Phylogeographic structure of Hippophae tibetana (Elaeagnaceae) highlights the highest microrefugia and the rapid uplift of the Qinghai-Tibetan Plateau

Molecular Ecology

Volumn 19, Issue 14, 2010, Pages 2964-2979

  Wang, Hao ^a   Qiong, La ^b   Sun, Kun ^c   Lu, Fan ^a   Wang, Yuguo ^a   Song, Zhiping ^a   Wu, Qianhong ^a   Chen, Jiakuan ^a   Zhang, Wenju ^a  

^a FUDAN UNIVERSITY   (China)

^b TIBET UNIVERSITY   (China)

^c NORTHWEST NORMAL UNIVERSITY   (China)

Author keywords

cpDNA trnT trnF; Hippophae tibetana; microrefugia; phylogeographic structure; plateau uplift; Qinghai Tibetan Plateau

Indexed keywords

CHLOROPLAST DNA; PLANT DNA;

ARTICLE; ASIA; DNA SEQUENCE; ELAEAGNACEAE; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION GENETICS;

ASIA; DNA, CHLOROPLAST; DNA, PLANT; ELAEAGNACEAE; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

ELAEAGNACEAE; HIPPOPHAE RHAMNOIDES; HIPPOPHAE THIBETANA;

EID: 77954556391     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04729.x     Document Type: Article

References (121)

