Species / Lat Range / Pop/Ind / Marker* / Var¶ / Clu / FST / Reference / Main findings§
Abies homolepis / 33.8 / 35.9 / 9/17 / cpSeq / - / 1 / 0.23 / Tsumura et al. (2000)
Abies mariesii / 36.1 / 40.7 / 7/28 / cpSeq / - / 1 / - / Tsumura et al. (1994) / Higher diversity in CJ than NJ due to past survival in CJ during the LGM, northwards expansion to its present range after the LGM
36.1 / 40.7 / 11/91 / allozyme / S>M>N / 6? / 0.14 / Suyama et al. (1997)
36.1 / 40.7 / 13/40 / cpSeq / - / 1 / 0.14 / Tsumura et al. (2000)
Abies sachalinensis / 41.9 / 44.8 / 5/28 / cpSeq / - / 1 / 0.02 / Tsumura et al. (2000)
Abies veitchii / 33.8 / 37.7 / 13/22 / cpSeq / - / 1 / 0.04 / Tsumura et al. (2000)
Arcterica nana / 35.4 / 44.1 / 22/9 / cpSeq / S<M<N / 1 / 0.42 / Ikeda and Setoguchi (2006) / Homogeneous structure caused by southward migration during the LGM
35.4 / 44.1 / 21/8 / AFLP / S<M<N / 1 / 0.21 / Ikeda and Setoguchi (2009)
Cardamine nipponica / 35.5 / 43.7 / 19/15 / cpSeq / - / 3 / 1.00 / Ikeda et al. (2008a) / Differentiation between NJ and CJ
35.5 / 43.7 / 19/15 / nSeq / - / 3-5 / 0.85 / Ikeda et al. (2008a)
Diapensia lapponica subsp. / 35.5 / 45.2 / 22/7 / cpSeq / S>M>N / 2 / 0.73 / Ikeda et al. (2008c) / Differentiation between NJ and CJ
Parasenecio adenostyloides / 33.7 / 40.5 / 11/38 / allozyme / S<M=N / 2? / 0.18 / Nakagawa (2008) / Strong geographical isolation
Pedicularis chamissonis / 35.5 / 45.5 / 23/2 / cpSeq / - / 2 / - / Fujii et al. (1997) / Differentiation between NJ and CJ
Pedicularis ser. / 35.3 / 39.8 / 15/5 / cpSeq / - / 2 / - / Fujii (2007) / Differentiation between PO and JS
Phyllodoce nipponica / 33.9 / 43.6 / 19/8 / cpSeq / S<M>N / 2? / 0.67 / Ikeda and Setoguchi (2007) / Higher diversity in CJ due to past survival
Picea alcoquiana / 35.3 / 37.0 / 9/32 / nSSR / S=M>N / 2 / 0.08 / Aizawa et al. (2008) / Southwards retreat to CJ after the LGM, bottlenecks in the isolated populations in the northern periphery
35.3 / 37.0 / 9/19 / cpRFLP / S=M=N / 1? / -0.01 / Aizawa et al. (2008)
35.3 / 37.0 / 9/8 / mtRFLP / S=M=N / 2? / 0.62 / Aizawa et al. (2008)
Picea jezoensis / 34.2 / 45.3 / 25/17 / cpRFLP / S<M<N / 2 / 0.17 / Aizawa et al. (2007) / Differentiation between Hokkaido and Honshu due to different migration routes from the continent
34.2 / 45.3 / 25/8 / mtRFLP / S=M=N / 2 / 0.87 / Aizawa et al. (2007)
34.2 / 45.3 / 25/31 / nSSR / S<M=N / 2 / <0.10 / Aizawa et al. (2009)
Pinus parviflora / 32.8 / 42.1 / 16/41 / allozyme / S<M<N / 1 / 0.04 / Tani et al. (2003) / Northward and upward migrations after the LGM, differentiation in mtDNA
32.8 / 42.1 / 16/11 / mtRFLP / S=M=N / 2 / 0.87 / Tani et al. (2003)
Pinus pumila / 36.2 / 45.2 / 18/48 / allozyme / S<M<N / 2 / 0.17 / Tani et al. (1996) / Differentiation between NJ and CJ
Potentilla matsumurae / 35.5 / 43.6 / 22/9 / cpSeq / S>M>N / 2 / 0.68 / Ikeda et al. (2006) / Differentiation in cpDNA between NJ and CJ, fragmentation within a single distribution
35.5 / 43.6 / 22/7 / AFLP / S>M>N / 1? / - / Ikeda et al. (2008b)
Primula cuneifolia / 36.2 / 45.2 / 14/6 / cpSeq / - / 3 / - / Fujii et al. (1999) / Three clades caused by several glacial cycles
Notes) Lat Range, Latitudinal range; Pop/Ind, Number of populations and mean number of individuals examined per population; Marker, the genetic marker used; Var, Latitudinal change of intra-population genetic variation (generally expected heterozygosity); Clu, Likely number of geographically differentiated clusters based on dendrogram and/or clustering analysis; FST, The ratio of inter-population variation to all genetic variation (represented by FST or GST)
Notes) The data given in Italics were estimated by us based on the location names or genotype data provided in the studies we examined and their supplementary data.
