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  1. Article ; Online: Contrasting genetic diversity between Planchonella obovata sensu lato (Sapotaceae) on old continental and young oceanic island populations in Japan.

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

    PLoS ONE, Vol 17, Iss 9, p e

    2022  Volume 0273871

    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.
    Keywords Medicine ; R ; Science ; Q
    Subject code 590 ; 580
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus

    Eun-Kyeong Han / Won-Bum Cho / Ichiro Tamaki / In-Su Choi / Jung-Hyun Lee

    International Journal of Molecular Sciences, Vol 22, Iss 7237, p

    2021  Volume 7237

    Abstract: The dynamic evolution of mitochondrial gene and intron content has been reported across the angiosperms. However, a reference mitochondrial genome (mitogenome) is not available in Rubiaceae. The phylogenetic utility of mitogenome data at a species level ... ...

    Abstract The dynamic evolution of mitochondrial gene and intron content has been reported across the angiosperms. However, a reference mitochondrial genome (mitogenome) is not available in Rubiaceae. The phylogenetic utility of mitogenome data at a species level is rarely assessed. Here, we assembled mitogenomes of six Damnacanthus indicus (Rubiaceae, Rubioideae) representing two varieties (var. indicus and var. microphyllus ). The gene and intron content of D. indicus was compared with mitogenomes from representative angiosperm species and mitochondrial contigs from the other Rubiaceae species. Mitogenome structural rearrangement and sequence divergence in D. indicus were analyzed in six individuals. The size of the mitogenome in D. indicus varied from 417,661 to 419,435 bp. Comparing the number of intact mitochondrial protein-coding genes in other Gentianales taxa (38), D. indicus included 32 genes representing several losses. The intron analysis revealed a shift from cis to trans splicing of a nad1 intron (nad1i728) in D. indicus and it is a shared character with the other four Rubioideae taxa. Two distinct mitogenome structures (type A and B) were identified. Two-step direct repeat-mediated recombination was proposed to explain structural changes between type A and B mitogenomes. The five individuals from two varieties in D. indicus diverged well in the whole mitogenome-level comparison with one exception. Collectively, our study elucidated the mitogenome evolution in Rubiaceae along with D. indicus and showed the reliable phylogenetic utility of the whole mitogenome data at a species-level evolution.
    Keywords coffee family ; organelle genome evolution ; heteroplasmy ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 590
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
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  3. Article ; Online: The genetic structure and demographic history of Zabelia tyaihyonii, endemic to Korean limestone karst forests, based on genome‐wide SNP markers

    In‐Su Choi / Eun‐Kyeong Han / Martin F. Wojciechowski / Tae‐Im Heo / Jong‐Soo Park / Jong‐Cheol Yang / Amarsanaa Gantsetseg / Kyeong‐Sik Cheon / Ichiro Tamaki / Jung‐Hyun Lee

    Ecology and Evolution, Vol 13, Iss 7, Pp n/a-n/a (2023)

    2023  

    Abstract: Abstract Similar to the global phenomenon, many plant species endemic to Korean limestone karst forests are at risk of extinction due to human intervention. Zabelia tyaihyonii is a familiar shrub, called “Hardy abelia” and “Fragrant abelia” growing in ... ...