1. Abbott RJ, Brochmann C (2003) History and evolution of the arctic flora: in the footsteps of Eric Hultén. Molecular Ecology, 12, 299 313.
2. Abbott RJ, Smith LC, Milne RI et al. (2000) Molecular analysis of plant migration and refugia in the Arctic. Science, 289, 1343 1346.
3. Aitchison JC, Ali JR, Davis AM (2007) When and where did India and Asia collide? Journal of Geophysical Research, 112, B05423, doi :.
4. Akgun F, Sozbilir H (2001) A palynostratigraphic approach to the SW Anatolian molasse basin: Kale-Tavas molasse and Denizli molasse. Geodinamica Acta, 14, 71 93.
5. An ZS, Kutzbach JE, Prell WL, Porter SC (2001) Evolution of Asian monsoons and phased uplift of the Himalaya-Tibetan plateau since Late Miocene times. Nature, 411, 62 66.
6. Anderson LL, Hu FS, Nelson DM, Petit RJ, Paige KN (2006) Ice-age endurance: DNA evidence of a white spruce refugium in Alaska. Proceedings of the National Academy of Sciences, USA, 103, 12447 12450.
7. Avise JC (2000) Phylogeography: the History and Formation of Species. Harvard University Press
8. Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37 48.
9. Bartish IV, Jeppsson N, Bartish GI, Lu R, Nybom H (2000) Inter- and intraspecific genetic variation inHippophae (Elaeagnaceae) investigated by RAPD markers. Plant Systematics and Evolution, 225, 85 101.
10. Bartish IV, Jeppsson N, Nybom H, Swenson U (2002) Phylogeny of Hippophae (Elaeagnaceae) inferred from parsimony analysis of chloroplast DNA and morphology. Systematic Botany, 27, 41 54.
11. Bartish IV, Kadereit JW, Comes HP (2006) Late Quaternary history of Hippophae rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (Chsi) sequences and chloroplast DNA variation. Molecular Ecology, 15, 4065 4083.
12. Chase MW, Soltis DE, Olmstead RG et al. (1993) Phylogenetics of seed plants - an analysis of nucleotide-sequences from the plastid gene rbcL. Annals of the Missouri Botanical Garden, 80, 528 580.
13. Chen XL, Ma RJ, Sun K, Lian YS (2003) Germplasm resource and habitat types of Seabuckthorn in China. Acta Botanica Boreali-Occidentalia Sinica, 23, 451 455.
14. Chung SL, Lo CH, Lee TY et al. (1998) Diachronous uplift of the Tibetan plateau starting 40 Myr ago. Nature, 394, 769 773.
15. Coleman M, Hodges K (1995) Evidence for Tibetan Plateau Uplift before 14-Myr ago from a new minimum age for east-west extension. Nature, 374, 49 52.
16. Cui ZJ, Gao QZ, Liu GN, Pan BT, Chen HL (1996) Planation surfaces, palaeokarst and uplift of Xizang (Tibet) plateau. Science in China Series D-Earth Sciences, 39, 391.
17. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochemical Bulletin, 19, 11 15.
18. Du YJ, Wang YJ, Yang J, Zhang H, Sun K (2008) Morphological analysis of Hippophae rhamnoides ssp. Sinensis × Hippophae neurocarpa ssp. neurocarpa hybrid zone. Journal of Northwest Normal University (Natural Science), 44, 73 77.
19. Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Molecular Ecology, 11, 2571 2581.
20. Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Molecular Ecology, 13, 853 864.
21. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
22. Fang XM, Lu LQ, Yang SL et al. (2002) Loess in Kunlun Mountains and its implications on desert development and Tibetan Plateau uplift in west China. Science in China Series D-Earth Sciences, 45, 289 299.
23. Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics, 22, 521 565.
24. Frenzel B, Bräuning A, Adamczyk S. (2003) Possible last-glacial forest-refuge-areas within the deep valleys of eastern Tibet. Erdkunde, 57, 182 198.
25. Fu Y-X (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915 925.
26. Gao LM, Moller M, Zhang XM et al. (2007) High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam. Molecular Ecology, 16, 4684 4698.
27. Godbout J, Jaramillo-Correa JP, Beaulieu J, Bousquet J (2005) A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer. Molecular Ecology, 14, 3497 3512.
28. Hampe A, Arroyo J, Jordano P, Petit RJ (2003) Rangewide phylogeography of a bird-dispersed Eurasian shrub: contrasting Mediterranean and temperate glacial refugia. Molecular Ecology, 12, 3415 3426.
29. Harrison TM, Copeland P, Kidd WSF, Yin A (1992) Raising Tibet. Science, 255, 1663 1670.
30. Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society, 58, 247 276.
31. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907 913.
32. Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 359, 183 195.
