Response of a desert shrub to past geological and climatic change: A phylogeographic study of Reaumuria soongarica (Tamaricaceae) in western China

Journal of Systematics and Evolution

Volumn 50, Issue 4, 2012, Pages 351-361

  Li, Zhong Hu ^a,b,c   Chen, Jian ^a   Zhao, Gui Fang ^b   Guo, Yu Peng ^a   Kou, Yi Xuan ^a   Ma, Ya Zheng ^a   Wang, Gang ^a   Ma, Xiao Fei ^c  

^a LANZHOU UNIVERSITY   (China)

^b BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

^c Chinese Academy of Sciences   (China)

Author keywords

CpDNA; Desert plant; Genetic variation; Range expansion; Reaumuria soongarica

Indexed keywords

REAUMURIA SOONGARICA; TAMARICACEAE;

EID: 84864615345     PISSN: 16744918     EISSN: 17596831     Source Type: Journal    
DOI: 10.1111/j.1759-6831.2012.00201.x     Document Type: Article

References (80)

1. Abbott RJ, Brochmann C. 2003. History and evolution of the arctic flora: In the footsteps of Eric Hultén. Molecular Ecology 12: 299-313. (Pubitemid 36144711)
2. Abbott RJ, Smith LC, Milne RI, Crawford RM, Wolff K, Balfour J. 2000. Molecular analysis of plant migration and refugia in the Arctic. Science 289: 1343-1346. (Pubitemid 30656049)
3. Anderson LL, Hu FS, Nelson DM, Petit RJ, Paige KN. 2006. Iceage endurance: DNA evidence of a white spruce refugium in Alaska. Proceedings of the National Academy of Sciences USA 103: 12447-12450. (Pubitemid 44267279)
4. Avise JC. 1987. Identification and interpretation of mitochondrial DNA stocks in marine species. In: Kumpf H, Nakamura EL eds. Proceedings of the stock identification workshop. Panama: National Oceanographic and Atmospheric Administration. 105-136.
5. Avise JC. 2004. Molecular markers, natural history, and evolution. Sunderland: Sinauer Associates.
6. Bennett KD. 1997. Evolution and ecology: The pace of life. Cambridge: Cambridge University Press.
7. Bush ABG, Little EC, Rokosh D, White D, Rutter NW. 2004. Investigation of the spatio-temporal variability in Eurasian Late Quaternary loess-paleosol sequences using a coupled atmosphere-ocean general circulation model. Quaternary Science Reviews 23: 481-498. (Pubitemid 38225105)
8. Chaves MM, Maroco JP, Pereira JS. 2003. Understanding plant responses to drought - from genes to the whole plant. Functional Plant Biology 30: 239-264. (Pubitemid 36409032)
9. 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. Molecular Ecology 17: 4276-4288.
10. Clement M, Posada D, Crandall KA. 2000. TCS: A computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659.
11. Comes HP, Kadereit JW. 1998. The effect of Quaternary climatic changes on plant distribution and evolution. Trends in Plant Science 3: 432-438. (Pubitemid 28542007)
12. Cui DF, Liao WB, Zhang B. 2000. Determination of flavonoid compounds of Reaumuria L. (Tamaricaceae) and their taxonomical significance. Acta Botanica Boreali Occidentalia Sinica 20: 283-287.
13. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
14. Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161: 1307-1320. (Pubitemid 34831453)
15. Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47-50.
16. Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
17. Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
18. Gaskin JF, Schaal BA. 2003. Molecular phylogenetic investigation of US invasive Tamarix. Systematic Botany 28: 86- 95. (Pubitemid 36317720)
19. Gaskin JF, Ghahremani-nejad F, Zhang DY, Londo JP. 2004. A systematic overview of Frankeniaceae and Tamaricaceae from nuclear rDNA and plastid sequence data. Annals of the Missouri Botanical Garden 91: 401-409. (Pubitemid 39428768)
20. Guo YP, Zhang R, Chen CY, Zhou DW, Liu JQ. 2010. Allopatric divergence and regional range expansion of Juniperus sabina in China. Journal of Systematics and Evolution 48: 153-160.
21. Guo ZT, Ruddiman WF, Hao QZ, Wu HB, Qiao YS, Zhu RX, Peng SZ, Wei JJ, Yuan BY, Liu TS. 2002. Onset of Asian desertification by 22 Myr ago inferred from loess deposits in China. Nature 416: 159-163. (Pubitemid 34246469)
22. Hamilton MB. 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 8: 521-523. (Pubitemid 29170549)
23. Harpending HC. 1994. Signature of ancient population growth in a low-resolutionmitochondrial DNA mismatch distribution. Human Biology 66: 591-600. (Pubitemid 2117524)
24. 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. (Pubitemid 26389802)
25. Hewitt GM. 2000. The genetic legacy of the Quaternary ice ages. Nature 405: 907-913.
26. Hudson RR. 1990. Gene genealogies and the coalescent process. In: Futuyma D, Antonovics J eds. Oxford surveys in evolutionary biology. Oxford: Oxford University Press. 1-44.
