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  1. Article ; Online: Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: genetic, phenotypic, and environmental insights.

    Setsuko, Suzuki / Sugai, Kyoko / Tamaki, Ichiro / Hayama, Kayo / Kato, Hidetoshi

    Heredity

    2024  

    Abstract: Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial ... ...

    Abstract Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.
    Language English
    Publishing date 2024-05-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2423-5
    ISSN 1365-2540 ; 0018-067X
    ISSN (online) 1365-2540
    ISSN 0018-067X
    DOI 10.1038/s41437-024-00684-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Diversity profiling of soil bacterial and fungal communities in the Ogasawara (Bonin) Islands, Japan.

    Shigyo, Nobuhiko / Shichi, Koji / Sugai, Kyoko / Setsuko, Suzuki

    Microbiology resource announcements

    2023  Volume 12, Issue 10, Page(s) e0064423

    Abstract: Island biogeography research provides insight into microbial diversity patterns; however, little is known about the diversity and distribution of soil microbial communities on remote and poorly accessible islands. Here, we present amplicon sequencing ... ...

    Abstract Island biogeography research provides insight into microbial diversity patterns; however, little is known about the diversity and distribution of soil microbial communities on remote and poorly accessible islands. Here, we present amplicon sequencing data from bacterial and fungal communities in the surface soils of the Ogasawara (Bonin) Islands, Japan.
    Language English
    Publishing date 2023-09-21
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00644-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Environmental and genetic effects on phenotypic differences between Elaeocarpus photiniifolia (Elaeocarpaceae) ecotypes in dry and mesic habitats on a Japanese oceanic island

    Sugai, Kyoko / Setsuko, Suzuki / Nagamitsu, Teruyoshi / Murakami, Noriaki / Kato, Hidetoshi / Yoshimaru, Hiroshi

    Plant Species Biology. 2023 Mar., v. 38, no. 2 p.67-78

    2023  

    Abstract: Ecological speciation is a consequence of phenotypic and genetic differentiation, which is driven by divergent selection and reproductive isolation between different environments. In Elaeocarpus photiniifolia, a plant species endemic to the Bonin Islands, ...

    Abstract Ecological speciation is a consequence of phenotypic and genetic differentiation, which is driven by divergent selection and reproductive isolation between different environments. In Elaeocarpus photiniifolia, a plant species endemic to the Bonin Islands, genetic differentiation between a shrub ecotype in dry habitats and a tree ecotype in mesic habitats occurs in the Chichijima Island Group, while gene flow between the ecotypes and migration between the habitats are feasible. To clarify environmental and genetic effects on traits different between the ecotypes, we examined the soil moisture content, nuclear microsatellite genotypes, plant height, and flowering phenology in dry and mesic habitats in two areas on Chichijima Island. The soil moisture content decreased from June to July in both areas and tended to be lower in dry habitats than in mesic habitats in July. Genetic structure indicated not only genetic differentiation between the ecotypes but also admixture between them and migration between the habitats. Both environmental and genetic effects were detected in plant height and flowering phenology: lower height and earlier flowering of the shrub ecotype in the dry habitats, indicating phenotypic plasticity in response to drought, and genetic variation between ecotypes in both traits. These findings indicate that phenotypic plasticity in response to different environments results in different flowering phenology, which facilitates reproductive isolation and genetic differentiation, leading to genetic variation in adaptive traits associated with the environments.
    Keywords Elaeocarpus ; drought ; ecotypes ; gene flow ; genetic structure ; genetic variation ; microsatellite repeats ; phenology ; phenotype ; phenotypic plasticity ; plant height ; reproductive isolation ; shrubs ; soil water content ; trees
    Language English
    Dates of publication 2023-03
    Size p. 67-78.
    Publishing place John Wiley & Sons Australia, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 2020484-X
    ISSN 1442-1984 ; 0913-557X
    ISSN (online) 1442-1984
    ISSN 0913-557X
    DOI 10.1111/1442-1984.12397
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  4. Article ; Online: Contrasting genetic diversity between Planchonella obovata sensu lato (Sapotaceae) on old continental and young oceanic island populations in Japan.

