The Pleistocene demography of an alpine juniper of the Qinghai-Tibetan Plateau: Tabula rasa, cryptic refugia or something else?

Journal of Biogeography

Volumn 38, Issue 1, 2011, Pages 31-43

  Li, Zhonghu ^a,b   Zhang, Qian ^a   Liu, Jianquan ^a   Källman, Thomas ^c   Lascoux, Martin ^b,c  

^a LANZHOU UNIVERSITY   (China)

^b MAX PLANCK INSTITUTE   (Germany)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

Coalescent tests; Demographic history; Juniperus przewalskii; Nucleotide variation; Qinghai Tibetan Plateau; Refugia

Indexed keywords

CHLOROPLAST; CLIMATE OSCILLATION; COALESCENCE; DEMOGRAPHIC HISTORY; EVERGREEN TREE; GENETIC STRUCTURE; PALEOECOLOGY; PLEISTOCENE; POPULATION SIZE; REFUGE;

CHINA; QINGHAI-XIZANG PLATEAU;

CONIFEROPHYTA; CUPRESSACEAE; JUNIPERUS; JUNIPERUS PRZEWALSKII;

EID: 78650003883     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2010.02400.x     Document Type: Article

References (59)

1. Akey, J.M., Eberle, M.A., Rieder, M.J., Carlson, C.S., Shriver, M.D., Nickerson, D.A. & Kruglyak, L. (2004) Population history and natural selection shape patterns of genetic variation in 132 genes. PloS Biology, 2, 1591-1599.
2. Bandelt, H.J., Forster, P. & Röhl, A. (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48.
3. Binney, H.A., Willis, K.J., Edwards, M.E., Bhagwat, S.A., Anderson, P.M., Andreev, A.A., Blaauw, M., Damblon, F., Haesaerts, P., Kienast, F., Kremenetski, K.V., Krivonogov, S.K., Lozhkin, A.V., MacDonald, G.M., Novenko, E.Y., Oksanen, P., Sapelko, T.V., Väliranta, M. & Vazhenina, L. (2009) The distribution of late-Pleistocene woody taxa in northern Eurasia: evidence from a new macrofossil database. Quaternary Science Reviews, 28, 2445-2464.
4. Birks, J.H.B. & Willis, K.J. (2008) Alpines, trees, and refugia in Europe. Plant Ecology & Diversity, 1, 147-160.
5. De Mita, S., Ronfort, J., McKhann, H.I., Poncet, C., Malki, R.E. & Bataillon, T. (2007) Investigation of the demographic and selective forces shaping the nucleotide diversity of genes involved in Nod factor signaling in Medicago truncatula. Genetics, 177, 2123-2133.
6. Doyle, J.J. & Doyle, J.L. (1987) A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochemical Bulletin, 19, 11-15.
7. Dvornyk, V., Sirviö, A., Mikkonen, M. & Savolainen, O. (2002) Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris. Molecular Biology and Evolution, 19, 179-188.
8. Eckert, A.J., Wegrzyn, J.L., Pande, B., Jermstad, K.D., Lee, J.M., Liechty, J.D., Tearse, B.R., Krutovsky, K.V. & Neale, D.B. (2009) Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas fir (Pseudotsuga menziesii var. menziesii). Genetics, 183, 289-298.
9. Evanno, G., Regnaut, S. & Goudet, J. (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology, 14, 2611-2620.
10. 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.
11. Fay, J.C. & Wu, C.I. (2000) Hitchhiking under positive Darwinian selection. Genetics, 131, 479-491.
12. Fu, Y.X. & Li, W.H. (1993) Statistical tests of neutrality of mutations. Genetics, 133, 693-709.
13. Fujimoto, A., Kado, T., Yoshimaru, H., Tsumura, Y. & Tachida, H. (2008) Adaptive and slightly deleterious evolution in a conifer, Cryptomeria japonica. Journal of Molecular Evolution, 67, 201-210.
14. Grivet, D., Sebastiani, F., González-Martínez, S.C. & Vendramin, G.G. (2009) Patterns of polymorphism resulting from long-range colonization in the Mediterranean conifer Aleppo pine. New Phytologist, 184, 1016-1028.
15. Hampe, A. & Petit, R.J. (2010) Cryptic forest refugia on the 'Roof of the World'. New Phytologist, 185, 5-7.
