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The molecular clock in long-lived tropical trees is independent of growth rate

Akiko Satake, Ryosuke Imai, Takeshi Fujino, Sou Tomimoto1 Kayoko Ohta,

Mohammad Na’iem, Sapto Indrioko, Widiyatno, Susilo Purnomo, Almudena Mollá–Morales, Viktoria Nizhynska, Naoki Tani, Yoshihisa Suyama, Eriko Sasaki, Masahiro Kasahara.

eLife
https://doi.org/10.7554/eLife.88456.1

Somatic mutation rates scale with time not growth rate in long-lived tropical trees

Akiko Satake, Ryosuke Imai, Takeshi Fujino, Sou Tomimoto, Kayoko Ohta, Mohammad Na’iem, Sapto Indrioko,Widiyatno, Susilo Purnomo, Almudena  Mollá–

Morales, Viktoria Nizhynska, Naoki Tani, Yoshihisa Suyama, Eriko Sasaki, Masahiro

Kasahara

eLife, 2023.

DOI: https://doi.org/10.1101/2023.01.26.525665

Carbon use strategies in shoot and acorn growth of two evergreen broadleaf trees unraveled by seasonal carbohydrate measurements and carbon isotope analysis

Qingmin Han, Daisuke Kabeya, Yoshiyuki Inagaki, Tatsuro Kawasaki, Akiko Satake

Tree Physiology, tpad072, 2023.

DOI: 10.1093/treephys/tpad072

Typhoon-induced Lammas growth promotes the non-dormant life-cycle of the Great Orange Tip butterfly Hebomoia glaucippe

Kota Ogawa, Wataru Nakamizo, Fukashi Ishiwata, Yu Matsuura, Akiko Satake

bioRxiv, 2023.

https://doi.org/10.1101/2023.05.09.539972

AGAMOUS regulates various target genes via cell cycle-coupled H3K27me3 dilution in floral meristems and stamens

Margaret Anne Pelayo, Fumi Morishita, Haruka Sawada, Kasumi Matsushita, Hideaki Iimura, Zemiao He, Liang Sheng Looi, Naoya Katagiri, Asumi Nagamori, Takamasa Suzuki, Marek Širl, Aleš Soukup, Akiko Satake, Toshiro Ito, Nobutoshi Yamaguchi

Plant Cell, Volume 35, Issue.8, Pages.2821-2847, 2023.

https://doi.org/10.1093/plcell/koad123

Characterization of Leaf Transcriptome in a Tropical Tree Species, Shorea curtisii, over a Flowering Season

Ahmad Husaini SUHAIMI, Masaki J. KOBAYASHI, Akiko SATAKE, Soon Leong LEE, Norwati MUHAMMAD, Tatsuya OTANI, Toshiaki KONDO, Naoki TANI, Suat Hui YEOH

J -STAGE, Vol.57, Issue.2, Pages.139-144, 2023.

https://doi.org/10.6090/jarq.57.139

Modelling somatic mutation accumulation and expansion in a long-lived tree with hierarchical modular architecture

Sou Tomimoto, Akiko Satake

Journal of Theoretical Biology, Vol.565, 111465, 2023.

DOI: 10.1016/j.jtbi.2023.111465

Contributions to the flora of Myanmar IX: five new distributional records of flowering plants from Chin State, Kachin State and Tanintharyi Region

Ai Nagahama, Takashi Sugawara, Mu Mu Aung, Axel Dalberg Poulsen, Kate E. Armstrong, Shuichiro Tagane, Nobuyuki Tanaka

Bulletin of the National Museum of Nature and Science Series B (Botany), Vol.49, Issue.2, Pages.49-55, 2023.

https://doi.org/10.50826/bnmnsbot.49.2_49

The transcriptional changes underlying the flowering phenology shift of Arabidopsis halleri in response to climate warming

Hideyuki Komoto, Ai Nagahama, Atsuko Miyawaki-Kuwakado, Yuki Hata, Junko Kyozuka, Yui Kajita, Hironori Toyama, Akiko Satake

Plant, Cell & Environment, Vol.47, Issue.1, Pages.174-186, 2023.

DOI: 10.1111/pce.14716

Assessing the impacts of genetic defects on starch metabolism in Arabidopsis plants using the carbon homeostasis model

Shuichi N. Kudo, Carolina C. M. Bello, Anthony Artins, Camila Caldana, Akiko Satake

Journal of the Royal Society Interface, Vol.20, Issue.208, 2023.

 DOI: 10.1098/rsif.2023.0426

An ecological transcriptome approach to capture the molecular and physiological mechanisms of mass flowering in Shorea curtisii

Ahmad Husaini Suhaimi, Masaki J. Kobayashi, Akiko Satake, Ching Ching Ng, Soon Leong Lee, Norwati Muhammad, Shinya Numata, Tatsuya Otani, Toshiaki Kondo, Naoki Tani​, Suat Hui Yeoh​

PeerJ, Vol.11, e16368, 2023.

DOI: 10.7717/peerj.16368

Plant Molecular Phenology and Climate Feedbacks Mediated by BVOCs

Akiko Satake, Tomika Hagiwara, Atsushi J. Nagano, Nobutoshi Yamaguchi, Kanako Sekimoto, Kaori Shiojiri, and Kengo Sudo

Annual Review of Plant Biology, Vol.75, Pages.605-627, 2024.

DOI: 10.1146/annurev-arplant-060223-032108

Altered Trends in Spring- and Autumn-Flowering Species in Japan in Response to Global Warming

Ai Nagahama , Hitomi Uemura, Taro Nikaido

Bulletin of the National Museum of Nature and Science Series B (Botany)

Vol.50, Issue.2, Pages.59-69, 2024.

https://doi.org/10.50826/bnmnsbot.50.2_59

The genetic structure within a single tree is determined by the behavior of the stem cells in the meristem

Yoh Iwasa, Sou Tomimoto, Akiko Satake

Genetics, Vol.223, Issue.4, 2023.

https://doi.org/10.1093/genetics/iyad020

Seasonal gene expression signatures of delayed fertilization in Fagaceae

Akiko Satake, Kayoko Ohta, Noriko Takeda-Kamiya, Kiminori Toyooka, Junko Kusumi

Molecular Ecology, Vol.32, Issue.17, Pages.4801-4813, 2023.

https://doi.org/10.1111/mec.17079

Impacts of climate change on the transcriptional dynamics and timing of bud dormancy release in Yoshino-cherry tree

Atsuko Miyawaki-Kuwakado, Qingmin Han, Keiko Kitamura, Akiko Satake

Plants, People, Planet, 2024.

