Interspecific phylogenetic analysis enhances intraspecific phylogeographical inference: A case study in Pinus lambertiana

Molecular Ecology

Volumn 16, Issue 18, 2007, Pages 3926-3937

  Liston, Aaron ^a   Parker Defeniks, Mariah ^a   Syring, John V ^b,c   Willyard, Ann ^a,d   Cronn, Richard ^b  

^a OREGON STATE UNIVERSITY   (United States)

^b PACIFIC NORTHWEST RESEARCH STATION   (United States)

^c W O Farber Center for Civic Leadership   (United States)

^d MONTANA STATE UNIVERSITY BILLINGS   (United States)

Author keywords

Chloroplast introgression; Cronartium ribicola; Phylogeography; Pinus lambertiana; Pinus subsect. Strobus; White pine blister rust resistance

Indexed keywords

ARTICLE; CHLOROPLAST; CLASSIFICATION; DNA SEQUENCE; GENETICS; GEOGRAPHY; HAPLOTYPE; HYBRIDIZATION; MOLECULAR EVOLUTION; PHYLOGENY; PINE; SPECIES DIFFERENCE; UNITED STATES;

CALIFORNIA; CHLOROPLASTS; EVOLUTION, MOLECULAR; GEOGRAPHY; HAPLOTYPES; HYBRIDIZATION, GENETIC; OREGON; PHYLOGENY; PINUS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

CONIFEROPHYTA; CRONARTIUM RIBICOLA; FUNGI; PINUS ALBICAULIS; PINUS LAMBERTIANA; STROBUS;

EID: 34548595410     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03461.x     Document Type: Article

References (64)

