Skip to main content

Advertisement

SpringerLink
Log in

Phylogeography and genetic diversity of East Asian Neolitsea sericea (Lauraceae) based on variations in chloroplast DNA sequences

  • Regular Paper
  • Published:
Journal of Plant Research Aims and scope Submit manuscript

Abstract

Neolitsea sericea is an evergreen broad leaved tree in the warm-temperate regions of East Asia. This area is a hotspot for plant species richness and endemism caused by dynamic changes in land configuration during the Quaternary. However, the historical migration of such evergreen tree species is still poorly understood. In an attempt to reconstruct the phylogeographic history of N. sericea during the Quaternary, we identified the chloroplast DNA haplotypes of 287 individuals from 33 populations covering almost all of its geographic range. Analyses were based on sequence data from the trnL–F, psbC–trnS, and rps16 regions. Nine haplotypes were identified. The majority included ancestral types in the southwestern part of the main islands of Japan, with other region-specific haplotypes being found in populations on the Korean Peninsula, Taiwan (Isl. Lanyu), and elsewhere in Japan. A statistical parsimony network revealed two lineages derived from Japanese main islands. One was represented on the Korean Peninsula, the other on Isl. Lanyu. The current distribution of N. sericea has been shaped by colonization via land bridges. During the glacial periods, two primary, but separate migration routes were followed—from the southwestern part of the Japanese main islands to either the Korean Peninsula or Taiwan. In addition, we believe the Zhoushan populations were shaped by post-glacial processes through an ECS land bridge (East China Sea basin) from northern refugia that existed during the late Pleistocene.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • 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. J Plant Res 117:77–94

    Article  PubMed  Google Scholar 

  • Aoki K, Matsumura T, Hattori T, Murakami N (2006) Chloroplast DNA phylogeography of Photinia glabra (Rosaceae) in Japan. Am J Bot 93:1852–1858

    Article  PubMed  CAS  Google Scholar 

  • Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge

    Google Scholar 

  • Bai WN, Liao WJ, Zhang DY (2010) Nuclear and chloroplast DNA phylogeography reveal two refuge areas with asymmetrical gene flow in a temperate walnut tree from East Asia. New Phytol 188:892–901

    Article  PubMed  Google Scholar 

  • Chen KC, Pan FJ (1997) New findings on the genus Neolitsea (Lauraceae) in Taiwan (in Chinese with English summary). Taiwan J For Sci 12:155–166

    Google Scholar 

  • Chen KM, Abbott RJ, Milne RI, Tian XM, Liu JQ (2008) Phylogeography of Pinus tabulaeformis Carr. (Pinaceae), a dominant species of coniferous forest in northern China. Mol Ecol 17:4276–4288

    Article  PubMed  CAS  Google Scholar 

  • Cheng YP, Hwang SY, Lin TP (2005) Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae). Mol Ecol 14:2075–2085

    Article  PubMed  CAS  Google Scholar 

  • Chung MG, Chung MY, Oh GS, Epperson B (2000) Spatial genetic structure in a Neolitsea sericea population (Lauraceae). Heredity 85:490–497

    Article  PubMed  Google Scholar 

  • Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1659

    Article  PubMed  CAS  Google Scholar 

  • Corriveau JL, Coleman AW (1988) Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. Am J Bot 75:1443–1458

    Article  Google Scholar 

  • Duminil J, Fineschi S, Hampe A, Jordano P, Salvini D, Vendramin GG, Petit RJ (2007) Can population genetic structure be predicted from life-history traits? Am Nat 169:662–672

    Article  PubMed  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

    Article  PubMed  CAS  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: applications to human mitochondrial DNA restriction data. Genetics 131:479–491

    PubMed  CAS  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50

    CAS  Google Scholar 

  • Hampe A, Arroyo J, Jordano P, Petit RJ (2003) Rangewide phylogeography of a bird-dispersed Eurasian shrub: contrasting Mediterranean and temperate glacial refugia. Mol Ecol 12:3415–3426

    Article  PubMed  CAS  Google Scholar 

  • Harrison SP, Yu G, Takahara H, Prentice IC (2001) Palaeovegetation: diversity of temperate plants in East Asia. Nature 413:129–130

    Article  PubMed  CAS  Google Scholar 

  • Hatusima S (1969) On some species of the Lauraceae from Japan and Taiwan (in Japanese). J Geobot 17:106–107

    Google Scholar 

  • Hayata B (1911) Materials for a flora of Formosa. Journal of the College of Science, Imperial University, Tokyo, Japan

  • Heuertz M, Fineschi S, Anzidei M, Pastorelli R, Salvini D, Paule L, Frascaria-Lacoste N, Hardy OJ, Vekemans X, Vendramin GG (2004) Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe. Mol Ecol 13:3437–3452

    Article  PubMed  CAS  Google Scholar 

  • Hewitt GM (1999) Post-glacial re-colonization of European biota. Biol J Linn Soc 68:87–112

    Article  Google Scholar 

  • Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913

    Article  PubMed  CAS  Google Scholar 

  • Hewitt G (2003) Ice ages: species distributions, and evolution. In: Rothschild LJ, Lister AM (eds) Evolution on planet earth. Academic Press, Amsterdam