History of the terrestrial isopod genus Ligidium in Japan based on phylogeographic analysis

Wakana Harigai, Aya Saito, Chika Zemmoto, Shigenori Karasawa, Touta Yokoi, Atsushi J. Nagano, Hitoshi Suzuki & Masanobu Yamamoto.
BMC Ecology and Evolution, Vol.23, Issue.1, 2023.
https://doi.org/10.1186/s12862-023-02144-8

A low-coverage 3' RNA-seq to detect homeolog expression in polyploid wheat

Jianqiang Sun, Moeko Okada, Toshiaki Tameshige, Rie Shimizu-Inatsugi, Reiko Akiyama, Atsushi J Nagano, Jun Sese, Kentaro K Shimizu.
NAR Genom Bioinform, Vol.5, Issue.3, 2023.
DOI: 10.1093/nargab/lqad067

Development and validation of novel SNP markers for the rapid identification of natural hybrids of the 11 closely related pufferfish species (Takifugu spp.) distributed in Japan

Hiroshi Takahashi, Ryo Kakioka, Atsushi J. Nagano

Aquaculture Reports, Vol.31, 2023.

DOI:https://doi.org/10.1016/j.aqrep.2023.101650

Genetic differentiation and evolution of broad-leaved evergreen shrub and tree varieties of Daphniphyllum macropodum (Daphniphyllaceae)

Watanabe Yoichi, Sae Matsuzawa, Ichiro Tamaki, Atsushi J. Nagano & Sang-Hun Oh.
Heredityi, Vol.131, Issue.3, Pages.211-220, 2023.
https://doi.org/10.1038/s41437-023-00637-2

Multiple colonizations and hybridization of a freshwater fish group on a satellite island of Sulawesi

Ixchel F. Mandagi, Bayu K. A. Sumarto, Handung Nuryadi, Daniel F. Mokodongan, Sjamsu A. Lawelle, Kawilarang W.A. Masengi, Atsushi J. Nagano, Ryo Kakioka, Jun Kitano, Satoshi Ansai, Junko Kusumi, Kazunori Yamahira.
Molecular Phylogenetics and Evolution, Vol.5, Issue.3, 2023.
https://doi.org/10.1016/j.ympev.2023.107804

Induction of leaf curling in cassava plants by the cassava mealybug Phenacoccus manihoti (Hemiptera: Pseudococcidae)

Shun-ichiro Takano, Yoshinori Utsumi, Atsushi Nagano, Satoshi Takahashi, Akihiro Ezoe, Motoaki Seki, Thi Xuyen Le & Keiji Takasu.
Applied Entomology and Zoology, Vol.58, Pages.279-290, 2023.
https://doi.org/10.1007/s13355-023-00832-x

Apoplast-Localized β-Glucosidase Elevates Isoflavone Accumulation in the Soybean Rhizosphere

Hinako Matsuda, Yumi Yamazaki, Eiko Moriyoshi, Masaru Nakayasu, Shinichi Yamazaki, Yuichi Aoki, Hisabumi Takase, Shin Okazaki, Atsushi J Nagano, Akito Kaga, Kazufumi Yazaki, Akifumi Sugiyama.
Plant and Cell Physiology, Vol.65, Issue.5,Pages.486-550, 2023.
https://doi.org/10.1093/pcp/pcad012

Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes) 

Nozomu Muto, Takuma Kawasaki, Ryo Kakioka, Atsushi J Nagano, Yuta Shimizu, Shu Inose, Yohei Shimizu, Hiroshi Takahashi.
Journal of Heredity, Vol.114, Issue.3, Pages.231-245, 2023.
https://doi.org/10.1093/jhered/esad007

Genetic population structure of the precious coral Corallium japonicum in the Northwest Pacific

Hiroki Kise, Akira Iguchi, Naoki Saito, Yuki Yoshioka, Koji Uda, Tomohiko Suzuki, Atsushi J. Nagano, Atsushi Suzuki, Nozomu Iwasaki.
Frontiers in Marine Science, Vol.10, 2023.
https://doi.org/10.3389/fmars.2023.1052033

The detailed population genetic structure of the rare endangered latid fish akame Lates japonicus with extremely low genetic diversity revealed from single-nucleotide polymorphisms

Takuya Naito, Kouji Nakayama, Hirohiko Takeshima, Yasuyuki Hashiguchi, Tetsuya Akita, Yo Y. Yamasaki, Tappei Mishina, Naohiko Takeshita, Atsushi J. Nagano & Hiroshi Takahashi.
Conservation Genetics, Vol.24, Pages.523-535, 2023.
https://doi.org/10.1007/s10592-023-01517-2

The evolutionary history of rice azaleas (Rhododendron tschonoskii alliance) involved niche evolution to a montane environment

Watanabe Yoichi, Ichiro Tamaki, Sang-Hun Oh, Atsushi J Nagano, Koichi Uehara, Nobuhiro Tomaru, Harue Abe.
American Journal of Botany, Vol.110, Issue.4, e16166, 2023.
DOI: 10.1002/ajb2.16166

An ecological network approach for detecting and validating influential organisms for rice growth

Masayuki Ushio, Hiroki Saito, Motoaki Tojo, Atsushi J Nagano

eLife, Vol.12, RP87202, 2023.

DOI:10.7554/eLife.87202.3

RAD-Seq analysis of wild Japanese garlic (Allium macrostemon Bunge) growing in Japan revealed that this neglected crop was previously actively utilized

Wiwit Probowati, Shogo Koga, Kentaro Harada, Yukio Nagano, Atsushi J. Nagano, Kanji Ishimaru, Kazusato Ohshima & Shinji Fukuda

Scientific Reports, Vol.13, 2023.

