Journal of Plant Research - <Virtual Issue No. 5>
Phylogeographic studies in the Japanese Archipelago: from geographic patterns of genetic variation to biodiversity in plants
Edited by Hajime Ikeda
Phylogeographic studies have investigated genetic variation and structure within species or closely related lineages and are fundamental for understanding factors and processes of genetic divergence as well as speciation. This virtual issue collects 35 papers on phylogeographic studies published in the Journal of Plant Research and focuses on three major topics in biodiversity: (1) biogeography, (2) systematics, and (3) evolution.
Table of contents
Editorial - Free access!
Ikeda H (2023) Phylogeographic studies in the Japanese Archipelago: from geographic patterns of genetic variation to biodiversity in plants. (this opens in a new tab) Journal of Plant Research. https://doi.org/10.1007/s10265-023-01478-0
(1) Biogeographic insights
Range shifts in the Japanese Archipelago:
Photo credit © Hajime Ikeda
Hiraoka K, Tomaru N (2009) Genetic divergence in nuclear genomes between populations of Fagus crenata along the Japan Sea and Pacific sides of Japan. (this opens in a new tab) Journal of Plant Research 122:269-282
Ohsawa T, Tsuda Y, Saito Y, Ide Y (2011) The genetic structure of Quercus crispula in northeastern Japan as revealed by nuclear simple sequence repeat loci. (this opens in a new tab) Journal of Plant Research 124:645-654
Sugahara K, Kaneko Y, Ito S, Yamanaka K, Sakio H, Hoshizaki K, Suzuki W, Yamanaka N, Setoguchi H (2011) Phylogeography of Japanese horse chestnut (Aesculus turbinata) in the Japanese Archipelago based on chloroplast DNA haplotypes. (this opens in a new tab) Journal of Plant Research 124:75-83.
Tsuda Y, Kimura M, Kato S, Katsuki T, Mukai Y, Tsumura Y (2009) Genetic structure of Cerasus jamasakura, a Japanese flowering cherry, revealed by nuclear SSRs: implications for conservation. (this opens in a new tab) Journal of Plant Research 122:367-375
Iwasaki T, Aoki K, Seo A, Murakami N (2012) Comparative phylogeography of four component species of deciduous broad-leaved forests in Japan based on chloroplast DNA variation. (this opens in a new tab) Journal of Plant Research 125:207-221
Aoki K, Suzuki T, Hsu TW, Murakami N (2004) Phylogeography of the component species of broad-leaved evergreen forests in Japan, based on chloroplast DNA variation. (this opens in a new tab) Journal of Plant Research 117:77-94
Toyama H, Yahara T (2009) Comparative phylogeography of two closely related Viola species occurring in contrasting habitats in the Japanese archipelago. (this opens in a new tab) Journal of Plant Research 122:389-401
Aizawa M, Yoshimaru H, Takahashi M, Kawahara T, Sugita H, Saito H, Sabirov RN (2015) Genetic structure of Sakhalin spruce (Picea glehnii) in northern Japan and adjacent regions revealed by nuclear microsatellites and mitochondrial gene sequences. (this opens in a new tab)Journal of Plant Research 128:91-102
Ikeda H, Setoguchi H (2006) Phylogeography of Arcterica nana (Ericaceae) suggests another range expansion history of Japanese alpine plants. (this opens in a new tab) Journal of Plant Research 119:489-495
Ikeda H, Setoguchi H (2009) The homogenous genetic structure and inferred unique history of range shifts during the Pleistocene climatic oscillations of Arcterica nana (Maxim.) Makino (Ericaceae). (this opens in a new tab) Journal of Plant Research 122:141-151
Fujii N, Ueda K, Watano Y, Shimizu T (1997) Intraspecific sequence variation of chloroplast DNA in Pedicularis chamissonis Steven (Scrophulariaceae) and geographic structuring of the Japanese ''Alpine'' plants. (this opens in a new tab) Journal of Plant Research 110:195-207
Fujii N, Ueda K, Watano Y, Shimizu T (1999) Further analysis of intraspecific sequence variation of chloroplast DNA in Primula cuneifolia Ledeb. (Primulaceae): Implications for biogeography of the Japanese alpine flora. (this opens in a new tab) Journal of Plant Research 112:87-95
Tsuda Y, Ide Y (2010) Chloroplast DNA phylogeography of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in Japan. (this opens in a new tab) Journal of Plant Research 123:343-353
Tamaki I, Kawashima N, Setsuko S, Lee JH, Itaya A, Yukitoshi K, Tomaru N (2019) Population genetic structure and demography of Magnolia kobus: variety borealis is not supported genetically. (this opens in a new tab)Journal of Plant Research 132:741-758 [Open Access]
Ikeda H (2022) Decades-long phylogeographic issues: complex historical processes and ecological factors on genetic structure of alpine plants in the Japanese Archipelago. (this opens in a new tab) Journal of Plant Research 135:191-201 [Open Access]
Dispersal to and around the Japanese Archipelago:
Photo credit © Hajime Ikeda
Setoguchi H, Yukawa T, Tokuoka T, Momohara A, Sogo A, Takaso T, Peng CI (2006) Phylogeography of the genus Cardiandra based on genetic variation in cpDNA sequences. (this opens in a new tab) Journal of Plant Research 119:401-405
Hiraoka Y, Tamaki I, Watanabe A (2018) The origin of wild populations of Toxicodendron succedaneum on mainland Japan revealed by genetic variation in chloroplast and nuclear DNA. (this opens in a new tab) Journal of Plant Research 131:225-238