27. Huelsenbeck JP, Rannala B. 1997. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276: 227-232. (Pubitemid 27172674)
28. Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755. (Pubitemid 32851390)
29. Jia DR, Abbott RJ, Liu TL, Mao KS, Bartish IV, Liu JQ. 2012. Out of the Qinghai-Tibet Plateau: Evidence for the origin and dispersal of Eurasian temperate plants from a phylogeographic study of Hippophae rhamnoides (Elaeagnaceae). New Phytologist 194: 1123-1133.
30. Jia DR, Liu TL, Wang LY, Zhou DW, Liu JQ. 2011. Evolutionary history of an alpine shrub Hippophae tibetana (Elaeagnaceae): Allopatric divergence and regional expansion. Biological Journal of the Linnean Society 102: 37-50.
31. Kropf M, Kandereit JW, Comes HP. 2003. Differential cycles of range contraction and expansion in European high mountain plants during the late Quaternary: Insight from Pritzelago alpine (L.) O. Kuntze (Brassicaceae). Molecular Ecology 12: 931-949. (Pubitemid 36524287)
32. Kuhner MK. 2006. LAMARC 2.0: Maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22: 768-770.
33. Li JJ, Shi YF, Li BY. 1995. Uplift of the Qinghai-Xizang (Tibet) Plateau and global change. Lanzhou: Lanzhou University Press.
34. Li ZH, Zhang Q, Liu JQ, Kãllman T, Lascoux M. 2011. The Pleistocene demography of an alpine juniper of the Qinghai- Tibetan Plateau: Tabula rasa, cryptic refugia or something else? Journal of Biogeography 38: 31-43.
35. Li ZH, Zou JB, Mao KS, Lin K, Li HP, Liu JQ, Kãllman T, Lascoux M. 2012. Population genetic evidence for complex evolutionary histories of four high altitude juniper species in the Qinghai-Tibetan Plateau. Evolution 66: 831-845.
36. Librado P, Rozas J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
37. Little DP, Barrington DS. 2003. Major evolutionary events in the origin and diversification of the fern genus Polystichum (Ryopteridaceae). American Journal ofBotany 90: 508-514. (Pubitemid 38161900)
38. Liu JQ, Chen ZD, Lu AM. 2000. The phylogenetic relationships of an endemic genus Sinadoxa in the Qinghai-Xizang Plateau: Evidence from ITS sequence analysis. Journal of Integrative Plant Biology 42: 656-658.
39. Liu JQ, Gao TG, Chen ZD, Lu AM. 2002. Molecular phylogeny and biogeography of the Qinghai-Tibet Plateau endemic Nannoglottis (Asteraceae). Molecular Phylogenetics and Evolution 23: 307-325.
40. Liu JQ, Qiu MX, Pu JC, Lu ZM. 1982. The typical extreme xerophyte Reaumuria soongorica in the desert of China. Acta Botanica Sinica 24: 485-488 (in Chinese).
41. Liu JQ, Wang YJ, Wang AL, Hideaki O, Abbott RJ. 2006. Radiation and diversification within the Ligularia- Cremanthodium-Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau. Molecular Phylogenetics and Evolution 38: 31-49. (Pubitemid 41773272)
42. Liu YF, Wang Y, Huang HW. 2009. Species-level phylogeographical history of Myricaria plants in the mountain ranges of western China and the origin of M. laxiflora in the three gorges mountain region. Molecular Ecology 18: 2700-2712.
43. Ma JY, Chen T, Qiang WY, Wang G. 2005. Correlations between foliar stable carbon isotope composition and environmental factors in desert plant Reaumuria soongorica (Pall.)Maxim. Journal of Integrative Plant Biology 47: 1065-1073. (Pubitemid 41794339)
44. Mao KS, Hao G, Liu JQ, Adams RP, Milne RI. 2010. Diversification and biogeography of Juniperus (Cupressaceae): Variable diversification rates and multiple intercontinental dispersals. New Phytologist 188: 254-272.
45. Meng LH, Yang R, Abbott RJ, George M, Hu TH, Liu JQ. 2007. Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom (Pinaceae) in the Qinghai-Tibetan Plateau and adjacent highlands.Molecular Ecology 16: 4128-4137. (Pubitemid 47481047)
46. Petit RJ, Grivet D. 2002. Optimal randomization strategies when testing the existence of a phylogeographic structure. Genetics 161: 469-471. (Pubitemid 34564072)
47. Petit RJ, Aguinagalde I, de Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Mohanty A, Muller-Starck G, Demesure-Musch B, Palme A, Martin JP, Rendell S, Vendramin GG. 2003. Glacial refugia: Hotspots but not melting pots of genetic diversity. Science 300: 1563-1565. (Pubitemid 36682886)
48. Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG. 2005. Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations.Molecular Ecology 14: 689-701. (Pubitemid 40346461)
49. Pons O, Petit RJ. 1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144: 1237-1245. (Pubitemid 26378263)
50. Posada D, Crandall KA. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14: 817-818. (Pubitemid 28552116)