DOI: 10.1038/s41598-023-43537-5

Ghost introgression in ricefishes of the genus Adrianichthys in an ancient Wallacean lake

Kazunori Yamahira, Hirozumi Kobayashi, Ryo Kakioka, Javier Montenegro, Kawilarang W. A. Masengi, Noboru Okuda, Atsushi J. Nagano, Rieko Tanaka, Kiyoshi Naruse, Shoji Tatsumoto, Yasuhiro Go, Satoshi Ansai, Junko Kusumi

Journal of Evolutionary Biology, Vol.36, Issue.10, 2023.

DOI: 10.1111/jeb.14223

Identification of Novel Quantitative Trait Loci for Culm Thickness of Rice Derived from Strong-Culm Landrace in Japan, Omachi

Koki Chigira, Masanori Yamasaki, Shunsuke Adachi, Atsushi J. Nagano & Taiichiro Ookawa

Rice, Vol.16, Issue.1, 2023.

DOI:10.1186/s12284-023-00621-8

Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

Mohammad Ibrahim Haqani, Michiharu Nakano, Atsushi J. Nagano, Yoshiaki Nakamura & Masaoki Tsudzuki

Scientific Reports, Vol.13, Issue.1, 2023.

DOI:10.1038/s41598-023-48293-0

Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes

Shuya Kato, Seiji Arakaki, Atsushi J. Nagano, Kiyoshi Kikuchi, Shotaro Hirase

Molecular Ecology, 2023.

https://doi.org/10.1111/mec.17216

A transcriptional program for circannual clock in medaka

Tomoya Nakayama, Miki Tanikawa, Yuki Okushi, Thoma Itoh, Tsuyoshi Shimmura, Michiyo Maruyama, Taiki Yamaguchi, Akiko Matsumiya, Ai Shinomiya, Ying-Jey Guh, Junfeng Chen, Kiyoshi Naruse, Hiroshi Kudoh, Yohei Kondo, Honda Naoki, Kazuhiro Aoki, Atsushi J Nagano, Takashi Yoshimura

Proceedings of the National Academy of Sciences of the United Sates of America, Vol.120, Issue.52, e2313514120, 2023.

DOI: 10.1073/pnas.2313514120

Genome-wide association study of leaf photosynthesis using a high-throughput gas exchange system in rice

Sotaro Honda, Ayumu Imamura, Yoshiaki Seki, Koki Chigira, Marina Iwasa, Kentaro Hayami, Tomohiro Nomura, Satoshi Ohkubo, Taiichiro Ookawa, Atsushi J. Nagano, Makoto Matsuoka, Yu Tanaka & Shunsuke Adachi

Photosynthesis Research, Vol.159, Pages.17-28, 2024.

https://doi.org/10.1270/jsbbs.23053

Single candidate gene for salt tolerance of Vigna nakashimae (Ohwi) Ohwi & Ohashi identified by QTL mapping, whole genome sequencing and triplicated RNA-seq analyses

Miho Ito, Honami Ohashi, Masahiro Takemoto, Chiaki Muto, Takashi Seiko, Yusaku Noda, Eri Ogiso-Tanaka, Atsushi J. Nagano, Yu Takahashi, Jun Furukawa, Yuki Monden, Ken Naito

Breeding Science, Vol.74, Issue.2, Pages.93-102, 2024.

https://doi.org/10.1270/jsbbs.23053

Hybridization and its impact on the ontogenetic allometry of skulls in macaques

Tsuyoshi Ito, Ryosuke Kimura, Hikaru Wakamori, Mikiko Tanaka, Ayumi Tezuka, Atsushi J Nagano, Yuzuru Hamada, Yoshi Kawamoto

Evolution, Vol.78, Issue.2, Pages.284-299, 2024.

https://doi.org/10.1093/evolut/qpad206

Application of ethanol alleviates heat damage to leaf growth and yield in tomato

Daisuke Todaka, Do Thi Nhu Quynh, Maho Tanaka, Yoshinori Utsumi, Chikako Utsumi, Akihiro Ezoe, Satoshi Takahashi, Junko Ishida, Miyako Kusano, Makoto Kobayashi, Kazuki Saito, Atsushi J Nagano, Yoshimi Nakano, Nobutaka Mitsuda, Sumire Fujiwara, Motoaki Seki

Frontiers in Plant Science, Vol.15, 2024.

https://doi.org/10.3389/fpls.2024.1325365

Non-prey biotic interactions in carnivorous plants Unlocking the secrets of peristome geometry in pitcher plants

Montero H, Fukushima K

Current Biology, Vol.33, Issue.11, Pages.R497-R500, 2023.

https://doi.org/10.1016/j.cub.2023.01.053

Carnivorous plants: Unlocking the secrets of peristome geometry in pitcher plants

Fukushima K

Current Biology, Vol.33, Issue.21, Pages.R1155-R1157, 2023.

https://doi.org/10.1016/j.cub.2023.09.056

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Saul F, Scharmann M, Wakatake, T, Rajaraman S, Marques A, Freund M, Bringmann G, Channon L, Becker D, Carroll E, Low YW, Lindqvist C, Gilbert KJ, Renner T, Masuda S, Richter M, Vogg G, Shirasu K, Michael TP, Hedrich R, Albert VA, Fukushima K

Nature Plants, Vol.9, Issue.12, 2023.

