Demographic History of Shorea curtisii (Dipterocarpaceae) Inferred from Chloroplast DNA Sequence Variations

Biotropica

Volumn 44, Issue 5, 2012, Pages 577-585

  Kamiya, Koichi ^a   Nanami, Satoshi ^b   Kenzo, Tanaka ^c   Yoneda, Reiji ^c   Diway, Bibian ^d   Chong, Lucy ^d   Azani, Mohamad A ^e   Majid, Nik M ^e   Lum, Shawn K Y ^f   Wong, Khoon Meng ^g   Harada, Ko ^a  

^a EHIME UNIVERSITY   (Japan)

^b Osaka Prefecture University   (Japan)

^c FORESTRY AND FOREST PRODUCTS RESEARCH INSTITUTE   (Japan)

^d Botanical Research Centre   (Malaysia)

^e UNIVERSITY PUTRA MALAYSIA   (Malaysia)

^f NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^g SINGAPORE BOTANIC GARDENS   (Singapore)

Author keywords

Demographic expansion; Genetic variation; Haplotype; Phylogeography; Sundaland

Indexed keywords

CHLOROPLAST; DEMOGRAPHIC HISTORY; DICOTYLEDON; GENETIC DIFFERENTIATION; GEOGRAPHICAL REGION; HILL; ISOLATED POPULATION; MITOCHONDRIAL DNA; MONTANE FOREST; MUTATION; PHYLOGENETICS; PHYLOGEOGRAPHY; PLEISTOCENE; POPULATION BOTTLENECK; SEED DISPERSAL;

BORNEO; MALAY PENINSULA; SUNDA ISLES;

DIPTEROCARPACEAE; SHOREA; SHOREA CURTISII;

EID: 84865729058     PISSN: 00063606     EISSN: 17447429     Source Type: Journal    
DOI: 10.1111/j.1744-7429.2011.00834.x     Document Type: Article

References (55)

