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Phylogeography of Medicinal Plant

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Molecular Pharmacognosy

Abstract

This chapter introduces the background, the basic theories, research methods in phylogeography and their application in biological evolution research, including the definition and formation of species, the evolutionary history of species, the identification of priority protected areas, and the origin of domestic animals and cultivated plants. In addition, the application of phylogeography in the evolution of medicinal plants is described, including research on the genetic basis of medicinal plants and the origin of cultivation. Case studies were also carried out.

Dan Jiang, Xiao-Lei Jin and Jia-Hui Sun are equally contributed for this chapter.

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References

  1. Arbogast BS: Phylogeography. The history and formation of species. Integr Comp Biol. 2001;41(1):134–5.

    Google Scholar 

  2. Moritz CDT, Brown WM. The mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst. 1987;18:269–92.

    Article  Google Scholar 

  3. Bai WN, Zhang DY. Current status and future directions in plant phylogeography. Chin Bull Life Sci. 2014;26(2):125–37.

    Google Scholar 

  4. Avise JC, Arnold J, Ball RM, et al. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst. 1987;18:489–522.

    Article  Google Scholar 

  5. Avise JC. Phylogeography: the history and formation of species. London: Harvard University Press; 2000.

    Google Scholar 

  6. Ge XJ, Chiang YC, Chou CH, et al. Nested clade analysis of Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle DNA sequences. Conserv Genet. 2002;3(4):351–62.

    Article  CAS  Google Scholar 

  7. Ge XJ, Liu MH, Wang WK, et al. Population structure of wild bananas, Musa balbisiana, in China determined by SSR fingerprinting and cpDNA PCR-RFLP. Mol Ecol. 2005;14(4):933–44.

    Article  CAS  PubMed  Google Scholar 

  8. Wang HW, Ge S. Phylogeography of the endangered Cathaya argyrophylla (Pinaceae) inferred from sequence variation of mitochondrial and nuclear DNA. Mol Ecol. 2006;15:4109–23.

    Article  CAS  PubMed  Google Scholar 

  9. Gao LM, Möller M, Zhang XM, et al. High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam. Mol Ecol. 2007;16(22):4684–98.

    Article  CAS  PubMed  Google Scholar 

  10. Yuan QJ, Zhang ZY, Peng H, et al. Chloroplast phylogeography of Dipentodon (Dipentodontaceae) in southwest China and northern Vietnam. Mol Ecol. 2008;17:1054–65.

    Article  CAS  PubMed  Google Scholar 

  11. Tian S, Li DR, Wang HW, et al. Mitochondrial DNA phylogeography of a montane pine (Pinus kwangtungensis Chun ex Tsiang) in south China: interglacial refugia and southward migration during cold stages. Ann Bot. 2008;102:69–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Xu XW, Ke WD, Yu XP, et al. A preliminary study on population genetic structure and phylogeography of the wild and cultivated Zizania latifolia (Poaceae) based on Adh1a sequences. Theor Appl Genet. 2008;116:835–43.

    Article  PubMed  Google Scholar 

  13. Rosenberg NA, Norborg M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet. 2002;2002(3):380–90.

    Article  CAS  Google Scholar 

  14. Lei M, Wang Q, Wu ZJ, et al. Molecular phylogeography of Fagus engleriana (Fagaceae) in subtropical China: limited admixture among multiple refugia. Tree Genet Genomes. 2012;8:1203–12.

    Article  Google Scholar 

  15. Templeton AR, Routman E, Philips CA. Separating population structure from population history: a cladistic analysis the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics. 1995;140:767–82.

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Mayden RL. A hierarchy of species concepts: The denouement in the saga of the species problem. London: The units of biodiversity Chapman and Hall; 1997. p. 381–424.

    Google Scholar 

  17. Slade RW, Moritz C. Phylogeography of Bufo marinus from its natural and introduced ranges. R Soc. 1998;265:769–77.

    Article  CAS  Google Scholar 

  18. Roca AL, Georgiadis N, Pecon-Slattery J, et al. Genetic evidence for two species of elephant in Africa. Science. 2001;293(5534):1473–7.

    Article  CAS  PubMed  Google Scholar 

  19. Gao J, Wang B, MAO JF, et al. Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau. Mol Ecol. 2012;21(19):4811–27.

    Article  PubMed  Google Scholar 

  20. Vandergast AG, Bohonak AJ, Hathaway SA, et al. Are hotspots of evolutionary potential adequately protected in southern California? Biol Conserv. 2008;141(6):1648–64.