    Setsuko, Suzuki / Sugai, Kyoko / Tamaki, Ichiro / Takayama, Koji / Kato, Hidetoshi

    PloS one

    2022  Volume 17, Issue 9, Page(s) e0273871

    Abstract: Genetic diversity of plant populations on islands is likely to be influenced by characteristics such as island origin (oceanic or continental) and their age, size, and distance to continental landmasses. In Japan, Planchonella obovata sensu lato which is ...

    Abstract Genetic diversity of plant populations on islands is likely to be influenced by characteristics such as island origin (oceanic or continental) and their age, size, and distance to continental landmasses. In Japan, Planchonella obovata sensu lato which is found on both continental and oceanic islands of varying age, size, and distance to East Asian continental areas-is an ideal system in which to investigate the factors influencing genetic diversity of island plant species. In this study, we examined the genetic diversity of P. obovata s.l. populations, in the context of the species population genetic structure, demography, and between island migration, from 668 individuals, 28 populations and 14 islands including both continental (the Yaeyama Islands) and oceanic islands (the Daito, Bonin, and Volcano Islands) using 11 microsatellite markers. The Yaeyama and Volcano Islands respectively had the highest and lowest genetic diversity, and island origin and age significantly affected genetic diversity. Clustering analysis revealed that populations were grouped into Bonin, Volcano, and Yaeyama + Daito groups. However, Bonin and Volcano groups were distinct despite the relatively short geographical distance between them. Approximate Bayesian Computation analysis suggested that the population size was stable in Bonin and Yaeyama + Daito groups, whereas population reduction occurred in Volcano group, and migration between groups were very limited. Younger oceanic islands showed lower genetic diversity, probably due to limited gene flow and a lack of time to accumulate unique alleles. Genetic structure was generally consistent with the geographic pattern of the islands, but in Volcano, a limited number of founders and limited gene flow among islands are likely to have caused the large genetic divergence observed.
    MeSH term(s) Bayes Theorem ; Genetic Variation ; Genetics, Population ; Humans ; Japan ; Microsatellite Repeats/genetics ; Sapotaceae
    Language English
    Publishing date 2022-09-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0273871
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago

    Kikuchi, Satoshi / Mimura, Makiko / Naruhashi, Naohiro / Setsuko, Suzuki / Suzuki, Wajiro

    Plant systematics and evolution. 2022 June, v. 308, no. 3

    2022  

    Abstract: This study aimed to reveal the evolutionary timescale and processes underlying the diversity of Rubus in the Japanese Archipelago. We conducted molecular phylogenetic analyses of most native species (35 species), along with previously published data from ...