DOI: 10.1038/s41477-023-01562-2

AGAMOUS regulates various target genes via cell cycle-coupled H3K27me3 dilution in floral meristems and stamens

Margaret Anne Pelayo, Fumi Morishita, Haruka Sawada, Kasumi Matsushita, Hideaki Iimura, Zemiao He, Liang Sheng Looi, Naoya Katagiri, Asumi Nagamori, Takamasa Suzuki, Marek Širl, Aleš Soukup, Akiko Satake, Toshiro Ito, Nobutoshi Yamaguchi.
Plant Cell, Vol.35, Issue.8, Pages.2821–2847, 2023.
https://doi.org/10.1093/plcell/koad123

The regulation of chromatin configuration at AGAMOUS locus by LFR-SYD-containing complex is critical for reproductive organ development in Arabidopsis

Xiaowei Lin, Tingting Yuan Hong Guo, Yi Guo, Nobutoshi Yamaguchi, Shuge Wang, Dongxia Zhang, Dongmei, Jiayu Li, Qiang Chen, Xinye Liu, Long Zhao, Jun Xiao, Doris Wagner, Sujuan Cui and Hongtao Zhao

Plant Journal, Vol.116, Issue.2, Pages.478-496, 2023.

https://onlinelibrary.wiley.com/doi/10.1111/tpj.16385

Seed Halopriming: A Promising Strategy to Induce Salt Tolerance in Indonesian Pigmented Rice

Yekti Asih Purwestri , Siti Nurbaiti, Sekar Pelangi Manik Putri, Ignasia MargiWahyuni,

Siti Roswiyah Yulyani, Alfino Sebastian, Tri Rini Nuringtyas, and Nobutoshi Yamaguchi

PlantsI, Vol.12, Issue.15, 2023.

https://doi.org/10.3390/plants12152879

Statistical analysis of organelle movement using state-space models

Haruki Nishio, Satoyuki Hirano, Yutaka Kodama

Plant Methods, Vol.19, Issue.1, e67, 2023.

DOI: 10.1186/s13007-023-01038-6

Transcriptome profiles of rice roots under simulated microgravity conditions and following gravistimulation

Noriyuki Kuya, Ryo Nishijima, Yuka Kitomi, Taiji Kawakatsu, Yusaku Uga

Frontiers in Plant Science, Vol.14, 1193042, 2023.

DOI: 10.3389/fpls.2023.1193042

Transcriptional Regulators of Plant Adaptation to Heat Stress

Xuejing Wang, Wui Kiat Nicholas Tan, Fong Yi Chung, Nobutoshi Yamaguchi, Eng Seng Gan, Toshiro Ito

International Journal of Molecular Sciences, Vol.24, Issue.17, 13297, 2023.

https://doi.org/10.3390/ijms241713297

SHI family transcription factors regulate an interspecific barrier

Fujii S, Yamamoto E, Ito S, Tangpranomkorn S, Kimura Y, Miura H, Yamaguchi N, Kato Y, Niidome M, Yoshida A, Shimosato-Asano H, Wada Y, Ito T, Takayama S.

Nature Plants, Vol.9, Pages.1862-1873, 2023.

https://www.nature.com/articles/s41477-023-01535-5

Beyond heat waves: Unlocking epigenetic heat stress memory in Arabidopsis

Haruki Nishio; Taiji Kawakatsu; Nobutoshi Yamaguchi

Plant Physiology, Vol.194, Issue.4, Pages.1934-1951, 2023.

https://doi.org/10.1093/plphys/kiad558

AGAMOUSによる花メリステムの細胞増殖停止機構

古田優生, 山口暢俊, 伊藤寿朗
アグリバイオ, 7巻, 14号, Pages.61-66, 2023.

An improved method for the highly specific detection of transcription start sites

Seki M, Kuze Y, Zhang X, Kurotani K, Notaguchi M, Nishio H, Kudoh H, Suzaki T, Yoshida S, Sugano S, Matsushita T, Suzuki Y.
Nucleic Acids Research. Vol.52, Issue.2, Page.e7, 2023.

https://doi.org/10.1093/nar/gkad1116

Petal abscission is promoted by jasmonic acid-induced autophagy at Arabidopsis petal bases.

Yuki Furuta1, Haruka Yamamoto1, Takeshi Hirakawa1, Akira Uemura1, Margaret Anne Pelayo1,2, Hideaki Iimura1,3, Naoya Katagiri1, Noriko Takeda-Kamiya4, Kie Kumaishi5, Makoto Shirakawa1,6, Sumie Ishiguro7, Yasunori Ichihashi5, Takamasa Suzuki8, Tatsuaki Goh1, Kiminori Toyooka4, Toshiro Ito1,* and Nobutoshi Yamaguchi1,*
Nature Communications, 15, Article number: 1098, 2023.

DOI: 10.1038/s41467-024-45371-3

Life-cycle multiomics of rice shoots reveals growth stage-specific effects of drought stress and time-lag drought responses

Soma F, Kitomi Y, Kawakatsu T, Uga Y

Plant and Cell Physiology, Vol.65, Issue.1, Pages.156-168, 2024.

https://doi.org/10.1093/pcp/pcad135

Genome- and transcriptome-wide association studies to discover candidate genes for diverse root phenotypes in cultivated rice

Wei S, Tanaka R, Kawakatsu T, Teramoto S, Tanaka N, Shenton M, Uga Y, Yabe S

Rice, Vol.16, 55, 2023.

https://doi.org/10.1186/s12284-023-00672-x

Generation of major glutelin-deficient (GluA, GluB, and GluC) semi-dwarf Koshihikari rice line.

Wakasa Y, Kawakatsu T, Ishimaru K, Ozawa K

Plant Cell Reports, Vol.43, 51, 2024.

https://doi.org/10.1007/s00299-023-03131-5

Old school, new rules: floral meristem development revealed by 3D gene expression atlases and high-resolution transcription factor-chromatin dynamics

Margaret Anne Pelayo, Nobutoshi Yamaguchi

Frontiers in Plant Science, Vol.14, 2023.

DOI: 10.3389/fpls.2023.1323507

Analysis of Volatile Esters and Alkanoic Acids by an Atmospheric Pressure Corona Discharge Ionization Collision-Induced Dissociation Mass Spectrometry in Positive-Ion Mode: Ionization, Fragmentation Patterns, and Discrimination between Isomeric Compounds

Yuto Nishikido, Kanako Sekimoto.
Mass Spectrometry, Vol.12, Issue.1, Pages. A0127, 2023.

https://doi.org/10.5702/massspectrometry.A0127

Fuel-type Independent Parameterization of Volatile Organic Compound Emissions from Western US Wildfires

Kanako Sekimoto, Matthew M. Coggon, Georgios I. Gkatzelis, Chelsea E. Stockwell, Jeff Peischl, Amber Soja, Carsten Warneke.
Environmental Science & Technology, Vol.57, Issue.35, Pages.13193-13204, 2023.

DOI:10.1021/acs.est.3c00537

Measurement report: Assessment of Asian emissions of ethane, propane, carbon monoxide, and NOx based on observations from the island of Hateruma

dedeji, A. R., Andrews, S. J., Rowlinson, M. J., Evans, M. J., Lewis, A. C., Hashimoto, S., Mukai, H., Tanimoto, H., Tohjima, Y., and Saito.
Atmos. Chem. Phys, Vol.23, Issue.16, Pages.9229-9224, 2023.

https://doi.org/10.5194/acp-23-9229-2023

Functional Group Analysis of a-Pinene Oxidation Products Using Derivatization Reactions and High-Reslution Electrospray Inoization Collision-Induced Dissociation Mass Spectrometry

Daisuke Fukuyama, Kanako Sekimoto

Journal of the American Society for Mass Spectrometry, Vol.35, Issue.4, Pages.728-737, 2024.

DOI: 10.1021/jasms.3c00415

A high-accuracy dynamic dilution method for generating reference gas mixtures of carbonyl sulfide at sub-nanomole-per-mole levels for long-term atmospheric observation

Hideki Nara, Takuya Saito, Taku Umezawa, Yasunori Tohjima

Atmos. Meas. Tech. Discuss, 2024.

DOI:10.5194/amt-2024-16

When to help juveniles, adults, or both: analyzing the evolutionary models of stage-structured mutualism

Takefumi Nakazawa, Noboru Katayama, Shunsuke Utsumi, Akira Yamawo, Masato Yamamichi.
Frontiers in ecology and evolution, Vol.11, Pages.1138138, 2023.

DOI:10.3389/fevo.2023.1138138

The exposure of field-grown maize seedlings to weed volatiles affects their growth and seed quality

Yusuke Sakurai , Satomi Ishizaki , Shota Izumi ,
Takuma Yoshida, Kaori Shiojiri, Junji Takabayashi.
Frontiers in Plant Science, Vol.14, Pages.1141338, 2023.

https://doi.org/10.3389/fpls.2023.1141338

Fuel-Type Independent Parameterization of Volatile Organic Compound Emissions from Western US Wildfires

Kanako Sekimoto*, Matthew M. Coggon, Georgios I. Gkatzelis, Chelsea E. Stockwell, Jeff Peischl, Amber J. Soja, and Carsten Waeneke.
Environmental Science & Technology, August 23, 2023.
https://doi.org/10.1021/acs.est.3c00537

Elevated O3 threatens biological communications

Noboru Masuia , Kaori Shiojiri , Evgenios Agathokleousc , Akira Tania ,  Takayoshi Koike.
Critical Reviews in Environmental Science and Technology, Volume 53, P.1982-2001, 2023.
https://doi.org/10.1080/10643389.2023.2202105

Seasonal patterns of sugar components and their functions in branches of Fagus crenata in association with three reproduction events

Daisuke Kabeya and Qingmin Han

Ecological Research, Vol.38, Issue.6, Pages.782-794, 2023.

https://doi.org/10.1111/1440-1703.12370

Resurrection of Spicantopsis hancockii (Blechnaceae) as an endemic species to Taiwan -Reidentification of Spicantopsis in the Tokara Islands, Japan

Atsushi Ebihara, Shuichiro Tagane, Shun K. Hirota, Yoshihisa Suyama, Narumi Nakato, Li-Yaung Kuo

Taiwania, Vol.68, Issue.2, Pages.148-154, 2023.

Spiranthes hachijoensis (Orchidaceae), a new species within the S. sinensis species complex in Japan, based on morphological, phylogenetic, and ecological evidence

Suetsugu K, Hirota SK, Hayakawa H, Fujimori S, Ishibashi M, Hsu TC, Suyama Y

Journal of Plant Research, Vol.136, Issue.3, Pages.333-348, 2023.

Spiranthes minamitaniana (Orchidaceae), a new orchid species from Japan based on morphological and phylogenetic data

Kenji Suetsugu, Shun K. Hirota, Yoshihisa Suyama

Phytotaxa, Vol.599, Issue.3, Pages.139-149, 2023.

https://hdl.handle.net/20.500.14094/0100489465

Phylogeography of the temperate grassland plant Tephroseris kirilowii (Asteraceae) inferred from multiplexed inter‑simple sequence repeat genotyping by sequencing (MIG‑seq) data

Tomoka Sakaba, Akiko Soejima, Shinji Fujii, Hajime Ikeda, Takaya Iwasaki, Hiroaki Saito, Yoshihisa Suyama, Ayumi Matsuo, Andrey E. Kozhevnikov, Zoya V. Kozhevnikova, Hongfeng Wang, Siqi Wang, Jae‑Hong Pak, Noriyuki Fujii

Journal of Plant Research, Vol.136, Pages.437-452, 2023.

https://doi.org/10.1007/s10265-023-01452-w

Geographical genetic structure of Lespedeza cuneata var. cuneata in Japan: Necessity of genetic considerations in slope revegetation

Junichi Imanishi, Ayumi Imanishi, Yoshihisa Suyama, Yuji Isagi

Landscape and Ecological Engineering, Vol.19, Pages.583-596, 2023.

https://doi.org/10.1007/s11355-023-00564-8

Aphids increase their rate of survival on emergent aquatic plants through niche construction.