1. Aagaard JE, Krutovskii KV, Strauss SH (1998) RAPD markers of mitochondrial origin exhibit lower population diversity and higher differentiation than RAPDs of nuclear origin in Douglas fir. Molecular Ecology, 7, 801 812.
2. Bingham RT, Hoff RJ, Steinhoff RJ (1972) Genetics of Western White Pine, USDA Forest Service Research Paper WO-12. USDA Forest Service, Washington, D.C.
3. Brubaker LB, Anderson PM, Edwards ME, Lozhkin AV (2005) Beringia as a glacial refugium for boreal trees and shrubs: new perspectives from mapped pollen data. Journal of Biogeography, 32, 833 848.
4. Chiang YC, Hung KH, Schaal BA et al 2006) Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex. Molecular Ecology, 15, 765 779.
5. Conkle MT (1996) Patterns of variation in isozymes of sugar pine. In: Sugar Pine: Status, Values, and Roles in Ecosystems: Proceedings of a Symposium Presented by the California Sugar Pine Management Committee (eds Kinloch BB, Marosy M, Huddleston ME p. 99. University of California Division of Agriculture and Natural Resources, Davis, California.
6. Critchfield WB (1986) Hybridization and classification of the white pines (Pinus section Strobus). Taxon, 35, 647 656.
7. Critchfield WB, Kinloch BB (1986) Sugar pine and its hybrids. Silvae Genetica, 35, 138 145.
8. Critchfield WB, Little EL Jr. (1966) Geographic Distribution of the Pines of the World, Forest Service Miscellaneous Publication 991. USDA Forest Service, Washington, D.C.
9. Devey ME, Delfino-Mix A, Kinloch BB, Neale DB (1995) Random amplified polymorphic DNA markers tightly linked to a gene for resistance to white pine blister rust in sugar pine. Proceedings of the National Academy of Sciences, USA, 92, 2066 2070.
10. Eckert AJ, Hall BD (2006) Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): phylogenetic tests of fossil-based hypotheses. Molecular Phylogenetics and Evolution, 40, 166 182.
11. Fernando DD, Long SM, Sniezko RA (2005) Sexual reproduction and crossing barriers in white pines: the case between Pinus lambertiana (sugar pine) and P. monticola (western white pine). Tree Genetics and Genomes, 1, 143 150.
12. Gadek PA, Alpers DL, Heslewood MM, Quinn CJ (2000) Relationships within Cupressaceae sensu lato: a combined morphological and molecular approach. American Journal of Botany, 87, 1044 1057.
13. Gernandt DS, Gaeda López G, Ortiz García S, Liston A (2005) Phylogeny and classification of Pinus. Taxon, 54, 29 42.
14. Hall TA (1999) bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95 98.
15. Hausner G, Olson R, Simon D et al 2006) Origin and evolution of the chloroplast trnK (matK) intron: a model for evolution of group II intron RNA structures. Molecular Biology and Evolution, 23, 380 391.
16. Hickman JC (1993) Geographic subdivisions of California. In: The Jepson Manual: Higher Plants of California (ed. Hickman JC pp. 37 48. University of California, Berkeley, California.
17. Hong Y-P, Krupkin AB, Strauss SH (1993) Chloroplast DNA transgresses species boundaries and evolves at variable rates in the California closed-cone pines (P. radiata, P. muricata, and P. attenuata). Molecular Phylogenetics and Evolution, 2, 322 329.
18. Hood GM (2006) PopTools Version 2.7.5. CSIRO, Canberra, Australia. http://www.cse.csiro.au/poptools/.
19. Johansen AD, Latta RG (2003) Mitochondrial haplotype distribution, seed dispersal and patterns of postglacial expansion of ponderosa pine. Molecular Ecology, 12, 293 298.
20. Kidd DM, Ritchie MG (2006) Phylogeographic information systems: putting the geography into phylogeography. Journal of Biogeography, 33, 1851 1865.
21. Kinloch BB (1992) Distribution and frequency of a gene for resistance to white pine blister rust in natural populations of sugar pine. Canadian Journal of Botany, 70, 1319 1323.
22. Kinloch BB (2003) White pine blister rust in North America: past and prognosis. Phytopathology, 93, 1044 1047.
23. Kinloch BB, Scheuner WH (2004) Pinus lambertiana Dougl., Sugar Pine. USDA Forest Service, Washington, D.C. http://na.fs.fed.us/spfo/pubs/silvics_manual/ Volume_1/vol1_Table_of_contents.htm.
24. Krutovskii KV, Politov DV, Altukhov YP (1995) Isozyme study of population genetic structure, mating system and phylogenetic relationships of the five stone pine species (subsection Cembrae, section Strobi, subgenus Strobus). In: Population Genetics and Genetic Conservation of Forest Trees (eds Baradat P, Adams WT, Müller-Starck G pp. 279 304. Academic Publishing, Amsterdam.
25. Latta RG, Mitton JB (1999) Historical separation and present gene flow through a zone of secondary contact in ponderosa pine. Evolution, 53, 769 776.
26. Ledig FT (1998) Genetic variation in Pinus. In: Ecology and Biogeography of Pinus (ed. Richardson DM pp. 251 280. Cambridge University Press, Cambridge, UK.
27. Liston A (1992) Variation in the chloroplast genes rpoC1 and rpoC2 of the genus Astragalus (Fabaceae): evidence from restriction site mapping of a PCR-amplified fragment. American Journal of Botany, 79, 953 961.
28. Liston A, Robinson WA, Piñero D, Alvarez-Buylla ER (1999) Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer sequences. Molecular Phylogenetics and Evolution, 11, 95 109.
