Advertisement

Journal of Plant Biology

, Volume 62, Issue 1, pp 14–26 | Cite as

Phylogeographical Study of Camellia japonica Inferred from AFLP and Chloroplast DNA Haplotype Analyses

  • Youngil Ryu
  • Il Ryong Kim
  • Mong Huai Su
  • Jongduk Jung
  • Hong-Keun ChoiEmail author
  • Changkyun KimEmail author
Original Article
  • 2 Downloads

Abstract

Intraspecific genetic variation provides the information on the distributional pattern of plant species by inducing local adaptation, range shifts, and range reduction. Here, genetic variation of amplified fragment length polymorphism (AFLP) and three chloroplast DNA (cpDNA) regions (atpI-atpH, trnD-psbM, and trnT-L) is investigated in 37 populations of Camellia japonica to assess the genetic diversity and population structure. We also infer the phylogeographical history of C. japonica distributed in South Korea, Japan (Kyushu and Okinawa), and Taiwan of East Asia. The AFLP results reveal high levels of genetic diversity in C. japonica across East Asia. At the regional level, the Kyushu populations display the highest level of genetic variation, whereas the mainland populations of South Korea exhibit the lowest level of variation. Our results show trends of loss of genetic diversity along with latitude. On the basis of 154 polymorphic sites of the combined three cpDNA regions, 11 haplotypes (A-K) were identified across the East Asian C. japonica populations. Haplotypes A-C are dominant and widespread in South Korea and Japan, while Haplotypes G, I, and J in Taiwan. In addition, five haplotypes (A, B, D-F) are exclusively occur in South Korea/Japan and five (G-K) are in Taiwan. Our molecular dating analysis estimates the age of initial diversification of C. japonica haplotypes in the late Tertiary. The phylogeographic patterns of C. japonica coupled with molecular dating suggest vicariance as key mechanism for initial diversification between South Korea/Japan and Taiwan. In contrast, the haplotypes of Japan are shared with those of South Korea indicating that they had insufficient time to form population structures at the regional level.

Keywords

AFLP Camellia japonica cpDNA Haplotype Genetic diversity Phylogeography 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

12374_2017_292_MOESM1_ESM.pdf (631 kb)
Supplementary material, approximately 631 KB.