Kodera T., Ohsaki H., Yamawo A.
Journal of Evolutionary Biology,2024

Potential contribution of floral thermogenesis to cold adaptation, distribution pattern, and population structure in skunk cabbage

Mitsuhiko P. Sato, Ayumi Matsuo, Koichi Otsuka, Kohei Takenaka Takano, Masayuki Maki, Kunihiro Okano, Yoshihisa Suyama, Yasuko Ito-Inaba

Ecology and Evolution, Vol.13, Pages.e10319,

https://doi.org/10.1002/ece3.10319

Molecular phylogeny and taxonomy of the genus Nanocnide (Urticaceae) with particular attention to the Ryukyu Islands endemic N. lobata

Satoshi Aoki, Pan Li, Ayumi Matsuo, Yoshihisa Suyama, Motomi Ito

Phytotaxa, Vol.607, No.1, Pages.23-40, 2023.

http://dx.doi.org/10.11646/phytotaxa.607.1.3

First record of Thrixspermum annamense (Orchidaceae) from Iriomote Island, Ryukyu Islands, Japan, with discussions on its intraspecific taxonomy

Kenji Suetsugu, Shun K. Hirota, Koji Yonekura, Atsushi Abe, Yoshihisa Suyama and Tian-Chuan Hsu

Acta Phytotaxonomica et Geobotanica, 74巻, 2号, Pages.121-129, 2023.

https://doi.org/10.18942/apg.202306

MIG-seq 法を用いたゲノムワイドSNP 分析による森林遺伝学研究

陶山佳久

森林遺伝育種, 12巻, 2号, Pages.63-67, 2023.

https://doi.org/10.32135/fgtb.12.2_63

Wax on the surface of Phragmites australis leaves provides enemy-free space for the aphid Hyalopterus pruni

Yamawo A., Mukai H.
Biological Journal of the Linnean Society, 2023.

Plant size, latitude, and phylogeny explain variability in global herbivory

Robinson ML et al. (Herbvar Network, including Yamawo A.)
Science 382 (6671), 2023.
DOI: 10.1126/science.adh8830

Aphids increase their rate of survival on emergent aquatic plants through niche construction.

Kodera T., Ohsaki H., Yamawo A.

Journal of Evolutionary Biology, Vol.37, Issue.3, Pages.283–289, 2024.

https://doi.org/10.1093/jeb/voae011

Plant–mycorrhizal associations may explain the latitudinal gradient of plant community assembly.

Shinohara N., Kobayashi Y., Nishizawa K., Kadowaki K., Yamawo A.

Oikos, Vol.2024, Issue.6, e10367, 2024.

https://doi.org/10.1111/oik.10367

Facilitative interaction networks in experimental microbial community dynamics

Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H

Frontiers in Microbiology, Vol.14, 1153952, 2023.

https://doi.org/10.3389/fmicb.2023.1153952

Computational capability of ecological dynamics

Ushio M, Watanabe K, Fukuda Y, Tokudome Y, Nakajima K

Royal Society Open Science, Vol.10, 221614, 2023.

https://doi.org/10.1098/rsos.221614

Changes of soil chemical properties, microbial biomass and enzymatic activities along a gradient of forest degradation in logged over tropical rain forests, Borneo

Jiang L, Ushio M, Kitayama K

Plant and Soil, Vol.485, Pages.525-536, 2023.

https://doi.org/10.1007/s11104-022-05848-w

Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant

Yoneya K, Ushio M, Miki T

Scientific Reports, Vol.13, 7125, 2023.

https://doi.org/10.1038/s41598-023-32862-4

Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities

Ushio M, Sado T, Fukuchi T, Sasano S, Masuda R, Osada Y, Miya M

eLife, Vol.12, RP85795, 2023.

https://doi.org/10.7554/eLife.85795.2

The effects of the floral infection by a bacterial pathogen in a dioecious plant, Mallotus japonicus (Euphorbiaceae)

Maxime M, Ushio M, Sakai S

Population Ecology, Vol.65, Issue.4, Pages.232-239, 2023.

https://doi.org/10.1002/1438-390X.12110

Collection of environmental DNA from stemflow for monitoring arboreal biodiversity: preliminary validation using lichens

Sakata A, Sado T, Oka S-I, Ushio M, Miya M

MethodsX, Vol.11, 102448,

https://doi.org/10.1016/j.mex.2023.102448

Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics

Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H

Frontiers in Microbiology, Vol.14, 1261137, 2023.

https://doi.org/10.3389/fmicb.2023.1261137

Masting is uncommon in trees that depend on mutualist dispersers in the context of global climate and fertility gradients

Qiu et al. (MASTIF network, including Han Q)

Nature Plants, Vol.9,Issue.7, Pages.1044-1056, 2023.

https://doi.org/10.1038/s41477-023-01446-5

Plant Molecular Phenology and Climate Feedbacks Mediated by BVOCs

Satake, A., Hagiwara, T., Nagano, A., Yamaguchi, N., Sekimoto, K., Shiojiri,K., Sudo, K.
Annual Review of Plant Biology, Vol.75, 2023

DOI:10.1146/annurev-arplant-060223-032108

Linking seed size and number to trait syndromes in trees

Bogdziewicz et al. (MASTIF network, including Han Q)

Global Ecology and Biogeography, Vol.32, Issue.5, Pages.683-694, 2023.

https://doi.org/10.1111/geb.13652

Effects of species traits and ecosystem characteristics on species detection by eDNA metabarcoding in lake fish communities

Doi H, Matsuoka S, Matsuzaki SS, Nagano M, Sato H, Yamanaka H, Matsuhashi S, Yamamoto S, Minamoto T, Araki H,  Ikeda K, Kato A, Kumei K, Maki N, Mitsuzuka T, Takahara T, Toki K, Ueda N, Watanabe T, Yamazoe K, Miya M.

Freshwater Biology, Vol.68, Issue.8, Pages.1346-1358, 2023.

https://doi.org/10.1111/fwb.14107

Synergistic effects of succession and microtopography of moraine on the fungal spatial diversity in a glacier forefield.

Masumoto S,  Mori AS, Nishizawa K, Naka M, Matsuoka S, Wong S, Uchida M

FEMS Microbiology Ecology, Vol.99, Issue.9, fiad090, 2023.

https://doi.org/10.1093/femsec/fiad090

eDNA metabarcoding analysis reveals the consequence of creating ecosystem-scale refugia from deer grazing for the soil microbial communities.

Kadowaki K, Honjo M, Nakamura N, Kitagawa Y, Ishihara MI, Matsuoka S, Tachiki Y, Fukushima K, Sakaguchi S, Miizuki I, Fujiki D, Sakai M, Takayanagi A, Yamasaki M, Tokuchi N, Takahashi D, Nagasawa K, Masuda K.