1. Ashton, P. S. 1969. Speciation among tropical forest trees, some deductions in the light of recent evidence. Biol. J. Linn. Soc. 1: 155-196.
2. Ashton, P. S. 1982. Dipterocarpaceae. In C. G. G. J. van Steenis (Ed.) Flora Malesiana, Ser. 1, 9: 237-552. Martinus Nijhoff Publishers, The Netherlands.
3. Ashton, P. S. 1998a. Niche specificity among tropical trees: a question of scales. In D. M. Newbery, H. T. T. Prins, and N. Brown (Eds.) Dynamics of tropical communities, pp. 491-514. 37th Symposium of the British Ecology Society, RoyalHolloway College, University of London. Blackwell Science, Oxford.
4. Ashton, P. S. 1998b. Shorea curtisii. In IUCN 2010. IUCN Red List of Threatened Species. Version 2010.4. Available at www.iucnredlist.org. (accessed 24 November 2010).
5. Ashton, P. S. 2004. Dipterocarpaceae. In E. Soepadmo, L. G. Saw, and R. C. K. Chung (Eds.) Tree flora of Sabah and Sarawak, vol 5. pp. 63-388. Forest Research Institute, Malaysia.
6. Ashton, P. S. 2010. Conservation of Borneo biodiversity: Do small lowland parks have a role, or are big inland sanctuaries sufficient? Brunei as an example. Biodivers. Conserv. 19: 343-356.
7. Avise, J. J. 2000. Phylogeography: The history of formation of species. Harvard University Press Cambrige, Massachusetts.
8. Bänfer, G., U. Moog, B. Fiala, M. Mohamed, K. Weising, and F. R. Blattner 2006. A chloroplast genealogy of myrmecophytic Macaranga species (Euphorbiaceae) in Southeast Asia reveals hybridisation, vicariance and long-distance dispersal. Mol. Ecol. 15: 4409-4424.
9. Cannon, C. H. 2011. Quaternary dynamics of lowland forest in Sundaland and its implications for the management and conservation of the Dipterocarpaceae. Biotropica (in press).
10. Cannon, C. H., and P.S. Manos 2003. Phylogeography of the Southeast Asian stone oaks (Lithocarpus). J. Biogeogr. 30: 211-226.
11. Cannon, C. H., R. J. Morley, and A. B. G. Bush 2009. The current refugial rainforests of Sundaland are unrepresentative of their biogeographic past and highly vulnerable to disturbance. Proc. Nat. Acad. Sci. U.S.A. 106: 11188-11193.
12. Clement, M., D. Posada, and K. A. Crandall 2000. TCS: A computer program to estimate gene genealogies. Mol. Ecol. 9: 1657-1659.
13. Demesure, B., N. Sodzii, and R. J. Petit 1995. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol. Ecol. 4: 129-134.
14. Excoffier, L., and H. E. L. Lischer 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10: 564-567.
15. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
16. Frascaria, N, L. Maggia, M. Michaud, and J. Bousquet 1993. The rbcL gene sequence from chestnut indicates a slow rate of evolution in the Fagaceae. Genome 36: 668-671.
17. Fu, Y. X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking, and background selection. Genetics 147: 915-925.
18. Fu, Y. X., and W. H. Li 1993. Statistical tests of neutrality of mutations. Genetics, 133: 693-709.
19. Gathorne-Hardy, F. J., F. J., Syaukani, R. G. Davies, P. Eggleton, and D. T. Jones 2002. Quaternary rainforest refugia in south-east Asia: using termites (Isoptera) as indicators. Biol. J. Linn. Soc. 75: 453-466.
20. Gorog, A. J., M. H. Sinaga, and M. D. Engstrom 2004. Vicariance or dispersal? Historical biogeography of three Sunda shelf murine rodents (Maxomys surifer, Leopoldamys sabanus and Maxomys whiteheadi). Biol. J. Linn. Soc. 81: 91-109.
21. Guicking, D., B. Fiala, F. R. Blattner, F. Slik, M. Mohamed, and K. Weising 2011. Comparative chloroplast DNA phylogeography of two tropical pioneer trees, Macaranga gigantea and Macaranga pearsonii (Euphorbiaceae). Tree Genet. Genomes 7: 573-585.
22. Harpending, H. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biol. 66: 591-600.
23. Hudson, R. R. 2000. A new statistic for detecting genetic differentiation. Genetics 155: 2011-2014.
24. Hudson, R. R., D. D. Boos, and N. L. Kaplan 1992. A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9: 138-151.
25. Ishiyama, H., N. Inomata, T. Yamazaki, N. Ab Shukor, and A. E. Szmidt 2008. Demographic history and interspecific hybridization of four Shorea species (Dipterocarpaceae) from Peninsular Malaysia inferred from nucleotide polymorphism in nuclear gene regions. Can. J. For. Res. 38: 996-1007.
26. Jakob, S. S., and F. R. Blattner 2006. A chloroplast genealogy of Hordeum (Poaceae): long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference. Mol. Biol. Evol. 23: 1602-1612.
27. Kamiya, K., Y. Y. Gan, S. K. Y. Lum, M. S. Khoo, S. C. Chua, and N. N. H. Faizu 2011. Morphological and molecular evidence of natural hybridization in Shorea (Dipterocarpaceae). Tree Genet. Genomes 7: 297-306.