33. Hsü J, Tao J-R, Sun X-J (1973) On the discovery of a Quercus semicarpifolia bed in Mount Shisha Pangma and its significance in botany and geology. Journal of Integrative Plant Biology, 15, 103 119.
34. Huang WP, Ji HX (1979) Discovery of Hipparion fauna in Xizang. Chinese Science Bulletin, 24, 885 885.
35. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294, 2310 2314.
36. Jaramillo-Correa JP, Beaulieu J, Bousquet J (2004) Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer. Molecular Ecology, 13, 2735 2747.
37. Kapp P, DeCelles PG, Gehrels GE, Heizier M, Ding L (2007) Geological records of the Lhasa-Qiangtang and Indo-Asian collisions in the Nima area of central Tibet. Geological Society of America Bulletin, 119, 917 932.
38. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111 120.
39. Kimura M (1981) Estimation of evolutionary distances between homologous nucleotide sequences. Proceedings of the National Academy of Sciences, USA, 78, 454 458.
40. Kuhle M (1990) The cold deserts of high Asia (Tibet and contiguous mountains). GeoJournal, 20, 319 323.
41. Lehmkuhl F, Owen LA (2005) Late Quaternary glaciation of Tibet and the bordering mountains: a review. Boreas, 34, 87 100.
42. Li JJ, Wen SX, Zhang QS et al. (1979) A discussion on the period, amplitude and type of the uplift of the Qinghai-Xizang (Tibetan) Plateau. Scientia Sinica, 22, 1314 1328.
43. Li B, Li J, Cui Z et al. (1991) Quaternary Glacial Distribution Map of Qinghai-Xizang (Tibet) Plateau. Science Press (Map)
44. Li JJ, Fang XM, Ma HZ et al. (1996) Geomorphological and environmental evolution in the upper reaches of the Yellow River during the late Cenozoic. Science in China Series D-Earth Sciences, 39, 380 390.
45. Li JJ, Fang XM, Pan BT, Zhao ZJ, Song YG (2001) Late Cenozoic intensive uplift of Qinghai-Xizang Plateau and its impacts on environments in surrounding area. Quaternary Sciences, 21, 381 391.
46. Li SC, Xu L, Guo YX, Qian WH, Zhang GQ, Li C (2007) Change of annual precipitation over Qinghai-Xizang Plateau and sub-regions in recent 34 Years. Journal of Desert Research, 27, 307 314.
47. Lian YS, Chen XL, Lian H (1998) Systematic classification of the genus Hippophae L. Seabuckthorn Research, 1, 13 23.
48. Lisiecki LE, Raymo ME (2005) A Pliocene-Pleistocene stack of 57 globally distributed benthic °18O records. Paleoceanography, 20, PA1003, doi :.
49. Liu XD, Yin ZY (2002) Sensitivity of East Asian monsoon climate to the uplift of the Tibetan Plateau. Palaeogeography, Palaeoclimatology, Palaeoecology, 183, 223 245.
50. Liu T, Lu Y, Zheng H (1985) Loess and Environment. Science Press
51. Liu T, Zheng M, Guo Z (1998) Initiation and evolution of the Asian monsoon system timely coupled with the ice-sheet growth and the tectonic movements in Asia. Quaternary Sciences, 3, 194 198.
52. Liu S, Wang N, Duan Ke et al. (2004) Recent progress of glaciological studies in China. Journal of Geographical Sciences, 14, 401 410.
53. Magri D, Fineschi S, Bellarosa R et al. (2007) The distribution of Quercus suber chloroplast haplotypes matches the palaeogeographical history of the western Mediterranean. Molecular Ecology, 16, 5259 5266.
54. Mardulyn P (2001) Phylogeography of the Vosges mountains populations of Gonioctena pallida (Coleoptera : Chrysomelidae): a nested clade analysis of mitochondrial DNA haplotypes. Molecular Ecology, 10, 1751 1763.
55. Meng LH, Yang R, Abbott RJ et al. (2007) Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom. (Pinaceae) in the Qinghai-Tibetan Plateau and adjacent highlands. Molecular Ecology, 16, 4128 4137.
56. Myers N, Mittermeier R, Mittermeier C, Fonseca G, Kent J (2000) Biodiversity hotspots for conversation priorities. Nature, 403, 853 858.
57. Nei M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, USA, 70, 3321 3323.
58. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press
59. Ni J (2000) A simulation of biomes on the Tibetan Plateau and their responses to global climate change. Mountain Research and Development, 20, 80 89.
60. Opgenoorth L, Vendramin GG, Mao KS et al. (2010) Tree endurance on the Tibetan Plateau marks the world's highest known tree line of the Last Glacial Maximum. New Phytologist, 185, 332 342.
61. Petit RJ, Grivet D (2002) Optimal randomization strategies when testing the existence of a phylogeographic structure. Genetics, 161, 469 471.