Environmental DNA, Vol.5, Issue.6, Pages.1732-1742, 2023.

https://doi.org/10.1002/edn3.498

Host-shift speciation proceeded with gene flow in algae covering shells

Osamu Kagawa, Shun K. Hirota, Takumi Saito, Shota Uchida, Hiroaki Watanabe, Ryusuke Miyazoe, Takanobu Yamaguchi, Taiki Matsuno, Kouta Araki, Hinata Wakasugi, Sayaka Suzuki, Genki Kobayashi, Hikaru Miyazaki, Yoshihisa Suyama, Takeaki Hanyuda, Satoshi Chiba

The American Naturalist, Vol.202, No.5, Pages.721-732, 2023.

http://dx.doi.org/10.1086/726221

Twenty-year changes in the composition of a mixed stock of foraging green turtles in the Yaeyama Islands of Japan

Tomoko Hamabata, Masakado Kawata, Satomi Kondo, Ayumi Matsuo, Yoshihisa Suyama, Kazuyuki Suzuki, Kazunari Kameda

Marine Ecology Progress Series, Vol.716, Pages.93-105, 2023.

https://doi.org/10.3354/meps14367

Range shift and introgression of three Japanese Abies species: insights from population genetic data and species distribution modeling

Kentaro Uchiyama, Sayaka Fujii, Ikutaro Tsuyama, Nobuyuki Tanaka, Suzuki Setsuko, Megumi K. Kimura, Yoshihisa Suyama, Yoshihiko Tsumura

Tree Genetics & Genomes, Vol.19, Article number.41, 2023.

https://doi.org/10.1007/s11295-023-01617-7

Demographic history and conservation aspects of two relict shrubs (Daphnimorpha spp., Thymelaeaceae) showing disjunct and restricted distribution in the southern part of Japan

Daiki Takahashi, Yoshihisa Suyama

Tree Genetics & Genomes, Vol.19, Article number.43, 2023.

https://doi.org/10.1007/s11295-023-01618-6

Phylogeographical evidence for historical long-distance dispersal in the flightless stick insect Ramulus mikado

Kenji Suetsugu, Tomonari Nozaki, Shun K Hirota, Shoichi Funaki, Katsura Ito, Kazuki Kurita, Yuji Isagi, Yoshihisa Suyama, Shingo Kaneko

Proceedings of the Royal Society B, Vol.290, Issue.2008, 2023.

https://doi.org/10.1098/rspb.2023.1708

Introduction pathways and evolutionary mechanisms of alien species of Lolium spreading across sandy coasts in Japan

Momoko Hirata, Yumiko Higuchi, Ayumi Matsuo, Mitsuhiko P Sato, Yoshihisa Suyama, Kiyoshi Takako, Akihiro Konuma, Tohru Tominaga, Yoshiko Shimono

Journal of Ecology, Vol.111, Issue.12, Pages.2583-2596, 2023.

https://doi.org/10.1111/1365-2745.14206

Molecular phylogeny and taxonomy of Hosta (Asparagaceae), including five new species, H.kagamiriparia,H.longipedicellata,H.minazukiflora,H.samukazemontana,andH.takiminazukiflora, on Shikoku Island, Japan

Tetsukazu Yahara, Shun Hirota, Seiko Fujii, Yasushi Kokami, Kengo Fuse, Hiroyuki Sato, Shuichiro Tagane, Yoshihisa Suyama

PhytoKeys, Vol.235, Issue.12, Pages.137-187, 2023.

https://doi.org/10.3897/phytokeys.235.99140

Discrimination of Camellia cultivars using iD-NA analysis

Hitomi S. Kikkawa, Mitsuhiko P. Sato, Ayumi Matsuo, Takanori Sasaki, Yoshihisa Suyama, Kouichiro Tsuge

Scientific Reports, Vol.13, Issue.1, Article number.17674, 2023.

https://doi.org/10.1038/s41598-023-44404-z

Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced

Ichiro Tamaki, Mizuo Mizuno, Tatsuo Ohtsuki, Kohtaroh Shutoh, Ryoichi Tabata, Yoshihiro Tsunamoto, Yoshihisa Suyama, Yusuke Nakajima, Naoki Kubo, Takeru Ito, Naohiko Noma, Emiko Harada

Scientific Reports, Vol.13, Article number.20746, 2023.

https://doi.org/10.1038/s41598-023-48079-4

天然記念物ウツクシマツの遺伝構造と自生地保全

前迫ゆり・陶山佳久・廣田峻

保全生態学研究I, 28巻, 2号, Pages.379-391, 2023.

https://doi.org/10.18960/hozen.2228

Genome-wide SNPs reveal clonality and population genetic structure of Nymphoides peltata in Japan (Menyanthaeae)

Akira Asakawa, Shoki Murakami, Sachiko Horie, Ayumi Matsuo, Yoshihisa Suyama, Shinji Fujii, Masayuki Maki

Aquatic Botany, Vol.190, 103720, 2024.

https://doi.org/10.1016/j.aquabot.2023.103720

The phylogenetic reconstruction of the Neotropical cycad genus Ceratozamia (Zamiaceae) reveals disparate patterns of niche evolution

José Said Gutiérrez-Ortega, Miguel Angel Pérez-Farrera*, Ayumi Matsuo, Mitsuhiko P. Sato, Yoshihisa Suyama, Michael Calonje, Andrew P. Vovides, Tadashi Kajita, Yasuyuki Watano

Molecular Phylogenetics and Evolution, Vol.190, 107960, 2024.

https://doi.org/10.1016/j.ympev.2023.107960

Genetic consequences of Last Glacial–Holocene changes in snowfall regime in Arnica mallotopus populations—a plant confined to heavy-snow areas of Japan

Kazutoshi Masuda, Hiroaki Setoguchi, Koki Nagasawa, Shun K. Hirota, Yoshihisa Suyama, Kazuhiro Sawa, Shigeru Fukumoto, Masae Iwamoto Ishihara, Harue Abe, Hayato Tsuboi, Tsuguoki Tango, Sayoko Mori, Shota Sakaguchi

American Journal of Botany, Vol.111, Issue.2, e16275, 2024.

https://doi.org/10.1002/ajb2.16275

Ice-age land bridges to continental islands: repeated migration of the forest-dwelling sable in northeastern Asia

