Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex

Molecular Ecology

Volumn 15, Issue 3, 2006, Pages 765-779

  Chiang, Y C ^a   Hung, K H ^b   Schaal, B A ^c,f   Ge, X J ^d   Hsu, T W ^b,e   Chiang, T Y ^b  

^a NATIONAL PINGTUNG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Taiwan)

^b NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d SUN YAT SEN UNIVERSITY   (China)

^e ENDEMIC SPECIES RESEARCH INSTITUTE   (Taiwan)

^f UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Genetic diversity; Island colonization; Organelle DNAs; Phylogeography; Pinus luchuensis complex; Postglacial expansion; Stepping stone migration

Indexed keywords

CHLOROPLAST DNA; MITOCHONDRIAL DNA;

ARTICLE; CHINA; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PINE; TAIWAN;

CHINA; DNA, CHLOROPLAST; DNA, MITOCHONDRIAL; GEOGRAPHY; MOLECULAR SEQUENCE DATA; PHYLOGENY; PINUS; SEQUENCE ANALYSIS, DNA; TAIWAN; VARIATION (GENETICS);

PINUS LUCHUENSIS;

EID: 33644778606     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2005.02833.x     Document Type: Article

References (71)

1. Boyer WD 1958 Longleaf pine seed dispersal in south Alabama Journal of Forestry 56 265 268
2. Burban C Petit R 2003 Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance Molecular Ecology 12 1487 1495
3. Chen SF 2004 ) Phylogeography of Fatsia (Araliaceae): An endemic genus in East Asia. Master's Thesis Department of Biology, Cheng Kung University Tainan, Taiwan
4. Chiang TY 2000 Lineage sorting accounting for the disassociation between chloroplast and mitochondrial lineages in oaks of southern France Genome 43 1090 1094
5. Chiang TY Schaal BA 1999 Phylogeography of ten North American Hylocomium splendens based on nrDNA ITS sequences Molecular Ecology 8 1037 1042
6. Chiang TY Schaal BA 2000 Molecular evolution and phylogeny of the atpB-rbcL spacer of chloroplast DNA in true mosses Genome 43 417 426
7. Chiang TY Schaal BA Peng CI 1998 Universal primers for amplification and sequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA Botanical Bulletin of Academia Sinica 39 245 250
8. Chiang TY Chiang YC Chen YJ et al. 2001 Phylogeography of Kandelia candel in East Asiatic mangroves based on nucleotide variation of chloroplast and mitochondrial DNAs Molecular Ecology 10 2697 2710
9. Chiang YC Schaal BA Chou CH Huang S Chiang TY 2003 Contrasting selection modes at the Adh1 locus in outcrossing Miscanthus sinensis vs. inbreeding Miscanthus condensatus (Poaceae) American Journal of Botany 90 561 570
10. Chiang TY Chiang YC Pan CH et al. 2004a Comparative genomics of horizontal transfer between chloroplast and nuclear genomes in rice and Arabidopsis In Plant Evolutionary Genetics and Biology of Weeds (eds Schaal BA et al. ), pp 1 10 Taiwan Endemic Species Research Institute Nantou, Taiwan
11. Chiang TY Hung KH Hsu TW Wu WL 2004b Lineage sorting and phylogeography in Lithocarpus formosanus and L. dodonaeifolius (Fagaceae) form Taiwan Annals of Missouri Botanical Garden 91 207 222
12. Cronk QCB 1992 Relict floras of the Atlantic islands: patterns assessed Biological Journal of Linnean Society 46 91 103
13. Darwin CR 1859 On the Origin of Species John Murray London
14. 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
15. Dong J Wagner DB 1993 Taxonomic and population differentiation of mitochondrial diversity in Pinus banksiana and Pinus conforta Theoretical and Applied Genetics 86 573 378
16. Donnelly P Tavaré S 1986 The ages of alleles and a coalescent Advanced Applied Probabilities 18 1 19
17. Dyer RJ Sork VL 2001 Pollen pool heterogeneity in shortleaf pine, Pinus echinata Mill Molecular Ecology 10 859 866
18. Emerson BC 2002 Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and process Molecular Ecology 11 951 966
