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Ikeda H. Decades-long phylogeographic issues: complex historical processes and ecological factors on genetic structure of alpine plants in the Japanese Archipelago. JOURNAL OF PLANT RESEARCH 2022; 135:191-201. [PMID: 35166981 PMCID: PMC8894158 DOI: 10.1007/s10265-022-01377-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Mountain regions are important places for biodiversity, where organisms could persist throughout prolonged periods and accumulate genetic divergence as well as promote speciation. Roles of mountains for biodiversity have been exclusively discussed in regions that have specifically diverse species or covered with ice-sheets during the Pleistocene glacial periods, whereas the importance of mountainous regions in East Asia has been less disputed. High mountains in the Japanese Archipelago, located at the eastern edge of the Eurasia continent, have one of southernmost populations of alpine and arctic-alpine plants that are also distributed in the northern Pacific and/or the circumarctic regions. Phylogeographic studies on the Japanese alpine plants have excluded their possible ephemeral occurrence during the current warm period, and rather, suggest persistence of alpine plants throughout several cycles of climate changes in the Pleistocene on high mountains in central Honshu, the main island of the Japanese Archipelago. In this review, I look through decade long phylogeographic studies and show complicated patterns of range dynamics of Japanese alpine plants. In addition, I note recent findings of genetic relationships of Japanese populations of alpine and/or arctic-alpine plants with those in northern regions and their possible ecological divergence in the Japanese Archipelago. Taken together, I provide several issues for understanding historical processes that established distribution of alpine plants following climate changes as well as their diversification and propose importance of Japanese populations of alpine plants on biodiversity in alpine communities across broader range, especially in the northern Pacific region.
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Affiliation(s)
- Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
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2
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Ikeda H, Suzuki T, Oka Y, Gustafsson ALS, Brochmann C, Mochizuki N, Nagatani A. Divergence in red light responses associated with thermal reversion of phytochrome B between high- and low-latitude species. THE NEW PHYTOLOGIST 2021; 231:75-84. [PMID: 33817798 DOI: 10.1111/nph.17381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Phytochromes play a central role in mediating adaptive responses to light and temperature throughout plant life cycles. Despite evidence for adaptive importance of natural variation in phytochromes, little information is known about molecular mechanisms that modulate physiological responses of phytochromes in nature. We show evolutionary divergence in physiological responses relevant to thermal stability of a physiologically active form of phytochrome (Pfr) between two sister species of Brassicaceae growing at different latitudes. The higher latitude species (Cardamine bellidifolia; Cb) responded more strongly to light-limited conditions compared with its lower latitude sister (C. nipponica; Cn). Moreover, CbPHYB conferred stronger responses to both light-limited and warm conditions in the phyB-deficient mutant of Arabidopsis thaliana than CnPHYB: that is Pfr CbphyB was more stable in nuclei than CnphyB. Our findings suggest that fine tuning Pfr stability is a fundamental mechanism for plants to optimise phytochrome-related traits in their evolution and adapt to spatially varying environments, and open a new avenue to understand molecular mechanisms that fine tune phytochrome responses in nature.