29. Martinson SR (1997) Association among geographic, allozyme, and growth variables for sugar pine (Pinus lambertiana Dougl.) in southwest Oregon and throughout the species range. PhD Thesis, North Carolina State University.
30. Matos JA, Schaal BA (2000) Chloroplast evolution in the Pinus montezumae complex: a coalescent approach to hybridization. Evolution, 54, 1218 1233.
31. May RH (1974) An observation of some sugar pine relicts. Madroño, 22, 276.
32. Mielke JL (1943) White Pine Blister Rust in Western North America, Bulletin no. 52, Yale University School of Forestry, New Haven, Connecticut.
33. Millar CI, King JC, Westfall RD, Alden HA, Delany DL (2006) Late Holocene forest dynamics, volcanism, and climate change at Whitewing Mountain and San Joaquin Ridge, Mono County, Sierra Nevada, CA, USA. Quaternary Research, 66, 273 287.
34. Mirov NT (1967) The Genus Pinus. The Ronald Press Co., New York.
35. Mohr JA, Whitlock C, Skinner CN (2000) Postglacial vegetation and fire history, eastern Klamath mountains, California, USA. Holocene, 10, 587 601.
36. Murray M (2005) Our threatened timberlines: the plight of whitebark pine ecosystems. Kalmiopsis, 12, 25 29.
37. Muse SV, Weir BS (1992) Testing for equality of evolutionary rates. Genetics, 132, 269 276.
38. Navascues M, Vaxevanidou Z, Gonzalez-Martinez SC et al 2006) Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine. Molecular Ecology, 15, 2691 2698.
39. 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.
40. Petit RJ, Bodénès C, Ducousso A, Roussel G, Kremer A (2003) Hybridization as a mechanism of invasion in oaks. New Phytologist, 161, 151 164.
41. Petit RJ, Duminil J, Fineschi S et al 2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Molecular Ecology, 14, 689 701.
42. Posada D, Crandall KA (1998) modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817 818.
43. 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.
44. Richardson DM, Rundel PW (1998) Ecology and biogeography of Pinus: an introduction. In: Ecology and Biogeography of Pinus (ed. Richardson DM pp. 3 46. Cambridge University Press, Cambridge, UK.
45. Rieseberg LH, Soltis DE (1991) Phylogenetic consequences of cytoplasmic gene flow in plants. Evolutionary Trends in Plants, 5, 65 84.
46. Rieseberg LH, Whitton J, Linder CR (1996) Molecular marker incongruence in plants hybrid zones and phylogenetic trees. Acta Botanica Neerlandica, 45, 243 262.
47. Rozas J, Sánchez-De I, Barrio JC, Messeguer X, Rozas R (2003) dnasp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
48. Scharpf RF (1993) Diseases of Pacific Coast Conifers, Handbook 521. USDA Forest Service, Washington D.C.
49. Shaw J, Lickey EB, Beck JT et al 2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany, 92, 142 166.
50. Soltis DE, Gitzendanner MA, Strenge DD, Soltis PS (1997) Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Systematics and Evolution, 206, 353 373.
51. Swofford DL (2002) Paup*, Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, Massachusetts.
52. Syring J, Farrell K, Businský R, Cronn R, Liston A (2007) Widespread genealogical nonmonophyly in species of Pinus subgenus Strobus. Systematic Biology, 56, 163 181.
53. Syring J, Willyard A, Cronn R, Liston A (2005) Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. American Journal of Botany, 92, 2086 2100.
54. Thayer TC, Vander Wall SB (2005) Interactions between Steller's jays and yellow pine chipmunks over scatter-hoarded sugar pine seeds. Journal of Animal Ecology, 74, 364 375.
55. 14C yr bp reconstructed from pollen and packrat midden data. Journal of Biogeography, 27, 555 584.
56. Tomback DF (2005) The impact of seed dispersal by Clark's nutcracker on whitebark pine: multi-scale perspective on a high mountain mutualism. In: Mountain Ecosystems: Studies in Treeline Ecology (eds Broll G, Keplin B pp. 181 201. Springer, Berlin.
57. Tsitrone A, Kirkpatrick M, Levin DA (2003) A model for chloroplast capture. Evolution, 57, 1776 1782.
58. 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.
59. Wefald M (2001) TRS2LL, http://www.geocities.com/jeremiahobrien/trs2ll. html.
60. Wei XX, Wang XQ (2003) Phylogenetic split of Larix: evidence from paternally inherited cpDNA trnT-trnF region. Plant Systematics and Evolution, 239, 67 77.
61. Wendel JF, Doyle JJ (1998) Phylogenetic incongruence: window into genome history and molecular evolution. In: Molecular Systematics of Plants: DNA Sequencing (eds Soltis DE, Soltis PS, Doyle JJ pp. 265 296. Kluwer, Boston, Massachusetts.
62. Willyard A, Syring J, Gernandt DS, Liston A, Cronn R (2007) Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Molecular Biology and Evolution, 24, 90 101.
63. Zhang M-L, Uhink CH, Kadereit JW (2007) Phylogeny and biogeography of Epimedium/Vancouveria (Berberidaceae): western North American-East Asian disjunctions, the origin of European mountain plant taxa, and East Asian species diversity. Systematic Botany, 32, 81 92.
64. Zhu Y-P, Wen J, Zhang Z-Y, Chen Z-D (2006) Evolutionary relationships and diversification of Stachyuraceae based on sequences of four chloroplast markers and the nuclear ribosomal ITS region. Taxon, 55, 931 940.