62. Petit RJ, Pineau E, Demesure B et al. (1997) Chloroplast DNA footprints of postglacial recolonization by oaks. Proceedings of the National Academy of Sciences, USA, 94, 9996 10001.
63. Petit RJ, Hampe A, Cheddadi R (2005) Climate changes and tree phylogeography in the Mediterranean. Taxon, 54, 877 885.
64. Polzin T, Daneschmand SV (2003) On Steiner trees and minimum spanning trees in hypergraphs. Operations Research Letters, 31, 12 20.
65. Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics, 144, 1237 1245.
66. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817 818.
67. Qiu Z, Li C (2005) Evolution of Chinese mammalian faunal regions and elevation of the Qinghai-Xizang (Tibet) Plateau. Science in China Series D-Earth Sciences, 48, 1246 1258.
68. Raunkiaer C (1934) Life Forms of Plants and Statistical Plant Geography. Arno Press
69. Ray N, Currat M, Excoffier L (2003) Intra-deme molecular diversity in spatially expanding populations. Molecular Biology and Evolution, 20, 76 86.
70. Raymo ME, Ruddiman WF (1992) Tectonic forcing of Late Cenozoic climate. Nature, 359, 117 122.
71. Richardson JE, Fay MF, Cronk QCB, Bowman D, Chase MW (2000) A phylogenetic analysis of Rhamnaceae using rbcL and trnL-F plastid DNA sequences. American Journal of Botany, 87, 1309 1324.
72. Richardson JE, Pennington RT, Pennington TD, Hollingsworth PM (2001) Rapid diversification of a species rich genus of Neotropical rain forest trees. Science, 293, 2242 2245.
73. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552 569.
74. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572 1574.
75. Rowley DB, Currie BS (2006) Palaeo-altimetry of the late Eocene to Miocene Lunpola basin, central Tibet. Nature, 439, 677 681.
76. Royden LH, Burchfiel BC, van der Hilst RD (2008) The geological evolution of the Tibetan plateau. Science, 321, 1054 1058.
77. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
78. Ruddiman WF, Kutzbach JE (1989) Forcing of Late Cenozoic northern hemisphere climate by plateau uplift in Southern Asia and the American West. Journal of Geophysical Research-Atmospheres, 94, 18409 18427.
79. Savolainen V, Chase MW, Hoot SB et al. (2000) Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Systematic Biology, 49, 306 362.
80. Searle M (1995) Plate-tectonics - the rise and fall of Tibet. Nature, 374, 17 18.
81. Shi Y (2002) Characteristics of late Quaternary monsoonal glaciation on the Tibetan Plateau and in East Asia. Quaternary International, 97-8, 79 91.
82. Shi YF, Zheng BX, Yao TD (1997) Glaciers and environments during the Last Glacial Maximum (LGM) on the Tibetan Plateau. Journal of Glaciology and Geocryology, 19, 97 113.
83. Shi YF, Li JJ, Li BY (1998) Uplift and Environmental Changes of Qinghai-Tibetan Plateau in the Late Cenozoic. Guangdong Science and Technology Press
84. Shi YF, Li JJ, Li BY (1999) Uplift of the Qinghai-Xizang (Tibetan) Plateau and East Asia environmental change during late Cenozoic. Acta Geographica Sinica, 54, 10 20.
85. Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129, 555 562.
86. Smith SA, Donoghue MJ (2008) Rates of molecular evolution are linked to life history in flowering plants. Science, 322, 86 89.
87. Soltis DE, Soltis PS, Morgan DR et al. (1995) Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms. Proceedings of the National Academy of Sciences, USA, 92, 2647 2651.
88. Soltis DE, Soltis PS, Nickrent DL et al. (1997) Angiosperm Phylogeny Inferred from 18S Ribosomal DNA Sequences. Annals of the Missouri Botanical Garden, 84, 1 49.
89. Soltis DE, Morris AB, Lachlan JM, Manos PS, Soltis PS (2006) Comparative phylogeography of unglaciated eastern North America. Molecular Ecology, 15, 4261 4293.
90. Song BH, Wang XQ, Wang XR, Ding KY, Hong DY (2003) Cytoplasmic composition in Pinus densata and population establishment of the diploid hybrid pine. Molecular Ecology, 12, 2995 3001.
91. Spicer RA, Harris NB, Widdowson M et al. (2003) Constant elevation of southern Tibet over the past 15 million years. Nature, 421, 622 624.
92. Stehlik I, Schneller JJ, Bachmann K (2001) Resistance or emigration: response of the high-alpine plant Eritrichium nanum (L.) Gaudin to the ice age within the Central Alps. Molecular Ecology, 10, 357 370.
93. Sun Y, An Z (2002) History and variability of Asian interior aridity recorded by eolian flux in the Chinese Loess Plateau during the past 7 Ma. Science in China Series D-Earth Sciences, 45, 420 429.
