記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Ecology and Evolution  

The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100–150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.

DOI： 10.1002/ece3.11584

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Scopus

PubMed

掲載種別：研究論文（学術雑誌）   出版者・発行元：Magnolia Press  

During our investigation of the genetic and morphological variation within the distribution range of Paepalanthus calvus, we observed that specimens from Juiz de Fora municipality, Minas Gerais (Brazil) were morphologically divergent. Through genome-wide analyses using MIG-seq and detailed morphological comparisons, we were able to establish consistent differences between P. calvus and the Juiz de Fora specimens, which supported the recognition of a new species, Paepalanthus salimenae sp. nov. This new species is primarily distinguished by the narrow leaves; trichomes on the leaves, spathes, and scapes; densely pilose involucral bracts; and the tufted apex of some floral organs. Paepalanthus salimenae exhibits low genetic diversity and strong population structure. A preliminary conservation risk assessment suggests this species as Critically Endangered, highlighting the urgent need for conservation efforts to protect its habitat and intraspecific diversity. We provide photographs, line drawings and additional commentaries on the distribution, habitat, and morphological affinities of P. salimenae to congeneric taxa.

DOI： 10.11646/phytotaxa.655.2.5

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掲載種別：研究論文（学術雑誌）  

DOI： 10.1007/s10722-024-02020-4

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掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

Abstract

Ungulate overbrowsing is a growing problem in forests worldwide due to its prolonged and pervasive impact on plant biodiversity and ecosystem functioning. It has been shown that overbrowsing not only reduces plant species diversity and biomass (i.e., direct effects) but also causes a loss of associated trophic levels that could potentially feedback to influence plant community structure (i.e., indirect effects). One of the primary pathways of such indirect effects that have not been fully examined is the impact of overbrowsing on soil microorganisms. Recent studies have shown that soil microorganisms maintain vegetation diversity and drive succession, so it is of critical importance to understand how soil microbial communities might be affected by or protected from the deer impact. To assess the consequence of creating artificial grazing refugia on the structure and composition of soil microbial communities, we compared the distribution and abundance of soil microbial taxa (bacteria, archaea, fungi) at the fenced versus unfenced control sites in the context of a catchment‐scale field experiment in Japan. The eDNA metabarcoding analysis of soil microbial communities showed that the numbers of archaea and basidiomycetes fungal species were greater in the fenced site than in the control, while no such pattern was found for bacteria and ascomycetes fungi. Despite the lack of significant influence of the fence treatment on taxonomic composition in the soil fungal communities, their functional guild composition was influenced by the fenced treatment, with significant changes in the abundance of animal pathogens. Thus, although the effect of fencing on soil microbial communities is characterized by complex responses that vary from taxon to taxon, our work suggests that creating ecosystem‐scale refugia from deer overgrazing might help sustain certain, if not all, taxa of soil microbial communities.

DOI： 10.1002/edn3.498

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

Abstract

GenusAsarum(Aristolochiaceae) shows diverse floral morphology and is hypothesized to have diversified as a result of pollinator‐mediated selection. Yet most aspects of their reproductive ecology, including pollinators, remain unclear. This study focuses onA. costatumandA. minamitanianumin Japan, a sister species pair having remarkable differences in calyx lobe length (10–20 mm and 70–180 mm, respectively). The objectives of this study are to elucidate multiple aspects of reproductive ecology of these two species and obtain evolutionary insights into floral organ elongation.

We adopted combined approaches, including field observations, molecular analyses and cultivation experiments, such as pollinator observation for 3 years, fine‐scale spatial genetic analysis of 769 individuals, paternity analysis based on 566 seeds over 4 years, and control pollination experiments.

BothAsarumspecies had strong spatial genetic structures, indicating limited seed dispersal. Pollinator observation revealed that flies and ground‐dwelling insects visited flowers of both species, but that the pollinator fauna differed between the species. The visitation rate of flies was extremely low but was more than twice as high in the species with an elongated floral appendage. Paternity analysis revealedA. minamitanianumwas predominantly outcrossing, whileA. costatumshowed a wide range of selfing rates among fruits.

These twoAsarumspecies are likely adapted to fly pollination in the shady forest understorey, where available pollinator fauna is limited. In addition, although its function remains unclear, the elongated calyx lobe ofA. minamitanianumcould have evolved for effective pollen dispersal by attracting fly visitors.