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Affiliation(s)
- Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Tomomi Suzuki
- Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo, Kyoto, 606-8502, Japan
| | - Yoshito Oka
- Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo, Kyoto, 606-8502, Japan
| | - A Lovisa S Gustafsson
- Natural History Museum, University of Oslo, PO Box 1172, Blindern, Oslo, NO-0318, Norway
| | - Christian Brochmann
- Natural History Museum, University of Oslo, PO Box 1172, Blindern, Oslo, NO-0318, Norway
| | - Nobuyoshi Mochizuki
- Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo, Kyoto, 606-8502, Japan
| | - Akira Nagatani
- Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo, Kyoto, 606-8502, Japan
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Kobayashi H, Haino Y, Iwasaki T, Tezuka A, Nagano AJ, Shimada S. ddRAD-seq based phylogeographic study of Sargassum thunbergii (Phaeophyceae, Heterokonta) around Japanese coast. MARINE ENVIRONMENTAL RESEARCH 2018; 140:104-113. [PMID: 29895505 DOI: 10.1016/j.marenvres.2018.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Using genome-wide SNP data obtained from high-throughput techniques based on double digest restriction site-associated DNA sequencing (ddRAD-seq), we elucidated the migration history and genetic diversity of the Japanese population of the ecologically important brown seaweed Sargassum thunbergii (Mertens ex Roth) Kuntze. STRUCTURE and NeighborNet analyses showed a clear genetic differentiation among populations of four geographic regions: Kyushu (POP1); Sea of Japan (POP2); Hokkaido and Tohoku (POP3); and Pacific coast from Kyushu to Kanto (POP4). Approximate Bayesian Computation (ABC) analysis indicated that POP4 diverged first, followed by the separation between POP2 (the largest effective population size) and POP3; POP1 was the last to form, shaped by the mixture of POP2 (73%) and POP4 (27%). High genetic diversity was detected in POP1 and POP2, whereas low genetic diversity was detected in POP3 and POP4. These results indicated that S. thunbergii populations of Kyushu and the Sea of Japan might have been maintained as large and stable populations gathered different lineages from China, Korea and/or Japan.
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Affiliation(s)
- Honoka Kobayashi
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan
| | - Yuka Haino
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan
| | - Takaya Iwasaki
- Faculty of Science, Kanagawa University, Tsuchiya 2946, Hiratsuka, Kanagawa, 259-1293, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
| | - Satoshi Shimada
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan.
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Ikeda H, Eidesen PB, Yakubov V, Barkalov V, Brochmann C, Setoguchi H. Late Pleistocene origin of the entire circumarctic range of the arctic-alpine plant Kalmia procumbens. Mol Ecol 2017; 26:5773-5783. [PMID: 28815785 DOI: 10.1111/mec.14325] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 08/06/2017] [Accepted: 08/08/2017] [Indexed: 01/18/2023]
Abstract
The circumarctic ranges of arctic-alpine plants are thought to have been established in the late Pliocene/early Pleistocene, when the modern arctic tundra was formed in response to climate cooling. Previous findings of range-wide genetic structure in arctic-alpine plants have been thought to support this hypothesis, but few studies have explicitly addressed the temporal framework of the genetic structure. Here, we estimated the demographic history of the genetic structure in the circumarctic Kalmia procumbens using sequences of multiple nuclear loci and examined whether its genetic structure reflects prolonged isolation throughout the Pleistocene. Both Bayesian clustering and phylogenetic analyses revealed genetic distinction between alpine and arctic regions, whereas detailed groupings were somewhat discordant between the analyses. By assuming a population grouping based on the phylogenetic analyses, which likely reflects a deeper intraspecific divergence, we conducted model-based analyses and demonstrated that the intraspecific genetic divergence in K. procumbens likely originated during the last glacial period. Thus, there is no need to postulate range separation throughout the Pleistocene to explain the current genetic structure in this species. This study demonstrates that range-wide genetic structure in arctic-alpine plants does not necessarily result from the late Pliocene/early Pleistocene origin of their circumarctic ranges and emphasizes the importance of a temporal framework of the current genetic structure for understanding the biogeographic history of the arctic flora.
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Affiliation(s)
- Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | | | - Valentin Yakubov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Vyacheslav Barkalov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | | | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto, Japan
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Yoichi W, Tamaki I, Sakaguchi S, Song JS, Yamamoto SI, Tomaru N. Population demographic history of a temperate shrub, Rhododendron weyrichii (Ericaceae), on continental islands of Japan and South Korea. Ecol Evol 2016; 6:8800-8810. [PMID: 28035270 PMCID: PMC5192946 DOI: 10.1002/ece3.2576] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/04/2016] [Accepted: 10/06/2016] [Indexed: 01/18/2023] Open
Abstract
Continental islands provide opportunities for testing the effects of isolation and migration on genetic variation in plant populations. In characteristic of continental islands is that the geographic connections between these islands, which are currently distinguished by seaways, have experienced fluctuations caused by sea‐level changes due to climate oscillations during the Quaternary. Plant populations on the islands have migrated between these islands via the exposed seafloors or been isolated. Here, we examined the demographic history of a temperate shrub, Rhododendron weyrichii, which is distributed in the southwestern parts of the Japanese archipelago and on an island of South Korea, using statistical phylogeographic approaches based on the DNA sequences of two chloroplast and eight nuclear loci in samples analyzed from 18 populations on eight continental islands, and palaeodistribution modeling. Time estimates for four island populations indicate that the durations of vicariance history are different between these populations, and these events have continued since the last glacial or may have predated the last glacial. The constancy or expansion of population sizes on the Japanese islands, and in contrast a bottleneck in population size on the Korean island Jeju, suggests that these islands may have provided different conditions for sustaining populations. The result of palaeodistribution modeling indicates that the longitudinal range of the species as a whole has not changed greatly since the last glacial maximum. These results indicate that exposed seafloors during the glacial period formed both effective and ineffective migration corridors. These findings may shed light on the effects of seafloor exposure on the migration of plants distributed across continental islands.