16. Herzschuh, U., Kürschner, H. & Mischke, S. (2006) Temperature variability and vertical vegetation belt shifts during the last -50, 000-yr in the Qilian Mountains (NE margin of the Tibetan Plateau, China). Quaternary Research, 66, 133-146.
17. Herzschuh, U., Birks, H.J.B., Mischke, S., Zhang, C. & Böhner, J. (2010) A modern pollen-climate calibration set based on lake sediments from the Tibetan Plateau and its application to a Late Quaternary pollen record from the Qilian Mountains. Journal of Biogeography, 37, 752-766.
18. Heuertz, M., De Paoli, E., Källman, T., Larsson, H., Jurman, I., Morgante, M., Lascoux, M. & Gyllenstrand, N. (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics, 174, 2095-2105.
19. Hubisz, M.J., Falush, D., Stephens, M. & Pritchard, J.K. (2009) Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources, 9, 1322-1332.
20. Hudson, R.R. & Kaplan, N.L. (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics, 111, 147-164.
21. Hudson, R.R., Kreitman, M. & Aguadé, M. (1987) A test of neutral molecular evolution based on nucleotide data. Genetics, 116, 153-159.
22. Kado, T., Yoshimaru, H., Tsumura, Y. & Tachida, H. (2003) DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). Genetics, 164, 1547-1559.
23. Kado, T., Matsumoto, A., Ujino-Ihara, T. & Tsumura, Y. (2008) Amounts and patterns of nucleotide variation within and between two Japanese conifers, sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) (Cupressaceae sensu lato). Tree Genetics & Genomes, 4, 133-141.
24. Keller, S.R., Olson, M.S., Silim, S., Schroeder, W. & Tiffin, P. (2010) Genomic diversity, population structure, and migration following rapid range expansion in the balsam poplar, Populus balsamifera. Molecular Ecology, 19, 1212-1226.
25. Kumar, S., Nei, M., Dudley, J. & Tamura, K. (2008) mega: a biologist-centric software for evolutionary analysis of DNA and protein sequence. Briefings in Bioinformatics, 9, 299-306.
26. Kusumi, J., Tsumura, Y., Yoshimaru, H. & Tachida, H. (2002) Molecular evolution of nuclear genes in Cupressacea, a group of conifer trees. Molecular Biology and Evolution, 19, 736-747.
27. Lascoux, M., Palmé, A.E., Cheddadi, R. & Latta, R.G. (2004) Impact of ice ages on the genetic structure of trees and shrubs. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 197-207.
28. Lascoux, M., Pyhäjärvi, T., Källman, T. & Savolainen, O. (2008) Past demography in forest trees: what can we learn from nuclear DNA sequences that we do not already know? Plant Ecology & Diversity, 1, 209-215.
29. Li, Y., Stocks, M., Hemmilä, S., Källman, T., Zhu, H.T., Zhou, Y.F., Chen, J., Liu, J.Q. & Lascoux, M. (2010) Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci. Molecular Biology and Evolution, 27, 1001-1014.
30. Librado, P. & Rozas, J. (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
31. Ma, X.F., Szmidt, A.E. & Wang, X.R. (2006) Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci. Molecular Biology and Evolution, 23, 807-816.
32. Marjoram, P. & Tavaré, S. (2006) Modern computational approaches for analysing molecular genetic variation data. Nature Reviews Genetics, 7, 759-770.
33. Miehe, G., Winiger, M., Böhner, J. & Zhang, Y.L. (2001) The climatic diagram map of High Asia: purpose and concepts. Erdkunde, 55, 94-97.
34. Miehe, G., Miehe, S., Kaiser, K., Reudenbach, C., Behrendes, L., Duo, L. & Schlütz, F. (2009) How old is pastoralism in Tibet? An ecological approach to the making of a Tibetan landscape. Palaeogeography, Palaeoclimatology, Palaeoecology, 276, 130-147.
35. Nei, M. (1987) Molecular evolutionary genetics. Columbia University Press, New York.
36. Nei, M. & Li, W.H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences USA, 76, 5269-5273.
37. 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.
38. Opgenoorth, L., Vendramin, G.G., Mao, K.S., Miehe, G., Miehe, S., Liepelt, S., Liu, J.Q. & Ziegenhagen, B. (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.
39. Petit, R.J., Hu, F.S. & Dick, C.W. (2008) Forests of the past: a window to future changes. Science, 320, 1450-1452.
40. Pritchard, J.K., Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
41. Provan, J. & Bennett, K.D. (2008) Phylogeographic insights into cryptic glacial refugia. Trends in Ecology and Evolution, 23, 564-571.
42. Pyhäjärvi, T., García-Gil, M.R., Knürr, T., Mikkonen, M., Wachowiak, W. & Savolainen, O. (2007) Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics, 177, 1713-1724.
43. Rosenberg, N. (2004) distruct: a program for the graphical display of population structure. Molecular Ecology Notes, 4, 137-138.
44. Rousset, F. (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219-1228.
45. Royden, L.H., Burchfiel, B.C. & van der Hilts, R.D. (2008) The geological evolution of the Tibetan Plateau. Science, 321, 1054-1058.
46. Rull, V. (2009) Microrefugia. Journal of Biogeography, 36, 481-484.
47. Schlütz, F. & Lehmkuhl, F. (2009) Holocene climatic change and the nomadic Anthropocene in Eastern Tibet: palynological and geomorphological results from the Nianbaoyeze Mountains. Quaternary Science Reviews, 28, 1449-1471.
48. Städler, T., Haubold, B., Merino, C., Stephan, W. & Pfaffelhuber, P. (2009) The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics, 182, 205-216.
49. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
50. Tang, L.Y. & Shen, C.M. (1996) Late Cenozoic vegetational history and climatic characteristics of Qinghai-Xizang Plateau. Acta Micropalaeontologica Sinica, 13, 321-337.
51. Tani, N., Tsumura, Y. & Sato, H. (2003) Nuclear gene sequences and DNA variation of Cryptomeria japonica samples from the postglacial period. Molecular Ecology, 12, 859-868.
52. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876-4882.
53. Tsumura, Y., Suyama, Y., Yoshimura, K., Shirato, N. & Mukai, Y. (1997) Sequence-tagged-sites (STSs) of cDNA clones in Cryptomeria japonica and their evaluation as molecular markers in conifers. Theoretical and Applied Genetics, 94, 764-772.
54. Ujino-Ihara, T., Yoshimura, K., Ugawa, Y., Yoshimaru, H., Nagasaka, K. & Tsumura, Y. (2000) Expression analysis of ESTs derived from the inner bark of Cryptomeria japonica. Plant Molecular Biology, 43, 451-457.
55. Watterson, G.A. (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256-276.
56. Wright, S. (1951) The genetic structure of populations. Annals of Eugenics, 15, 323-354.
57. Wright, S.I. & Gaut, B.S. (2005) Molecular population genetics and the search for adaptive evolution in plants. Molecular Biology and Evolution, 22, 506-519.
58. Zhang, Q., Chiang, T.Y., George, M., Liu, J.Q. & Abbot, R.J. (2005) Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Molecular Ecology, 14, 3513-3524.
59. Zhang, X.S., Yang, D.A., Zhou, G.S., Liu, C.Y. & Zhang, J. (1996) Model expectation of impacts of global climate change on biomes of the Tibetan Plateau. Climate change and plants in East Asia (ed. by K. Omasa, K. Kai, H. Taodao, Z. Uchijima and M. Yoshino), pp. 25-38. Springer-Verlag, Tokyo.