DOI： 10.1111/plb.13456

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PubMed

その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1111/plb.13456

担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY  

Tertiary relicts often show evolutionary stasis in morphology and ecology and have been hypothesized to retain stable population sizes in refugia. However, recent studies have reported that some relicts evolutionarily shifted their physiology, ecology, and morphology and experienced various patterns of demography. To understand the historical survival of relict plants, a multidimensional study investigating the evolution of ecological and morphological traits as well as population demographic history is needed. The genus Tanakaea (Saxifragaceae) comprises two species in China and Japan. These species share most vegetative characteristics and are sometimes treated as a single species. The distribution pattern is relictual, as the populations are confined to small areas in mesic warm temperate forests less influenced by Quaternary glacial climates. Focusing on the relictual plant group, this study tested the hypotheses of evolutionary stasis and population stability in long-term refugia. Genetic analyses using plastome sequences and genome-wide single-nucleotide polymorphisms revealed divergence of the two species approximately 6.8 million years ago and strong genetic differentiation of the regional populations. Demographic analysis revealed that almost all populations retained stable population sizes during glacial-interglacial climate changes, supporting the traditional view. However, morphological assessments revealed a simultaneous shift in breeding systems (from hermaphrodite to dioecy/non-clonal to clonal reproduction) in Japanese species and intraspecific differentiation of leaf traits. Therefore, the relict species do not show evolutionary stasis in every aspect. Changes in reproductive characteristics may have contributed to their long-term in situ survival.

DOI： 10.1111/jse.12849

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記述言語：英語   出版者・発行元：日本植物分類学会  

<i>Ribes fujisanense </i>S. Sakag. & Mit. Oishi (Grossulariaceae), an obligate epiphytic gooseberry, is de- scribed here for the first time. It is narrowly endemic in the cool-temperate forests of Mt. Fuji and adja- cent areas of central Japan. <i>Ribes fujisanense </i>is morphologically most similar to <i>R. ambiguum </i>Maxim., but is distinguished by the reddish apex of the calyx lobes, branchlets armed with prickles, petioles with long glandular trichomes and more deeply lobed leaf blades. Phylogenetic analysis based on genome- wide markers showed that the two species are considerably divergent, even though <i>R. fujisanense </i>fully overlaps the distribution of the wide-ranging <i>R. ambiguum</i>, indicating that they are biologically isolated species.

DOI： 10.18942/apg.202109

CiNii Research

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ACADEMIC PRESS INC ELSEVIER SCIENCE  

Phenotypic polymorphism within a species is a notable phenomenon in evolutionary biology to understand the process of adaptive speciation and other historical events. The Saxifraga fortunei complex is a widespread herb found in East Asia. It includes several ecotypic taxa corresponding to their habitat environments. The distribution of the various ecotypes in a limited area of the Japanese Archipelago makes the species a suitable model to investigate the impact of population demographic history and natural selection on lineage diversification. Here, Sanger-based sequencing was used to estimate the divergence timeframe between populations of the Eurasian continent and Japan. Genome-wide SNPs obtained by ddRAD sequencing were used to investigate the phylogeographic origins of ecotypic taxa. The phylogenetic analyses revealed the divergence of the Japanese population from the continental population in the late Miocene. Two distinct regional clades of North and South Japan were identified; phenotypic diversification was evident only in the southern clade. The South Japan clades displayed a historical distribution expansion from north to south. The phenotypic variations appeared to have generated during the expansion. The ecotypic boundaries were incongruent with the genetic grouping. We propose that morphological and ecological specialization in Japanese populations was repeatedly generated by local natural selection.

DOI： 10.1016/j.ympev.2021.107230

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PubMed

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：日本植物分類学会  

Repeated adaptation to similar environments can lead to divergence of phenotypes in different populations. Such evolutionary changes sometimes result in incongruence between morphology and molecular phylogeny, for which careful biological investigation is required. Natural phenotypic variation in rheophytic populations of the <i>Solidago virgaurea </i>L. complex (Asteraceae), which evolved multiple times from ancestral dryland forms in Japan, are here reported. Common garden experiments and population genetic analysis were used to evaluate the extent to which parallelly evolved rheophytes diverged in morphological, phenological and genotypic features to understand their complex evolutionary history. Significant divergence among rheophytic populations was detected in multiple traits, even in leaf morphological traits, which are similarly subjected to purifying selection by water pressure in riparian habitats. Whereas most of the variation were attributed to differences between specific pairs of populations, flowering phenology showed latitudinal variation, which likely evolved along a large-scale environmental cline. Multivariate analysis revealed that at least the population on Okinawa Isl., at the edge of the range of the species, is phenotypically distinguishable from rheophytic populations on the main islands. Phylogenetic analysis also suggested that the Okinawan rheophytes are genetically isolated from parapatric dryland populations. Based on the evidence, the Okinawan rheophytic plants are recognized as specifically distinct and are described as <i>Solidago yambaruensis </i>S. Sakaguchi & Mot. Ito.

