Nuclear and chloroplast DNA phylogeography reveal two refuge areas with asymmetrical gene flow in a temperate walnut tree from East Asia

New Phytologist

Volumn 188, Issue 3, 2010, Pages 892-901

  Bai, Wei Ning ^a,b   Liao, Wan Jin ^b   Zhang, Da Yong ^b  

^a INSTITUTE OF BOTANY   (China)

^b BEIJING NORMAL UNIVERSITY   (China)

Author keywords

Gene flow; Glacial refugia; Juglans mandshurica; Northern and northeastern China; Phylogeography

Indexed keywords

CHLOROPLAST DNA; MICROSATELLITE DNA; PLANT DNA;

CHLOROPLAST; DECIDUOUS TREE; GENE FLOW; GENETIC ANALYSIS; GENETIC MARKER; LAST GLACIAL MAXIMUM; PHYLOGEOGRAPHY; PLEISTOCENE; REFUGE; TEMPERATE ENVIRONMENT;

ARTICLE; ASIA; ECOSYSTEM; GENE FLOW; GENETICS; HAPLOTYPE; HISTORY; METHODOLOGY; PHYLOGEOGRAPHY; WALNUT;

ASIA; DNA, CHLOROPLAST; DNA, PLANT; ECOSYSTEM; GENE FLOW; HAPLOTYPES; HISTORY, ANCIENT; JUGLANS; MICROSATELLITE REPEATS; PHYLOGEOGRAPHY;

FAR EAST;

JUGLANDACEAE; JUGLANS; JUGLANS MANDSHURICA;

EID: 77958617036     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2010.03407.x     Document Type: Article

References (69)

