摘要
揭示物种自然群体遗传变异的进化力量和近缘物种间物种形成机制一直以来都是进化生物学的中心议题之一。西藏圆柏(Juniperus tibetica)及其复合体物种密枝圆柏(J. convallium)、方枝柏(J. saltuaria)和祁连圆柏(J. przewalskii)是青藏高原特有的高山植物物种,隶属于柏科(Cupressaceae),刺柏属(Juniperus),圆柏组(Sabina)。四个物种形态上鳞叶或刺叶兼有,均具一粒种子,但种子大小和生鳞叶的末次分枝形状存在较大差异。西藏圆柏、密枝圆柏和方枝柏主要分布在青藏高原的东南部边缘地区,存在同域和邻域分布现象。这三个物种和分布在高原东北部的祁连圆柏一起构成了刺柏属圆柏组物种在青藏高原现代地理分布的典型的圆柏物种复合体。本论文通过取样多个核基因座位,运用现代分子群体遗传学的分析方法研究了四个物种的核苷酸多态性和种群遗传结构,并运用隔离-迁移(IM)模型探索了物种形成与分化的分子机制。
对西藏圆柏复合体物种自然分布区内53个种群共219个个体的胚乳(单倍体)DNA进行了13套核基因的扩增和测序。四个物利·在13个基因座上平均核苷酸多态性呈现低水平。方枝柏沉默位点平均多态性最高(θwsil=0.0055,πsil=0.0042),密枝圆柏最低(θwsil=0.00420,πsil=0.00211)。AMOVA分析表明四个物种存在高水平的群体间遗传分化：密枝圆柏的平均FST值最高(0.291),接着是祁连圆柏(0.266),方枝柏最低(0.173)。物种的进化历史、所受选择压力以及青藏高原复杂的地形可能一起导致了这些高山物种低水平的核苷酸多态性和较高的遗传分化。物种成对IM模拟表明祁连圆柏与密枝圆柏自起源以来,有效群体未发生剧烈的变化；西藏圆柏未得到明显的结论；但是方枝柏有效群体明显比其祖先有效群体大,说明该物种可能发生了扩张或杂交渐渗,但进一步的分析表明其迁出的基因流要远大于本身接受到的基因流,说明历史扩张是导致该物种有效群体增大的主要原因。
STRUCTURE分析表明四个物种不能单独成族,只能将祁连圆柏与西藏圆柏、密枝圆柏和方枝柏分开,而后三个物种之间聚集在一起,没有明显的分化。四个物种之间共享大量的基因多态性,可能是由于这些物种分化较晚,出于不完全的谱系筛选导致物种之间共享多态性。另一原因则可能是由于它们之间的分化始终是在基因流存在的情况下进行的,或者分化后存在反复的杂交,IM分析也表明它们存在明显的基因流。分子钟标记表明,西藏圆柏和密枝圆柏之间的分化时间最短,大约为71.6万年以前,其它物种对之间的分化大约发生在第三纪末与第四纪初,约为1.6-2.2百万年以前。第四纪气候变化以及青藏高原的进一步隆升可能促进了这些物种的分化以及它们分化之后的杂交。总之,基因流和不完全的谱系筛选是导致这些物种共享多态性和分化不明显的主要原因。
One of the long-standing questions in evolutionary biology is to reveal the evolutionary forces shaping genetic variations acted on the natural populations and infer the mechanisms of species divergence between closely related species. Juniperus tibetica and its closely related species, J. convallium, J. saltuaria, and J. przewalskii are the endemic alpine juniper species of the Qinghai-Tibetan Plateau (QTP), and they are subordinate to Cupressaceae family, Juniperus genera, Sabina section. All the four species are characteristic of branch with both scaly and spiny leaf and the cone with only one seed, but the size of cone and the shape of the last branches differentiated between them. J. tibetica, J. convallium, and J. saltuaria have a sympatric or parapatric distribution along the southern part of the QTP and J. przewalskii is mainly occurred at the northeastern plateau. The four junipers constitute a representative species-complex of the modern geographic distribution of juniper on the QTP. This dissertation studied the nucleotide diversity and population genetic structure of the four species inferred from the multiple nuclear loci, and revealed the process of species divergence based on the Isolation-with-Migration (IM) analysis of divergence population genetics.