DOI： 10.18942/apg.202012

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGERNATURE  

Climate relicts hold considerable importance because they have resulted from numerous historical changes. However, there are major interspecific variations among the ways by which they survived climate changes. Therefore, investigating the factors and timing that affected population demographics can expand our understanding of how climate relicts responded to historical environmental changes. Here, we examined herbaceous hydrangeas of genus Deinanthe in East Asia, which show limited distributions and a remarkable disjunction between Japan and central China. Chloroplast genome and restriction site-associated DNA sequencing revealed that speciation event occurred in the late Miocene (ca. 7-9 Mya) in response to global climate change. Two lineages apparently remained not branched until the middle Quaternary, and afterwards started to diverge to regional population groups. The narrow endemic species in central China showed lower genetic diversity (He = 0.082), as its population size rapidly decreased during the Holocene due to isolation in montane refugia. Insular populations in the three Japanese islands (He = 0.137-0.160) showed a genetic structure that was inconsistent with sea barriers, indicating that it was shaped in the glacial period when its range retreated to coastal refugia on the exposed sea floor. Demographic modelling by stairway-plot analysis reconstructed variable responses of Japanese populations: some experienced glacial bottlenecks in refugial isolation, while post-glacial range expansion seemingly exerted founder effects on other populations. Overall, this study demonstrated the involvement of not just one, but multiple factors, such as the interplay between climate changes, geography, and other population-specific factors, that determine the demographics of climate relicts.

DOI： 10.1038/s41437-020-00396-4

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PubMed

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

The Sino-Japanese Floristic Region (SJFR) in East Asia is one of the most diverse temperate floras in the world. However, the relative influence of Neogene palaeogeographical changes and Quaternary climatic fluctuations as causal mechanisms on species diversification remains largely controversial, because most divergence time estimates were inferred from single-locus data and have limited geographic or taxonomic sampling. To evaluate these influences, we use SNP markers from restriction site-associated DNA sequencing (RAD-Seq) loci and expressed sequence tags-simple sequence repeat (EST-SSR) markers to investigate the levels of genetic variation, speciation and demographic history of the temperate-deciduous forest (TDF) endemic Cardiocrinum (Endlicher) Lindley (Liliaceae), a genus comprising three species in China (C. giganteum, C. cathayanum) and Japan (C. cordatum). Phylogenomic and population genomic coalescent-based analyses demonstrated that Late Neogene tectonic/climatic events triggered speciation of Cardiocrinum, and Pleistocene climatic fluctuations had limited influence on its divergence history. Population demographic inference using Approximate Bayesian Computation from EST-SSRs and palaeoclimatic niche models both indicated that all three Cardiocrinum species experienced population expansions during the transition from the LIG to the LGM. We also discussed the implications of these results on the conservation of montane TDF species in the SJFR under ongoing environmental change. Our results improve our understanding of how the constituents of montane TDF across the SJFR responded to previous periods of rapid climate and environmental change in terms of speciation and population demographic processes.

DOI： 10.1016/j.ympev.2019.106693

DOI： 10.3390/d13050185_references_DOI_UPCvQBDBhI4af0tTEZHzkYuVuli

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：NATL TAIWAN UNIV PRESS  

Simple sequence repeat (SSR) markers were developed from expressed sequence tags (ESTs) for Mazus miquelii (Mazaceae), one of the most widespread species of the genus found in mainland China to Japan and North America, with the goal of elucidating the hidden genetic diversity and pollination ecology of the species. Of the initial 48 EST-SSR markers designed based on transcriptome data, 36 loci were successfully amplified, 16 of which were polymorphic. Polymorphisms for these markers were tested on 72 individuals from three populations in Japan. Two to eleven alleles per locus were detected, and the levels of observed and expected heterozygosity ranged from 0.181 to 0.708 and 0.154 to 0.715, respectively. Most loci were amplified successfully in five related Japanese and Taiwanese species. These markers will empower ecological and evolutionary studies in the creeping mazus and facilitate the disentanglement of phylogenetic relationships with related species.