    Article  Google Scholar 

  21. Médail F, Diadema K. Glacial refugia influence plant diversity patterns in the Mediterranean Basin. J Biogeogr. 2009;36(7):1333–45.

    Article  Google Scholar 

  22. Avise JC. Molecular population structure and the biogeographic history of a regional fauna, a case history with lessons for conservation biology. Oikos. 1992;63:62–76.

    Article  CAS  Google Scholar 

  23. Moritz C, Faith D. Comparative phylogeography and the identification of genetically divergent areas for conservation. Mol Ecol. 1998;7:419–29.

    Article  Google Scholar 

  24. Riddle BR, Hafner DJ, Alexander LF, et al. Cryptic vicariance in the historical assembly of a Baja California Peninsular Desert biota. Proc Natl Acad Sci. 2000;97(26):14438–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Zhang ZY, Wu R, Wang Q, et al. Comparative phylogeography of two sympatric beeches in subtropical China, Species-specific geographic mosaic of lineages. Ecol Evol. 2013;3(13):4461–72.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Vilà C, Savolainen P, Maldonado JE, et al. Multiple and ancient origins of the domestic dog. Science. 1997;276(5319):1687–9.

    Article  PubMed  Google Scholar 

  27. Adam RB. The domestic dog: man’s best friend in the genomic era. Genome Biol. 2011;12:216.

    Article  CAS  Google Scholar 

  28. Olsen KM, Schaal BA. Evidence on the origin of cassava, Phylogeography of Manihot esculenta. Proc Natl Acad Sci USA. 1999;96:5586–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Molina J, Sikora M, Garud N, et al. Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci. 2011;108(20):8351–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Huang X, Zhao Y, Wei X, et al. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet. 2012;44(1):32–9.

    Article  CAS  Google Scholar 

  31. Yuan QJ, Zhang ZY, Hu J, et al. Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae). BMC Genet. 2010;11:29.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  32. Huang S, Jing SNBC. (The divine farmer’s Materia Medica, translated by Yang SZ). Beijing: Traditional Chinese Medicine Ancient Books Press; 1982.

    Google Scholar 

  33. Joshee N, Mentreddy SR, Yadav AK. Mycorrhizal fungi and growth and development of micropropagated Scutellaria integrifolia plants. Ind Crop Prod. 2007;25:169–77.

    Article  CAS  Google Scholar 

  34. Kumagai T, Müller CI, Desmond JC, et al. Scutellaria baicalensis, a herbal medicine, anti-proliferative and apoptotic activity against acute lymphocytic leukemia, lymphoma and myeloma cell lines. Leuk Res. 2007;31(4):523–30.

    Article  CAS  PubMed  Google Scholar 

  35. Murch SJ, Rupasinghe HPV, Goodenowe D, et al. A metabolomic analysis of medicinal diversity in Huang-qin (Scutellaria baicalensis Georgi) genotypes, discovery of novel compounds. Plant Cell Rep. 2004;23(6):419–25.

    Article  CAS  PubMed  Google Scholar 

  36. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987;19:11–5.

    Google Scholar 

  37. Hamilton MB. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol Ecol. 1999;8:521–2.

    CAS  PubMed  Google Scholar 

  38. Sang T, Crawford DJ, Stuessy TF. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). Am J Bot. 1997;84:1120–36.

    Article  CAS  PubMed  Google Scholar 

  39. Thompson JD, Gibson TJ, Plewniak F, et al. The CLUSTAL_X windows interface, flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25(24):4876–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Caicedo AL, Schaal BA. Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Mol Ecol. 2004;13:1871–82.

    Article  CAS  PubMed  Google Scholar 

  41. Nei M. F-statistics and analysis of gene diversity in subdivided populations. Ann Hum Genet. 1977;41:225–33.

    Article  CAS  PubMed  Google Scholar 

  42. Nei M. Molecular evolutionary genetics. New York: Columbia University Press; 1987.

    Book  Google Scholar 

  43. Nei M. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA. 1973;70:3321–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Pons O, Petit RJ. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics. 1996;144:1237–45.

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Pons O, Petit RJ. Estimation, variance and optimal sampling of gene diversity. I. haploid locus. Theor Appl Genet. 1995;90:462–70.