References

  1. Aitken SN, Yeaman S, Holliday JA, Wang T, Curtis-McLane S (2008) Adaptation, migration or extirpation:climate change outcomes for tree populations. Evol Appl 1:95–111CrossRefGoogle Scholar
  2. Akaike H (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control 19:716–723CrossRefGoogle Scholar
  3. Alsos IG, Ehrich D, Thuiller W, Eidesen PB, Tribsch A, Schonswetter P, Lagaye C, Taberlet P, Brochmann C (2012) Genetic consequences of climate change for northern plants. Proc Biol Sci 279:2042–2051CrossRefGoogle Scholar
  4. Arrigo N, Holderegger R, Alvarez N (2012) Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library, In F Pompanon, A Bonin, eds, Data production and analysis in population genomics, Methods in Molecular Biology, Vol 888, Humana Press, Totowa, NJ, pp155−175CrossRefGoogle Scholar
  5. Brazil M (2009) Birds of East Asia:China, Taiwan, Korea, Japan, and Russia. Helm Field Guides, A & C Black Publishers Limited, London, 528 pagesGoogle Scholar
  6. Cao GX, Zhong ZC, Xie DT, Liu Y, Long Y (2003) RAPD analysis of Camellia roshorniana populations in different communities in Jinyun Mountain. Acta Ecol Sin 23:1583–1589Google Scholar
  7. Chen DH, Ronald PC (1999) A rapid DNA minipreparation method suitable for AFLP and other PCR applications. Plant Mol Biol Report 17:53–57CrossRefGoogle Scholar
  8. Chung MG, Kang SS (1996) Genetic variation within and among populations of Camellia japonica (Theaceae) in Korea. Can J For Res 26:537–542CrossRefGoogle Scholar
  9. Chung MY, Kang SS (1994) Genetic variation and population structure in Korean populations of Eurya japonica (Theaceae). Am J Bot 81:1077–1082CrossRefGoogle Scholar
  10. Chung MY, López-Pujol J, Chung MG (2014) Comparative biogeography of the congener lilies Lilium distichum and Lilium tsingtauense in Korea. Flora 209:435–445CrossRefGoogle Scholar
  11. Clement M, Posada D, Crandall KA (2000) TCS:a computer program to estimate gene genealogies. Mol Ecol 9:1657–1659CrossRefGoogle Scholar
  12. Demesure B, Comps B, Petit RJ (1996) Chloroplast DNA phylogeography of the common beech (Fagus sylvatica L.) in Europe. Evolution 50:2515–2520CrossRefGoogle Scholar
  13. Dieleman CM, Branfireun BA, McLaughlin JW, Lindo Z (2015) Climate change drives a shift in peatland ecosystem plant community:implications for ecosystem function and stability. Glob Change Biol 21:388–395CrossRefGoogle Scholar
  14. Drummond AJ, Rambaut A (2007) BEAST:Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214–222CrossRefGoogle Scholar
  15. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973CrossRefGoogle Scholar
  16. Dynesius M, Jansson R (2000) Evolutionary consequences of changes in species’ geographical distributions driven by Milankovitch climate oscillations. Proc Natl Acad Sci USA 97:9115–9120CrossRefGoogle Scholar
  17. Earl DA, von Holdt BM (2012) STRUCTURE HARVESTER:a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361CrossRefGoogle Scholar
  18. Ehrich D (2006) AFLPdat:a collection of R functions for convenient handling of AFLP data. Mol Ecol Notes 6:603–604CrossRefGoogle Scholar
  19. Elmendorf SC, Henry GHR, Hollister RD, Fosaa AM, Gould WA, Hermanutz L, Hofgaard A, Jonsdottir IS, Jorgenson JC, Levesque E, Magnusson B, Molau U, Myers-smith IH, Oberbauer SF, Rixen C, Tweedie CE, Walker MD (2015) Experiment, monitoring, and gradient methods used to infer climate change effects on plant communities yield consistent patterns. Proc Natl Acad Sci USA 112:448–452CrossRefGoogle Scholar
  20. Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567CrossRefGoogle Scholar
  21. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data:dominant markers and null alleles. Mol Ecol Notes 7:574–578CrossRefGoogle Scholar
  22. Ferris C, King RA, Väinölä R, Hewitt GM (1998) Chloroplast DNA recognizes three refugial sources of European oaks and suggests independent eastern and western immigrations to Finland. Heredity 80:584–593CrossRefGoogle Scholar
  23. Han Z, Han G, Wang Z, Shui B, Gao T (2015) The genetic divergence and genetic structure of two closely related fish species Lateolabrax maculatus and Lateolabrax japonicus in the Northwestern Pacific inferred from AFLP markers. Genes Genom 37:471–477CrossRefGoogle Scholar
  24. Harris SA, Ingram R (1991) Chloroplast DNA and biosystematics:the effects of intraspecific diversity and plastid transmission. Taxon 40:393–412CrossRefGoogle Scholar
  25. Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913CrossRefGoogle Scholar
  26. Holsinger KE, Lewis PO (2003) Hickory:a package for analysis of population genetic data v1. 0. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USAGoogle Scholar
  27. Holsinger KE, Lewis PO (2005) Hickory:A Package for Analysis of Population Genetic Data, ver. 1.0.4. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USAGoogle Scholar
  28. Jeong EK, Kim K, Kim JH, Suzuki M (2004) Fossil woods from Janggi Group (Early Miocene) in Pohang Basin, Korea. J Plant Res 117:183–189CrossRefGoogle Scholar
