High population differentiation and unusual haplotype structure in a shade-intolerant pioneer tree species, Zanthoxylum ailanthoides (Rutaceae) revealed by analysis of DNA polymorphism at four nuclear loci

Molecular Ecology

Volumn 17, Issue 10, 2008, Pages 2329-2338

  Kamiya, K ^a   Moritsuka, E ^a   Yoshida, T ^a   Yahara, T ^a   Tachida, H ^a  

^a KYUSHU UNIVERSITY   (Japan)

Author keywords

Nucleotide variation; Pioneer tree; Population structure; Zanthoxylum

Indexed keywords

PLANT DNA;

ARTICLE; CELL NUCLEUS; DNA SEQUENCE; GENETIC POLYMORPHISM; GENETICS; HAPLOTYPE; JAPAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; ZANTHOXYLUM;

BASE SEQUENCE; CELL NUCLEUS; DNA, PLANT; HAPLOTYPES; JAPAN; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; ZANTHOXYLUM;

CONIFEROPHYTA; HEXAPODA; RUTACEAE; ZANTHOXYLUM; ZANTHOXYLUM AILANTHOIDES; ZANTHOXYLUM SCHINIFOLIUM;

EID: 43049134825     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03756.x     Document Type: Article

References (53)

1. Arunyawat U, Stephan W, Städler T (2007) Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes. Molecular Biology and Evolution, 24, 2310 2322.
2. Chiang YC, Ge XJ, Chou CH, Wu WL, Chiang TY (2002) Nucleotide sequence diversity at the methionine synthase locus in endangered Dunnia sinensis (Rubiaceae): an evaluation of the positive selection hypothesis. Molecular Biology and Evolution, 19, 1367 1375.
3. Clement M, Posada D, Crandall K (2000) tcs: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657 1660.
4. Dalling JW, Hubbell SP (2002) Seed size, growth rate and gap microsite conditions as determinants of recruitment success for pioneer species. Journal of Ecology, 90, 557 568.
5. De A, Durrett R (2007) Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum. Genetics, 176, 969 981.
6. Dickinson DB, Preiss J (1969) ADP glucose pyrophosphorylase from maize endosperm. Archives of Biochemistry and Biophysics, 130, 119 128.
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. Evans RC, Alice LA, Campbell CS, Kellogg EA, Dickinson TA (2000) The granule-bound starch synthase (GBSSI) gene in the Rosaceae: multiple loci and phylogenetic utility. Molecular Phylogenetics Evolution, 17, 388 400.
9. Fu Y-X, Li W-H (1993) Statistical tests of neutrality of mutations. Genetics, 133, 693 709.
10. Fujita T, Itaya A, Miura M, Manabe T, Yamamoto S (2003) Long-term canopy dynamics analyzed by aerial photographs in a temperate old-growth evergreen broad-leaved forest. Journal of Ecology, 91, 686 693.
11. Galtier N, Depaulis F, Barton NH (2000) Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics, 155, 981 987.
12. Hamrick JL, Godt MJW (1989) Allozyme diversity in plant species. In : Plant Population Genetics, Breeding, and Genetic Resources (eds Brown ADH, Clegg MT, Kahler AL, Weir BS pp. 43 63. Sinauer & Associates, Sunderland, Massachusetts.
13. Hamrick JL, Godt MJW (1996) Conservation genetics of endemic plant species. In : Conservation Genetics (eds Avise JC, Hamrick JL pp. 281 304. Chapman & Hall, New York.
14. Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, Sherry ST (1998) Genetic traces of ancient demography. Proceedings of the National Academy of Sciences, USA, 95, 1961 1967.
15. Heuertz M, De Paoli E, Källman T et al 2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of norway spruce [Picea abies (L.) Karst]. Genetics, 174, 2095 2105.
16. Horikawa Y (1972) Atlas of the Japanese Flora. Gakken, Tokyo.
17. Hudson RR (2000) A new statistic for detecting genetic differentiation. Genetics, 155, 2011 2014.
18. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18, 337 338.
19. Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics, 111, 147 164.
20. Hudson RR, Kreitman M, Aguadé M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics, 116, 153 159.
21. Hudson RR, Slatkin M, Maddison WP (1992a) Estimation of levels of gene flow from DNA sequence data. Genetics, 132, 583 589.
22. Hudson RR, Boos DD, Kaplan NL (1992b) A statistical test for detecting geographic subdivision. Molecular Biology and Evolution, 9, 138 151.
23. Ingvarsson PK (2005) Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics, 169, 945 953.