    Article  CAS  PubMed  Google Scholar 

  46. Templeton AR, Crandall KA, Sing CF. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics. 1992;132:619–33.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Clement M, Posada D, Crandall KA. TCS, a computer program to estimate gene genealogies. Mol Ecol. 2000;9:1657–9.

    Article  CAS  PubMed  Google Scholar 

  48. Jensen JL, Bohonak AJ, Kelley ST. Isolation by distance, web service. BMC Genetics. 2005; 6:13 v.13.11. http://ibdws.sdsu.edu/.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. WenHsiung L. Molecular evolution. Sunderland: Sinauer Associates Incorporated; 1997.

    Google Scholar 

  50. Cavers S, Navarro C, Lowe AJ. A combination of molecular markers identifies evolutionarily significant units in Cedrela odorata L. (Meliaceae) in Costa Rica. Conserv Genet. 2003;4:571–80.

    Article  CAS  Google Scholar 

  51. Zhang Q, CHIANG TY, George M, et al. Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Mol Ecol. 2005;14(11):3513–24.

    Article  CAS  PubMed  Google Scholar 

  52. King RA, Ferris C. Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn. Mol Ecol. 1998;7:1151–61.

    Article  CAS  Google Scholar 

  53. Dumolin-lapegue S, Pemonge MH, Petit RJ. Association between chloroplast and mitochondrial lineages in oaks. Mol Biol Evol. 1998;15:1321–31.

    Article  CAS  PubMed  Google Scholar 

  54. Fineschi S, Salvini D, Taurchini D, et al. Chloroplast DNA variation of Tilia cordata (Tiliaceae). Can J For Res. 2003;33(12):2503–8.

    Article  Google Scholar 

  55. Huang H, Han X, Kang L, et al. Conserving native plants in China. Science (New York, NY). 2002;297(5583):935.

    Article  CAS  Google Scholar 

  56. Dutech C, Maggia L, Joly HI. Chloroplast diversity in Vouacapoua americana (Caesalpinaceae), a neotropical forest tree. Mol Ecol. 2000;9:1427–32.

    Article  CAS  PubMed  Google Scholar 

  57. Huang S, Chiang YC, Schaal BA, et al. Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan. Mol Ecol. 2001;10(11):2669–81.

    Article  CAS  PubMed  Google Scholar 

  58. Lu SY, Peng CI, Cheng YP, et al. Chloroplast DNA phylogeography of Cunninghamia konishii (Cupressaceae), an endemic conifer of Taiwan. Genome. 2001;44:797–807.

    Article  CAS  PubMed  Google Scholar 

  59. Petit RJ, Duminil J, Fineschi S, et al. Invited review, comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol. 2005;14(3):689–701.

    Article  CAS  PubMed  Google Scholar 

  60. Posada D, Crandall KA. Intraspecific gene genealogies, trees grafting into networks. Trends Ecol Evol. 2001;16:37–45.

    Article  CAS  PubMed  Google Scholar 

  61. Avise JC. Phylogeography, the history and formation of species. Cambridge, MA: Harvard University Press; 2000.

    Google Scholar 

  62. Hewitt GM. The genetic legacy of the quaternary ice ages. Nature. 2000;405:907–13.

    Article  CAS  PubMed  Google Scholar 

  63. TABERLET P, FUMAGALLI L, WUST-SAUCY AG, et al. Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol. 1998;7(4):453–64.

    Article  CAS  PubMed  Google Scholar 

  64. Abbott RJ, Smith LC, Milne RI, et al. Molecular analysis of plant migration and refugia in the Arctic. Science. 2000;289(5483):1343–6.

    Article  CAS  PubMed  Google Scholar 

  65. Willis KJ, Whittaker RJ. The refugial debate. Science. 2000;287:1406–7.

    Article  CAS  PubMed  Google Scholar 

  66. Mengel RM. The probable history of species formation in some northern wood warbles (Parulidae). Living Bird. 1964;3:9–43.

    Google Scholar 

  67. Klicka J, Zink RM. The impotence of recent ice ages in speciation: a failed paradigm. Science. 1997;277:1666–9.

    Article  CAS  Google Scholar 

  68. Doebley JF, Gaut BS, Smith BD. The molecular genetics of crop domestication. Cell. 2006;127:1309–21.

    Article  CAS  PubMed  Google Scholar 

  69. Londo JP, Chiang YC, Hung KH, et al. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci. 2006;103(25):9578–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Olsen KM, Gross BL. Detecting multiple origins of domesticated crops. Proc Natl Acad Sci USA. 2008;105:13701–2.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Allaby RG. The rise of plant domestication: Life in the slow lane. Biologist. 2008;55:94–9.