*) cp, chloroplast; n, nuclear; mt, mitochondria; Seq, sequencing
¶) S, M and N refer to the southern, middle and northern parts of the range examined. ‘>’, ‘<’ and ‘=’ indicate that the former is larger than, smaller than or equal to the latter respectively. ‘-‘ indicates no clear pattern because of insufficient polymorphisms and/or number of individuals examined.
§) CJ, central Japan; NJ, northern Japan; PO, Pacific Ocean side; JS, Japan Sea side; LGM, Last Glacial Maximum
App. 2. Previous studies of the phylogeographical and genetic structure of montane plant species in Japan excluding any foreign populations.
Species / Lat Range / Pop/Ind / Marker* / Var¶ / Clu / FST / Reference / Main findings§
Abies firma / 31.9 / 38.3 / 7/23 / cpSeq / - / 1 / 0.16 / Tsumura et al. (2000)
Arabis serrata / 35.4 / 42.8 / 10/33 / allozyme / S<M=N / 3 / 0.42 / Oyama (1998) / Differentiation between NJ and CJ
Betula maximowicziana / 36.1 / 44.5 / 23/44 / nSSR / S>M>N / 2 / 0.06 / Tsuda and Ide (2005) / Differentiation between NJ and CJ, cryptic refugia at 39ºN latitude
36.1 / 44.5 / 25/16 / cpRFLP / S<M>N / 2 / 0.95 / Tsuda and Ide (2010)
Cerasus jamasakura / 31.5 / 37.0 / 12/28 / nSSR / S<M<N / 2 / 0.04 / Tsuda et al. (2009) / Distinct populations in Kyushu Island
Chamaecyparis obtusa / 30.3 / 37.1 / 11/109 / allozyme / S>M>N / 2 / 0.05 / Uchida et al. (1997) / Differentiation at both margins of the distribution, higher diversity in CJ, evidence of recent bottlenecks in WJ
30.3 / 37.1 / 25/19 / nCAPS / S<M>N / 3 / 0.04 / Tsumura et al. (2007b)
30.3 / 37.1 / 25/19 / nSSR / S<M>N / 4 / 0.04 / Matsumoto et al. (2010)
Conocephalum conicum / 33.6 / 38.0 / 17/48 / allozyme / S<M<N / 3 / - / Akiyama and Hiraoka (1994) / Only one genotype in WJ
Cryptomeria japonica / 33.6 / 34.5 / 5/105 / allozyme / - / 1 / 0.02 / Tsumura and Ohba (1992) / Differentiation between the PO and JS sides of Japan revealed only by Tsumura et al. (2007), higher diversity in WJ due to the past survival during the LGM and northeastwards migration
30.2 / 40.3 / 17/51 / allozyme / - / 2? / 0.03 / Tomaru et al. (1994)
30.2 / 40.0 / 11/22 / nSTS / - / 1 / 0.05 / Tsumura and Tomaru (1999)
30.2 / 40.5 / 29/26 / nSSR / S=M=N / 2? / 0.03 / Takahashi et al. (2005)
30.2 / 40.5 / 29/20 / nCAPS / S>M=N / 8 / 0.05 / Tsumura et al. (2007a)
Erigeron thunbergii / 36.7 / 45.2 / 22/7 / nSeq / - / 2? / - / Kawase et al. (2007) / Two clades resulting from different origins
Fagus crenata / 31.5 / 42.7 / 23/27 / allozyme / S>M>N / ? / 0.04 / Tomaru et al. (1997) / Differentiation between the PO and JS revealed by most studies, differentiation between Hokkaido and Honshu (Hiraoka and Tomaru 2009b), higher diversity in WJ due to the past survival during the LGM and northeastwards migration
31.5 / 42.7 / 17/24 / mtRFLP / - / ? / 0.96 / Tomaru et al. (1998)
31.5 / 42.7 / 45/2 / cpSeq / - / 2 / - / Fujii et al. (2002)
32.5 / 42.6 / 21/17 / cpSeq / - / 4 / 0.95 / Okaura and Harada (2002)