    Abstract This study aimed to reveal the evolutionary timescale and processes underlying the diversity of Rubus in the Japanese Archipelago. We conducted molecular phylogenetic analyses of most native species (35 species), along with previously published data from 116 foreign species, based on nuclear ribosomal internal transcribed spacer (ITS) and chloroplast DNA sequences. Most of the northern species of Japan, that is, Rubus chamaemorus, R. pedatus, R. vernus, R. pseudojaponicus, and R. ikenoensis, were found to belong to anciently diverged lineages; in particular, R. ikenoensis formed a unique lineage distinct from other species. The other species diverged into two evolutionary groups. One included subg. Malachobatus, Chamaebatus, and sects. Pungentes, Idaeanthi, and Parvifolii (subg. Idaeobatus), which was further divided into two clades in the chloroplast phylogenies. Although the phylogenetic structures within this group were unresolved, R. sieboldii has been proven to be recently derived. The second group represented a well-supported clade, comprising sects. Microphylli, Corchorifolii, Peltati, and Rosifolii (subg. Idaeobatus) and suggested early Miocene diversification of this Asian lineage associated with character specialization in vegetative reproduction and leaf shape. This clade was further resolved into lower clades primarily representing the sectional classifications, although the placement of the earliest diverged species, R. sumatranus, R. peltatus, R. corchorifolius, and R. chingii, was incongruent among gene trees. At the lower taxonomic levels, R. illecebrosus, R. grayanus, and the thornless species of sect. Microphylli showed earlier divergence.
    Keywords Japan ; Miocene epoch ; Rubus chamaemorus ; asexual reproduction ; chloroplast DNA ; chloroplasts ; genes ; geographical distribution ; indigenous species ; internal transcribed spacers ; leaves ; phylogeny ; plant taxonomy
    Language English
    Dates of publication 2022-06
    Size p. 20.
    Publishing place Springer Vienna
    Document type Article
    ZDB-ID 1463027-8
    ISSN 1615-6110 ; 0378-2697
    ISSN (online) 1615-6110
    ISSN 0378-2697
    DOI 10.1007/s00606-022-01810-6
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  6. Article ; Online: Risk factors associated with asymptomatic hypoxemia among COVID-19 patients

    Yutaro Akiyama / Shinichiro Morioka / Yusuke Asai / Lubna Sato / Setsuko Suzuki / Sho Saito / Nobuaki Matsunaga / Kayoko Hayakawa / Norio Ohmagari

    Journal of Infection and Public Health, Vol 15, Iss 3, Pp 312-

    a retrospective study using the nationwide Japanese registry, COVIREGI-JP

    2022  Volume 314

    Abstract: Deaths of home-care patients with coronavirus disease (COVID-19) have become a social problem. One of their causes is hypoxemia without dyspnea which delays seeking medical attention.This was a retrospective study including patients registered in the ... ...

    Abstract Deaths of home-care patients with coronavirus disease (COVID-19) have become a social problem. One of their causes is hypoxemia without dyspnea which delays seeking medical attention.This was a retrospective study including patients registered in the COVID-19 Registry Japan, in which hospitalized patients with COVID-19 in 227 participating healthcare facilities were enrolled. The enrolled patients were divided into two groups: non-dyspneic patients with a peripheral capillary oxygen saturation (SpO2) ≤ 93% on admission (the hypoxemia without dyspnea group) and non-dyspneic patients with an SpO2> 93% (the control group). We conducted a multivariate logistic regression analysis to identify the factors associated with hypoxemia without dyspnea.21544 patients were enrolled, 1035 (4.8%) patients were in the hypoxemia without dyspnea group, and 20509 (95.2%) patients were in the control group. The median respiratory rate (RR) of the hypoxemia without dyspnea group was higher than that of the control group (31/min vs. 18/min, p < 0.001). Age> 65, male, body mass index> 25, smoking, chronic obstructive pulmonary disease, other chronic lung disease, and diabetes mellitus were the independent factors associated with hypoxemia without dyspnea. Patients with those background should be closely monitored. RR is an important indicator of hypoxemia, even in the absence of dyspnea.
    Keywords COVID-19 ; Silent hypoxia ; Risk factors ; Respiratory rate ; Registry ; Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270
    Subject code 610
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: DNA meta-barcoding revealed that sika deer foraging strategies vary with season in a forest with degraded understory vegetation

    Nakahama, Naoyuki / Furuta, Tomohiro / Ando, Haruko / Setsuko, Suzuki / Takayanagi, Atsushi / Isagi, Yuji

    Forest ecology and management. 2021 Mar. 15, v. 484

    2021  

    Abstract: Overbrowsing by the explosively increasing deer has a huge impact on forest vegetation in the temperate zone. Although it was expected that, over the years, the decline of forest floor vegetation would lead to a decrease in deer population, such a ... ...