    Google Scholar 

  72. He J, Chen L, Si Y, et al. Population structure and genetic diversity distribution in wild and cultivated populations of the traditional Chinese medicinal plant Magnolia officinalis subsp. biloba (Magnoliaceae). Genetica. 2009;135(2):233–43.

    Article  PubMed  Google Scholar 

  73. Kilian B, Özkan H, Walther A, et al. Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum (Einkorn) domestication, implications for the origin of agriculture. Mol Biol Evol. 2007;24(12):2657–68.

    Article  CAS  PubMed  Google Scholar 

  74. Miller A, Schaal B. Domestication of a Mesoamerican cultivated fruit tree, Spondias purpurea. Proc Natl Acad Sci USA. 2005;102:12801–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Miller AJ, Schaal BA. Domestication and the distribution of genetic variation in wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea L. (Anacardiaceae). Mol Ecol. 2006;15:1467–80.

    Article  CAS  PubMed  Google Scholar 

  76. Guo HB, Lu BR, Wu QH, et al. Abundant genetic diversity in cultivated Codonopsis pilosula populations revealed by RAPD polymorphisms. Genet Resour Crop Evol. 2007;54(5):917–24.

    Article  CAS  Google Scholar 

  77. Shi W, Yang CF, Chen JM, et al. Genetic variation among wild and cultivated populations of the Chinese medicinal plant Coptis chinensis (Ranunculaceae). Plant Biol 2008. 1985;10(4):485–91.

    Google Scholar 

  78. Ellstrand NC, Marshall DL. The impact of domestication on distribution of allozyme variation within and among cultivars of radish, Raphanus sativus L. Theor Appl Genet. 1985;69:393–8.

    Article  CAS  PubMed  Google Scholar 

  79. Hamrick JL, Godt MJW. Allozyme diversity in cultivated crops. Crop Sci. 1997;37:26–30.

    Article  CAS  Google Scholar 

  80. Brown AHD. Isozymes, plant population genetic structure and genetic conservation. Theor Appl Genet. 1978;52:145–57.

    Article  CAS  PubMed  Google Scholar 

  81. Hyten DL, Song Q, Zhu Y, et al. Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci. 2006;103(45):16666–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Blanca JM, Prohens J, Anderson GJ, et al. AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae), implications for evolution and domestication. Am J Bot. 2007;94(7):1219–29.

    Article  CAS  PubMed  Google Scholar 

  83. Altieri MA, Merrick LC. In situ conservation of crop genetic resources through maintenance of traditional farming systems. Econ Bot. 1987;41:86–96.

    Article  Google Scholar 

  84. Vargas-Ponce O, Zizumbo-Villarreal D, Martínez-Castillo J, et al. Diversity and structure of landraces of Agave grown for spirits under traditional agriculture: A comparison with wild populations of A. angustifolia (Agavaceae) and commercial plantations of A. tequilana. Am J Bot. 2009;96(2):448–57.

    Article  PubMed  Google Scholar 

  85. Allendorf FW, Luikart G. Conservation and the genetics of populations. Mammalia. 2007;2007:189–97.

    Google Scholar 

  86. Storfer A. Gene flow and endangered species translocations, a topic revisited. Biol Conserv. 1999;87:173–80.

    Article  Google Scholar 

  87. Bower AD, Aitken SN. Ecological genetics and seed transfer guidelines for Pinus albicaulis (Pinaceae). Am J Bot. 2008;95:66–76.

    Article  PubMed  Google Scholar 

  88. Canter PH, Thomas H, Ernst E. Bringing medicinal plants into cultivation, opportunities and challenges for biotechnology. Trends Biotechnol. 2005;23:180–5.

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Qing-Jun Yuan .

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Jiang, D., Jin, XL., Sun, JH., Yuan, QJ., Chiang, YC., Zhang, ZY. (2019). Phylogeography of Medicinal Plant. In: Huang, Lq. (eds) Molecular Pharmacognosy. Springer, Singapore. https://doi.org/10.1007/978-981-32-9034-1_4

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