    Google Scholar 

  • Hikida T, Ota H (1997) Biogeography of reptiles in the subtropical East Asian islands. In: Lue KY, Chen T-H (eds) Proceedings of the Symposium on the Phylogeny, Biogeography and Conservation of Fauna and Flora of East Asian Region. National Science Council, Taipei, pp 11–28

  • Hong SK, Nakagoshi N, Fu B, Morimoto Y (2007) Landscape ecological applications in man-influenced areas: linking man and nature systems. Springer, New York

    Book  Google Scholar 

  • Huang S, Chiang YC, Schaal BA, Chou CH, Chiang TY (2001) Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan. Mol Ecol 10:2669–2681

    Article  PubMed  CAS  Google Scholar 

  • Huang SSF, Hwang SY, Lin TP (2002) Spatial pattern of chloroplast DNA variation of Cyclobalanopsis glauca in Taiwan and East Asia. Mol Ecol 11:2349–2358

    Article  PubMed  CAS  Google Scholar 

  • Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Kimura M (1996) Quaternary paleogeography of the Ryukyu Arc (in Japanese with English summary). J Geogr 105:259–285

    Article  Google Scholar 

  • Kimura M (2000) Paleography of the Ryukyu Islands. Tropics 10:5–24

    Article  Google Scholar 

  • Kitamura A, Kimoto K (2006) History of the inflow of the warm Tsushima Current into the Sea of Japan between 3.5 and 0.8 Ma. Palaeogeogr Palaeoclimatol Palaeoecol 236:355–366

    Article  Google Scholar 

  • Kizaki K, Oshiro I (1977) Paleogeography of the Rytkyu [sic] Islands (in Japanese with English summary). Marine Sci Mon 9:543–547

    Google Scholar 

  • Kominami Y, Sato T, Takeshita K, Manabe T, Endo A, Noma N (2003) Classification of bird-dispersed plants by fruiting phenology, fruit size, and growth form in a primary lucidophyllous forest: an analysis, with implications for the conservation of fruit-bird interactions. Ornithol Sci 2:3–23

    Article  Google Scholar 

  • Lee JH, Choi BH (2010) Distribution and northernmost limit on the Korean Peninsula of three evergreen trees (in Korean with English summary). Korean J Pl Taxon 40:267–273

    Article  Google Scholar 

  • Lee JH, Lee BY, Choi BH (2011) Preliminary search of intraspecific chloroplast DNA variation of nine evergreen broad leaved plants in East Asia. Korean J Pl Taxon 41:194–201

    Google Scholar 

  • Li EX, Yi S, Qiu YX, Guo JT, Comes HP, Fu CX (2008) Phylogeography of two East Asian species in Croomia (Stemonaceae) inferred from chloroplast DNA and ISSR fingerprinting variation. Mol Phylogenet Evol 49:702–714

    Article  PubMed  CAS  Google Scholar 

  • Liao JC (1996) Neolitsea Merr. In: Editorial Committee of the Flora of Taiwan (eds) Flora of Taiwan, vol 2. Tah Jinn Printing Company Ltd., Taipei, pp 484–496

  • Mantel N (1967) The detection of disease clustering and generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • Miyazaki T, Yamaguchi YY, Hoshino Y, Ohba H (2003) Neolitsea sericea (Blume) Koidz. var. aurata (Hayata) Hatus. and the occurrence in Toshima, the Izu Islands, Japan (in Japanese with English summary). J Jpn Bot 78:311–312

    Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Oxford University Press, New York

    Google Scholar 

  • Nishizawa T, Watano Y (2000) Primer pairs suitable for PCR-SSCP analysis of chloroplast DNA in angiosperms. J Phytogeogr Taxon 48:63–66

    Google Scholar 

  • Ohashi H, Sasaki Y, Ohashi K (2006) The northern limit of distribution of Neolitsea sericea (Blume) Koidz. (Lauraceae) on the Pacific side of Japan (in Japanese with English summary). J Jpn Bot 81:248–249

    Google Scholar 

  • Ohi T, Kajita T, Murata J (2003a) Distinct geographic structure as evidenced by chloroplast DNA haplotypes and ploidy level in Japanese Aucuba (Aucubaceae). Am J Bot 90:1645–1652

    Article  PubMed  Google Scholar 

  • Ohi T, Wakabayashi M, Wu S, Murata J (2003b) Phylogeography of Stachyurus praecox (Stachyuraceae) in the Japanese Archipelago based on chloroplast DNA haplotypes. J Jpn Bot 78:1–14

    Google Scholar 

  • Ota H (1998) Geographic patterns of endemism and speciation in amphibians and reptiles of the Ryukyu Archipelago, Japan, with special reference to their paleogeographical implications. Res Popul Ecol 40:189–204