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Affiliation(s)
- Watanabe Yoichi
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan; Present address: Graduate School of Horticulture Chiba University Matsudo 648 Matsudo Chiba 271-8510 Japan
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture Mino Gifu Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
| | - Jong-Suk Song
- Department of Biological Science College of Natural Sciences Andong National University Andong Gyeongbuk Korea
| | | | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
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Burgarella C, Chantret N, Gay L, Prosperi J, Bonhomme M, Tiffin P, Young ND, Ronfort J. Adaptation to climate through flowering phenology: a case study in
Medicago truncatula. Mol Ecol 2016; 25:3397-415. [DOI: 10.1111/mec.13683] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Concetta Burgarella
- UMR 232 DIADE/DYNADIV Institut de Recherche pour le Developpement (IRD) 911 avenue Agropolis BP 64501, 34394 Montpellier France
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Nathalie Chantret
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Laurène Gay
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Jean‐Marie Prosperi
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Maxime Bonhomme
- UPS Laboratoire de Recherche en Sciences Végétales Université de Toulouse BP42617, Auzeville F‐31326 Castanet‐Tolosan France
- Laboratoire de Recherche en Sciences Végétales CNRS BP42617, Auzeville F‐31326 Castanet‐Tolosan France
| | - Peter Tiffin
- Department of Plant Biology University of Minnesota St. Paul MN 55108 USA
| | - Nevin D. Young
- Department of Plant Biology University of Minnesota St. Paul MN 55108 USA
- Department of Plant Pathology University of Minnesota St. Paul MN 55108 USA
| | - Joelle Ronfort
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
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Importance of demographic history for phylogeographic inference on the arctic-alpine plant Phyllodoce caerulea in East Asia. Heredity (Edinb) 2015; 116:232-8. [PMID: 26531250 DOI: 10.1038/hdy.2015.95] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 11/08/2022] Open
Abstract
Arctic-alpine plants have enormous ranges in the Northern Hemisphere. Phylogeographic studies have provided insights into their glacial survival as well as their postglacial colonization history. However, our understanding of the population dynamics of disjunct alpine populations in temperate regions remains limited. During Pleistocene cold periods, alpine populations of arctic-alpine species in East Asia were either connected to an ice-free Beringia refugium or they persisted with prolonged isolation after their establishment. To estimate which of these scenarios is more likely, we elucidated the genetic structure of Phyllodoce caerulea (Ericaceae) in Beringia and northern Japan, East Asia. Sequence variation in multiple nuclear loci revealed that P. caerulea can be distinguished into northern and southern groups. A demographic analysis demonstrated that the north-south divergence did not predate the last glacial period and detected introgression from Phyllodoce aleutica, relative widely distributed in East Asia, exclusively into the southern group. Therefore, although there has been genetic divergence between northern Japan and Beringia in P. caerulea, the divergence is unlikely to have resulted from their prolonged geographic separation throughout several cycles of glacial and interglacial periods. Instead, our study suggests that the introgression contributed to the genetic divergence of P. caerulea and that the range of P. caerulea was plausibly connected between northern Japan and Beringia during the last glacial period. Overall, our study not only provides a biogeographic insight into alpine populations of arctic-alpine plants in East Asia but also emphasizes the importance of careful interpretation of genetic structure for inferring phylogeographic history.