  29. Jin Y (2003) Phytosociological Studies on the Distribution Zone of Camellia japonica in Korean peninsula, A part of doctoral dissertation, Graduate School Changwon National University, ChangwonGoogle Scholar
  30. Jombart T (2008) adegenet:a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405Google Scholar
  31. Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components:a new method for the analysis of genetically structured populations. BMC Genetics 11:94CrossRefGoogle Scholar
  32. Karp A, Kresovich S, Bhat KV, Ayad WG, Hodgkin T (1997) Molecular tools in plant genetic resources conservation:a guide to the technologies, IPGRI, RomeGoogle Scholar
  33. Keiper FJ, McConchie R (2000) An analysis of genetic variation in natural populations of Sticherus flabellatus [R. Br. (St John)] using amplified fragment length polymorphism (AFLP) markers. Mol Ecol 9:571–581Google Scholar
  34. Kim C, Shin H, Choi H-K (2009) Genetic diversity and population structure of diploid and polyploid species of Isoëtes in East Asia based on amplified fragment length polymorphism markers. Int J Plant Sci 170:496–504CrossRefGoogle Scholar
  35. Kim IR, Yu D, Choi H-K (2015) A phytogeographical study of Sasa borealis populations based on AFLP analysis. Korean J Plant Taxon 45:29–35CrossRefGoogle Scholar
  36. Lee C, Wen J (2004) Phylogeny of Panax using chloroplast trnC–trnD intergenic region and the utility of trnC–trnD in interspecific studies of plants. Mol Phylogenet Evol 31:894–903CrossRefGoogle Scholar
  37. Lee JH, Lee DH, Choi BH (2013) Phylogeography and genetic diversity of East Asian Neolitsea sericea (Lauraceae) based on variations in chloroplast DNA sequences. J Plant Res 126:193–202CrossRefGoogle Scholar
  38. Li CY, Wang CM, Hsiao JY, Yang CH (2003) Two fossil dicotyledonous woods from the Kungkuan Tuff (Early Miocene), Northern Taiwan. Collection and Research 16:71–78Google Scholar
  39. Li EX, Sun Y, 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 49:702–714CrossRefGoogle Scholar
  40. Li J (2007) Flora of China. Harvard Papers in Botany 12:367–412Google Scholar
  41. Liao Y, Gichira AW, Wang Q, Chen J (2016) Molecular phylogeography of four endemic Sagittaria species (Alismataceae) in the Sino-Japanese Floristic Region of East Asia. Bot Linn J Soc 180:6–20CrossRefGoogle Scholar
  42. Librado P, Rozas J (2009) DnaSP v5:a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452CrossRefGoogle Scholar
  43. Lim JD, Jeong EK, Kim K, Suzuki M, Paik IS, et al. (2010) Miocene woods of the Janggi Basin in Korea:Implications for paleofloral changes. Geosci J 14:11–22CrossRefGoogle Scholar
  44. Lin L, Hu Z-Y, Ni S, Li J-Y, Qiu Y-X (2013) Genetic diversity of Camellia japonica (Theaceae), a species endangered to East Asia, detected by inter-simple sequence repeat (ISSR). Biochem Syst Ecol 59:199–206CrossRefGoogle Scholar
  45. Liu ZJ, Cordes JF (2004) DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238:1–37CrossRefGoogle Scholar
  46. Lu S-Y, Hong K-H, Liu S-L, Cheng Y-P, Wu W-L, Chiang T-Y (2002) Genetic variation and population differentiation of Michelia formosana (Magnoliaceae) based on cpDNA variation and RAPD fingerprints:relevance to post-Pleistocene recolonization. J Plant Res 115:203–216CrossRefGoogle Scholar
  47. Milne RI (2006) Northern hemisphere plant disjunctions:a window on Tertiary land bridges and climate change? Ann Bot 98:465–472CrossRefGoogle Scholar
  48. Min TL, Bartholomew B (2007) Theaceae. In:Wu ZY, Raven PH (eds) Flora of China, vol 12. Science Press:Beijing and Missouri Botanical Garden Press, St. LouisGoogle Scholar
  49. Mosca E, Eckert AJ, Pierro EAD, Rocchini D, Porta NL, Belletti P, Neale DB (2012) The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps. Mol Ecol 21:5530–5545CrossRefGoogle Scholar
  50. Nei M and Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273CrossRefGoogle Scholar
  51. Nei. H (1973) Analysis of gene diversity in subdivided populations, Proc Natl Acad Sci USA 70:3321–3323CrossRefGoogle Scholar
  52. 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.CrossRefGoogle Scholar
  53. Petit RJ, Brewer S, Bordács S, Burg K, Cheddadi R, Coart E, Cottrellg J, Csaikle UM, van Damh B, Deansi JD, Espinelj S, Fineschik S, Finkeldeyl R, Glaza I, Goicoecheaj PG, Jensenn JS, Königo AO, Lowei AJ, Madsenp SF, Mátyásk G, Munroi RC, Popescua F, Sladea D, Tabbenerg H, de Vriesh SMG, Ziegenhageno B, Beaulieu JL, Kremer A (2002) Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. For Ecol Manage 156:49–74CrossRefGoogle Scholar
  54. Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144:1237–1245Google Scholar
  55. Posada D, Crandall KA (1998) MODELTEST:testing the model of DNA substitution. Bioinformatics 14:817–818CrossRefGoogle Scholar
  56. Qian H, Ricklefs RE (2000) Large-scale processes and the Asian bias in species diversity of temperate plants. Nature 407:108–182CrossRefGoogle Scholar
  57. Qiu Y-X, Fu C-X, 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 59:225–244CrossRefGoogle Scholar
