Quaternary range-shift history of Japanese wingnut (Pterocarya rhoifolia) in the Japanese Archipelago evidenced from chloroplast DNA and ecological niche modeling

References

• Bard E, Hamelin B, Arnold M, Montaggioni L, Cabioch G, Faure G, Rougerie F. 1996. Deglacial sea-level record from Tahiti corals and the timing of global meltwater discharge. Nature. 382:241–174.
   Google Scholar
• Bhagwat SA, Willis KJ. 2008. Species persistence in northerly glacial refugia of Europe: a matter of chance or biogeographical traits? J Biogeogr. 35:464–482.
   Web of Science ®Google Scholar
• Brito PH. 2005. The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe. Mol Ecol. 14:3077–3094.
   PubMed Web of Science ®Google Scholar
• Carnaval AC, Moritz C. 2008. Historical climate modelling predicts patterns of current biodiversity in the Brazilian Atlantic forest. J Biogeogr. 35:1187–1201.
   Web of Science ®Google Scholar
• Chung C-H. 2007. Vegetation response to climate change on Jeju Island, South Korea, during the last deglaciation based on pollen record. Geosciences J. 11:147–155.
   Google Scholar
• Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Mol Ecol. 9:1657–1659.
   PubMed Web of Science ®Google Scholar
• Collins WD, Bitz CM, Blackmon ML, Bonan GB, Bretherton CS, Carton JA, Chang P, Doney SC, Hack JJ, Henderson TB. 2006. The community climate system model version 3 (CCSM3). J Clim. 19:2122–2143.
   Web of Science ®Google Scholar
• Comes HP, Kadereit JW. 1998. The effect of Quaternary climatic changes on plant distribution and evolution. Trends Plant Sci. 3:432–438.
   Web of Science ®Google Scholar
• Demesure B, Sodzi NPetit RJ. 1995. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast dna in plants. Mol Ecol. 4:129-131.
   PubMed Web of Science ®Google Scholar
• Doyle JJ. 1990. Isolation of plant DNA from fresh tissue. Focus. 12:13–15.
   Google Scholar
• Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Mol Ecol. 11:2571–2581.
   PubMed Web of Science ®Google Scholar
• 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. 232:21–33.
   Web of Science ®Google Scholar
• Furuichi M. 1982. A note on the Pollen Analysis of the Bisan-seto submarine deposits, Kagawa Prefecture, Japan (In Japanese). Kagawa Seibutsu. 10:69–75.
   Google Scholar
• Guisan A, Thuiller W. 2005. Predicting species distribution: offering more than simple habitat models. Ecol Lett. 8:993–1009.
   PubMed Web of Science ®Google Scholar
• Hamilton MB. 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol Ecol. 8:521–523.
   PubMed Web of Science ®Google Scholar
• Hampe A, Petit RJ. 2005. Conserving biodiversity under climate change: the rear edge matters. Ecol Lett. 8:461–467.
   PubMed Web of Science ®Google Scholar
• Harrison S, Yu G, Takahara H, Prentice I. 2001. Palaeovegetation (Communications arising): diversity of temperate plants in East Asia. Nature. 413:129–130.
   PubMed Web of Science ®Google Scholar
• Hashimoto S, Minato M. 1955. Quaternary Geology of Hokkaido. 1st Report: on the Ice-ages and Post glacial age of the Hidaka Mountain-range. J Fac Sci, Hokkaido University. Ser 4, Geol Mineralogy. 9:7–20.
   Google Scholar
• Hatanaka K, editor. 1989. Pollen fossil assemblages of the elephant fossil bearing formations in Yoshinohara, Ono-machi, Oita. Okayama: Okayama University.
   Google Scholar
• Hatanaka K, Noi H. 1994. Pollen assemblages during the Last Glacial Maximum in northern Kyushu. J Fac Humanities, Univ Kyushu (Department Hum Relations). 1:9–13.
   Google Scholar
• Heuertz M, Fineschi S, Anzidei M, Pastorelli R, Salvini D, Paule L, Frascaria‐Lacoste N, Hardy OJ, Vekemans X, Vendramin G. 2004. Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe. Mol Ecol. 13:3437–3452.