A total of 13 nuclear loci were amplified and sequenced for 219 individuals (megagametophyte) of 53 populations through the entire distribution ranges of J. tibetica complex. Average value of nucleotide diversity across all 13 loci was low in the four species. Juniperus saltuaria had the highest diversity (θwsil= 0.0055,πsil= 0.0042). and J. convallium maintained the lowest (θwsil= 0.00420,πsil=0.00211). These juniper species have a high between-population differentiation based on the AMOVA analysis:J. convallium had the highest average value of FST(0.291), followed by J. przewalskii (0.266), and J. saltuaria had the lowest (0.173). The evolutionary history of species, selective pressures and complex topography of the QTP may have together led to the low level nucleotide variability and significant population genetic differentiation.J.przewalskii and J. convallium have maintained the relative stable population sizes since divergence from their common ancestral species based on the 1M analysis. We got no clear signs about population size of J. tibetica. However, J. saltuaria has the largest effective population size compared to the other three species and this species may have experienced population or range expansion in the past.
STRUCTURE analysis revealed two clusters, one composed of the southern QTP species, J. tibetica, J. saltuaria, and J. convallium, and the other one J. przewalskii individuals in the northeastern QTP. Two possibilties may have contributed to the large amount of shared polymorphisms between species. One may be incomplete lineage sorting due to the recently species divergence and the other one the species divergence in the face of gene flow or the introgression after speciation which is supported by IM analysis. Molecular calibration revealved the latest divergence, between J. tibetica and J. convallium, maybe 0.716 Mya while the other species diverged 1.6-2.2 Mya. The Quaternary climatic oscillations and uplift of the QTP may have together drived the speciation or the introgression between juniper species. In summary, we proposed that incomplete lineage sorting and/or species divergence in the face of gene flow have resulted in the shared polymorphisms among the J. tibetica complex.
引文
1. Abbott RJ, Comes HP.2004. Evolution in the Arctic:a phylogeographic analysis of the circumarctic plant (Purple saxifrage). New Phytologist 161:211-224.
2. Abbott RJ, Ritchie MG, Hollingsworth PM.2008. Speciation in plants and animals:pattern and process. Philosophical Transactions of the Royal Society B:Bological Science 363: 2965-2969.
3. Adams RP.2008. Junipers of the World:The genus Juniperus,2nd ed.. Vancouver, B.C., Canada:Trafford Publishing.
4. Aguade M.2001. Nucleotide sequence variation at two genes of thephenylpropanoid pathway, the FAH1 and F3H Genes, in Arabidopsis thaliana. Molecular Phylogenetics and Evolution 18:1-9.
5. Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, Kruglyak L. 2004. Population history and natural selection shape patterns of genetic variation in 132 genes. PloS Biology 2:1591-1599.
6. Allnutt TR, Newton AC, Premoli A, Lara A.2003. Genetic variation in the threatened south American conifer Pilgerodendron uviferum (Cupressaceae), detected using RAPD markers. Biological Conservation 114:245-253.
7. Amos W, Harwood J.1998. Factors affecting levels of genetic diversity in natural populations. Philosophical Transactions of the Royal Society of London Series B 353:177-186.
8. Andolfatto P.2001. Adaptive hitchhiking effects on genome variability. Current Opinion in Genetics & Development 11:635-641.
9. Artyukova EV, Kozyrenko MM, Gorovoy PG, Zhuravlev YN.2009. Plastid DNA variation in highly fragmented populations of Microbiota decussata Kom. Cupressaceae), an endemic to Sikhote Alin mountains. Genelica 137:201-212.
10. Ayala FJ, Kiger JA.1984. Modern genetics. Benjamin-Cummings. Menlo. Park, California.
11. Ayunyawat U, Stephan W, Stadler T.2007. Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wildtomatoes. Molecualr Biology and Evolution 24:2310-2322.
12. Barluenga M., Stolting KN, Salzburger W, Muschick M, Meyer A.2006. Sympatric speciation in Nicaraguan crater lake cichlid fish. Nature 439:719-723
13. Barraclough TG, Nee S.2001. Phylogenetics and speciation. Trends in Ecology and Evolution 16:391-399.
14. Bawa KS, Pin Koh L, Lee TM, Liu J, Ramakrishnan PS, Yu DW, Zhang Y-P, Raven PH. 2010. China, India and the environment. Science 327:1457-1458.