Aizawa M, Kim ZS, Yoshimaru H (2012) Phylogeography of the Korean pine (Pinus koraiensis) in northeast Asia: inferences from organelle gene sequences. (this opens in a new tab) Journal of Plant Research 125:713-723
Lee JH, Lee DH, Choi BH (2013) Phylogeography and genetic diversity of East Asian Neolitsea sericea (Lauraceae) based on variations in chloroplast DNA sequences. (this opens in a new tab) Journal of Plant Research 126:193-202
Jin DP, Lee JH, Xu B, Choi BH (2016) Phylogeography of East Asian Lespedeza buergeri (Fabaceae) based on chloroplast and nuclear ribosomal DNA sequence variations. (this opens in a new tab) Journal of Plant Research 129:793-805
Sata H, Shimizu M, Iwasaki T, Ikeda H, Soejima A, Kozhevnikov AE, Kozhevnikova ZV, Im HT, Jang SK, Azuma T, Nagano AJ, Fujii N (2021) Phylogeography of the East Asian grassland plant, Viola orientalis (Violaceae), inferred from plastid and nuclear restriction site-associated DNA sequencing data. (this opens in a new tab) Journal of Plant Research 134:1181-1198
Sakaba T, Soejima A, Fujii S, Ikeda H, Iwasaki T, Saito H, Suyama Y, Matsuo A, Kozhevnikov AE, Kozhevnikova ZV, Wang H, Wang S, Pak JH, Fujii N (2023) Phylogeography of the temperate grassland plant Tephroseris kirilowii (Asteraceae) inferred from multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) data. (this opens in a new tab) Journal of Plant Research 136:437-452
Polezhaeva MA, Tikhonova NA, Marchuk EA, Modorov MV, Ranyuk MN, Polezhaev AN, Badmayeva NK, Semerikov VL (2021) Genetic structure of a widespread alpine shrub Rhododendron aureum (Ericaceae) across East Asia. (this opens in a new tab) Journal of Plant Research 134:91-104
Higashi H, Ikeda H, Setoguchi H (2012) Population fragmentation causes randomly fixed genotypes in populations of Arabidopsis kamchatica in the Japanese Archipelago. (this opens in a new tab) Journal of Plant Research 125:223-233
Ikeda H, Yoneta Y, Higashi H, Eidesen PB, Barkalov V, Yakubov V, Brochmann C, Setoguchi H (2015) Persistent history of the bird-dispersed arctic-alpine plant Vaccinium vitis-idaea L. (Ericaceae) in Japan. (this opens in a new tab) Journal of Plant Research 128:437-444
Ikeda H (2022) Decades-long phylogeographic issues: complex historical processes and ecological factors on genetic structure of alpine plants in the Japanese Archipelago. (this opens in a new tab) Journal of Plant Research 135:191-201 [Open Access]
Sakata Y, Itami J, Isagi Y, Ohgushi T (2015) Multiple and mass introductions from limited origins: genetic diversity and structure of Solidago altissima in the native and invaded range. (this opens in a new tab) Journal of Plant Research 128:909-921
(2) Systematic insights
Inamura A, Ohashi Y, Sato E, Yoda Y, Masuzawa T, Ito M, Yoshinaga K (2000) Intraspecific sequence variation of chloroplast DNA reflecting variety and geographical distribution of Polygonum cuspidatum (Polygonaceae) in Japan. (this opens in a new tab) Journal of Plant Research 113:419-426
Fujii N (2007) Chloroplast DNA phylogeography of Pedicularis ser. Gloriosae (Orobanchaceae) in Japan. (this opens in a new tab) Journal of Plant Research 120:491-500
Kaneko S, Matsuki Y, Qiu YX, Isagi Y (2017) Chloroplast DNA sequencing and detailed microsatellite genotyping of all remnant populations suggests that only a single genet survives of the critically endangered plant Rehmannia japonica. (this opens in a new tab) Journal of Plant Research 130:117-124
Takayama K, Sun BY, Stuessy TF (2013) Anagenetic speciation in Ullung Island, Korea: genetic diversity and structure in the island endemic species, Acer takesimense (Sapindaceae). (this opens in a new tab) Journal of Plant Research 126:323-333
Gil HY, Maki M, Pimenova EA, Taran A, Kim SC (2020) Origin of the critically endangered endemic species Scrophularia takesimensis (Scrophulariaceae) on Ulleung Island, Korea: implications for conservation. (this opens in a new tab) Journal of Plant Research 133:765-782
Tamaki I, Kawashima N, Setsuko S, Lee JH, Itaya A, Yukitoshi K, Tomaru N (2019) Population genetic structure and demography of Magnolia kobus: variety borealis is not supported genetically. (this opens in a new tab) Journal of Plant Research 132:741-758 [Open Access]
(3) Evolutionary insights
Photo credit © Hajime Ikeda
Aizawa M, Worth JRP (2021) Phylogenetic origin of two Japanese Torreya taxa found in two regions with strongly contrasting snow depth. (this opens in a new tab) Journal of Plant Research 134:907-919
Kameoka S, Sakio H, Abe H, Ikeda H, Setoguchi H (2017) Genetic structure of Hepatica nobilis var. japonica, focusing on within population flower color polymorphism. (this opens in a new tab) Journal of Plant Research 130:263-271
Kubota S, Ohara M (2009) The evolution of self-compatible and self-incompatible populations in a hermaphroditic perennial, Trillium camschatcense (Melanthiaceae). (this opens in a new tab) Journal of Plant Research 122:497-507. doi: 10.1007/s10265-009-0245-5
Tono A, Iwasaki T, Seo A, Murakami N (2015) Environmental factors contribute to the formation and maintenance of the contact zone observed in deciduous broad-leaved tree species in Japan. (this opens in a new tab) Journal of Plant Research 128:535-551