32.5 / 42.6 / 21/1 / cpSeq / - / 4 / - / Okaura and Harada (2002)
31.5 / 42.7 / 23/35 / nSSR / S>M>N / 2 / 0.03 / Hiraoka and Tomaru (2009b)
Fagus japonica / 32.5 / 40.2 / 16/34 / nSSR / S=M=N / 2-3 / 0.02 / Hiraoka and Tomaru (2009a) / Effect of the I-S Tectonic Line
Fraxinus mandshurica var. / 36.5 / 44.1 / 15/27 / nSSR / S<M<N / 2-3 / 0.08 / Hu et al. (in press) / Sub-structuring especially in Honshu
Hemerocallis spp. / 33.7 / 44.1 / 35/1? / cpSeq / - / 3 / - / Noguchi et al. (2004) / Different movements between the PO and JS
Polygonum cuspidatum / 31.6 / 40.8 / 38/2 / cpSeq / - / 5 / - / Inamura et al. (2000) / Effect of the I-S Tectonic Line
Quercus crispula / 31.9 / 44.1 / 44/11 / cpSeq / S>M>N / 2 / 0.85 / Okaura et al. (2007) / Differentiation across the I-S Tectonic Line, higher diversity in NJ than WJ (Quang et al. 2008), lower diversity in NJ than CJ (Ohsawa et al. 2011)
32.5 / 44.1 / 6/20seq / nSeq / S<N<N / - / 0.02 / Quang et al. (2008)
32.5 / 44.1 / 9/19seq / nSeq / S=M=N / - / 0.09 / Quang et al. (2008)
35.4 / 45.4 / 16/23 / nSSR / S>M>N / 2 / 0.02 / Ohsawa et al. (2011)
Quercus spp. / 32.0 / 45.4 / 122/4 / cpSeq / - / 2 / - / Kanno et al. (2004) / C-type restricted to EJ
Ranunculus subgenus. / 32.8 / 43.6 / 46/5 / cpSeq / - / 2 / - / Koga et al. (2008) / Differentiation between NJ and CJ/WJ
Rhododendron ripense / 33.2 / 35.3 / 9/6 / cpSeq / S>M>N / 2? / - / Kobayashi et al. (2008) / Higher diversity in Shikoku
Viola chaerophylloides var. / 32.9 / 35.9 / 11/5 / AFLP / S<M>N / 1 / 0.68 / Toyama and Yahara (2009) / A single refugium in WJ (Sanbe Volcano)
Viola eizanensis / 32.9 / 36.5 / 11/6 / AFLP / S<M=N / 2 / 0.68 / Toyama and Yahara (2009) / Differentiation between EJ and WJ
Notes) Lat Range, Latitudinal range; Pop/Ind, Number of populations and mean number of individuals examined per population; Marker, genetic marker used; Var, Latitudinal change in intra-population genetic variation (generally expected heterozygosity); Clu, Likely number of geographically differentiated clusters based on dendrogram and/or clustering analysis; FST, The ratio of inter-population variation to all genetic variation (represented by FST or GST)
Notes) The data given in Italics were estimated by us based on the location names provided in the articles we reviewed and their supplementary data.
*) cp, chloroplast; n, nuclear; mt, mitochondria; Seq, sequencing
¶) S, M and N refer to southern, middle and northern parts of range examined . ‘>’, ‘<’ and ‘=’ indicate that the former is larger than, smaller than or equal to the latter respectively. ‘-' indicates no clear pattern because of insufficient polymorphisms and/or number of individuals examined.
§) CJ, central Japan; NJ, northern Japan; EJ, eastern Japan; WJ, western Japan; PO, Pacific Ocean side; JS, Japan Sea side; LGM, Last Glacial Maximum
App. 3. Previous studies of the phylogeographical and genetic structure of lowland plant species in Japan excluding any foreign populations.