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Tao J, Qi Q, Kang M, Huang H. Adaptive Molecular Evolution of PHYE in Primulina, a Karst Cave Plant. PLoS One 2015; 10:e0127821. [PMID: 26030408 PMCID: PMC4452542 DOI: 10.1371/journal.pone.0127821] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 04/19/2015] [Indexed: 12/24/2022] Open
Abstract
Limestone Karst areas possess high levels of biodiversity and endemism. Primulina is a typical component of Karst endemic floras. The high species richness and wide distribution in various Karst microenvironments make the genus an idea model for studying speciation and local adaptation. In this study, we obtained 10 full-length sequences of the phytochrome PHYE from available transcriptome resources of Primulina and amplified partial sequences of PHYE from the genomic DNA of 74 Primulina species. Then, we used maximum-likelihood approaches to explore molecular evolution of PHYE in this Karst cave plant. The results showed that PHYE was dominated by purifying selection in both data sets, and two sites were identified as potentially under positive selection. Furthermore, the ω ratio varies greatly among different functional domains of PHYE and among different species lineages. These results suggest that potential positive selection in PHYE might have played an important role in the adaption of Primulina to heterogeneous light environments in Karst regions, and different species lineages might have been subjected to different selective pressures.
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Affiliation(s)
- Junjie Tao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingwen Qi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (MK); (HH)
| | - Hongwen Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (MK); (HH)
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Ikeda H, Yoneta Y, Higashi H, Eidesen PB, Barkalov V, Yakubov V, Brochmann C, Setoguchi H. Persistent history of the bird-dispersed arctic-alpine plant Vaccinium vitis-idaea L. (Ericaceae) in Japan. JOURNAL OF PLANT RESEARCH 2015; 128:437-444. [PMID: 25773306 DOI: 10.1007/s10265-015-0709-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 12/21/2014] [Indexed: 06/04/2023]
Abstract
Arctic-alpine plants have expanded and contracted their ranges in response to the Pleistocene climate oscillations. Today, many arctic-alpine plants have vast distributions in the circumarctic region as well as marginal, isolated occurrences in high mountains at lower latitudes. These marginal populations may represent relict, long-standing populations that have persisted for several cycles of cold and warm climate during the Pleistocene, or recent occurrences that either result from southward step-wise migration during the last glacial period or from recent long-distance dispersal. In light of these hypotheses, we investigated the biogeographic history of the marginal Japanese populations of the widespread arctic-alpine plant Vaccinium vitis-idaea (Ericaceae), which is bird-dispersed, potentially over long distances. We sequenced three nuclear loci and one plastid DNA region in 130 individuals from 65 localities covering its entire geographic range, with a focus on its marginal populations in Japan. We found a homogenous genetic pattern across its enormous range based on the loci analysed, in contrast to the geographically structured variation found in a previous study of amplified fragment length polymorphisms in this species. However, we found several unique haplotypes in the Japanese populations, excluding the possibility that these marginal populations result from recent southward migration. Thus, even though V. vitis-idaea is efficiently dispersed via berries, our study suggests that its isolated populations in Japan have persisted during several cycles of cold and warm climate during the Pleistocene.
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Affiliation(s)
- Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan,
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Ikeda H, Yakubov V, Barkalov V, Setoguchi H. Molecular evidence for ancient relicts of arctic-alpine plants in East Asia. THE NEW PHYTOLOGIST 2014; 203:980-988. [PMID: 24889813 DOI: 10.1111/nph.12863] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/22/2014] [Indexed: 06/03/2023]
Abstract
Following climate cooling at the end of the Tertiary, arctic-alpine plants attained most of their extant species diversity. Because East Asia was not heavily glaciated, the importance of this region as a location for the long-term persistence of these species and their subsequent endemism during the Pleistocene was proposed in early discussions of phytogeography. However, this hypothesis remains to be fully tested. Here, we address this hypothesis by elucidating the phylogenetic history of Phyllodoce (Ericaceae). A phylogenetic tree based on multiple nuclear loci revealed that Phyllodoce nipponica was not derived from widespread species such as the arctic-alpine Phyllodoce caerulea, but rather represented an independent lineage sister to the clade of widespread relatives. Molecular dating indicated a mid-Pleistocene divergence of P. nipponica. These findings exclude the hypothesis that P. nipponica was derived from an arctic-alpine species that extended its range southwards during recent glacial periods. Instead, our results support the hypothesis that P. nipponica is an ancestral species which persisted in the Japanese archipelago during the mid- and late Pleistocene. Our findings demonstrate support for the early proposal and shed light on the importance of the Japanese archipelago for the evolution and persistence of arctic-alpine species.