51. Qian ZQ, Xu L, Wang YL, Yang J, Zhao GF. 2008. Ecological genetics of Reaumuria soongorica (Pall.) Maxim. population in the oasis-desert ecotone in Fukang, Xinjiang, and its implications for molecular evolution. Biochemical Systematics and Ecology 36: 593-601. (Pubitemid 351992885)
52. 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. Molecular Phylogenetics and Evolution 59: 225-244.
53. Rhodes TE, Gasse F, Ruifen L, Fontes JC, Keqin W, Bertrand P, Gibert E, Mélières F, Tucholka P, Wang ZX, Cheng ZY. 1996. A Late Pleistocene-Holocene lacustrine record from Lake Manas, Zunggar (northern Xinjiang, western China). Palaeogeography, Paleoclimatology, Palaeoecology 120: 105-121.
54. Rogers A, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9: 552-569.
55. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574. (Pubitemid 37038874)
56. Schneider S, Excoffier L. 1999. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: Application to human mitochondrial DNA. Genetics 152: 1079-1089. (Pubitemid 29330907)
57. Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF. 1998. The tortoise and the hare: Choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85: 1301-1315.
58. Sun JM, Liu TS. 2006. The age of the Taklimakan Desert. Science 312: 1621.
59. Sun JM, Ding ZL, Liu TS. 1998. Desert distributions during the glacial maximum and climatic optimum: Example of China. Episodes 21: 28-31.
60. Sun JM, Zhang ZQ, Zhang LY. 2009. New evidence on the age of the Taklimakan Desert. Geology 37: 159-162.
61. Sun YS, Wang AL, Wan DS, Wang Q, Lu JQ. 2012. Rapid radiation of Rheum (Polygonaceae) and parallel evolution of morphological traits. Molecular Phylogenetics and Evolution 63: 150-158.
62. Swofford DL. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods. Beta version 4.0b10). Sunderland: Sinauer Associates.
63. 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.
64. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585- 595. (Pubitemid 19274682)
65. 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 Research 25: 4876- 4882. (Pubitemid 28022245)
66. Wang AL, Yang MH, Liu JQ. 2005a. Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences. Annals of Botany 96: 489- 498.
67. Wang LY, Abbott RJ, Zheng W, Chen P, Wang YJ, Liu JQ. 2009a. History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae). Molecular Ecology 18: 709-721.
68. Wang LY, Ikeda H, Liu TL, Wang YJ, Liu JQ. 2009b. Repeated range expansion and glacial endurance of Potentilla glabra (Rosaceae) in the Qinghai-Tibetan Plateau. Journal of Integrative Plant Biology 51: 698-706.
69. Wang SM, Zhang X, Li Y, Zhang L, Xiong YC, Wang G. 2005b. Spatial distribution patterns of the soil seed bank of Stipagrostis pennata (Trin.) de Winter in the Gurbantonggut Desert of north-west China. Journal of Arid Environments 63: 203-222. (Pubitemid 40782608)
70. Wolfe KH, Li WH, Sharp PM. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences USA 84: 9054-9058.
71. Wu LL, Cui XK, Milne RI, Sun YS, Liu JQ. 2010. Multiple autopolyploidizations and range expansion of Allium przewalskianum Regel. (Alliaceae) in the Qinghai-Tibetan Plateau. Molecular Ecology 19: 1691-1704.
72. Xu L, Wang YL, Wang XM, Zhang LJ, Yue M, Gu FX, Pan XL, Zhao GF. 2003. Genetic structure of Reaumuria soongorica population in Fukang Desert, Xinjiang and its relationship with ecological factors. Acta Botanica Sinica 45: 787- 794. (Pubitemid 37212095)
73. Xu TT, Abbott RJ, Milne RI, Mao KS, Du FK, Wu GL, Zhaxi CR, Miehe G, Liu JQ. 2010. Phylogeography and allopatric divergence of cypress species (Cupressus L.) in the Qinghai- Tibetan Plateau and adjacent regions. BMC Evolutionary Biology 10: 194.
74. Yang D, Fang XM, Dong GR, Peng ZC, Li JJ. 2006. Aeolian deposit evidence for formation and evolution of the Tengger Desert in the north of China since early Pleistocene. Marine Geology and Quaternary Geology 26: 93-100.
75. 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.
76. Yang XP, Zhu ZD, Jaekel D, Owen LA, Han JM. 2002. Late Quaternary palaeoenvironment change and landscape evolution along the Keriya River, Xinjiang, China: The relationship between high mountain glaciation and landscape evolution in foreland desert regions. Quaternary International 97-98: 155-166. (Pubitemid 35259191)
77. Young ND, Healy J. 2003. GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinformatics 4: 6.
78. Zhang ML, Fritsch PW. 2010. Evolutionary response of Caragana (Fabaceae) to Qinghai-Tibetan uplift and Asian interior aridification. Plant Systematics and Evolution 288: 191-199.
79. 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.
80. 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 97-98: 93-101.