiguration of future reefs by filling empty niches and functional roles left open by the regression of scleractinian corals. Scleractinian corals are the principal engineers of modern-day shallow water tropical coral reefs. The scleractinians originated approximately 450 mya from a solitary and azooxanthellate ancestor 1. But it was not until the middle Triassic (ca. 240 Ma) in tandem with dinoflagellate diversification events 2 that the modern shallow-water Scleractinia underwent their first major radiations. Since that time, scleractinian corals have endured massive climate changes, but the modern combination of contemporary climate and anthropogenic impacts has surpassed coral tolerance limits, and at many locations, scleractinians are retreating 3. The vulnerability of scleractinians threatens to jeopardize the accretion potential and productivity of coral reef ecosystems as a whole and as a result, coral reefs are predicted to transform in unprecedented ways. The most anticipated reconfiguration of future reefs involves transitions from hard coral to non-calcifying macroalgal communities or non-reef-building soft coral communities 4-6. Progressive shifts to altered reef states dominated by non-constructional taxa would jeopardize the biological functions and ecosystem services that coral reefs provide. Hence, maintaining the accretion potential and three dimensional structure of coral reefs is a priority 7. In this regard, it is important to note that there is another, often overlooked genus of cnidarian that also contributes to reef-building-Heliopora de Blainville, 1830. Heliopora coerulea is one of the two extant members of the Anthozoan Order Helioporacea 8 and the single extant member of the Family Helioporidae (Moseley, 1876). This species of octocoral, commonly called the 'blue coral' due to
Conservation biology : the journal of the Society for Conservation Biology, Jan 23, 2018
Mangroves comprise of tropical and sub-tropical intertidal plant communities. Theyprovide essenti... more Mangroves comprise of tropical and sub-tropical intertidal plant communities. Theyprovide essential ecosystem services (e.g. carbon sequestration and coastal protection) that are severely undermined by widespread habitat degradation and destruction, and were predicted to be lost or impaired by the end of this century (Duke et al. 2007). This article is protected by copyright. All rights reserved.
PhytoKeys, 2018
The taxonomy of and its relatives in Vietnam and Cambodia have been revised based on evidence obt... more The taxonomy of and its relatives in Vietnam and Cambodia have been revised based on evidence obtained from field observations, morphological comparison of herbarium specimens and molecular analyses using both classic and next generation DNA markers. Based on Bayesian inference using L, K and ITS regions and Neighbour-joining tree using genome-wide sequences amplified with multiplexed inter-simple sequence repeat (ISSR) primers (MIG-seq), the authors recognised ten species in the complex in Vietnam and Cambodia, three of which are newly described in this paper: , and . These new species are all phenotypically similar to in having lanceolate to oblanceolate leaf shape, upper 4-5/6-serrated leaf margin, acute or acuminate leaf apex and bracts of cupule arranged in 5-9 rings but distinguished both morphologically and phylogenetically. In molecular phylogenetic reconstructions, is not close to any other species. In the Bayesian tree, is sister to both and that are found in the same loca...
PhytoKeys, 2018
A new species, Quercus xuanlienensis Binh, Ngoc & Bon, is described from Xuan Lien Nature Reserve... more A new species, Quercus xuanlienensis Binh, Ngoc & Bon, is described from Xuan Lien Nature Reserve, Vietnam. The new species is morphologically similar to Q. edithiae Skan, in having 8-11 pairs of secondary veins, bowl-shaped cupules and ellipsoid to cylindrical-ellipsoid and basally convex nuts. It differs in having serrulate leaf margins only at apical 1/5-1/7, almost entire margins of bracts on cupule and much longer nuts. The species is also similar to Q. fleuryi Hickel & A. Camus in having leaves glabrous on both surfaces with only an apically serrulate margin but differs in having shorter petioles, cupules enclosing 1/5 of the nut and much longer nuts. In addition, Q. disciformis Chun & Tsiang. and Q. bella Chun & Tsiang., previously known from China, are newly recorded from Ba Vi National Park, Vietnam.
Tohoku Journal of Agricultural Research, 2009
Microbes and Environments, 2012
The distribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in cattle, swine, and chic... more The distribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in cattle, swine, and chicken manure compost was analyzed. PCR-denaturing gradient gel electrophoresis (DGGE) showed that a Candidatus Nitrososphaera gargensis-like sequence dominated in cattle manure compost, while few AOA were detected in other composts. In the case of AOB, Nitrosomonas-like sequences were detected with higher diversity in cattle and swine manure composts. The relative abundance of ammonia oxidizers by real-time PCR revealed that more AOB was present in compost except in one swine manure compost. Our results indicated that AOB rather than AOA are widely distributed in animal manure compost.
Japanese beech is widely distributed throughout Japan, and investigating adaptation of Japanese b... more Japanese beech is widely distributed throughout Japan, and investigating adaptation of Japanese beech to the variety of atmospheric and soil water conditions is important to understand gas exchange of forest ecosystems under climate exchange. Therefore, the purpose of this study is to clarify geographical variation in control transpiration of Japanese beech trees under various climate conditions. Toward this goal, canopy stomatal conductance at tree level and hydraulic conductivity of the trees were evaluated in 3 beech stands. Stomata of beech trees with high hydraulic conductivity have high gas exchange ability, and its stomata respond to D sensitively to avoid loss more water and cavitations at high D. On the other hand, beech trees in SH have smaller hydraulic conductivity with low sensitivity to D to keep stomata opened under high D condition. The relationship between transpiration characteristics and morphological differences among sites will be discussed.