DOI： 10.6165/tai.2020.65.249

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記述言語：日本語   掲載種別：研究論文（学術雑誌）  

DOI： 10.18942/CHIRIBUNRUI.0682-01

担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

Clinal variation is a major pattern of observed phenotypic diversity and identifying underlying demographic processes is a necessary step to understand the establishment of clinal variation. The wild ginger series Sakawanum (genus Asarum) comprises four taxa, which exhibit intertaxonomic clinal variation in calyx lobe length across two continental islands isolated by a sea strait. To test alternative hypotheses of the evolutionary history and to determine the implications for the formation of clinal variation, we conducted approximate Bayesian computation (ABC) analysis and ecological niche modeling (ENM). ABC analysis indicated that the scenario assuming multiple admixture events was strongly supported. This scenario assumed two admixture events occurred between morphologically distinct taxa, likely leading to the generation of intermediate taxa. One of the admixture events was estimated to have occurred during the last glacial maximum (LGM), during which the taxa were estimated to have formed a common refugia in southern areas by ENM analysis. Although four taxa are currently distributed allopatrically on different islands and trans-oceanic dispersal appears unlikely, the formation of a land bridge and the geographic range shift to refugia would have allowed secondary contact between previously isolated taxa. This study suggests that clinal variation can be shaped by demographic history including multiple admixtures due to climatic oscillations.

DOI： 10.1016/j.ympev.2019.05.003

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PubMed

CiNii Research

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Science and Business Media LLC  

Climatic perturbation during the Pleistocene era has played a major role in plant evolutionary history by altering species distribution range. However, the relative roles of climatic and geographic factors in the distribution dynamics remain poorly understood; in particular, the edaphic endemics. In this paper, we examine the evolutionary history of two ultramafic primroses, Primula hidakana and Primula takedana. These species are ecologically and morphologically distinct with disjunct distributions on Hokkaido Island, Japan. Primula hidakana is found on various rocks in southern Hokkaido and P. takedana in serpentine areas in northern Hokkaido. We performed population genetics analyses on nuclear and chloroplast data sets and tested alternative phylogenetic models of divergence using approximate Bayesian computation (ABC) analyses. Nuclear microsatellite loci clearly distinguished the two sister taxa. In contrast, chloroplast sequence variations were shared between P. takedana and P. hidakana. ABC analyses based on nuclear data supported a secondary contact scenario involving asymmetrical gene flow from P. hidakana to P. takedana. Paleodistribution modeling also supported the divergence model, and predicted their latitudinal range shifts leading to past secondary contact. Our findings highlight the importance of the distribution dynamics during the Pleistocene climatic oscillations in the evolution of serpentine plants, and demonstrate that tight species cohesion between serpentine and nonserpentine sister taxa has been maintained despite past interspecific gene flow across soil boundaries.

DOI： 10.1038/s41437-019-0245-8

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その他リンク： http://www.nature.com/articles/s41437-019-0245-8

記述言語：英語   掲載種別：研究論文（学術雑誌）  

担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Informa UK Limited  

Series Sakawanum (genus Asarum, Aristolochiaceae) comprises four taxa of forest understory herbaceous plants, which exhibits a geographical cline of calyx lobe length across taxonomic units. To understand the formation process of this series, it is necessary to investigate the evolutionary history based on maternally inherited seed-mediated plastid markers. Using pyrosequencing technique, nearly complete chloroplast genomes of two species (A. minamitanianum and A. costatum) were obtained. Furthermore, nine polymorphic chloroplast single nucleotide polymorphisms (SNPs) and 11 simple sequence repeat (SSR) markers were developed. Most of these markers showed interspecific variations and all markers showed transferability to other Asarum species, while most of markers showed little intra-population variations. These chloroplast genomes and markers can be applied in future studies investigating the contributions of the maternal lineage in shaping the population genetic structure of series Sakawanum and the evolutionary processes underlying their morphological diversification including the characteristic calyx lobe length variation. Moreover, this study showed the applicability of comparative chloroplast genome analysis to develop the chloroplast markers for species group for which it is difficult to obtain polymorphism data using the universal primers.

DOI： 10.1080/13416979.2018.1518649

DOI： 10.1016/j.ympev.2019.05.003_references_DOI_Zi5zmZKQHkJHWuVI0agWuM7BcPd

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その他リンク： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16H04831/

記述言語：英語   出版者・発行元：National Museum of Nature and Science  

CiNii Books

CiNii Research

担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Oxford University Press (OUP)  

