Genetic diversity and population demography of Geranium soboliferum var. kiusianum: a glacial relict plant in the wetlands of Japan

  • Seikan KurataEmail author
  • Shota Sakaguchi
  • Motomi Ito
Research Article


Geranium soboliferum var. kiusianum and var. hakusanense (Geraniaceae) are believed to be relict plants that migrated southward from the Eurasian continent to the Japanese archipelago during the last glacial period. G. soboliferum var. kiusianum individuals and populations, which occur in wetlands in the Aso-Kuju region of Kyushu Island, are declining as a result of the deteriorating quality of the microhabitat, a process that is associated with the decrease in semi-natural grasslands. Using 10 polymorphic microsatellite markers, we evaluated the genetic diversity and population structure of the G. soboliferum complex, with the aim of understanding the species’ genetic characteristics to facilitate efficient conservation. Genetic demographic analysis suggested that Japanese G. soboliferum populations branched off from the Eurasian continental G. soboliferum var. soboliferum during the last glacial period and that, thereafter, the Japanese populations of the plant diverged into two lineages at the beginning of the Holocene epoch. The genetic diversity of G. soboliferum var. kiusianum was significantly lower than that of var. hakusanense, which is more widely distributed in central Honshu Island (mean Ar = 3.288 vs. 3.830 and He = 0.366 vs. 0.546). Genetic differentiation among populations was significantly higher (mean FST = 0.368 vs. 0.184) in var. kiusianum populations and, notably, exhibited non-significant patterns of isolation by distance, indicating that the populations underwent strong genetic drift independent of adjacent populations. Our findings suggested that the population’s isolation, and its associated habitat specialization and limited inter-population gene flow, would have accelerated genetic differentiation in var. kiusianum. Overall, G. soboliferum var. kiusianum, which is genetically unique to wetland habitats in the Aso-Kuju region, merits conservation, and appropriate human intervention and management are critical to maintaining its remaining habitats in semi-natural grasslands.


Geranium soboliferum Kom. Semi-natural grassland Glacial relict plant Wetland plant Genetic diversity Genetic demography 



The authors are grateful to Dr. Yuki Mitsui for granting access to his collection of materials (G. soboliferum var. soboliferum) in China, and to Dr. Akiko Soejima for guiding us to the natural habitats of G. soboliferum var. kiusianum. We are grateful to Drs. Takaya Iwasaki and Naoyuki Nakahama for their useful suggestions regarding genetic analyses. We are grateful to Dr. Hyeok Jae Choi for letting us know the distribution of G. soboliferum in Korea. We are also grateful to the Ministry of the Environment, and the prefectural offices of Kumamoto, Nagano, Shizuoka, and Yamanashi for granting us permission to conduct surveys. This study was partly supported by JSPS KAKENHI Grant Number JP16H04827 and the National BioResource Project (18 km0210136j0002) from AMED.

Supplementary material

10592_2018_1141_MOESM1_ESM.pdf (56 kb)
Fig. S1 Posterior probability of each demographic scenario in DIYABC analysis. (PDF 48 KB)
10592_2018_1141_MOESM2_ESM.pdf (27 kb)
Fig. S2 The demographic scenario based on a single-population model in DIYABC analysis. The populations are those of Tadewara, Ide Farm, and Mt. Daikanbou. (PDF 26 KB)
10592_2018_1141_MOESM3_ESM.pdf (63 kb)
Fig. S3 Population-based PCoA. GSvk_Td, G. soboliferum var. kiusianum (Tadewara); GSvk_Id, G. soboliferum var. kiusianum (Ide Farm); GSvk_Dk, G.soboliferum var. kiusianum (Mt. Daikanbou); GSvh_Ns, G. soboliferum var. hakusanense (Nasu); GSvh_Tc, G. soboliferum var. hakusanense (Tochigi); GSvh_Sk, G. soboliferum var. hakusanense (Saku); GSvh_Kr, G. soboliferum var. hakusanense (Kirigamine); GSvh_Nb, G. soboliferum var. hakusanense (Nobeyama); GSvh_Ky, G. soboliferum var. hakusanense (Kiyosato); GSvh_Fj, G. soboliferum var. hakusanense (Fujinomiya); GSvs_Ji, G. soboliferum var. soboliferum (Jilin). (PDF 63 KB)
10592_2018_1141_MOESM4_ESM.docx (44 kb)
Supplementary material 4 (DOCX 55 KB)
10592_2018_1141_MOESM5_ESM.docx (15 kb)
Supplementary material 5 (DOCX 14 KB)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and SciencesThe University of TokyoTokyoJapan
  2. 2.Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan

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