19. Excoffier L Smouse PE 1994 Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony Genetics 136 343 359
20. Fu Y Li W 1993 Statistical tests of neutrality of mutations Genetics 133 693 709
21. Gernandt D Lopez GG Garcia SO Liston A 2005 Phylogeny and classification of Pinus Taxon 54 29 42
22. Graur D Li WH 1999 Fundamentals of Molecular Evolution Sinauer Associates Sunderland, Massachusetts
23. Hewitt G 2000 The genetic legacy of the Quaternary ice ages Nature 405 907 913
24. Hikida T Ota H 1997 Biogeography of reptiles in the subtropical East Asian Islands In The Symposium on the Phylogeny, Biogeography and Conservation of Fauna and Flora of East Region pp 11 18 National Taiwan Normal University Taipei, Taiwan
25. Huang S Chiang YC Schaal BA Chou CH Chiang TY 2001 Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan Molecular Ecology 10 2669 2681
26. Juan II Emerson BC Orom II Hewitt GM 2000 Colonization and diversification: towards a phylogeographic synthesis for the Canary Islands Trends in Ecology & Evolution 15 104 109
27. Kimura M 1980 A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences Journal of Molecular Evolution 7 1151 1161
28. Kumar S Tamura K Jakobsen IB Nei M 2001 mega 2: molecular evolutionary genetics analysis software Bioinformatics 17 1244 1245
29. Lanner RM 1998 Seed dispersal in Pinus In Ecology and Biogeography of Pinus (ed Richardson DM pp 281 295 Cambridge University Press Cambridge, UK
30. Latta RG Mitton JB 1997 A comparison of population differentiation across four classes of gene marker in limber pine (Pinus flexilis James) Genetics 146 1153 1163
31. Latta RG Mitton JB 1999 Historical separation and present gene flow through a zone of secondary contact in ponderosa pine Evolution 53 769 776
32. Ledig FT 1998 Genetic variation in Pinus In Ecology and Biogeography of Pinus (ed Richardson DM pp 251 280 Cambridge University Press Cambridge, UK
33. Li DZ 1997 A reassessment of Pinus subgenus Pinus in China Edinburgh Journal of Botany 54 337 349
34. Liu J Ye P 1977 Quaternary pollen assemblages in Shanghai and Zheijiang Province and their stratigraphic and paleoclimatic significance Acta Palaeontologica Sinica 16 10 33
35. Liu KB Sun S Jiang X 1992 Environmental change in the Yangtze River delta since 12000 yr BP Quarterly Research 38 32 45
36. Matos JA Schaal BA 2000 Chloroplast evolution in the Pinus montezumae complex: a coalescent approach to hybridization Evolution 54 1218 1233
37. Millar CI 1998 Early evolution of pines In Ecology and Biogeography of Pinus (ed Richardson DM pp 69 91 Cambridge University Press Cambridge, UK
38. Mirov NT 1967 The Genus Pinus The Ronald Press New York
39. Mitton JB Kreiser BR Latta RG 2000 Glacial refugia of limber pine (Pinus flexilis James) inferred from the population structure of mitochondrial DNA Molecular Ecology 9 91 97
40. Murray MG Thompson WF 1980 Rapid isolation of high molecular weight DNA Nucleic Acids Research 8 4321 4325
41. Neale DB Sederoff RR 1989 Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine Theoretical and Applied Genetics 77 212 216
42. Newton AC Allnutt TR Dvorak WS del Castillo RF Ennos RA 2002 Patterns of genetic variation in Pinus chiapensis, a threatened Mexican pine, detected by RAPD and mitochondrial DNA RFLP markers Heredity 89 191 198
43. Petit RJ Duminil J Fineschi S Hampe A Salvini DA Vendramin GG 2005 Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations Molecular Ecology 14 689 701
44. Pons O Petit RJ 1996 Measuring and testing genetic differentiation with ordered versus unordered alleles Genetics 144 1237 1245