    Abstract Abstract Similar to the global phenomenon, many plant species endemic to Korean limestone karst forests are at risk of extinction due to human intervention. Zabelia tyaihyonii is a familiar shrub, called “Hardy abelia” and “Fragrant abelia” growing in the karst forests of Korea, where it is one of the most threatened species. We investigated the genetic structure and demographic history of Z. tyaihyonii, which allow us to develop appropriate conservation and management strategies. The genetic structure was evaluated using a total of 187 samples from 14 populations, covering the entire distribution of Z. tyaihyonii in South Korea. We utilized 254 and 1753 SNP loci obtained via MIG‐seq (Multiplexed ISSR Genotyping by sequencing) for structure and demographic analyses, respectively. The population demographic modeling was performed with site frequency spectrum. To gain further historical insights, we also employed ENM (Ecological Niche Modeling). We found two distinct clusters (CLI and CLII) of ancient origin (ca. 490 ka). Despite CLII experiencing a more severe bottleneck, both clusters showed similar levels of genetic diversity, indicating mutual historical gene flow. Their historical distribution range seems to have changed very little. We proposed a historical distribution scenario for Z. tyaihyonii, taking into account its intrinsic factors, and emphasized a more complex response to Quaternary climate change beyond simple allopatric speciation models. These findings provide valuable insights for conservation and management strategies for Z. tyaihyonii.
    Keywords conservation ; demographic history ; limestone karst forests ; MIG‐seq ; Zabelia tyaihyonii ; Ecology ; QH540-549.5
    Subject code 333
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
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  4. Article: The origin of wild populations of Toxicodendron succedaneum on mainland Japan revealed by genetic variation in chloroplast and nuclear DNA

    Hiraoka, Yuichiro / Ichiro Tamaki / Atsushi Watanabe

    Journal of plant research. 2018 Mar., v. 131, no. 2

    2018  

    Abstract: Toxicodendron succedaneum: (L.) Kuntze is a tree cultivated for the production of sumac wax, which is extracted from the mesocarp. There are several hypotheses regarding the origin of T. succedaneum on mainland Japan. In this study, the geographical ... ...

    Abstract Toxicodendron succedaneum: (L.) Kuntze is a tree cultivated for the production of sumac wax, which is extracted from the mesocarp. There are several hypotheses regarding the origin of T. succedaneum on mainland Japan. In this study, the geographical distribution of genetic variation in 13 wild populations on Honshu, Shikoku, Kyushu, and Ryukyu Islands, Japan was investigated and compared with that of individuals from continental Asia. Seven chloroplast DNA haplotypes of T. succedaneum were observed in Japan and could be divided into three lineages based on relatedness between haplotypes. One of these lineages was also observed in continental Asia, and the others were genetically distant from the haplotypes that originated on the continent, with one considered to have originated on the Ryukyu Islands, and the other on mainland Japan. The genetic diversity of both chloroplast and nuclear DNA was lower in populations from Ryukyu Islands than in populations from mainland Japan. Bayesian clustering based on nuclear genotypes showed a clear difference between the groups from Ryukyu Islands and mainland Japan. Based on approximate Bayesian computation analysis of polymorphic data for both genomes, it was inferred that wild populations of T. succedaneum on mainland Japan consist of both lineages with natural distribution on mainland Japan and those introduced from Ryukyu Islands and continental Asia.
    Keywords Bayesian theory ; Toxicodendron succedaneum ; chloroplast DNA ; chloroplasts ; genetic variation ; geographical distribution ; haplotypes ; mesocarp ; nuclear genome ; trees ; Ryukyu Archipelago
    Language English
    Dates of publication 2018-03
    Size p. 225-238.
    Publishing place Springer Japan
    Document type Article
    ZDB-ID 2077362-6
    ISSN 1618-0860 ; 0918-9440
    ISSN (online) 1618-0860
    ISSN 0918-9440
    DOI 10.1007/s10265-017-0992-7
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  5. Article ; Online: Genetic Distinctiveness but Low Diversity Characterizes Rear-Edge Thuja Standishii (Gordon) Carr. (Cupressaceae) Populations in Southwest Japan

    James R. P. Worth / Ichiro Tamaki / Ikutaro Tsuyama / Peter A. Harrison / Kyoko Sugai / Hitoshi Sakio / Mineaki Aizawa / Satoshi Kikuchi

    Diversity, Vol 13, Iss 185, p

    2021  Volume 185

    Abstract: Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in ... ...