   PubMed Web of Science ®Google Scholar
• Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature. 405:907–913.
   PubMed Web of Science ®Google Scholar
• Hewitt G, editor. 2003. Ice ages: their impact on species distributions and evolution. Amsterdam: Academic Press.
   Google Scholar
• Hewitt G. 2004. Genetic consequences of climatic oscillations in the Quaternary. Philosophical Trans Royal Soc London B: Biol Sci. 359:183–195.
   PubMed Web of Science ®Google Scholar
• Hewitt GM. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol Journal Linnean Soc. 58:247–276.
   Web of Science ®Google Scholar
• Hewitt GM. 1999. Post glacial re-colonization of European biota. Biol Journal Linnean Soc. 68:87–112.
   Web of Science ®Google Scholar
• Hiraoka K, Tomaru N. 2009a. Genetic divergence in nuclear genomes between populations of Fagus crenata along the Japan Sea and Pacific sides of Japan. J Plant Res. 122:269–282.
   Web of Science ®Google Scholar
• Hiraoka K, Tomaru N. 2009b. Population genetic structure of Fagus japonica revealed by nuclear microsatellite markers. Int J Plant Sci. 170:748–758.
   Google Scholar
• Hugall A, Moritz C, Moussalli A, Stanisic J. 2002. Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proc Natl Acad Sci. 99:6112–6117.
   PubMed Web of Science ®Google Scholar
• 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. J Plant Res. 125:207–221.
   PubMed Web of Science ®Google Scholar
• Kaneko Y. 2009. Pterocarya rhoifolia. Tokyo: Japan Forestry Investigation Committee.
   Google Scholar
• Kaneko Y, Kawano S. 2002. Demography and matrix analysis on a natural Pterocarya rhoifolia population developed along a mountain stream. J Plant Res. 115:341–354.
   Google Scholar
• Kaneko Y, Takada T. 2008. Population dynamics and key stages in two Japanese riparian elements Ecology of Riparian Forests in Japan. Tokyo: Springer; p. 91–105.
   Google Scholar
• Kanno M, Yokoyama J, Suyama Y, Ohyama M, Itoh T, Suzuki M. 2004. Geographical distribution of two haplotypes of chloroplast DNA in four oak species (Quercus) in Japan. J Plant Res. 117:311–317.
   PubMed Web of Science ®Google Scholar
• Kawahara T, Watanabe S, Matsui T, Takahashi M, editors. 2009. Distribution map. Tokyo: Japan Forestry Investigation Committee. Japanese.
   Google Scholar
• Kobayashi K. 1958. Quaternary glaciation of the Japan Alps. J Faculty Liberal ArtsSci Shinshu University. 8:13–67.
   Google Scholar
• Kozlowski T. 1976. Water supply and leaf shedding. Soil Water Measurements, Plant Responses, and Breeding for Drought Resistance. 4:191–231.
   Google Scholar
• Lu A, Stone DE, Grauke LJ. 1999. Juglandaceae. Flora of China. 4:277–285.
   Google Scholar
• Maliouchenko O, Palmé AE, Buonamici A, Vendramin G, Lascoux M. 2007. Comparative phylogeography and population structure of European Betula species, with particular focus on B. pendula and B. pubescens. J Biogeogr. 34:1601–1610.
   Web of Science ®Google Scholar
• Morita M. 2007. Palynological analysis in Aranuma, Shirataka lake group in Yamagata Prefecture, Japan. Naturalistae. 11:75–94.
   Google Scholar
• Morita Y, Yagi H, Inokuchi T, Yamazaki T. 2002. Vegetation history of the southern Tohoku district, based on pollen analysis of Aranuma in the Shirataka Lakes, Yamagata prefecture (In Japanese). Quat Res. 41:375–387.
   Google Scholar
• Nishizawa TWatano Y. 2000. Primer pairs suitable for pcr-sscp analysis of chloroplast dna in angiosperms. J Phytogeogr Taxon. 48:63-66.
   Google Scholar
• Okaura T, Harada K. 2002. Phylogeographical structure revealed by chloroplast DNA variation in Japanese beech (Fagus crenata Blume). Heredity. 88:322–329.