    Abstract Overbrowsing by the explosively increasing deer has a huge impact on forest vegetation in the temperate zone. Although it was expected that, over the years, the decline of forest floor vegetation would lead to a decrease in deer population, such a decline has not been observed. A dietary analysis of deer is necessary to establish the survival mechanisms of deer populations in forests with degraded understory vegetation. This study explores the foraging strategy of sika deer, Cervus nippon, in Ashiu Research Forest, Kyoto, Japan, where the understory vegetation is severely degraded. A total of 177 fecal samples of sika deer were collected during each season and their food resources identified using DNA meta-barcoding technology and local plant DNA database. The results of the DNA meta-barcoding revealed that sika deer depended on non-preferred plants and preferred plants from early winter to spring. From summer to autumn, sika deer mainly feed on preferred plants. In all seasons, the percent cover of preferred plants for sika deer is also scarce in the forest floor. Biomass of preferred plants, such as litterfalls, play a significant role in maintaining the population density of sika deer when the understory vegetation is degraded in the forest habitat. Therefore, the degradation of the understory vegetation might not necessarily lead to a decrease in the population density of sika deer.
    Keywords Cervus nippon ; DNA ; Japan ; administrative management ; autumn ; biomass ; databases ; deer ; forest habitats ; forest litter ; forests ; population density ; summer ; temperate zones ; understory ; winter
    Language English
    Dates of publication 2021-0315
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 751138-3
    ISSN 0378-1127
    ISSN 0378-1127
    DOI 10.1016/j.foreco.2020.118637
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  8. Article ; Online: A DNA barcode reference library for the native woody seed plants of Japan

    Setsuko, Suzuki / Yoshimura, Kensuke / Ueno, Saneyoshi / Worth, James Raymond Peter / Ujino‐Ihara, Tokuko / Katsuki, Toshio / Noshiro, Shuichi / Fujii, Tomoyuki / Arai, Takahisa / Yoshimaru, Hiroshi

    Molecular Ecology Resources. 2023 May, v. 23, no. 4 p.855-871

    2023  

    Abstract: DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode‐based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed ... ...

    Abstract DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode‐based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, and comprising 77.3% of the genera and 72.2% of the species of native woody seed plants in Japan. A total of 6216 plant specimens were collected from 223 sites across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This reference library utilized three chloroplast DNA regions (rbcL, trnH‐psbA and matK) and consists of 14,403 barcode sequences. Individual regions varied in their identification rates, with species‐level and genus‐level rates for rbcL, trnH‐psbA and matK based on blast being 57.4%/96.2%, 78.5%/99.1% and 67.8%/98.1%, respectively. Identification rates were higher using region combinations, with total species‐level rates for two region combinations (rbcL & trnH‐psbA, rbcL & matK and trnH‐psbA & matK) ranging between 90.6% and 95.8%, and for all three regions being equal to 98.6%. Genus‐level identification rates were even higher, ranging between 99.7% and 100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode reference library is an effective resource for investigations of native woody seed plants in Japan using DNA barcodes and provides a useful template for the development of libraries for other components of the Japanese flora.
    Keywords DNA barcoding ; Japan ; chloroplast DNA ; ecology ; flora ; genetic databases ; libraries
    Language English
    Dates of publication 2023-05
    Size p. 855-871.
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 2406816-0
    ISSN 1471-8286 ; 1755-098X
    ISSN (online) 1471-8286
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13748
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  9. Article ; Online: Novel microsatellite markers for Distylium lepidotum (Hamamelidaceae) endemic to the Ogasawara Islands.

    Sugai, Kyoko / Setsuko, Suzuki

    BMC research notes

    2016  Volume 9, Page(s) 332

    Abstract: Background: Distylium lepidotum is a small tree endemic to the Ogasawara Islands located in the northwestern Pacific Ocean. This species is a sole food for an endemic locust, Boninoxya anijimensis. Here, we developed microsatellite markers to ... ...