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Affiliation(s)
- Hajime Ikeda
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, 305-0005, Ibaraki, Japan
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Ikeda H, Higashi H, Yakubov V, Barkalov V, Setoguchi H. Phylogeographical study of the alpine plantCassiope lycopodioides(Ericaceae) suggests a range connection between the Japanese archipelago and Beringia during the Pleistocene. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hajime Ikeda
- Department of Botany; National Museum of Nature and Science; 4-1-1 Amakubo Tsukuba Ibaraki 305-0005 Japan
- Institute of Plant Science and Resources; Okayama University; 2-20-1 Chuo Kurashiki Okayama 710-0046 Japan
| | - Hiroyuki Higashi
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-nihonmatsu-cho Sakyo-ku Kyoto 606-8501 Japan
| | - Valentin Yakubov
- Institute of Biology and Soil Sciences; Russian Academy of Sciences; Far East Branch Vladivostok 690022 Russia
| | - Vyacheslav Barkalov
- Institute of Biology and Soil Sciences; Russian Academy of Sciences; Far East Branch Vladivostok 690022 Russia
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-nihonmatsu-cho Sakyo-ku Kyoto 606-8501 Japan
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McEwen JR, Vamosi JC, Rogers SM. Natural selection and neutral evolution jointly drive population divergence between alpine and lowland ecotypes of the allopolyploid plant Anemone multifida (Ranunculaceae). PLoS One 2013; 8:e68889. [PMID: 23874801 PMCID: PMC3715535 DOI: 10.1371/journal.pone.0068889] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 06/02/2013] [Indexed: 11/18/2022] Open
Abstract
Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst = 0.074-0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST = 0.041-0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.
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Affiliation(s)
- Jamie R McEwen
- University of British Columbia, Department of Botany, Vancouver, BC, Canada.
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Ikeda H, Setoguchi H. A multilocus sequencing approach reveals the cryptic phylogeographical history ofPhyllodoce nipponica Makino (Ericaceae). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Hajime Ikeda
- Department of Botany; National Museum of Nature and Science; 4-1-1 Amakubo; Tsukuba; Ibaraki; 305-0005; Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-nihonmatsu-cho; Sakyo-ku; Kyoto; 606-8501; Japan
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References. Mol Ecol 2012. [DOI: 10.1002/9780470979365.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Schoville SD, Barreto FS, Moy GW, Wolff A, Burton RS. Investigating the molecular basis of local adaptation to thermal stress: population differences in gene expression across the transcriptome of the copepod Tigriopus californicus. BMC Evol Biol 2012; 12:170. [PMID: 22950661 PMCID: PMC3499277 DOI: 10.1186/1471-2148-12-170] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 08/30/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Geographic variation in the thermal environment impacts a broad range of biochemical and physiological processes and can be a major selective force leading to local population adaptation. In the intertidal copepod Tigriopus californicus, populations along the coast of California show differences in thermal tolerance that are consistent with adaptation, i.e., southern populations withstand thermal stresses that are lethal to northern populations. To understand the genetic basis of these physiological differences, we use an RNA-seq approach to compare genome-wide patterns of gene expression in two populations known to differ in thermal tolerance. RESULTS Observed differences in gene expression between the southern (San Diego) and the northern (Santa Cruz) populations included both the number of affected loci as well as the identity of these loci. However, the most pronounced differences concerned the amplitude of up-regulation of genes producing heat shock proteins (Hsps) and genes involved in ubiquitination and proteolysis. Among the hsp genes, orthologous pairs show markedly different thermal responses as the amplitude of hsp response was greatly elevated in the San Diego population, most notably in members of the hsp70 gene family. There was no evidence of accelerated evolution at the sequence level for hsp genes. Among other sets of genes, cuticle genes were up-regulated in SD but down-regulated in SC, and mitochondrial genes were down-regulated in both populations. CONCLUSIONS Marked changes in gene expression were observed in response to acute sub-lethal thermal stress in the copepod T. californicus. Although some qualitative differences were observed between populations, the most pronounced differences involved the magnitude of induction of numerous hsp and ubiquitin genes. These differences in gene expression suggest that evolutionary divergence in the regulatory pathway(s) involved in acute temperature stress may offer at least a partial explanation of population differences in thermal tolerance observed in Tigriopus.