28. Kamiya, K., K. Harada, H. Tachida, and P. S. Ashton 2005. Phylogeny of PgiC gene in Shorea and its closely related genera (Dipterocarpaceae), the dominant trees in Southeast Asian rain forests. Am. J. Bot. 92: 775-788.
29. Lee, S. L., K. C. Ang, and M. Norwati 2000b. Genetic diversity of Dryobalanops aromatica Gaertn. f. (Dipterocarpaceae) in Peninsular Malaysia and its pertinence to genetic conservation and tree improvement. Forest Genet. 7: 209-217.
30. Lee, H. S., S. J. Davies, J. V. LaFrankie, S. Tan, A. Itoh, T. Yamakura, and P. S. Ashton 2002a. Floristic and structural diversity of 52 hectares of mixed dipterocarp forest in Lambir Hills National Park, Sarawak, Malaysia. J. Trop. For. Sci. 14: 379-400.
31. Lee, S. L., K. K. S. Ng, L. G. Saw, A. Norwati, M. H. Siti Salwana, C. T. Lee, and M. Norwati 2002b. Population genetics of Intsia palembanica (Leguminosae) and genetic conservation of Virgin Jungle Reserves (VJRs) in Peninsular Malaysia. Am. J. Bot. 89: 447-459.
32. Lee, S. L., R. Wickneswari, M. C. Mahani, and A. H. Zakri 2000a. Genetic diversity of Shorea leprosula Miq. (Dipterocarpaceae) in Malaysia: Implications for conservation of genetic resources and tree improvement. Biotropica 32: 213-224.
33. Librado, P., and J. Rozas 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
34. Meijer, W. 1974. Plant geographic studies on Dipterocarpaceae in Malesia. Ann. Missouri. Bot. Gard. 61: 806-811.
35. Morley, R. J. 1998. Palynological evidence for tertiary plant dispersals in the SE Asian region in relation to plate tectonics and climate. In R. Hall, and J. D. Holloway (Eds.) Biogeography and geological evolution of SE Asia, pp. 211-234. Backhuys Publishers, Leiden, The Netherlands.
36. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, NY.
37. Nordborg, M., and H. Innan 2002. Molecular population genetics. Curr. Opinion Plant Biol. 5: 69-73.
38. Petit, R. J., J. Duminil, S. Fineschi, A. Hampe, D. Salvini, and G. G. Vendramin 2005. Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol. Ecol. 14: 689-701.
39. Pons, O., and R. J. Petit 1995. Estimation, variance and optimal sampling of gene diversity I. Haploid locus. Theor. Appl. Genet. 90: 462-470.
40. Pons, O., and R. J. Petit 1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics, 144: 1237-1245.
41. Quek, S. P., S. J. Davies, P. S. Ashton, T. Itino, and N. E. Pierce 2007. The geography of diversification in mutualistic ants: a gene's-eye view into the Neogene history of Sundaland rain forests. Mol. Ecol. 16: 2045-2062.
42. Ramos-Onsins, S. E., and J. Rozas 2002. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 19: 2092-2100.
43. Smith, S. A., and M. J. Donoghue 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86-89.
44. Soltis, D. E., A. M. Gitzendanner, D. D. Strenge, and P. S. Soltis 1997. Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Pl. Syst. Evol. 206: 353-373.
45. Swofford, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer Associates, Sunderland, Massachusetts.
46. Symington, C. F. 1943. Foresters' manual of Dipterocarps. Malayan Forest Records 16. Forestry Department, Peninsular Malaysia.
47. Taberlet, P., L. Fumagalli, A. G. Wust Saucy, and J. F. Cosson 1998. Comparative phylogeography and postgracial colonization routes in Europe. Mol. Ecol. 7: 453-464.
48. Taberlet, P., L. Gielly, G. Pautou, and J. Bouvet 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17: 1105-1109.
49. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
50. Tsumura, Y., T. Kado, K. Yoshida, H. Abe, M. Ohtani, Y. Taguchi, Y. Fukue, N. Tani, S. Ueno, K. Yoshimura, K. Kamiya, K. Harada, Y. Takeuchi, B. Diway, F. Reiner, N. Mohamad, I. Sapto, K. K. S. Ng, N. Muhammad, and S. L. Lee 2011. Molecular database for classifying Shorea species (Dipterocarpaceae) and techniques for checking the legitimacy of timber and wood products. J. Plant. Res. 124: 35-48.
51. Tsumura, Y., T. Kawahara, R. Wickneswari, and K. Yoshimura 1996. Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes. Theor. Appl. Genet. 93: 22-29.
52. Ueda, S., S. P. Quek, T. Itioka, K. Murase, and T. Itino 2010. Phylogeography of the Coccus scale insects inhabiting myrmecophytic Macaranga plants in Southeast Asia. Popul. Ecol. 52: 137-146.
53. Watterson, G. A. 1975. On the number of segregating sites in genetical models without recombination. Theor. Pop. Biol. 7: 256-276.
54. Weir, B. S., and C. C. Cockerham 1984. Estimating F-statistics for the analysis of population structure. Evolution, 38: 1358-1370.
55. Wolfe, K. H., W. H. Li, and P. M. Sharp 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, nuclear DNAs. Proc. Natl. Acad. Sci. U.S.A. 84: 9054-9058.