    Abstract Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in life-history traits, demographic histories and human impacts. Using 13 EST-microsatellites, we investigated the genetic diversity and differentiation of rear-edge populations of the Japanese endemic conifer Thuja standishii (Gordon) Carr. in southwest Japan from the core-range in northeast Japan. Range-wide genetic differentiation was moderate ( Fst = 0.087), with northeast populations weakly differentiated ( Fst = 0.047), but harboring high genetic diversity (average population-level Ar = 4.76 and Ho = 0.59). In contrast, rear-edge populations were genetically diverged ( Fst = 0.168), but contained few unique alleles with lower genetic diversity ( Ar = 3.73, Ho = 0.49). The divergence between rear-edge populations exceeding levels observed in the core-range and results from ABC analysis and species distribution modelling suggest that these populations are most likely relicts of the Last Glacial Maximum. However, despite long term persistence, low effective population size, low migration between populations and genetic drift have worked to promote the genetic differentiation of southwest Japan populations of T. standishii without the accumulation of unique alleles.
    Keywords approximate Bayesian computation ; central-marginal hypothesis ; gene-flow ; genetic drift ; Japanese endemic conifer ; leading edge ; Biology (General) ; QH301-705.5
    Subject code 580
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
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  6. Article: Contrasting diversification history between insular and continental species of three‐leaved azaleas (Rhododendron sect. Brachycalyx) in East Asia

    Yoichi, Watanabe / Ching‐I Peng / Ichiro Tamaki / Nobuhiro Tomaru / Xiao‐Feng Jin

    Journal of biogeography. 2017 May, v. 44, no. 5

    2017  

    Abstract: AIM: To reconstruct the diversification history of Rhododendron sect. Brachycalyx (Ericaceae), and to elucidate the differences in evolutionary history between 18 insular and two continental species. LOCATION: Islands of Japan, South Korea and Taiwan and ...

    Abstract AIM: To reconstruct the diversification history of Rhododendron sect. Brachycalyx (Ericaceae), and to elucidate the differences in evolutionary history between 18 insular and two continental species. LOCATION: Islands of Japan, South Korea and Taiwan and the mainland of China in East Asia. METHODS: Sequences of seven non‐coding chloroplast DNA regions (3971 bp) were obtained from 74 populations covering all 20 species in Rhododendron sect. Brachycalyx. The diversification history of the section was estimated by phylogenetic analysis and molecular dating. Genetic diversity estimates within species and species groups (continental and insular species) were calculated. Differences in patterns of genetic structure within each species group were estimated by analysis of the spatial genetic structure. RESULTS: The section was monophyletic and started to diversify in the late Miocene or Pliocene. We detected 61 haplotypes in the section, of which 44 were observed in the insular species and 17 in the continental species. The two species groups were almost monophyletic. Genetic diversity across species was higher for the group of insular species than for the group of continental species, corresponding to the difference in species richness. In contrast, the insular species showed a tendency towards low genetic diversity within species and populations, whereas the continental species showed the opposite trend. MAIN CONCLUSIONS: The rapid diversification in the insular species during the Quaternary may be a result of genetic drift due to population isolation and population decline on the islands. In contrast, widespread migration or colonization may have prevented allopatric speciation in the continental species.
    Keywords allopatric speciation ; chloroplast DNA ; genetic drift ; genetic variation ; haplotypes ; islands ; monophyly ; population dynamics ; Rhododendron ; China ; Japan ; South Korea ; Taiwan
    Language English
    Dates of publication 2017-05
    Size p. 1065-1076.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 188963-1
    ISSN 0305-0270
    ISSN 0305-0270
    DOI 10.1111/jbi.12924
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    Z 2005/722: Show issues
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  7. Article: Thinning operations increase the demographic performance of the rare subtree species Magnolia stellata in a suburban forest landscape

    Matsushita, Michinari / Ichiro Tamaki / Michiko Nakagawa / Naoyuki Nishimura / Nobuhiro Tomaru / Suzuki Setsuko

    Landscape and ecological engineering. 2016 July, v. 12, no. 2

    2016  

    Abstract: To ensure the persistence of populations and species that maintain unique biodiversity in suburban landscapes, it is necessary to establish an efficient management system for abandoned suburban secondary forests. Thinning operations seem to be an ... ...

    Abstract To ensure the persistence of populations and species that maintain unique biodiversity in suburban landscapes, it is necessary to establish an efficient management system for abandoned suburban secondary forests. Thinning operations seem to be an effective management approach to inhibiting the progress of forest succession, which could lower the level of species diversity. To evaluate the effect of thinning operations on the demographic performance (growth, survival, and sexual reproduction) of the rare subtree species Magnolia stellata, we set up a field experiment and monitored the population dynamics over 9 years. The results revealed that stem survival and flower production per genet showed a decreasing trend in the nonthinned site. However, thinning operations increased the demographic performance, in particular the stem growth and survival rates as well as flower and seed production. The findings suggested that thinning operations may decrease the extinction probability of not only the targeted local population but also the metapopulation, because the thinned population serves as a better seed source. Thus, the creation of well-lit sites by thinning operations would be a useful conservation strategy for M. stellata.
    Keywords extinction ; field experimentation ; flowers ; forest succession ; landscapes ; Magnolia stellata ; population dynamics ; probability ; secondary forests ; sexual reproduction ; species diversity ; stem elongation ; survival rate
    Language English
    Dates of publication 2016-07
    Size p. 179-186.
    Publishing place Springer Japan
    Document type Article
    ZDB-ID 2266588-2
    ISSN 1860-188X ; 1860-1871
    ISSN (online) 1860-188X
    ISSN 1860-1871
    DOI 10.1007/s11355-015-0281-3
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    In stock of ZB MED Bonn / Germany

    Z 7644: Show issues

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  8. Article: Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations

    Izuno, Ayako / Masaomi Hatakeyama / Tomoaki Nishiyama / Ichiro Tamaki / Rie Shimizu-Inatsugi / Ryuta Sasaki / Kentaro K. Shimizu / Yuji Isagi

    Journal of plant research. 2016 July, v. 129, no. 4

    2016  

    Abstract: Whole genome sequences, which can be provided even for non-model organisms owing to high-throughput sequencers, are valuable in enhancing the understanding of adaptive evolution. Metrosideros polymorpha, a tree species endemic to the Hawaiian Islands, ... ...

    Abstract Whole genome sequences, which can be provided even for non-model organisms owing to high-throughput sequencers, are valuable in enhancing the understanding of adaptive evolution. Metrosideros polymorpha, a tree species endemic to the Hawaiian Islands, occupies a wide range of ecological habitats and shows remarkable polymorphism in phenotypes among/within populations. The biological functions of genetic variations observed within this species could provide significant insights into the adaptive radiation found in a single species. Here de novo assembled genome sequences of M. polymorpha are presented to reveal basic genomic parameters about this species and to develop our knowledge of ecological divergences. The assembly yielded 304-Mbp genome sequences, half of which were covered by 19 scaffolds with >5 Mbp, and contained 30 K protein-coding genes. Demographic history inferred from the genome-wide heterozygosity indicated that this species experienced a dramatic rise and fall in the effective population size, possibly owing to past geographic or climatic changes in the Hawaiian Islands. This M. polymorpha genome assembly represents a high-quality genome resource useful for future functional analyses of both intra- and interspecies genetic variations or comparative genomics.
    Keywords Metrosideros polymorpha ; adaptive radiation ; climate change ; evolutionary adaptation ; genes ; genetic variation ; genome assembly ; genomics ; habitats ; heterozygosity ; indigenous species ; nucleotide sequences ; phenotype ; phenotypic variation ; population size ; trees ; Hawaii
    Language English
    Dates of publication 2016-07
    Size p. 727-736.
    Publishing place Springer Japan
    Document type Article
    ZDB-ID 2077362-6
    ISSN 1618-0860 ; 0918-9440
    ISSN (online) 1618-0860
    ISSN 0918-9440
    DOI 10.1007/s10265-016-0822-3
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