Background and Aims Clines, the gradual variation in measurable traits along a geographical axis, play a major role in evolution and can contribute to our understanding of the relative roles of selective and neutral process in trait variation. Using genetic and morphological analyses, the relative contributions of neutral and non-neutral processes were explored to infer the evolutionary history of species of the series Sakawanum (genus Asarum), which shows significant clinal variation in calyx lobe length.Methods A total of 27 populations covering the natural geographical distribution of the series Sakawanum were sampled. Six nuclear microsatellite markers were used to investigate genetic structure and genetic diversity. The lengths of calyx lobes of multiple populations were measured to quantify their geographical and taxonomic differentiation. To detect the potential impact of selective pressure, morphological differentiation was compared with genetic differentiation (Q(CT) - F-ST comparison).Key Results Average calyx lobe length of A. minamitanianum was 124.11 mm, while that of A. costatum was 13.80 mm. Though gradually changing along the geographical axis within series, calyx lobe lengths were significantly differentiated among the taxa. Genetic differentiation between taxa was low (F-ST = 0.099), but a significant geographical structure along the morphological cline was detected. Except for one taxon pair, pairwise Q(CT) values were significantly higher than the neutral genetic measures of F-ST and G'(ST).Conclusions Divergent selection may have driven the calyx lobe length variation in series Sakawanum taxa, although the underlying mechanism is still not clear. The low genetic differentiation indicates recent divergence and/or gene flows between geographically close taxa. These neutral processes would also affect the clinal variation in calyx lobe lengths. Overall, this study implies the roles of population history and divergent selection in shaping the current cline of a flower trait in the series Sakawanum.

DOI： 10.1093/aob/mcx122

DOI： 10.1080/13416979.2018.1518649_references_DOI_3F9m49X4JgPnEvX01tqqgzYFSqQ

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CiNii Research

記述言語：英語   出版者・発行元：Wiley  

The genus Tanakaea is a plant genus that consists of one or two evergreen herbaceous species in Japan and China. As rithophytic plant species occur on shaded rocks, the populations are usually isolated and sporadically found in disjunct areas. To evaluate the genetic structure of the species at multiple spatial scales, 10 nuclear and mitochondrial microsatellite markers were developed. The novel markers showed high genetic variations (two to 15 alleles and H-e from 0.400 to 0.894). Clonal samples were identified with the probability of identity of 9.0E-8. When evaluated with 11 populations in Japan, significant genetic differentiation between regional population groups was detected (F-ST=0.313 between Shikoku and Honshu islands), suggesting they have long been isolated from each other. Overall, these markers will be useful for population genetic research to investigate clonal structure and genetic diversity and levels of genetic differentiation between the geographically isolated populations.

DOI： 10.1111/1442-1984.12196

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CiNii Research

その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1442-1984.12196

担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

The genus Asarum (Aristolochiaceae) encompasses approximately 120 species from five sections. Taxonomic controversies concerning the genus Asarum and/or its intrageneric classification remain unresolved. In particular, sect. Heterotropa accounts for a large percentage of the genus (80 of 120 species) and is well diverged in the Sino-Japanese Forest subkingdom. Reconstruction of Heterotropa phylogeny and estimation of its divergence times would provide significant insight into the process of species diversity in the Sino-Japanese floristic region. This study encompassed 106 operational taxonomic units (OTUs), and phylogenetic analyses were conducted based on internal transcribed spacer (ITS) and matK sequences. Although the matK sequences provided informative results solely for section Geotaenium, phylogenetic trees based on ITS regions yielded a clear result for several sections. Three sections, Asarum, Geotaenium and Asiasarum, were supported as robust monophyletic groups, whereas Heterotropa had low support. Sect. Hexastylis was revealed to be polyphyletic, suggesting taxonomic reconstruction would be needed. Sect. Heterotropa comprises two clades, which correspond to species distribution ranges: mainland China and the island arc from Taiwan to mainland Japan via the Ryukyu Islands. It is notable that the common ancestry of the latter clade in the eastern Asian islands was highly supported, suggesting that the present species diversity of Heterotropa was initially caused by allopatric range fragmentation in East Asia.

DOI： 10.1111/1442-1984.12189

DOI： 10.1080/13416979.2018.1518649_references_DOI_Y1M4adIuKKFggOKMZOJpwD9SsHs

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その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1442-1984.12189

担当区分：筆頭著者,　最終著者,　責任著者  

DOI： 10.1111/1442-1984.12156

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

Premise of the study: High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms.Methods: Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing.Results: Using this simple method, significant enrichment of chloroplast DNA-derived reads was attained, allowing deep sequencing of chloroplast genomes. As an example, the chloroplast genome of the conifer Callitris sulcata was assembled, from which polymorphic microsatellite loci were isolated successfully.Discussion: This chloroplast enrichment method from small amounts of plant tissue will be particularly useful for studies that use sequencers with relatively small throughput and that cannot use large amounts of tissue (e.g., for endangered species).

DOI： 10.3732/apps.1700002

DOI： 10.1080/13416979.2018.1518649_references_DOI_MhRpry5EP0H92GZk4ZcaUGLzpYi

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その他リンク： https://onlinelibrary.wiley.com/doi/pdf/10.3732/apps.1700002