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Affiliation(s)
- Sean D Schoville
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA.
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Keller SR, Levsen N, Olson MS, Tiffin P. Local Adaptation in the Flowering-Time Gene Network of Balsam Poplar, Populus balsamifera L. Mol Biol Evol 2012; 29:3143-52. [DOI: 10.1093/molbev/mss121] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Ludeña B, Chabrillange N, Aberlenc-Bertossi F, Adam H, Tregear JW, Pintaud JC. Phylogenetic utility of the nuclear genes AGAMOUS 1 and PHYTOCHROME B in palms (Arecaceae): an example within Bactridinae. ANNALS OF BOTANY 2011; 108:1433-44. [PMID: 21828068 PMCID: PMC3219496 DOI: 10.1093/aob/mcr191] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Molecular phylogenetic studies of palms (Arecaceae) have not yet provided a fully resolved phylogeny of the family. There is a need to increase the current set of markers to resolve difficult groups such as the Neotropical subtribe Bactridinae (Arecoideae: Cocoseae). We propose the use of two single-copy nuclear genes as valuable tools for palm phylogenetics. METHODS New primers were developed for the amplification of the AGAMOUS 1 (AG1) and PHYTOCHROME B (PHYB) genes. For the AGAMOUS gene, the paralogue 1 of Elaeis guineensis (EgAG1) was targeted. The region amplified contained coding sequences between the MIKC K and C MADS-box domains. For the PHYB gene, exon 1 (partial sequence) was first amplified in palm species using published degenerate primers for Poaceae, and then specific palm primers were designed. The two gene portions were sequenced in 22 species of palms representing all genera of Bactridinae, with emphasis on Astrocaryum and Hexopetion, the status of the latter genus still being debated. KEY RESULTS The new primers designed allow consistent amplification and high-quality sequencing within the palm family. The two loci studied produced more variability than chloroplast loci and equally or less variability than PRK, RPBII and ITS nuclear markers. The phylogenetic structure obtained with AG1 and PHYB genes provides new insights into intergeneric relationships within the Bactridinae and the intrageneric structure of Astrocaryum. The Hexopetion clade was recovered as monophyletic with both markers and was weakly supported as sister to Astrocaryum sensu stricto in the combined analysis. The rare Astrocaryum minus formed a species complex with Astrocaryum gynacanthum. Moreover, both AG1 and PHYB contain a microsatellite that could have further uses in species delimitation and population genetics. CONCLUSIONS AG1 and PHYB provide additional phylogenetic information within the palm family, and should prove useful in combination with other genes to improve the resolution of palm phylogenies.
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Affiliation(s)
- Bertha Ludeña
- Institut de Recherche pour le Développement (IRD), DYNADIV Group
| | - Nathalie Chabrillange
- IRD/CIRAD Palm Developmental Biology Group, UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Frédérique Aberlenc-Bertossi
- IRD/CIRAD Palm Developmental Biology Group, UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Hélène Adam
- IRD/CIRAD Palm Developmental Biology Group, UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - James W. Tregear
- IRD/CIRAD Palm Developmental Biology Group, UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
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Vermeer KMCA, Dicke M, de Jong PW. The potential of a population genomics approach to analyse geographic mosaics of plant--insect coevolution. Evol Ecol 2010. [DOI: 10.1007/s10682-010-9452-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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