  58. Qiu Y-X, Fu C-X, 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 59:225–244CrossRefGoogle Scholar
  59. Qiu Y-X, Qi X-S, Jin X-F, Tao X-Y, Fu C-X, 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 58:1226–1241Google Scholar
  60. Qiu Y-X, Sun Y, Zhang X-P, Lee J, Fu C-X, Comes HP (2009b) Molecular phylogeography of East Asian Kirengeshoma (Hydrangeaceae) in relation to Quaternary climate change and land bridge configurations. New Phytol 183:480–495CrossRefGoogle Scholar
  61. R Core Team (2015) R:A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, URL http://www.R-project.org/.Google Scholar
  62. Rambaut A (2009) FigTree, version 1.3.1 http://tree.Bio.ed.ac.uk/software/figtreeGoogle Scholar
  63. Rambaut A, Drummond AJ (2007) Tracer, version 1.5 <http://beast.bio.ed.ac.uk/Tracer>Google Scholar
  64. Schnitzer SA (2005) A mechanistic explanation for global patterns of liana abundance and distribution. Am Nat 166:262–276CrossRefGoogle Scholar
  65. Schoettle AW, Goodrich BA, Hipkins, V, Richards C, Kray J (2011) Geographic patterns of genetic variation and population structure in Pinus aristata, Rocky Mountain bristlecone pine. Can J For Res 42:23–37CrossRefGoogle Scholar
  66. Schönswetter P, Tribsch A (2005) Vicariance and dispersal in the alpine perennial Bupleurum stellatum L. (Apiaceae). Taxon 54:725–732CrossRefGoogle Scholar
  67. 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. J Plant Res 19:401–405CrossRefGoogle Scholar
  68. Spiegelhalter DJ, Best NG, Carlin BP, Van Der Linde A (2002) Bayesian measures of model complexity and fit. J. R. Stat. Soc. Series B (Statistical Methodology). 64:583–639CrossRefGoogle Scholar
  69. Su YJ, Liao WB, Wang T, Sun YF, Wei Q, Chang HT (2011) Phylogeny and evolutionary divergence times in Apterosperma and Eurydendron:Evidence of a Tertiary origin in south China. Biochem Syst Ecol 39:769–777CrossRefGoogle Scholar
  70. Suzuki M, Terada K (1996) Fossil wood flora from the lower Miocene Yanagida Formation, Noto Peninsula, central Japan. IAWA 17:365–392CrossRefGoogle Scholar
  71. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109CrossRefGoogle Scholar
  72. 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). J Plant Res 126:323–333CrossRefGoogle Scholar
  73. Tamura K, Stecher G, Peterson D, Filipski A and Kumar S (2013) MEGA6:molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefGoogle Scholar
  74. Tang S, Bin X, Wang L, Zhong Y (2006) Genetic diversity and population structure of yellow camellia (Camellia nitidissima) in China as revealed by RAPD and AFLP markers. Biochem Genet 44:449–461CrossRefGoogle Scholar
  75. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680CrossRefGoogle Scholar
  76. Tsumura Y, Kawahara T, Wickneswari R, Yoshimura K (1996) Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes. Theor Appl Genet 93:22–29CrossRefGoogle Scholar
  77. Ueno S, Tomaru N, Yoshimaru H, Manabe T, Yamamoto S (2000) Genetic structure of Camellia japonica L. in an old-growth evergreen forest, Tsushima, Japan. Mol Ecol 9:647–656CrossRefGoogle Scholar
  78. Vario SL, Chakraborty R, Nei M (1986) Genetic variation in subdivided populations and conservation genetics. Heredity 57:189–198CrossRefGoogle Scholar
  79. Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M (1995) AFLP:a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414CrossRefGoogle Scholar
  80. Weiser MD, Enquist BJ, Boyle B, Killeen TJ, Jørgensen PM, Fonseca G, Jennings MD, Kerkhoff AJ, Lacher TE, Monteagudo A, Núñez MP, Phillips OL, Swenson NG, Vásquez R. (2007) Latitudinal patterns of range size and species richness of New World woody plants. Glob Ecol Biogeogr 16:679–688CrossRefGoogle Scholar
  81. Wendel JF, Parks CR (1985) Genetic diversity and population structure in Camellia japonica L. (Theaceae). Am J Bot 72:52–65CrossRefGoogle Scholar
  82. 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 84:9054–9058CrossRefGoogle Scholar
  83. Xie GW (1997) On Phytogeographical affinities of the forest floras between East China and Japan. Chinese Geography Science 7:236–242CrossRefGoogle Scholar
  84. Yeh F, Yang RC, Boyle T (1997) POPGENE. A User-friendly Shareware for Population Genetic Analysis, ver. 1.31. Molecular and Biotechnology Center, University of Alberta, Edmonton, Alberta, CanadaGoogle Scholar
  85. Zhang W, Kan SL, Zhao H, Li ZY, Wang XQ (2014) Molecular phylogeny of tribe Theeae (Theaceae s.s.) and its implications for generic delimitation. PLoS One 9:e98133Google Scholar

Copyright information

© Korean Society of Plant Biologists and Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Biological ScienceAjou UniversitySuwonKorea
  2. 2.National Institute of EcologySeocheon-gun, ChongnamKorea
  3. 3.Department of Forestry and Nature ConservationChinese Culture UniversityTaipeiTaiwan
  4. 4.Institute of Northeast Asian PlantSeoulKorea
  5. 5.Department of Life ScienceGachon UniversitySeongnamKorea

Personalised recommendations