15. Begun DJ, Aquadro CF.1992. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356:519-520.
16. Boratynsky A, Lewandowski A, Boratynska K, Montserrat JM, Romo A.2009. High level of genetic differentiation of Juniperus phoenicea (Cupressaceae) in the Mediterranean region:geographic implications. Plant systematics and Evolution 277:163-172.
17. Bouille M, Bousquet J.2005. Trans-species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea(Pinaceae):implications for the long-term maintenance of genetic diversity in trees. American Journal of Botany 92:63-73.
18. Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB.2004. Nucleotide diversity and linkage disequilibrium in loblolly pine. Proceedings of the National Academy of Sciences, USA 101:15255-15260.
19. Chakravarti A.1999. Population genetics-making sense out of sequence. Nature Genetics 21: 56-60.
20. Charlesworth B, Charlesworth D, Barton NH.2003. The effects of genetic and geographic structure on neutral variation. Annual Review of Ecology, Evolution, and Systematics 34: 99-125.
21. Charlesworth B, Nordborg M, Charlesworth D.1997. The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genetical Research 70:155-174.
22. Chen J, Kallman T, Gyllenstrand N, Lascoux M.2010. New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict. Heredity 104:3-14.
23. Chung JD, Lin TP, Tan YC, Lin MY, Hwang SY.2004. Genetic diversity and biogeography of Cunninghamia konishii (Cupressaceae), an island species in Taiwan:a comparison with Cunninghamia lanceolata, a mainland species in China. Molecular Phylogenetics and Evolution 33:791-801.
24. Coyne JA, Orr H.A.2004. Speciation. Sunderland, MA:Sinauer Associates.
25. De Aguiar MAM, Baranger M, Baptestini EM, Kaufman L, Bar-Yam Y.2009. Global patterns of speciation and diversity. Nature 460:384-387.
26. Dieckman U, Doebeli M.1999. On the origin of species by sympatric speciation. Nature 400: 354-357.
27. Doebeli M, Dieckmann U.2003. Speciation along environmental gradients. Nature 421: 259-264.
28. Dvornyk V, SirviO A, Mikkonen M, Savolainen O.2002. Low nucleotide diversity at the pall locus in the widely distributed Pinus sylvestris. Molecualr Biology and Evolution 19: 179-188.
29. Eckert AJ, Wegrzyn JL, Pande B, Jermstad KD, Lee JM, Liechty, JD, Tearse, BR, Krutovsky KV, Neale DB.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.
30. 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.
31. Eveno E, Collada C, Guevara MA, Leger V, Soto A, Diaz L, Leger P, Gonzalez-Martinez SC, Cervera MT, Plomion C, Garnier-Gere PH.2008. Contrasting patterns of selection at Pinus pinaster ait. drought stress candidate genes as revealed by genetic differentiation analyses. Molecular Biology and Evolution 25:417-437.
32. 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.
33. Falush, D., M. Stephens and J. K. Pritchard.2003. Inference of population structure: Extensions to linked loci and correlated allele frequencies. Genetics 164:1567-1587.
34. Falush, D., M. Stephens and J. K. Pritchard.2007. Inference of population structure using multilocus genotype data:dominant markers and null alleles. Molecular Ecology Notes 7: 574-578.
35. Fay JC, Wu CI.2000. Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
36. Filatov DA, Charlesworth D.1999. DNA polymorphism, haplotype structure and balancing selection in the leavenworthia PgiC locus. Genetics 153:1423-1434.
37. Fu YX, Li WH.1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
38. Fu LG, Yu YF, Farjon A.1999. Cupressusaceae. In:Flora of China, pp.70-78. Science Press, Beijing and Missouri Botanical Garden Press, St. Louis.
39. Fujimoto A, Kado T, Yoshimaru H, Tsumura Y, Tachida H.2008. Adaptive slightly deleterious evolution in a conifer, Cryptomeria japonica. Journal of Molecular Evolution 67: 201-210.
40. Garcia-Gil MR, Mikkonen M, Savolainen O.2003. Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Molecular Ecology 12: 1195-1206.
41. Gaut BS, Clegg MT.1993. Nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (Poaceae). Genetics 135:1091-1097.
42. Gavrilets S, Li H, Vose M.D.2000. Patterns of parapatric speciation. Evolution 54: 1126-1134.
43. Goldstein DB.2001. Island of linkage disequilibrium. Nature Genetics 29:109-111.
44. Gonzalez-Martinez SC, Ersoz E, Brown GR, Wheeler NC, Neale DA.2006. DNA sequence variation and selection of tag single-polymorphisms at candidate genes for drought-stress response in Pinus taeda L. Genetics 172:1915-1926.
45. Grant V.1981. Plant speciation. Columbia Universty Press, New York.
46. Grivet D, Sebastiani F, Gonzalez-Martinez SC, Vendramin GG. 2009. Patterns of polymorphism resulting from long-range colonization in the Mediterranean conifer Aleppo pi ne. New Phytologisl 184:1016-1028.
47. Gross BL, Rieseberg LH.2005. The ecological genetics of homoploid hybrid speciation. Journal of Heredity 96:241-252.
48. Hamrick JL, Godt MJW.1990. Allozyme diversity in plant species. In:Brown AHD, Clegg MT, Kahler AL, Weir BS, eds. Plant population genetics, breeding and genetics resources. Sunderland:Sinauer Associates,43-63.
49. Hamrick JL, Godt MJW.1996. Effects of life history traits on genetic diversity in plant species. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 351:1291-1298.
50. Hamrick JL, Godt MJW, Sherman-Broyles SL.1992. Factors influencing levels of genetic diversity in woody plant species. New Forests 6:95-124.
51. Hamrick JL, Loveless M.D.1989. The genetic structure of tropical tree populations: association with reproductive biology, pp.129-146. In:Bock J, Linhart YB. (Eds) The Evolutionary Ecology of Plants, Westview Press, Boulder, Colorada.
52. Hare MP.2001. Prospects for nuclear gene phylogeography. Trends in Ecology:and Evolution 16:700-706.
53. Heuertz 1M., De Paoli E, Kallman 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.
54. Hewitt GM.2000. The genetic legacy of the quaternary ice ages. Nature 405:907-913.
55. Hey J, Nielsen R.2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760.
56. Hey J, Nielsen R.2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences, USA,104:2785-2790.
57. Hey J.2010a. Isolation with migration models for more than two populations. Molecular Biology and Evolution 27:905-920.
58. Hey J.2010b. The divergence of Chimpanzee species and subspecies as revealed in multipopulation isolation with migration analyses. Molecular Biology and Evolution 27: 921-933.
59. Hill WG, Robertson A.1968. Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38:226-231.
60. Hill WG, Weir BS.1988. Variances and covariances of squared linkagedisequilibrium in finite populations. Theoretical Population Biology 33:54-78.
61. Hilton H, Kliman RM, Hey J.1994. Using hitchhiking genes to study adaptatiuon and divergence during speciation within the Drosophila melanogaster species complex. Evolution 48:1900-1913.
62. Hubisz MJ, Falush D, Stephens M, Pritchard JK.2009. Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources 9: 1322-1332.
63. Hudson RR, Coyne JA.2002. Mathematical consequences of the genealogical species concept. Evolution 56:1557-1565.
64. Hudson RR.1990. Gene genealogies and the coalescent process, pp.1-44 in Oxford Surveys in Evolution Biology, Vol.7, edited by Futuyma DJ and Antonovics J. Oxford University Press, Oxford.
65. Hudson RR, Kaplan NL.1985. Statistical properties of the number of recombination events in the history of a sample of DN A sequences. Genetics 111:147-164.
66. Hudson RR, Kreitman M, Aguade M.1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
67. Huh MK, Huh HW.2000. Genetic diversity and population structure of Juniperus rigida (Cupressaceae) and Juniperus coreana. Evolutionary Ecology 14:87-98.
68. Huang SSF, Hwang SY, Lin TP.2002. Spatial pattern of chloroplast DNA variation of Cyclobalanopsis glauca in Taiwan and East Asia. Molecular Ecology 11:2349-2358.