1. Aizawa M, Yoshimaruth H, Saito H, Katsuki T, Kawahara T, Kitamura K, Shi F, Kaji M. 2007. Phylogeography of a northeast Asian spruce, Picea jezoensis, inferred from genetic variation observed in organelle DNA markers. Molecular Ecology 16: 3393-3405.
2. Alsos IG, Eidesen PB, Ehrich D, Skrede I, Westergaard K, Jacobsen GH, Landvik JY, Taberlet P, Brochmann C. 2007. Frequent long-distance plant colonization in the changing Arctic. Science 316: 1606-1609.
3. Aradhya KM, Potter D, Gao FY, Simon CJ. 2005. Cladistic biogeography of Juglans (Juglandaceae) based on chloroplast DNA inter-genic spacer sequences. In: Motley TJ, Zerega N, Cross H, eds. Darwin's harvest - new approaches to the origin, evolution, and conservation of crops. New York, NY, USA: Columbia University Press, 143-170.
4. Avise JC. 2000. Phylogeography: the history and formation of species. Cambridge, MA, USA: Harvard University Press.
5. Bai WN, Zeng YF, Liao WJ, Zhang DY. 2006. Flowering phenology and wind-pollination efficacy of heterodichogamous Juglans mandshurica (Juglandaceae). Annals of Botany 98: 397-402.
6. Bai WN, Zeng YF, Zhang DY. 2007. Mating patterns and pollen dispersal in a heterodichogamous tree, Juglans mandshurica (Juglandaceae). New Phytologist 176: 699-707.
7. Beerli P. 2006. Comparison of Bayesian and Maximum-likelihood inference of population genetic parameters. Bioinformatics 22: 341-345.
8. Beerli P, Felsenstein J. 1999. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152: 763-773.
9. Chen ZD. 1994. Phylogeny and phytogeography of the Betulaceae. Acta Phytotaxonomica Sinica 32: 1-153.
10. 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.
11. China EPA. 1998. Chinese country study on biological diversity. Beijing, China: China Environmental Science Press.
12. Crawford NG. 2010. SMOGD: software for the measurement of genetic diversity. Molecular Ecology Resources 10: 556-557.
13. Currat M, Ruedi M, Petit RJ, Excoffier L. 2008. The hidden side of invasions: massive introgression by local genes. Evolution 62: 1908-1920.
14. Dangl GS, Woeste K, Aradhya MK, Koehmstedt A, Simon C, Potter D, Leslie CA, McGranahan G. 2005. Characterization of 14 microsatellite markers for genetic analysis and cultivar identification of walnut. Journal of the American Society for Horticultural Science 130: 348-354.
15. Demesure B, Sodzi N, Petit RJ. 1995. A set of universal primers for amplification of polymorphic noncoding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology 4: 129-131.
16. Du FK, Petit RJ, Liu JQ. 2009. More introgression with less gene flow: chloroplast vs. mitochondrial DNA in the Picea asperata complex in China, and comparison with other Conifers. Molecular Ecology 18: 1396-1407.
17. Edh K, Widen B, Ceplitis A. 2007. Nuclear and chloroplast microsatellites reveal extreme population differentiation and limited gene flow in the Aegean endemic Brassica cretica (Brassicaceae). Molecular Ecology 16: 4972-4983.
18. 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.
19. Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
20. Goudet J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices, version 2.9.3.
21. Graur D, Li WH. 1999. Fundamentals of molecular evolution. Sunderland, MA, USA: Sinauer & Associates.
22. Hamilton MB. 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 8: 521-523.
23. Harrison SP, Yu G, Takahara H, Prentice IC. 2001. Palaeovegetation - diversity of temperate plants in east Asia. Nature 413: 129-130.
24. He JJ, Ju JH, Wen ZP, Lu JM, Jin QH. 2007. A review of recent advances in research on Asian monsoon in China. Advances in Atmospheric Sciences 24: 972-992.
25. Hedrick PW. 2005. A standardized genetic differentiation measure. Evolution 59: 1633-1638.
26. Hewitt GM. 2000. The genetic legacy of the Quaternary ice ages. Nature 405: 907-913.
27. Hewitt GM. 2004. Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society B: Biological Sciences 359: 183-195.
28. Hey J, Machado CA. 2003. The study of structured populations - new hope for a difficult and divided science. Nature Reviews Genetics 4: 535-543.
29. Hu LJ, Uchiyama K, Shen HL, Saito Y, Tsuda Y, Ide Y. 2008. Nuclear DNA microsatellites reveal genetic variation but a lack of phylogeographical structure in an endangered species, Fraxinus mandshurica, across north-east China. Annals of Botany 102: 195-205.
30. Huang X, Liu DS, Li Z. 1959. Natural scenery zone in the north of Changbai Mountains. Acta Geographica Sinica 25: 435-446.
31. Ju LX, Wang HK, Jiang DB. 2007. Simulation of the Last Glacial Maximum climate over East Asia with a regional climate model nested in a general circulation model. Palaeogeography Palaeoclimatology Palaeoecology 248: 376-390.
32. Kanno M, Yokoyama J, Suyama Y, Ohyama M, Itoh T, Suzuki M. 2004. Geographical distribution of two haplotypes of chloroplast DNA in four oak species (Quercus) in Japan. Journal of Plant Research 117: 311-317.
33. Li WY. 1998. Chinese Quaternary vegetation and environment. Beijing, China: Science Press.