45. Price RA Liston A Strauss SH 1998 Phylogeny and systematics of Pinus In Ecology and Biogeography of Pinus (ed Richardson DM pp 49 68 Cambridge University Press Cambridge, UK
46. Raven PH Evert RF Eichorn SE 1992 Biology of Plants 5th edn Worth New York
47. Rees DJ Emerson BC Oromi P Hewitt GM 2001 The diversification of the genus Nesotes (Coleoptera: Tenebrionidae) in the Canary Islands: evidence from mtDNA Molecular Phylogenetics and Evolution 21 321 326
48. 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
49. Richardson DM Rundel PW 1998 Ecology and biogeography of Pinus and introduction In Ecology and Biogeography of Pinus (ed Richardson DM pp 3 46 Cambridge University Press Cambridge, UK
50. Rozas J Rozas R 1999 dnasp (version 3.0): an integrated program for molecular population genetics and molecular evolution analysis Bioinformatics 15 174 175
51. Sanderson MJ 2002 ) r 8 s: Analysis of rates (' r 8 s ') of evolution (and other stuff), version 1.5. Section of Evolution and Ecology, University of California, Davis. Distributed at
52. Schuster WS Mitton JB 2000 Paternity and gene dispersal in limber pine (Pinus flexilis James) Heredity 84 348 361
53. Sibuet JC Hsu SK 1997 Geodynamics of the Taiwan arc-arc collision Tectonophysics 274 221 251
54. Sibuet JC Hsu SK 2004 How was Taiwan created? Tectonophysics 379 159 181
55. Sinclair W Morman JD Ennos RA 1999 The postglacial history of Scots pine (Pinus sylvestris L.) in western Europe: evidence from mitochondrial DNA variation Molecular Ecology 8 83 88
56. Slatkin M 1993 Isolation by distance in equilibrium and non-equilibrium populations Evolution 47 264279
57. Song BH Wang XQ Wang XR Sun LJ Hong DY Peng PH 2002 Maternal lineages of Pinus densata, a diploid hybrid Molecular Ecology 11 1057 1063
58. Strauss SH Hong YP Hipkins VD 1993 High levels of population differentiation for mitochondrial DNA haplotypes in Pinus radiata, muricata and attenuata Theoretical and Applied Genetics 86 605 611
59. Suzuki H Tsuchiya K Takezaki N 2000 A molecular phylogenetic framework for the Ryukyu endemic rodents Tokudaia osimensis and Diplothrix legata Molecular Phylogenetics and Evolution 15 15 24
60. Tajima F 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123 585 595
61. Tani N Maruyama K Tomaru N et al. 2003 Genetic diversity of nuclear and mitochondrial genomes in Pinus parviflora Sieb. & Zucc. (Pinaceae) populations Heredity 91 510 518
62. Vita-Finzi C 2000 Deformation and seismicity of Taiwan Proceedings of National Academy of Sciences, USA 97 11176 11180
63. Walter R Epperson BK 2004 Microsatellite analysis of spatial structure among seedling in populations of Pinus strobus (Pinaceae) American Journal of Botany 91 549 557
64. Wang JM 1987 The Fenwei rift and its recent periodic activity Tectonophysics 133 257 275
65. Wang WP Hwang CY Lin TP Hwang SY 2003 Historical biogeography and phylogenetic relationships of the genus Chamaecyparis (Cupressaceae) inferred from chloroplast DNA polymorphism Plant Systematics and Evolution 241 13 28
66. Wang XQ Tank DC Sang T 2000 Phylogeny and divergence times in Pinaceae: evidence from three genomes Molecular Biology and Evolution 17 773 781
67. 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
68. 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
69. Watterson GA 1975 On the number of segregating sites in genetical models without recombination Theoretical Population Biology 7 256 275
70. Wu CI Li WH 1985 Evidence for higher rates of nucleotide substitution in rodents than in man Proceedings of National Academy of Sciences, USA 82 1741 1745
71. Wu J Krutovskii Strauss S 1998 Abundant mitochondrial genome diversity, population differentiation and convergent evolution in pines Genetics 150 1605 1614