    Abstract Background: Distylium lepidotum is a small tree endemic to the Ogasawara Islands located in the northwestern Pacific Ocean. This species is a sole food for an endemic locust, Boninoxya anijimensis. Here, we developed microsatellite markers to investigate genetic diversity and genetic structure and to avoid a genetic disturbance after transplantation to restore the Ogasawara Islands ecosystem.
    Results: Microsatellite markers with perfect dinucleotide repeats were developed using the next-generation sequencing Illumina MiSeq Desktop Sequencer. Thirty-two primer pairs were characterized in two D. lepidotum populations on Chichijima and Hahajima Islands of the Ogasawara Islands. The number of alleles for the markers ranged from three to 23 per locus in the two populations. Expected heterozygosity per locus in each population ranged from 0.156 to 0.940 and 0.368 to 0.845, respectively.
    Conclusions: These microsatellite markers will be useful for future population genetics studies of D. lepidotum and provide a basis for conservation management of the Ogasawara Islands.
    MeSH term(s) Alleles ; Conservation of Natural Resources ; Ecosystem ; Genetic Loci ; Genetic Variation ; Genetics, Population ; Hamamelidaceae/classification ; Hamamelidaceae/genetics ; Heterozygote ; High-Throughput Nucleotide Sequencing ; Islands ; Japan ; Microsatellite Repeats ; Pacific Ocean ; Phylogeny ; Reproductive Isolation ; Trees/genetics
    Language English
    Publishing date 2016-07-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2413336-X
    ISSN 1756-0500 ; 1756-0500
    ISSN (online) 1756-0500
    ISSN 1756-0500
    DOI 10.1186/s13104-016-2137-9
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  10. Article ; Online: Genetic diversity, structure, and demography of Pandanus boninensis (Pandanaceae) with sea drifted seeds, endemic to the Ogasawara Islands of Japan: Comparison between young and old islands.

    Setsuko, Suzuki / Sugai, Kyoko / Tamaki, Ichiro / Takayama, Koji / Kato, Hidetoshi / Yoshimaru, Hiroshi

    Molecular ecology

    2020  Volume 29, Issue 6, Page(s) 1050–1068

    Abstract: Pandanus boninensis, endemic to the Ogasawara Islands, Japan, is distributed on both the older Bonin and younger Volcano Islands. In this study, we conducted population genetic analyses of P. boninensis on these islands to examine the population ... ...

    Abstract Pandanus boninensis, endemic to the Ogasawara Islands, Japan, is distributed on both the older Bonin and younger Volcano Islands. In this study, we conducted population genetic analyses of P. boninensis on these islands to examine the population diversity and structure across old and young islands, to assess potential differences in population demography with island age, and to collect any evidence of migration between old and young islands. We found that the genetic diversity of expressed sequence tag (EST)-based microsatellite (SSR) markers, the nucleotide diversity of nuclear DNA sequences, and the haplotype diversity of chloroplast DNA on young islands were lower than those on old islands. Clustering analyses of EST-SSR indicated that populations on old islands were strongly diverged from those on young islands. Approximate Bayesian computation analysis of EST-SSR suggested that population expansion occurred on old islands while population reduction occurred on young islands. We also found evidence of migration among old islands (mostly from south to north), while it appears that there have been very few migration events between old and young islands. These differences could be due to the fact that young islands tend to be geographically isolated and support smaller populations that began a shorter time ago from limited founders. The P. boninensis populations on the Volcano Islands are interesting from an evolutionary perspective as they constitute a classic example of the early stages of progressive colonization on oceanic islands with small effective population sizes and low genetic diversity.
    MeSH term(s) DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Expressed Sequence Tags ; Genetic Markers ; Genetic Variation ; Genetics, Population ; Haplotypes ; Islands ; Japan ; Microsatellite Repeats ; Pandanaceae/genetics
    Chemical Substances DNA, Chloroplast ; DNA, Plant ; Genetic Markers
    Language English
    Publishing date 2020-03-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.15383
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