94. Sun K, Chen X, Ma R, Li C, Wang Q, Ge S (2002) Molecular phylogenetics of Hippophae L. (Elaeagnaceae) based on the internal transcribed spacer (ITS) sequences of nrDNA. Plant Systematics and Evolution, 235, 121 134.
95. Swensen SM (1996) The evolution of actinorhizal symbioses: Evidence for multiple origins of the symbiotic association. American Journal of Botany, 83, 1503 1512.
96. Swofford DL (2002) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0. Sinauer Associates
97. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology, 17, 1105 1109.
98. Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF (1998) Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology, 7, 453 464.
99. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585 595.
100. Takhtajan A (1997) Diversity and Classification of Flowering Plants. Columbia University Press
101. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596 1599.
102. Tang LY, Shen CM (1996) Late Cenozoic vegetational history and climatic characteristics of Qinghai-Xizang Plateau. Acta Micropalaeontologica Sinica, 13, 321 337.
103. 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 analyses tools. Nucleic Acids Research, 24, 4876 4882.
104. Thorne R (1992) Classification and geography of the flowering plants. The Botanical Review, 58, 225 327.
105. Toumi L, Lumaret R (1998) Allozyme variation in cork oak (Quercus suber L.): the role of phylogeography and genetic introgression by other Mediterranean oak species and human activities. Theoretical and Applied Genetics, 97, 647 656.
106. Tremblay NO, Schoen DJ (1999) Molecular phylogeography of Dryas integrifolia: glacial refugia and postglacial recolonization. Molecular Ecology, 8, 1187 1198.
107. Turner S, Hawkesworth C, Liu JQ et al. (1993) Timing of Tibetan uplift constrained by analysis of volcanic rocks. Nature, 364, 50 54.
108. Wang CS, Zhao XX, Liu ZF et al. (2008) Constraints on the early uplift history of the Tibetan Plateau. Proceedings of the National Academy of Sciences, USA, 105, 4987 4992.
109. Wang LY, Abbott RJ, Zheng W et al. (2009) History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae). Molecular Ecology, 18, 709 721.
110. Willis KJ, Bennett KD, Birks HJB (2009) Variability in thermal and UV-B energy fluxes through time and their influence on plant diversity and speciation. Journal of Biogeography, 36, 1630 1644.
111. Wu SG, Yang YP, Fei Y (1995) On the flora of the alpine region in the Qinghai-Xizang (Tibet) Plateau. Acta Botanica Yunnanica, 17, 233 250.
112. Yan MD, Fang XM, Chen SY et al. (2001) Pleistocene magnetic susceptibility and paleomagnetism of the Tibetan loess and its implications on large climatic change events. Science in China Series D-Earth Sciences, 44, 227 232.
113. Yang XP, Rost KT, Lehmkuhl F, Zhenda Z, Dodson J (2004) The evolution of dry lands in northern China and in the Republic of Mongolia since the Last Glacial Maximum. Quaternary International, 118-19, 69 85.
114. Yang FS, Li YF, Ding X, Wang XQ (2008) Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change. Molecular Ecology, 17, 5135 5145.
115. Yuan QJ, Zhang ZY, Peng H, Ge S (2008) Chloroplast phylogeography of Dipentodon (Dipentodontaceae) in southwest China and northern Vietnam. Molecular Ecology, 17, 1054 1065.
116. Zhang Q, Chiang TY, George M, Liu JQ, Abbott RJ (2005) Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Molecular Ecology, 14, 3513 3524.
117. Zheng D (1996) The system of physico-geographical regions of the Qinghai-Tibet (Xizang) Plateau. Science in China Series D-Earth Sciences, 39, 410 417.
118. Zheng BX, Xu QQ, Shen YP (2002) The relationship between climate change and Quaternary glacial cycles on the Qinghai-Tibetan Plateau: review and speculation. Quaternary International, 97-8, 93 101.
119. Zheng W, Wang L, Meng L, Liu J (2008) Genetic variation in the endangered Anisodus tanguticus (Solanaceae), an alpine perennial endemic to the Qinghai-Tibetan Plateau. Genetica, 132, 123 129. (Pubitemid 350197750)
120. Zhong DL, Ding L (1996) Discovery of high-pressure basic granulite in Namjagbarwa area, Tibet, China. Chinese Science Bulletin, 41, 87 88.
121. Zurawski G, Clegg MT, Brown AHD (1984) The nature of nucleotide sequence divergence between barley and maize chloroplast DNA. Genetics, 106, 735 749.