Gohta Kinoshita, Takuma Sato, Shota Murakami, Vladimir Monakhov, Alexey P. Kryukov, Lyubov V. Frisman, Yoshihiro Tsunamoto, Yoshihisa Suyama, Takahiro Murakami, Hitoshi Suzuki, Jun J. Sato

Journal of Biogeography, Vol.51, Issue.5, Pages.924-939, 2024.

https://doi.org/10.1111/jbi.14797

Genetic divergence and ecological adaptation of an eastern North American spring ephemeral Sanguinaria canadensis

Mao-Qin Xia, Yu-Xin Luo, Yoshihisa Suyama, Ayumi Matsuo, Shota Sakaguchi, Yu-Guo Wang, Pan Li

Diversity and Distributions, Vol.30, Issue.4, e13813, 2024.

https://doi.org/10.1111/ddi.13813

The absence of bumblebees on an oceanic island blurs the species boundary of two closely related orchids

Kenji Suetsugu, Shun K. Hirota, Takuto Shitara, Kenya Ishida, Narumi Nakato, Hiroshi Hayakawa, Yoshihisa Suyama

New Phytologist, Vol.241, Issue.3, Pages.1321-1333, 2023.

https://doi.org/10.1111/nph.19325

Double migration of the endangered Tricyrtis formosana (Liliaceae) in Japan

Kaori Tsunenari, Takuro Ito, Masatsugu Yokota, Mayu Shibabayashi, Chiharu Endo, Kuo-Fang Chung, Yoshihisa Suyama, Ayumi Matsuo, Atsushi Abe, Akiyo Naiki, Hiroaki Setoguchi, Takashi Makino, Yuji Isagi

Scientific Reports, Vol.14, Article number.957, 2024.

http://dx.doi.org/10.1038/s41598-024-51431-x

Evolutionary and ecological trends in the Neotropical cycad genus Dioon (Zamiaceae): An example of success of evolutionary stasis

José Said Gutiérrez-Ortega, Miguel Angel Pérez-Farrera, Mitsuhiko P. Sato, Ayumi Matsuo, Yoshihisa Suyama, Andrew P. Vovides, Francisco Molina-Freaner, Tadashi Kajita, Yasuyuki Watano

Ecological Research, Vol.39, Issue.2, Pages.131-158, 2024.

https://doi.org/10.1111/1440-1703.12442

森で繰り広げられる植物間コミュニケーション

塩尻かおり・萩原幹花

Green Age, No.591, Pages.39-43, 2023.

https://www.jpgreen.shop/shopdetail/000000000187/

Small-scale dispersal and gene flow of the agricultural pest two-spotted spider mite in apple orchards: implication from landscape ecological and population genetic analyses

Yasuyuki Komagata, Takaho Oe, Takayuki Sekine, Yuta Kimura, Shun K. Hirota, Hiroya Taguchi, Yoshihisa Suyama

Ecological Research, Vol.39, Issue.3, Pages.341-352, 2024.

https://doi.org/10.1111/1440-1703.12463

Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow

Wei Zhao, Jie Gao, David Hall, Bea Andersson, Jade Bruxaux, Kyle Tomlinson, Andreas D. Drouzas, Yoshihisa Suyama, Xiao-Ru Wang

New Phytologist, Vol.242, Issue.5, Pages.2353-2368, 2024.

https://doi.org/10.1111/nph.19694

Phylogeographic incongruence between two related Geranium species with divergent habitat preferences in East Asia

Seikan Kurata, Shota Sakaguchi, Shun K. Hirota, Osamu Kurashima, Yoshihisa Suyama, Motomi Ito

Ecological Research, Vol.39, Issue.3, Pages.273-288, 2024.

http://dx.doi.org/10.1111/1440-1703.12458

The Emissions Model Intercomparison Project (Emissions-MIP): quantifying model sensitivity to emission characteristics

Ahsan, H., Wang, H. L., Wu, J. B., Wu, M. X., Smith, S. J., Bauer, S., Suchyta, H., Olivié, D., Myhre, G., Matsui, H., Bian, H. S., Lamarque, J. F., Carslaw, K., Horowitz, L., Regayre, L., Chin, M., Schulz, M., Skeie, R. B., Takemura, T., and Naik, V

Atmospheric Chemistry and Physics, Vol.23, Issue.23, Pages.14779-14799, 2023.

https://doi.org/10.5194/acp-23-14779-2023

Effectiveness of emission controls implemented since 2000 on ambient ozone concentrations in multiple timescales in Japan: An emission inventory development and simulation study

Chatani, S., Kitayama, K., Itahashi, S., Irie, H., and Shimadera, H.

Science of The Total Environment, Vol.894, 165058, 2023.

https://doi.org/10.1016/j.scitotenv.2023.165058

Interplay of Climate Change and Air Pollution- Projection of the under-5 mortality attributable to ambient particulate matter (PM2.5) in South Asia

Anita, W. M., Uttajug, A., Seposo, X. T., Sudo, K., Nakata, M., Takemura, T., Takano, H., Fujiwara, T., and Ueda, K.
Environ Res, Vol.248, ARTN 118292, 2024

DOI: 10.1016/j.envres.2024.118292

Air quality and urban climate improvements in the world's most populated region during the COVID-19 pandemic

Damiani, A., Irie, H., Belikov, D., Cordero, R. R., Feron, S., and Ishizaki, N. N.

Environmental Research Letters, Vol.19, No.3, 2023.

DOI 10.1088/1748-9326/ad25a2

Implementation of HONO into the chemistry-climate model CHASER (V4.0): roles in tropospheric chemistry

Ha, P. T. M., Kanaya, Y., Taketani, F., Hernández, M. D. A., Schreiner, B., Pfeilsticker, K., and Sudo, K.

Geoscientific Model Development, Vol.16, Issue.3, 2023.

https://doi.org/10.5194/gmd-16-927-2023

Historical (1960–2014) lightning and LNOx trends and their controlling factors in a chemistry–climate model

He, Y. and Sudo, K.

Atmospheric Chemistry and Physics, Vol.23, Issue.20, Pages.13061-13085, 2023.

https://doi.org/10.5194/egusphere-2023-301