34. Liepelt S, Bialozyt R, Ziegenhagen B. 2002. Wind-dispersed pollen mediates postglacial gene flow among refugia. Proceedings of the National Academy of Sciences, USA 99: 14590-14594.
35. Ma WL, Luo JC, Jing T, Kujansuu J. 2005. Ecological studies and prospect of cultivation on Juglans mandshurica population. Journal of Inner Mongolia Normal University 34: 489-492.
36. Nakagawa T, Tarasov PE, Kitagawa H, Yasuda Y, Gotanda K. 2006. Seasonally specific responses of the East Asian monsoon to deglacial climate changes. Geology 34: 521-524.
37. Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. New York, NY, USA: Oxford University Press.
38. Nei M, Tajima F, Tateno Y. 1983. Accuracy of estimated phylogenic trees from molecular data. Journal of Molecular Evolution 19: 153-170.
39. Ota T. 1993. DISPAN: genetic distance and phylogenetic analysis, Version 1.1. Pennsylvania State University, University Park.
40. Peakall R, Smouse PE. 2001. GENALEX (version 5.1): genetic analysis in Excel. Population genetic software for teaching and research. Canberra, Australia: Australian National University.
41. 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.
42. Petit R, El Mousadik A, Pons O. 1998. Identifying populations for conservation on the basis of genetic markers. Conservation Biology 12: 844-855.
43. Potter D, Gao FY, Baggett S, McKenna JR, McGranahan GH. 2002. Defining the sources of Paradox: DNA sequence markers for North American walnut (Juglans L.) species and hybrids. Scientia Horticulturae 94: 157-170.
44. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
45. Qian H, Ricklefs RE. 2000. Large-scale processes and the Asian bias in species diversity of temperate plants. Nature 407: 180-182.
46. Qian H, Ricklefs RE. 2001. Palaeovegetation - diversity of temperate plants in east Asia - Reply. Nature 413: 130.
47. Ren ME. 1985. Introduction to physical geography of China. Beijing, China: The Commercial Press.
48. Rice WR. 1989. Analyzing tables of statistical tests. Evolution 43: 223-225.
49. Rousset F. 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219-1228.
50. Schonswetter P, Stehlik I, Holderegger R, Tribsce A. 2005. Molecular evidence for glacial refugia of mountain plants in the European Alps. Molecular Ecology 14: 3547-3555.
51. Shang FD, Wang PJ, Feng GP. 1998. Study on the characteristics and causes of formation of plant diversity in the Funiushan transition region. Journal of Henan University (Natural Science) 28: 54-60.
52. Shaw J, Lickey EB, Schilling EE, Small RL. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. American Journal of Botany 94: 275-288.
53. Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF. 1998. Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology 7: 453-464.
54. 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.
55. 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.
56. Tian B, Liu RR, Wang LY, Qiu Q, Chen KM, Liu JQ. 2009. Phylogeographic analyses suggest that a deciduous species (Ostryopsis davidiana Decne., Betulaceae) survived in northern China during the Last Glacial Maximum. Journal of Biogeography 36: 2148-2155.
57. Wares JP, Cunningham CW. 2001. Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 55: 2455-2469.
58. Weaver AJ, Eby M, Augustus FF, Wiebe EC. 1998. Simulated influence of carbon dioxide, orbital forcing and ice sheets on the climate of the Last Glacial Maximum. Nature 394: 847-853.
59. Weir BS, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
60. Woeste K, Burns R, Rhodes O, Michler C. 2002. Thirty polymorphic nuclear microsatellite loci from black walnut. Journal of Heredity 93: 58-60.
61. Wright S. 1943. Isolation by distance. Genetics 28: 114-138.
62. Xu SY, Gao YX. 1962. The East Asia monsoon and season. In: Gao YX, ed. Several issues of the East Asia monsoon. Beijing, China: Science Press, 88-103.
63. Xu HG, Wang SQ, Xue DY. 1999. Biodiversity conservation in China: legislation, plans and measures. Biodiversity and Conservation 8: 819-837.
64. Zhang H, Yan J, Zhang GQ, Zhou KY. 2008. Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): evidence for independent refugia expansion and secondary contact. BMC Evolutionary Biology 8: 16.
65. Zhang JT, Xi Y, Li J. 2006. The relationships between environment and plant communities in the middle part of Taihang Mountain Range, North China. Community Ecology 7: 155-163.
66. Zhang JW, Zeng Y. 2000. Plant diversity and protection of Funiu Mountain. Journal of Henan University (Natural Science) 30: 76-81.
67. Zhang W, Niu YB, Yan L, Cui ZJ, Li CC, Mu KH. 2008. Late Pleistocene glaciation of the Changbai Mountains in northeastern China. Chinese Science Bulletin 53: 2672-2684.
68. Zheng Y, Xiao X, Guo Z, Howard T. 2001. A county-level analysis of the spatial distribution of forest resources in China. Journal of Forest Planning 7: 69-78.
69. Zhou FY, Abbott RJ, Jiang ZY, Du FK, Milne RI, Liu JQ. 2010. Gene flow and species delimitation: a case study of two pine species with overlapping distributions in southeast China. Evolution. doi: