Phylogeography of Pinus tabulaeformis Carr. (Pinaceae), a dominant species of coniferous forest in northern China

Molecular Ecology

Volumn 17, Issue 19, 2008, Pages 4276-4288

  Chen, Kangming ^a,b   Abbott, Richard J ^c   Milne, Richard I ^d   Tian, Xin Min ^b   Liu, Jianquan ^a,b  

^a LANZHOU UNIVERSITY   (China)

^b NORTHWEST INSTITUTE OF PLATEAU BIOLOGY   (China)

^c UNIVERSITY OF ST ANDREWS   (United Kingdom)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

cpDNA; Glacial refugia; mtDNA; North China; Phylogeography; Pinus tabulaeformis

Indexed keywords

MITOCHONDRIAL DNA; PLANT DNA;

ARTICLE; CHINA; CLIMATE; ECOSYSTEM; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; INTRON; ISOLATION AND PURIFICATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PINE; POPULATION GENETICS; TREE;

BASE SEQUENCE; CHINA; CLIMATE; DNA, MITOCHONDRIAL; DNA, PLANT; ECOSYSTEM; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; INTRONS; PHYLOGENY; PINUS; TREES;

CONIFERALES; PINACEAE; PINUS TABULIFORMIS;

EID: 52649152961     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03911.x     Document Type: Article

References (63)

1. Abbott RJ, Smith LC, Milne RI, Crawford RMM, Wolff K, Balfour J (2000) Molecular analysis of plant migration and refugia in the Arctic. Science, 289, 1343 1346.
2. Afzal-Rafii Z, Dodd A (2007) Chloroplast DNA supports a hypothesis of glacial refugia over postglacial recolonization in disjunct populations of black pine (Pinus nigra) in Western Europe. Molecular Ecology, 16, 723 736.
3. Aizawa M, Yoshimaru H, Saito H (2007) Phylogeography of a northeast Asian spruce, Picea jezoensis, inferred from genetic variation observed in organelle DNA markers. Molecular Ecology, 16, 3393 3405.
4. 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.
5. Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37 48.
6. Burban C, Petit RJ (2003) Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance. Molecular Ecology, 12, 1487 1495.
7. Demesure B, Sodzi N, Petit RJ (1995) A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology, 4, 129 131.
8. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochemical Bulletin, 19, 11 15.
9. Dumolin-Lapegue S, Pemonge M-H, Petit RJ (1997) An enlarged set of consensus primers for the study of organelle DNA in plants. Molecular Ecology, 6, 393 397.
10. Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Molecular Ecology, 11, 2571 2581.
11. Ennos RA (1994) Estimating the relative rates of pollen and seed migration among plant populations. Heredity, 72, 250 259.
12. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotype: application to human mitochondrial DNA restriction data. Genetics, 131, 479 491.
13. 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.
14. Gamache I, Jaramillo-Correa JP, Payette S, Bousquet J (2003) Diverging patterns of mitochondrial and nuclear DNA diversity in subarctic black spruce: imprint of a founder effect associated with postglacial colonization. Molecular Ecology, 12, 891 901.
15. 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.
16. Gonzales E, Hamrick JL, Chang SM (2008) Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum. Journal of Biogeography, 35, 844 852.
17. Hamper 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.
18. Harrison SP, Yu G, Takahara H (2001) Palaeovegetation: diversity of temperate plants in East Asia. Nature, 413, 129 130.
19. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907 913.
20. Hultén E (1937) Outline of the History of Arctic and Boreal Biota during the Quaternary Period. Lehre J. Cramer, New York.
21. Huntley B, Birks HJB (1983) An Atlas of Past and Present Pollen Maps for Europe: 0-13 000 Years Ago. Cambridge University Press, Cambridge, UK.
22. Jaramillo-Correa JP, Bousquet J (2005) Mitochondrial genome recombination in the zone of contact of two hybridising conifers. Genetics, 171, 1951 1962.
23. 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.
24. Jaramillo-Correa JP, Beaulieu J, Ledig FT, Bousquet J (2006) Decoupled mitochondrial and chloroplast DNA population structure reveals Holocene collapse and population isolation in a threatened Mexican-endemic conifer. Molecular Ecology, 15, 2787 2800.
25. Kropf M, Kandereit JW, Comes HP (2003) Differential cycles of range contraction and expansion in European high mountain plants during the Late Quaternary: insights from Pritzelago alpina (L.) O. Kuntze (Brassicaceae). Molecular Ecology, 12, 931 949.
26. Li JJ, Fang XM, Van der Voo R, Zhu JJ (1997) Magnetostratigraphic dating of river terraces: rapid and intermittent incision by the Yellow River of the northeastern margin of the Tibetan Plateau during the Quaternary. Journal of Geophysical Research, 102, 121 132.
27. Liepelt S, Bialozyt R, Ziegenhagen B (2002) Wind-dispersed pollen mediates postglacial gene flow among refugia. Proceedings of the National Academy of Sciences of the USA, 99, 14590 14594.
28. Lindbladh M, O'Connor R, Jacobson GL (2002) Morphometric analysis of pollen grains for paleoecological studies: classification of Picea from eastern North America. American Journal of Botany, 89, 1459 1467.
29. Liu KB (1988) Quaternary history of the temperate forests of China. Quaternary Science Reviews, 7, 1 20.
30. 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.
31. Marquardt PE, Epperson BK (2004) Spatial and population genetic structure of microsatellites in white pine. Molecular Ecology, 13, 3305 3315.
32. 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.
33. Naydenov K, Senneville S, Beaulieu J, Tremblay F, Bousquet J (2007) Glacial vicariance in Eurasia: mitochondrial DNA evidence from Scots pine for a complex heritage involving genetically distinct refugia at mid-northern latitudes and in Asia Minor. BMC Evolutionary Biology, 7, 233.
34. Nei M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, USA, 70, 3321 3323.
35. Petit RJ, Aguinagalde I, de Beaulieu JL et al 2003) Glacial refugia: hotspot but not melting pots of genetic diversity. Science, 300, 1563 1565.
36. 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.
37. Petit RJ, Grivet D (2002) Optimal randomization strategies when testing the existence of a phylogeographic structure. Genetics, 161, 469 471.
38. Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics, 144, 1237 1245.
39. Qian H, Ricklefs RE (2000) Large-scale processes and the Asian bias in species diversity of temperate plants. Nature, 407, 180 182.
40. Qian H, Ricklefs RE (2001) Diversity of temperate plants in East Asia - reply. Nature, 413, 130 130.
41. Richardson BA, Brunsfeld SJ, Klopfenstein NB (2002) DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis). Molecular Ecology, 11, 215 227.
42. Ronikier M, Cieslak EM, Korbecka G (2008) High genetic differentiation in the alpine plant Campanula alpina Jacq. (Campanulaceae): evidence for glacial survival in several Carpathian regions and long-term isolation between the Carpathians and the Alps. Molecular Ecology, 17, 1763 1775.
43. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219 1228.
44. 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.
45. Song BH, Wang XQ, Wang XR (2002) Maternal lineages of Pinus densata, a diploid hybrid. Molecular Ecology, 11, 1057 1063.
46. 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.
47. Taberlet P, Fumagalli L, Wust-Saucy AG, Cossons JF (1998) Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology, 7, 453 464.
48. Tang LY, Shen CM (1996) Late Cenozoic vegetation history and climatic characteristics of Qinghai-Xizang Plateau. Acta Micropalaeontologica Sinica, 13, 321 337.
49. 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, 24, 4876 4882.
50. Vasconcelos T, Horn A, Lieutier F, Branco M, Kerdelhue C (2006) Distribution and population genetic structure of the Mediterranean pine shoot beetle Tomicus destruens in the Iberian Peninsula and Southern France. Agricultural and Forest Entomology, 8, 103 111.
51. Wagner DB (1992) Nuclear, chloroplast and mitochondrial DNA polymorphisms as biochemical markers in population genetic analysis of forest trees. New Forests, 6, 373 390.
52. Wang P, Sun X (1994) Last Glacial Maximum in China: comparison between land and sea. Catena, 23, 341 353.
53. Wang XR, Tsumura Y, Yoshimaru H, Nagasaka K, Szmidt AE (1999) Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, matK, rpl20-rps18 spacer and trnV intron sequences. American Journal of Botany, 86, 1742 1753.
54. Wang XR, Szmidt AE, Savolainen O (2001) Genetic composition and diploid hybrid speciation of a high mountain pine, Pinus densata, native to the Tibetan plateau. Genetics, 159, 337 346.
55. Webb T, Bartlein PJ (1992) Global changes during the last 3 million years, climatic controls and biotic response. Annual Review of Ecology and Systematics, 23, 141 173.
56. Winkler MG, Wang PK (1993) The Late Quaternary vegetation and climate of China. In : Global Climates Since the Last Glacial Maximum (ed. Wright HE pp. 221 264. University of Minnesota Press, London.
57. 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.
58. Wright S (1978) Evolution and the Genetics of Populations 4. Variability Within and Among Natural Populations. University of Chicago Press, Chicago, Illinois.
59. Wu CL (1956) The taxonomic revision and phytogeographical study of Chinese pines. Acta Phytotaxonomica Sinica, 5, 131 163.
60. Wu CY (1995) Vegetation of China, 2nd edn. Science Press, Beijing.
61. Yu G, Chen XD, Ni J (2000) Palaeovegetation of China: a pollen data-based synthesis for the mid-Holocene and last glacial maximum. Journal of Biogeography, 27, 635 664.
62. 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.
63. Zhao SL, Li GG (1990) Deserts on the shelves adjacent China in the Later Pleistocene. Oceanography and Limnology of China, 8, 289 298.