    Article  Google Scholar 

  • Petit RJ, Brewer S, Bordács S, Burg K, Cheddadi R, Coart E, Cottrell J, Csaikl UM, van Dam BC, Deans JD, Fineschi S, Finkeldey R, Glaz I, Goicoechea PG, Jensen JS, König AO, Lowe AJ, Madsen SF, Mátyás G, Munro RC, Popescu F, Slade D, Tabbener H, de Vries SMG, Ziegenhagen B, Beauliey JL, Kremer A (2002) Identification of refugia and post-glacial colonization routes of European white oaks based on chloroplast DNA and fossil pollen evidence. For Ecol Manage 156:49–74

    Article  Google Scholar 

  • Petit RJ, Aguinagalde I, De Beaulieu J-L, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Mohanty A, Müller-Starck G, Demesure-Musch B, Palmé A, Martín JP, Rendell S, Vendramin GG (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300:1563–1565

    Article  PubMed  CAS  Google Scholar 

  • Pons O, Petit R (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144:1237–1245

    PubMed  CAS  Google Scholar 

  • Qian H, Ricklefs RE (2000) Large-scale processes and the Asian bias in species diversity of temperate plants. Nature 407:180–182

    Article  PubMed  CAS  Google Scholar 

  • Qiu YX, Qi XS, Jin XF, Tao XY, Fu CX, Naiki A, Comes HP (2009a) Population genetic structure, phylogeography, and demographic history of Platycrater arguta (Hydrangeaceae) endemic to East China and South Japan, inferred from chloroplast DNA sequence variation. Taxon 58:1226–1241

    Google Scholar 

  • Qiu YX, Sun Y, Zhang XP, Lee J, Fu CX, Comes HP (2009b) Molecular phylogeography of East Asian Kirengeshoma (Hydrangeaceae) in relation to Quaternary climate change and landbridge configurations. New Phytol 183:480–495

    Article  PubMed  CAS  Google Scholar 

  • Qiu YX, Fu CX, Comes HP (2011) Plant molecular phylogeography in China and adjacent regions: tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora. Mol Phylogenet Evol 59:225–244

    Article  PubMed  Google Scholar 

  • Rendell S, Ennos R (2003) Chloroplast DNA diversity of the dioecious European tree Ilex aquifolium L. (English holly). Mol Ecol 12:2681–2688

    Article  PubMed  CAS  Google Scholar 

  • Rozas J, Rozas R (1999) DNASP, version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174–175

    Article  PubMed  CAS  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

    Article  PubMed  Google Scholar 

  • Taberlet P, Gielly L, Patou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109

    Article  PubMed  CAS  Google Scholar 

  • Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF (1998) Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol 7:453–464

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Wang ZS, An SQ, Liu H, Leng X, Zheng JW, Liu YH (2005) Genetic structure of the endangered plant Neolitsea sericea (Lauraceae) from the Zhoushan Archipelago using RAPD markers. Ann Bot 95:305–313

    Article  PubMed  CAS  Google Scholar 

  • Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054–9058

    Article  PubMed  CAS  Google Scholar 

  • Xie GW (1997) On phytogeographical affinities of the forest floras between East China and Japan. Chin Geogr Sci 19:789–799

    Google Scholar 

  • Yiming L, Niemela J, Dianmo L (1998) Nested distribution of amphibians in the Zhoushan archipelago, China: can selective extinction cause nested subsets of species? Oecologia 113:557–564

    Article  Google Scholar 

  • Zhai SN, Comes HP, Nakamura K, Yan HF, Qiu YX (2012) Late Pleistocene lineage divergence among populations of Neolitsea sericea (Lauraceae) across a deep sea-barrier in Ryukyu Islands. J Biogeogr 37:1347–1360

    Article  Google Scholar 

Download references

Acknowledgments

The authors thank Emeritus Prof. H. Ohashi of Tohoku University, Dr. Y. Endo of Ibaraki University, Dr. T. Nemoto of Ishinomaki Senshu University, Dr. A. Yang of the National Museum of Natural Science, and Dr. S.H. Kang of Semyung University for help in collecting plant materials. They also thank all colleagues, J.Y. Lee, W.B. Cho, I.S. Choi, S.K. Jung, and D.P. Jin at the Plant Systematics Laboratory of Inha University for assisting with statistical analysis and commenting on the manuscript. This work was supported by Inha University and the National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST) (No. 2012R1A2A2A01011428).

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Inha University, Incheon, 402-751, Republic of Korea

    Jung-Hyun Lee, Dong-Hyuk Lee & Byoung-Hee Choi

Authors
  1. Jung-Hyun Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dong-Hyuk Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Byoung-Hee Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Byoung-Hee Choi.

Electronic supplementary material

Below is the link to the electronic supplementary material.

10265_2012_519_MOESM1_ESM.tif

Fig. S1. Maps showing a hypothesis by Kizaki and Oshiro (1977), then modified according to that of Hikida and Ota (1997). a and b show inferred land configurations in East Asia during the early and middle Pleistocene, respectively (TIFF 4709 kb)

Supplementary material 2 (XLS 77 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lee, JH., Lee, DH. & Choi, BH. Phylogeography and genetic diversity of East Asian Neolitsea sericea (Lauraceae) based on variations in chloroplast DNA sequences. J Plant Res 126, 193–202 (2013). https://doi.org/10.1007/s10265-012-0519-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10265-012-0519-1

Keywords

Search

Navigation