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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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Magota K, Sakaguchi S, Lee JS, Yamamoto M, Takahashi D, Nagano AJ, Setoguchi H. Phylogeographic analysis of Saxifraga fortunei complex (Saxifragaceae) reveals multiple origins of morphological and ecological variations in the Japanese Archipelago. Mol Phylogenet Evol 2021; 163:107230. [PMID: 34133947 DOI: 10.1016/j.ympev.2021.107230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
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.
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Affiliation(s)
- Kana Magota
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan.
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Jung-Sim Lee
- Korean National Arboretum, 415 Gwangneung Sumokwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-Province 11186, Republic of Korea
| | - Masaya Yamamoto
- Hyogo University of Teacher Education, 942-1 Shimokume, Kato, Hyogo 673-1494, Japan
| | - Daiki Takahashi
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
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Kurata S, Sakaguchi S, Hirota SK, Kurashima O, Suyama Y, Nishida S, Ito M. Refugia within refugium of Geranium yesoense (Geraniaceae) in Japan were driven by recolonization into the southern interglacial refugium. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Recent studies have found that geographical fragmentation and recurrent colonization result in complex genetic structures in refugial areas. This phenomenon, known as ‘refugia within refugium’, has been identified from many geographical locations. In Japan, the high-elevation mountains of central Honshu provided an interglacial refugium for alpine plants. Here we focused on the Geranium yesoense complex, which exhibits increased morphological variation in the refugial area, to determine whether this variation was shaped by recurrent colonization, range fragmentation or phenotypic changes independent of population history. We analysed single nucleotide polymorphism data and chloroplast genome sequences. Diversification in the G. yesoense species complex occurred in the mid-Pleistocene. The varieties are distinct entities and suggest the presence of a genetic cluster with highly disjunct distributions, occurring both in northern Japan and in southern refugial areas in central Honshu. Demographic analysis suggests that a single ancestral variety (var. nipponicum) evolved in the alpine region of central Honshu, and that subsequent migration from one of the two diverged northern varieties (var. pseudopratense) led to secondary contact with var. nipponicum during the last glacial period. Recolonization into refugial populations in central Honshu and hybridization between diverged populations have resulted in complex genetic structures among refugial populations.
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Affiliation(s)
- Seikan Kurata
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Aza-yomogida, Naruko Onsen, Osaki City, Miyagi, Japan
| | - Osamu Kurashima
- National Museum of Nature and Science, Ueno-koen, Taito-ku, Tokyo, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Aza-yomogida, Naruko Onsen, Osaki City, Miyagi, Japan
| | - Sachiko Nishida
- Nagoya University Museum, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Motomi Ito
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan
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Polezhaeva MA, Tikhonova NA, Marchuk EA, Modorov MV, Ranyuk MN, Polezhaev AN, Badmayeva NK, Semerikov VL. Genetic structure of a widespread alpine shrub Rhododendron aureum (Ericaceae) across East Asia. JOURNAL OF PLANT RESEARCH 2021; 134:91-104. [PMID: 33398441 DOI: 10.1007/s10265-020-01241-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
The vast territory of East Asia, including southwestern Beringia, is considered to have been almost ice free during the Pleistocene. Cold-resistant flora may have persisted in this region expanding or contracting its range during the climate cooling. Only a few plant genera have been studied with a sampling area across their entire geographic range in East Asia; therefore, the understanding of the biogeographic history of alpine flora in this region remains limited. In the present study, genetic variation and population structure in 21 populations of the alpine shrub Rhododendron aureum across its range in East Asia were assessed using 18 microsatellite loci. Phylogenetic analyses revealed three main genetic groups: Siberia, Northeast, and North Pacific. According to the geographical pattern of genetic diversity, the North Pacific group includes populations from Kamchatka, south of Russian Far East, and territories close to central Japan. This group is the most diverse and likely diverged earlier than the Siberia and Northeast groups. Ecological niche modeling predicts range expansion of this species during the period of cooling and, together with demographic history, suggests that the divergence between the three main genetic groups predated the Last Glacial Maximum. Similar to other cold-resistant species such as Larix sibirica and Juniperus communis, the pattern of genetic diversity of R. aureum supports the survival of the species at high latitudes during the Pleistocene with limited contribution of the southern populations to expansion of the species range to the Northeast region and Siberia.
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Affiliation(s)
- Maria A Polezhaeva
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia.
| | - Natalya A Tikhonova
- V. N. Sukachev Institute of Forest, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Elena A Marchuk
- Botanical Garden-Institute, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Makar V Modorov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Maryana N Ranyuk
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Alexey N Polezhaev
- Institute of the Biological Problems of the North, Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Natalya K Badmayeva
- Institute of General and Experimental Biology, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude, Russia
| | - Vladimir L Semerikov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
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Takaishi A, Kozhevnikov AE, Kozhevnikova ZV, Ikeda H, Fujii N, Soejima A. Phylogeography of Pulsatilla cernua (Ranunculaceae), a grassland species, in Japan. Ecol Evol 2019; 9:7262-7272. [PMID: 31380048 PMCID: PMC6662557 DOI: 10.1002/ece3.5298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/26/2019] [Accepted: 05/08/2019] [Indexed: 11/22/2022] Open
Abstract
The genetic diversity and structure of Pulsatilla cernua, a continental-grassland relict, were investigated using variations in chloroplast DNA (cpDNA) and microsatellites of nuclear DNA. In the analyses of three cpDNA regions, 17 haplotypes were found in 24 populations of P. cernua from Japan, Korea, and Russia. Although the route and time of migration between the continent of Asia and Japan could not be well resolved, the cpDNA haplotype network suggests the existence of several ancient lineages in Japan and a recent secondary migration from Japan to the continent. Microsatellite analyses did not indicate genetic structure among the Japanese populations, indicating the existence of gene flow across the distribution area until recently. These results indicate that the present fragmentation of P. cernua in Japan may reflect a rapid, recent reduction from a previously large, continuous distribution.
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Affiliation(s)
- Asuka Takaishi
- Department of Biological Science, Faculty of Advanced Science and TechnologyKumamoto UniversityKumamotoJapan
| | - Andrey E. Kozhevnikov
- Federal Scientific Center of the East Asia Terrestrial BiodiversityFar Eastern Branch of the Russian Academy of SciencesVladivostokRussia
| | - Zoya V. Kozhevnikova
- Federal Scientific Center of the East Asia Terrestrial BiodiversityFar Eastern Branch of the Russian Academy of SciencesVladivostokRussia
| | - Hajime Ikeda
- Institute of Plant Science and ResourcesOkayama UniversityKurashikiJapan
| | - Noriyuki Fujii
- Department of Biological Science, Faculty of Advanced Science and TechnologyKumamoto UniversityKumamotoJapan
| | - Akiko Soejima
- Department of Biological Science, Faculty of Advanced Science and TechnologyKumamoto UniversityKumamotoJapan
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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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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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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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