   Google Scholar
• Okaura T, Quang ND, Ubukata M, Harada K. 2007. Phylogeographic structure and late Quaternary population history of the Japanese oak Quercus mongolica var. crispula and related species revealed by chloroplast DNA variation. Genes Genet Syst. 82:465–477.
   Google Scholar
• Phillips SJ, Anderson RP, Schapire RE. 2006. Maximum entropy modeling of species geographic distributions. Ecol Modell. 190:231–259.
   Web of Science ®Google Scholar
• Phillips SJ, Dudík M. 2008. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography. 31:161–175.
   Web of Science ®Google Scholar
• Pons O, Petit R. 1995. Estimation, variance and optimal sampling of gene diversity. Theor Appl Genet. 90:462–470.
   PubMed Web of Science ®Google Scholar
• Pons O, Petit R. 1996. Measwring and testing genetic differentiation with ordered versus unordered alleles. Genetics. 144:1237–1245.
   PubMed Web of Science ®Google Scholar
• Provan J, Bennett K. 2008. Phylogeographic insights into cryptic glacial refugia. Trends Ecol Evol. 23:564–571.
   PubMed Web of Science ®Google Scholar
• Quang N, Ikeda S, Harada K. 2008. Nucleotide variation in Quercus crispula Blume. Heredity. 101:166–174.
   Google Scholar
• Sakaguchi S, Sakurai S, Yamasaki M, Isagi Y. 2010. How did the exposed seafloor function in postglacial northward range expansion of Kalopanax septemlobus? Evidence from ecological niche modelling. Ecological Res. 25:1183–1195.
   Google Scholar
• Sakaguchi S, Takeuchi Y, Yamasaki M, Sakurai S, Isagi Y. 2011. Lineage admixture during postglacial range expansion is responsible for the increased gene diversity of Kalopanax septemlobus in a recently colonised territory. Heredity. 107:338–348.
   Google Scholar
• Savolainen V, Manen JF, Douzery ESpichiger R. 1994. Molecular phylogeny of families related to celastrales based on rbcl 5' flanking sequences. Mol Phylogent Evol. 3:27-37.
   PubMed Web of Science ®Google Scholar
• Setoguchi H, Ohba H. 1995. Phylogenetic relationships in Crossostylis (Rhizophoraceae) inferred from restriction site variation of chloroplast DNA. J Plant Res. 108:87–92.
   Web of Science ®Google Scholar
• Shaw J, Edgar L, Edward SRandall S. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms. Amer J Bot. 94:275–288.
   PubMed Web of Science ®Google Scholar
• Siddall M, Rohling EJ, Almogi-Labin A, Hemleben C, Meischner D, Schmelzer I, Smeed D. 2003. Sea-level fluctuations during the last glacial cycle. Nature. 423:853–858.
   PubMed Web of Science ®Google Scholar
• Sommer RS, Zachos FE. 2009. Fossil evidence and phylogeography of temperate species:‘glacial refugia’and post-glacial recolonization. J Biogeogr. 36:2013–2020.
   Google Scholar
• 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. J Plant Res. 124:75–83.
   Google Scholar
• Suzuki W, Osumi K, Masaki T, Takahashi K, Daimaru H, Hoshizaki K. 2002. Disturbance regimes and community structures of a riparian and an adjacent terrace stand in the Kanumazawa Riparian Research Forest, northern Japan. For Ecol Manage. 157:285–301.
   Web of Science ®Google Scholar
• Taberlet P, Gielly L, Pautou GBouvet J. 1991. Universal primers for amplification of three non-coding regions of chloroplast dna. Plant Mol Biol. 17:1105-1109.
   PubMed Web of Science ®Google Scholar
• Takahara H. 1998. Vegetation history of Kinki region. In: Yasuda Y, Miyoshi N, editors. The vegetation history in the Japanese Islands. Tokyo: Asuka publishing Co. Ltd.; p. 114–137.
   Google Scholar
• Takahara H, Takeoka M. 1992. Postglacial vegetation history around Torihama, Fukui prefecture, Japan. Ecological Res. 7:79–85.
   Google Scholar
• Takahara H, Uemura Y, Danhara T, Takemura K, Nishida S. 1999. Vegetation history since the Last Glacial around Oofuke Moor, in the Tango Peninsula, Western Japan. Jpn J Palynology. 45:115–129.
   Google Scholar
• Takahashi T, Tani N, Taira H, Tsumura Y. 2005. Microsatellite markers reveal high allelic variation in natural populations of Cryptomeria japonica near refugial areas of the last glacial period. J Plant Res. 118:83–90.
   Google Scholar
• Takiya M, Hagiwara N. 1997. Vegetational history of Mt. Yokotsudake, southwestern Hokkaido, since the last glacial (in Japanese). Quat Res. 36:217–234.
   Google Scholar
• Tomaru N, Mitsutsuji T, Takahashi M, Tsumura Y, Uchida K, Ohba K. 1997. Genetic diversity in Fagus crenata (Japanese beech): influence of the distributional shift during the late-Quaternary. Heredity. 78:241–251.
   Google Scholar
• Tomaru N, Takahashi M, Tsumura Y, Ohba K. 1998. Intraspecific variation and phylogeographic patterns of Fagus crenata (Fagaceae) mitochondrial DNA. Am J Bot. 85:629–629.
   Google Scholar
• Tsukada M. 1982a. Cryptomeria japonica: glacial refugia and late-glacial and postglacial migration. Ecology. 63:1091–1105.
   Web of Science ®Google Scholar
• Tsukada M. 1982b. Late-Quaternary shift of Fagus distribution. Botanical Magazine= Shokubutsu-Gaku-Zasshi. 95:203–217.
   Google Scholar
• Tsukada M. 1983. Vegetation and climate during the last glacial maximum in Japan. Quaternary Res. 19:212–235.
   Google Scholar
• Tsukada M. 1984. A vegetation map in the Japanese Archipelago approximately 20, 000 years B. P. Jpn J Ecol. 34:203–208.
   Google Scholar
• Tsumura Y. 2006. The phylogeographic structure of Japanese coniferous species as revealed by genetic markers. Taxon. 55:53–66.
   Google Scholar
• Tsumura Y, Kado T, Takahashi T, Tani N, Ujino-Ihara T, Iwata H. 2007. Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics. 176:2393–2403.
   PubMed Web of Science ®Google Scholar
• Waltari E, Guralnick RP. 2009. Ecological niche modelling of montane mammals in the Great Basin, North America: examining past and present connectivity of species across basins and ranges. J Biogeogr. 36:148–161.
   Web of Science ®Google Scholar
• Waltari E, Hijmans RJ, Peterson AT, Nyári ÁS, Perkins SL, Guralnick RP. 2007. Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS One. 2:e563.
   PubMed Web of Science ®Google Scholar
• Woodward FI. 1987. Climate and plant distribution. Cambridge: Cambridge University Press.
   Google Scholar
• Worth JRP, Williamson GJ, Sakaguchi S, Nevill PG, Jordan GJ. 2014. Environmental niche modelling fails to predict Last Glacial Maximum refugia: niche shifts, microrefugia, or incorrect palaeoclimate estimates? Glob Ecol Biogeogr. 23:1186–1197.
   Web of Science ®Google Scholar
• Yagihashi T, Matsui T, Nakaya T, Tanaka N, Taoda H. 2007. Climatic determinants of the northern range limit of Fagus crenata forests in Japan. Plant Species Biol. 22:217–225.
   Google Scholar
• Yamanaka M, Kobayashi S, Setoguchi H. 2008. Distinct geographical structure across species units evidenced by chloroplast DNA haplotypes and nuclear ribosomal ITS genotypes of Corylopsis (Hamamelidaceae) in the Japanese islands. Bot J Linnean Soc. 157:501–518.
   Google Scholar
• Yu G, Chen X, Ni J, Cheddadi R, Guiot J, Han H, Harrison SP, Huang C, Ke M, Kong Z. 2000. Palaeovegetation of China: a pollen data‐based synthesis for the mid‐Holocene and last glacial maximum. J Biogeogr. 27:635–664.
   Web of Science ®Google Scholar