Species / Lat Range / Pop/Ind / Marker* / Var¶ / Clu / FST / Reference / Main findings§
Aucuba japonica / 26.6 / 40.8 / 124/2 / cytotypes / - / 2 / - / Ohi et al. (2003) / Eight “haplo-sytotypes”, non-adapting factors segregating cytotypes (at 134ºE longitude)
26.6 / 40.8 / 124/2 / cpSeq / - / 2 / - / Ohi et al. (2003)
Castanopsis spp. / 24.3 / 36.9 / 25/25 / nSSR / - / 3 / 0.26 / Yamada et al. (2006) / Differentiation between two species
Corylopsis spp. / 32.0 / 36.3 / 30/7 / cpSeq / S=M<N / 2 / 0.87 / Yamanaka et al. (2008) / Inconsistency between morphology-based taxonomy and gene genealogy
32.0 / 36.3 / 30/7 / nSeq / S=M<N / 3 / - / Yamanaka et al. (2008)
Glycine soja / 31.8 / 40.6 / 77/8 / nSSR / S=M=N / 38 / 0.76 / Kuroda et al. (2006) / Strong differentiation, low outcrossing rate
Hedyotis strigulosa var. / 24.5 / 35.7 / 30/25 / allozyme / S>M>N / ? / 0.75 / Maki et al. (2008) / Lower diversity in northern populations
Ludwigia peploides spp. / 31.5 / 35.7 / 10/1 / RAPD / - / 1? / - / Osawa et al. (2006)
Photinia glabra / 32.3 / 35.3 / 42/3 / cpSeq / - / 2? / 0.69 / Aoki et al. (2006) / Disjunct distributions
Pinus thunbergii / 31.5 / 41.1 / 22/72 / Allozyme / S>M>N / 2 / 0.07 / Miyata and Ubukata (1994) / Differentiation between WJ and EJ
Polygala reinii / 34.2 / 35.6 / 14/34 / allozyme / 3 / 0.40 / Nakagawa (2004) / Differentiation between PO and JS
Primula sieboldii / 32.9 / 42.6 / 66/4 / cpSeq / S<M>N / 3 / 0.92 / Honjo et al. (2004) / Higher diversity in the southern populations,
genetic isolation for Hokkaido populations
32.9 / 42.6 / 32/29 / nSSR / S>M>N / 4 / 0.22 / Honjo et al. (2009)
Raphanus sativus var. / 27.9 / 40.5 / 25/78 / allozyme / S=M=N / ? / 0.17 / Huh and Ohnishi (2001) / Relatively homogeneous structure, a very low pollen-to-seed flow ratio of 1.142
31.8 / 37.9 / 7/39 / cpRFLP / S=M=N / 1 / 0.39 / Ohsako and Ohnishi (2007)
Zanthoxylum ailanthoides / 31.4 / 35.5 / 10/27 / nSSR / S>M>N / 8 / 0.32 / Yoshida et al. (2010) / A putative refugium at the southern Kyushu
Notes) Lat Range, Latitudinal range; Pop/Ind, Number of populations and mean number of individuals examined per populations; Marker, genetic marker used; Var, Latitudinal change in intra-population genetic variation (generally expected heterozygosity); Clu, Likely number of geographically differentiated clusters based on dendrogram and/or clustering analysis; FST, The ratio of inter-population variation to all genetic variation (represented by FST or GST but exceptionally RST in Yamada et al. 2006)
Notes) The data written in Italics were estimated by us based on the location names provided in the cited articles and their supplementary data.
*) cp, chloroplast; n, nuclear; mt, mitochondria; Seq, sequencing
¶) S, M and N refer to the southern, middle and northern parts of range examined. ‘>’, ‘<’ and ‘=’ indicate that the former is larger than, smaller than or equal to the latter respectively. ‘-‘ indcates no clear pattern because of insufficient polymorphisms and/or the number of individuals examined.
§) CJ, central Japan; NJ, northern Japan; WJ, western Japan; PO, Pacific Ocean side; JS, Japan Sea side; LGM, Last Glacial Maximum
Supplementary references (not used in the article)
Aoki K, Matsumura T, Hattori T, Murakami N (2006) Chloroplast DNA phylogeography of Photinia glabra (Rosaceae) in Japan. Am J Bot 93:1852-1858.
Fujii N, Tomaru N, Okuyama K, Koike T, Mikami T, Ueda K (2002) Chloroplast DNA phylogeography of Fagus crenata (Fagaceae) in Japan. Plant Syst Evol 232(1-2):21-33.
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. J Plant Res 113(4):419-426.