Molecular ecology, 2008
The reproductive isolation barriers and the mating patterns among Pinus pumila, P. parviflora var... more The reproductive isolation barriers and the mating patterns among Pinus pumila, P. parviflora var. pentaphylla and their hybrids were examined by flowering phenology and genetic assays of three life stages: airborne-pollen grains, adults and seeds, in a hybrid zone on Mount Apoi, Hokkaido, Japan. Chloroplast DNA composition of the airborne-pollen was determined by single-pollen polymerase chain reaction. Mating patterns were analysed by estimating the molecular hybrid index of the seed parent, their seed embryos and pollen parents. The observation of flowering phenology showed that the flowering of P. pumila precedes that of P. parviflora var. pentaphylla by about 6 to 10 days within the same altitudinal ranges. Although this prezygotic isolation barrier is effective, the genetic assay of airborne-pollen showed that the two pine species, particularly P. pumila, still have chances to form F(1) hybrid seeds. Both parental species showed a strong assortative mating pattern; F(1) seeds ...
Limnology, 2012
This study describes a method of DNA extraction and amplification for ephippial cases of Daphnia ... more This study describes a method of DNA extraction and amplification for ephippial cases of Daphnia resting eggs from lake sediment. Recent studies have reconstructed succession records of Daphnia species by genetically analyzing Daphnia resting eggs stored in lake sediments and revealed changes in dominant Daphnia species that correspond well with environmental changes. However, this approach is not applicable to lakes where most of the resting eggs in the sediment have already hatched out. We modified conventional methods for DNA extraction and amplification to enable genetic analyses of the ephippial case that envelops and protects the resting eggs, and we compared the performance of the modified method to the conventional one. We confirmed that we could efficiently analyze the sequences of the ephippial cases collected in a sediment core using our modified method. It enables us to reconstruct changes in genetic structure of Daphnia populations regardless of hatching rates of the resting eggs.
The Journal of General and Applied Microbiology, 2009
Bacterial populations in epilithic biofi lms collected from two distinct oligotrophic rivers of J... more Bacterial populations in epilithic biofi lms collected from two distinct oligotrophic rivers of Japan were studied using denaturing gradient gel electrophoresis (DGGE). PCR-DGGE of the 16S rRNA gene and subsequent sequencing analysis suggested that in freshwater biofi lms, members of the Cytophaga-Flavobacterium-Bacteroides (CFB) group were the most dominant, followed by those of α-, β-, γ-, and δ-Proteobacteria; Leptospiraceae; and unidentifi ed bacteria. Members of the CFB group, α-Proteobacteria, and cyanobacteria/plastid DNA were also detected from the biofi lms collected from the estuary site, but the species in these samples differed from those detected in biofi lms in the freshwater areas of the rivers. A comparison between the determined sequences revealed that similar bacterial species existed in biofi lms at different sites of a river, and identical species existed in biofi lms of distinct rivers. The results suggested that bacterial species in biofi lms found in the estuary were different from those found in the freshwater areas of the rivers; however, the common bacterial species were distributed in biofi lms collected from not only different sites along the same river but also sites in distinct oligotrophic rivers.
Population Ecology, 2007
In this paper we first mathematically formulate spatial genetic models that rely on dispersal ker... more In this paper we first mathematically formulate spatial genetic models that rely on dispersal kernels, using the genetic inhomogeneous Poisson process. On the basis of mapped and genotyped data pertaining to adult and juvenile trees we are able to estimate three fundamental variables of population dynamics: individual female reproductive success, seed dispersal, and pollen flow. The model was applied to
Molecular Ecology Resources, 2011
In Japan, the three main crane species are the endangered red-crowned crane (Grus japonensis) inh... more In Japan, the three main crane species are the endangered red-crowned crane (Grus japonensis) inhabiting Hokkaido, the northernmost island of Japan; the vulnerable hooded crane (Grus monacha); and the vulnerable white-naped crane (Grus vipio). Both the hooded and white-naped cranes migrate in winter to Izumi in Kyushu, the southern island of Japan. In this study, we investigated the cranes and their coccidian parasites, through a targeted molecular approach using faecal DNA to develop a noninvasive method for infectious disease research. To determine the origin of noninvasively collected faecal samples, host species were identified by sequencing a region of approximately 470 bp of the mitochondrial 16S ribosomal RNA gene in the faecal DNA. Furthermore, to avoid sample redundancy, individual determination was performed by fragment analysis using microsatellite and sex-linked markers. For microsatellite genotyping, previously reported markers and markers isolated in this study were examined, and seven loci for red-crowned cranes, eight for hooded cranes and six for white-naped cranes displayed polymorphisms. A low error rate was demonstrated by comparing microsatellite data generated from faecal DNA samples with that generated from feather DNA samples, indicating a high reliability. Polymerase chain reaction-based capillary electrophoresis (PCR-CE), employing genetic markers in the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA, was employed to detect crane coccidia. The sensitivity of detection of PCR-CE using faecal DNA was inferior to that with traditional microscopy; however, our results suggest that PCR-CE can depict crane coccidia diversity with higher resolution and it is a useful tool to characterize community composition of coccidia in detail.
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Papers by Yoshihisa Suyama