24. Järvinen P, Lemmetyinen J, Savolainen O, Sopanen T (2003) DNA sequence variation in BpMADS2 gene in two populations of Betula pendula. Molecular Ecology, 12, 369 384.
25. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In : Mammalian Protein Metabolism III (ed. Munro HN pp. 21 132. Academic Press, New York and London.
26. Kado T, Yoshimaru H, Tsumura Y, Tachida H (2003) DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). Genetics, 164, 1547 1559.
27. Kim IJ, Kahng HY, Chung WI (1998) Characterization of cDNAs encoding small and large subunits of ADP-glucose pyrophosphorylases from watermelon (Citrus vulgaris S.). Bioscience, Biotechnology, and Biochemistry, 62, 550 555.
28. Kim IJ, Noh SJ, Lee BH, Jo J, Kim YS, Chung WI (2001) Molecular characterization of cDNA clones for ADP-glucose pyrophosphorylase from Citrus. Biochimica et Biophysica Acta, 1518, 324 328.
29. 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.
30. Miura M, Manabe T, Nishimura N, Yamamoto S (2001) Forest canopy and community dynamics in a temperate old-growth evergreen broad-leaved forest, south-western Japan: a 7-year study of a 4-ha plot. Journal of Ecology, 89, 841 849.
31. Moeller DA, Tenaillon MI, Tiffin P (2007) Population structure and its effects on patterns of nucleotide polymorphism in teosinte (Zea mays ssp. parviglumis). Genetics, 176, 1799 1809.
32. Naka K, Yoda K (1984) Community dynamics of evergreen broad-leaf forests in southwestern Japan II. Species composition and density of seeds buried in the soil of a climax evergreen oak forest. Botanical Magazine of Tokyo, 97, 61 79.
33. 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.
34. Nordborg M, Hu TT, Ishino Y, Jhaveri J et al 2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology, 3, e196.
35. Normile D (2004) Conservation takes a front seat as University builds new campus. Science, 305, 329 331.
36. Numata M (1961) Some problems in the secondary succession and judging the seral condition and trend. Seibutsu-Kagaku, 13, 146 152.
37. Park SW, Chung WI (1998) Molecular cloning and organ-specific expression of three isoforms of tomato ADP-glucose pyrophosphorylase gene. Gene, 206, 215 221.
38. Rambaut A (1996) se-al: Sequence Alignment Editor. Available at http://evolve.zoo.ox.ac.uk/.
39. Ramos-Onsins SE, Stranger BE, Mitchell-Olds T, Aguade M (2004) Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata. Genetics, 166, 373 388.
40. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) dnasp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
41. Savolainen O, Langley CH, Lazzaro BP, Fréville 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.
42. Shimoda K (1998) Studies on the buried seed strategy and establishment of Zanthoxylum ailanthoides. Dissertation, Graduate School of Science, Osaka City University, Osaka, Japan.
43. Stajich JE, Hahn MW (2005) Disentangling the effects of demography and selection in human history. Molecular Biology and Evolution, 22, 63 73.
44. Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437 460.
45. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585 595.
46. Tsukada M (1983) Vegetation and climate during the last glacial maximum in Japan. Quaternary Research, 19, 212 235.
47. Tsukada M (1985) Map of vegetation during the last glacial maximum in Japan. Quaternary Research, 23, 369 381.
48. Wakeley J (2000) The effects of subdivision on the genetic divergence of populations and species. Evolution, 54, 1092 1101.
49. Watanabe M (1979) Population dynamics of pioneer tree, Zanthoxylum ailanthoides, a host plant of the swallowtail butterfly. Papilio xuthus. Research on Population Ecology, 20, 265 277.
50. Whitt SR, Wilson LM, Tenaillon MI, Gaut BS, Buckler ES (2002) Genetic diversity and selection in the maize starch pathway. Proceedings of the National Academy of Sciences, USA, 99, 12959 12962.
51. Wright SI, Gaut BS (2005) Molecular population genetics and the search for adaptive evolution in plants. Molecular Biology and Evolution, 22, 506 519.
52. Wright SI, Lauga B, Charlesworth D (2003) Subdivision and haplotype structure in natural populations of Arabidopsis lyrata. Molecular Ecology, 12, 1247 1263.
53. Yamamoto S (1992) Gap characteristics and gap regeneration in primary evergreen broad-leaved forests of western Japan. Botanical Magazine of Tokyo, 105, 29 45.