69. Ingvarsson PK.2005. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae).Genetics 169: 945-953.
70. Ingvarsson PK.2008. Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics 180:329-340.
71. Innan H, Tajima F, Terauchi R, Miyashita T.1996. Intragenic recombination in the Adh locus of the wild plant Arabidopsis thaliana. Genetics 143:1761-1770.
72. Jordan DS.1905. The origin of species through isolation. Science 22:545-562.
73. Kado T, Matsumoto A, Ujino-1hara 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.
74. Kado T, Ushio Y, Yoshimaru H, Tsumura Y, Tachida H.2006. Contrasting patterns of DNA variation in natural populations of two related conifers, Cryptomeria japonica and Taxodium distichum (Cupressaceae sensu lato). Genes & Genetic Systems 81:103-113.
75. Kado T, Yoshimaru H, Tsumura Y, Tachida H.2003. DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). Genetics 164:1547-1559.
76. Kaplan NL, Hudson RR, Langley CH.1989. "Hitchhiking effect" revisited. Genetics 123: 887-899.
77. Kawabe A, Yamane K, Miyashita NT.2000. DNA polymorphism at the cytosolic phosphoglucose isomerase (PgiC locus of the wild plant Arabidopsis thaliana. Genetics 156: 1339-1347.
78. Kimura M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
79. Krutovsky KV, Neale DB.2005. Nucleotide diversity and linkage disequilibrium in cold-hardiness and wood quality-related candidate genes in Douglas fir. Genetics 171: 2029-2041.
80. Kuhle M.1988. Geomorphological finds on the bulit-up of Pleistocene glaciation in Southern Tibet and on the problem of inland ice. Geojournal 17:457-512.
81. Kuhle M.1998. Reconstruction of the 2.4 million km2 late Pleistocene ice sheet on the Tibet Plateau and its impact on the global climate. Quaternary International 45/46:71-108.
82. Kuittinen H, Aguade M.2000. Nucleotide variation at the chalcone isomerase locus in Arabidopsis thaliana. Genetics 155:863-872.
83. 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.
84. 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.
85. Ledig FT, Conkle MT.1983. Gene diversity, genetic structure in a narrow endemic, Torrey pine (Pines torreyana Parry ex c/arr,). Evolution 37:79-86.
86. Lexer C, Widmer A.2008. The genic view of plant speciation:recent progress and emerging questions. Philosophical Transactions of the Royal Society B:Biological Science 363: 3023-3036.
87. Li Y, Stocks M, Hemmila S, Kallman T, Zhu HT, Zhou YF, Chen J, Liu JQ, 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.
88. Librado P, Rozas J.2009. DnaSP v5:A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
89. Liu AZ, Burke JM.2006. Patterns of nucleotide diversity in wild and cultivated sunflower. Genetics 173:321-330.
90. Loveless M, Hamrick J.1984. Ecological determinant of genetic structure in plant populations. Annual Review of Ecology and Systematics 15:65-95.
91. Ma XF, Szmidt AE, Wang XR.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.
92. Mallet J.2007. Hybrid speciation. Nature 446:279-283.
93. Mao KS, Hao G, Liu JQ, Adams RP, Milne RI.2010. Diversification and biogeography of Juniperus (Cupressaceae):a Madrean-Tethyan tale? New Phytologist in press.
94. Maynard Smith J, Haigh J.1974. The hitch-hiking effect of a favorable gene. Genetics Research 23:23-35.
95. Me Vean G, Awadalla P, Fearnhead P.2002. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160:1231-1241.
96. Muller MH, Leppala J, Savolainen O.2008. Genome-wide effects of postglacial colonization in Arabidopsis lyrata. Heredity 100:47-58.
97. Nadachowska K, Babik W.2009. Divergence in the face of gene flow:the case of two Newts (Amphibia:Salamandridae). Molecular Biology:and Evolution 26:829-841.
98. Neale DB, Savolainen O.2004. Association genetics of complex traits in conifers. Trends in Plant Science 9:325-330.
99. Nei M.1975. Molecular Population Genetics and Evolution. North-Holland Publishing Company, Amsterdam. Oxford.
100. Nei M.1987. Molecular Evolutionary Genetics. Columbia University Press, New York, NY, USA.
101. Nei M, Li WH.1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, USA 76: 5269-5273.
102. Nei M, Tajima F.1981. DNA polymorphism detectable by restriction endonucleases. Genetics 97:145-63.
103. Ni J.2000. A simulation of biomes on the Plateau and their response to global climate change. Mountain Research and Development 20:80-89.
104. Nielimmer ML, Fitzpatrick BM, Miller BT.2008. Recent divergence-with-gene-flow in Tennessee cave salamanders (Plethodontidae:Gyrinophilus) inferred from gene genealogies. Molecular Ecology 17:2258-2275.
105. Nielsen R.2001. Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641-647.
106. Nielsen R, Wakeley J.2001. Distinguishing migration from isolation. A Markov chain Monte Carlo approach. Genetics 158:885-896.
107. Nordborg M.2000. Linkage disequilibrium, gene trees and selfing:an ancestral recombination graph with partial self-fertilization. Genetics 154:923-929.
108. Nordborg M.2001. Coalescent theory, pp.179-212 in Handbook of Statistical Genetics, edited by Balding DJ, Bishop M and Cannings C. Wiley Chichester, UK.
109. Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D.2002. The extant of linkage disequilibrium in Arabidopsis thaliana. Nature Genetics 30:190-193.
110. Nordborg M, Innan H.2002. Molecular population genetics. Current Opinion in Plant Biology 5:69-73.
111.Nosil P.2008. Speciation with gene flow could be common. Molecular Ecology 17: 2103-2106.
112. Opgenoorth L, Vend ram in GG, Mao KS, Miehe G, Miehe S, Liepelt S, Liu JQ, Ziegenhagen B.2010. Tree endurance on the Tibetan Plateau marks the world's highest known tree line of the Last Glacial Maximum. New Phylologist 185:332-342.
113. Palme A, Su Q, Palsson S, Lascoux M.2004. Extensive sharing of chloroplast haplotypes among European birches indicates hybridization among Betula pendula, B. pubescens and B. nana. Molecualr Ecology 13:167-178.
114. Petit RJ, Aguinagalde I, De Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M et al.2003. Glacial refugia:hotspots but not melting pots of genetic diversity. Science 300:1563-1565.
115. Pons O, Petit RJ.1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144:1237-1245.
116. Pot D, Mcmillan L, Echt C, Provost GL, Garnier-Gere P, Cato S, Plomion C.2005. Nucleotide variation in genes involved in wood formation in two pine species. New Phytologist 167:101-112.
117. Pritchard JK, Przeworski M.2001. Linkage disequilibrium in humans:Models and data. American Journal of Human Genetics 69:1-14.
118. Pritchard JK, Stephens M, Donnelly P.2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
119. Przeworski M.2002. The signature of positive selection at randomly chosen loci. Genetics 160:1179-1189.
120. Pyhajarvi T, Garcia-Gil MR, Knurr T, Mikkonen M, Wachowiak W, Savolainen O.2007. Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics 177:1713-1724.
121. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES.2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proceedings of the National Academy of Sciences, USA 98:11479-11484.
122. Rieseberg LH, Willis J.H.2007. Plant speciation. Science 317:910-914.
123. Ross-Ibarra J, Wright SI, Foxe JP, Kawabe A, DeRose-Wilson L, Gos G, Charlesworth D, Gaut BS.2008. Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PloS ONE 6:e2411.
124. Royden LH, Burchfiel BC, van der Hilst RD.2008. The geological evolution of the Tibetan plateau. Science.321:1054-10588.
125. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES.2006. Positive natural selection in thehuman lineage. Science 312:1614-1620.
126. Savolainen O, Langley CH, Lazzaro BP, Fr H.2000. Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana. Molecular Biology and Evolution 17:645-655.
127. Schmid, KJ, Ramos-Onsins S, Ringys-Beckstein H, Weisshaar B, Mitchell-Olds T.2005. A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. Genetics 169:1601-1615.
128. Shattuck-Eidens DM, Bell RN, Neuhausen SL, Helentjaris T.1990. DNA sequence variation within maize and melon:observation from polymerase chain reaction amplification and direct sequencing. Genetics 126:207-217.
129. Stahl EA, Dwyer G, Mauricio R, Krettman M, Bergelson J.1999. Dynamics of disease resistance polymorphism at the Rpm 1 locus of Arabidopsis. Nature 400:667-671.
130. Syring J, Farrell K, Businsky R, Cronn R, Liston A.2007. Widespread genealogical nonmonophyly in species of pinus subgenus strobes. Systematic Biology 56:163-181.
131.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.
132. Tajima F.1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
133. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS.2001. Patterns of DNA sequence polhmorphism chromosome 1 of maize (Zea mays ssp mays L.). Proceedings of the National Academy of Sciences, USA 98:9161-9166.
134. Tenaillon MI, U'Ren J, Tenaillon O, Gaut BS.2004. Selection versus demography:a multilocus investigation of the domestication process in maize. Molecular Biology and Evolution 21: 1214-1225.
135. 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.
136. Thompson LG, Yao T, Mosley-Thompson E, Davis ME, Henderson KA, Lin PN.2000. A high-resolution millennial record of the South Asian monsoon from Himalayan ice cores. Science 289:1916-1919.
137. Thornton KR, Jensen JD, Becquet C, Andolfatto P.2007. Progress and prospects in mapping recent selection in the genome. Heredity 98:340-348.
138. 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.
139. 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.
140. Wakeley J.1998. Segregating sites in Wright's island model. Theoretical Population Biology 53:166-174.
141. Wakeley J, Hey J.1997. Estimating ancestral population parameters. Genetics 145: 847-855.
142. Wang HW, Ge S.2006. Phylogeography of the endangered Cathaya argyrophylla (Pinaceae) inferred from sequence variation of mitochondrial and nuclear DNA. Molecular Ecology 15: 4109-4122.
143. Waters, E. R, and B. A. Schaal.1991. No variation is detected in the chloroplast genome of Pinus torreyana.Canadian Journal of Forrest Research 21:595-608.
144. Watterson GA.1975. On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7:256-276.
145. Wolfe KH, Li W-H, Sharp PH.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.
146. Willyard A, Cronn R, Liston A.2009. Reticulate evolution and incomplete lineage sorting among the ponderosa pines. Molecualr Phylogenelics and Evolution 52:498-511.
147. Willyard A, Syring J, Gernandt DS, Liston A, Cronn R.2007. Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Molecular Biology and Evolution 24:90-101.
148. Wright S.1951. The genetical structure of populations. Annals of Eugenics 15:323-354.
149. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS. 2005. The effects of artificial selection of the maize genome. Science 308:1310-1314.
150. Wright SI, Gaut BS.2005. Molecular population genetics and the search for adaptive evolution in plants. Molecular Biology and Evolution 22:506-519.
151. Wright SI, Lauga B, Charlesworth D.2003. Subdivision and haplotype structure in natural populations of Arabidopsis lyrata. Molecular Ecology 12:1247-1263.
152. Wu CI.2001. The genic view of the process of speciation. Journal of Evolutionary and Biology 14:851-865.
153. Wu CI, Ting CT.2004. Genes and Speciation. Nature Reviews of Genetics 5:114-121.
154. Zeng K, Fu YX, Shi SH, Wu CI.2006. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174:1431-1439.
155. Zhang X S.1983. The Tibetan Plateau in relation to the vegetation of China. Annals of Missouri Botanical Garden 70:564-570.
156. 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.
157. 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. In:Climate Change and Plants in East Asia. (eds. Omasa K, Kai K, Taodao H, Uchijima Z, Yoshino M).25-38, Springer-Verlag, Tokyo.
158. Zhang LQ, Peek AS, Dunams D, Gautier BS,2002. Population genetics of duplicated disease-defense genes, hml and hm 2. in maize (Zea mays ssp mays L.) and its wild ancestor (Zea mays ssp parviglumis). Genetics 162:851-860.
159. Zheng D.1996. The system of physico-geographical regions of the Qinghai-Tibet (Xizang) Plateau. Science in China (Series D) 39:410-417.
160. Zhou RC, Zeng K, Wu W, Chen XS, Yang ZH, Shi SH, Wu CI.2007. Population genetics of speciation in nonmodel organisms:I. ancestral polymorphism in mangroves. Molecular Biology and Evolution 24:2746-2754.
161.郑万钧,付立国.1978.中国植物志.北京：科学出版社7：347-351.
