Multiple nuclear loci reveal the distinctiveness of the threatened, neotropical Pinus chiapensis

Systematic Botany

Volumn 32, Issue 4, 2007, Pages 703-717

  Syring, John ^a   Del Castillo, Rafael F ^b   Cronn, Richard ^c   Liston, Aaron ^d  

^a MONTANA STATE UNIVERSITY BILLINGS   (United States)

^b INSTITUTO POLITÉCNICO NACIONAL   (Mexico)

^c PACIFIC NORTHWEST RESEARCH STATION   (United States)

^d OREGON STATE UNIVERSITY   (United States)

Author keywords

Lineage sorting; Nuclear phylogeny; Phylogenetic conflict; Pinaceae; Pinus strobus

Indexed keywords

PINACEAE; PINUS CHIAPENSIS; PINUS STROBUS;

EID: 38349121385     PISSN: 03636445     EISSN: 15482324     Source Type: Journal    
DOI: 10.1600/036364407783390836     Document Type: Article

References (56)

1. ANDRESEN, J. W. 1964. The taxonomic status of Pinus chiapensis. Phytologia 10: 417-421.
2. _. 1966. A multivariate analysis of the Pinus chiapensismonticola- strobus phylad. Rhodora 68: 1-24.
3. BAUM, D. A. and M. J. DONOGHUE. 1995. Choosing among alternative "phylogenetic" species concepts. Systematic Botany 20: 560-573.
4. CRITCHFIELD, W. B. and E. L. LITTLE Jr. 1966. Geographic distribution of the pines of the world. USDA Forest Service Miscellaneous Publication 991. Washington, D.C.
5. CRONN, R. C., R. L. SMALL, T. HASELKORN, and J. F. WENDEL. 2003. Cryptic repeated genomic recombination during speciation in Gossypium gossypioides. Evolution 57: 2475-2489.
6. DEL CASTILLO, R. F. and S. ACOSTA. 2002. Ethnobotanical notes on Pinus strobus var. chiapensis. Anales del Instituto de Biología, Universidad Nacional Autónoma de México, Serie Botánica 73: 319-327.
7. _, J. A. PÉREZ DE LA ROSA, G. V. AMADO, and R. RIVERA GARCÍA. 2004. Coníferas. Pp. 141-158 in Biodiversidad de Oaxaca, eds. A. García-Mendoza, M. J. Ordóñez, and M. A. Briones. México, México: Ediciones de la Universidad Nacional Autónoma de México, Instituto Estatal de Ecología de Oaxaca.
8. DONAHUE, J. K., W. S. DVORAK, and E. A. GUTIERREZ. 1991. The distribution, ecology, and gene conservation of Pinus ayacahuite and P. chiapensis in Mexico and Central America. Raleigh, North Carolina: CAMCORE.
9. DRESSLER, R. L. 1954. Some floristic relationships between Mexico and the United States. Rhodora 56: 81-96.
10. DVORAK, W. S., J. K. DONAHUE, and J. A. VASQUEZ. 1996. Provenance and progeny results for the tropical white pine, Pinus chiapensis, at five and eight years of age. New Forests 12: 125-140.
11. FAO. 1981. Report of the fifth session of the FAO panel of experts on forest gene resources. Rome: FAO.
12. FARJON, A. and B. T. STYLES. 1997. Pinus (Pinaceae). Flora Neotropica Monograph 75, New York: the New York Botanical Garden.
13. _ and C. N. PAGE. 1999. Conifers - status survey and conservation action plan. Cambridge: IUCN/SSC Conifer Specialist Group.
14. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
15. GAUSSEN, H. 1960. Pinus. Pp. 1-272 in Les gymnospermes actuelles et fossiles. Toulouse, France: Travaux du Laboratorie Forestier de Toulouse.
16. GERNANDT, D. S., G. G. LOPEZ, S. O. GARCIA, and A. LISTON. 2005. Phylogeny and classification of Pinus. Taxon 54: 29-42.
17. IGLESIAS, R. G. and M. J. BABIANO. 1999. Isolation and characterization of a cDNA encoding a late-embryogenesis-abundant protein (Accession No. AJ012483) from Pseudotsuga menziesii seeds. Plant Physiology 119: 806.
18. KRAL, R. 1993. Pinus. Pp. 373- 398. in Flora of North America (North of Mexico), vol. 2, eds. Flora of North America editorial committee. New York: Oxford Univerisity Press.
19. KRUTOVSKY, K. V., M. TROGGIO, G. R. BROWN, K. D. JERMSTAD, and D. B. NEALE. 2004. Comparative mapping in the Pinaceae. Genetics 168: 447-461.
20. _, C. G. ELSIK, M. MATVIENKO, A. KOZIK, and D. B. NEALE. 2006. . Conserved ortholog sets in forest trees. Tree Genetics and Genomes 3: 61-70.
21. KUMAR, S., K. TAMURA, I. B. JAKOBSEN, and M. NEI. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17: 1244-1245.
22. LANDRY, P. 1989. A revised synopsis of the white pines (Pinus, section Quinquefoliis). Phytologia 65: 467-474.
23. LISTON, A., W. A. ROBINSON, D. PINERO, and E. R. ALVAREZ-BUYLLA. 1999. Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Molecular Phylogenetics and Evolution 11: 95-109.
24. _, M. PARKER-DEFENIKS, J. V. SYRING, A. WILLYARD, and R. CRONN. 2007. Interspecific phyogenetic analysis enhances intraspecific phyogeographical inference: a case study in Pinus lambertiana. Molecular Ecology 16: 3926-3937.
25. LITTLE, E. L., Jr and W. B. CRITCHFIELD. 1969. Subdivisions of the genus Pinus. USDA Forest Service Miscellaneous Publication 1144. Washington, D.C.
26. MADDISON, W. P. and L. L. KNOWLES. 2006. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55: 21-30.
27. MARTIN, P. S. and B. E. HARRELL. 1957. The Pleistocene history of temperate biotas in Mexico and eastern United States. Ecology 38: 468-480.
28. MARTIN, D. P., C. WILLIAMSON, and D. POSADA. 2005. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21: 260-262.
29. MARTÍNEZ, M. 1940. Pinaceas Mexicanas. Anales del Instituto de Biología de México 11: 57-84.
30. MCGUIRE, G., F. WRIGHT, and M. J. PRENTICE. 1997. A graphical method for detecting recombination in phylogenetic data sets. Molecular Biology and Evolution 14: 1125-1131.
31. MILNE, I., F. WRIGHT, G. ROWE, D. F. MARSHALL, D. HUSMEIER, and G. MCGUIRE. 2004. TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 20: 1806-1807.
32. PERRY, J. P. 1991. The Pines of México and Central America. Portland, OR: Timber Press.
33. PETERS, J. L., K. G. MCCRACKEN, Y. N. ZHURAVLEV, Y. LU, R. E. WILSON, K. P. JOHNSON, and K. E. OMLAND. 2005. Phylogenetics of wigeons and allies (Anatidae: Anas): the importance of sampling multiple loci and multiple individuals. Molecular Phylogenetics and Evolution 35: 209-224.
34. POSADA, D. and K. A. CRANDALL. 2001. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proceedings of the National Academy of Sciences USA 98: 13757-13762.
35. PRICE, R. A., A. LISTON, and S. H. STRAUSS. 1998. Phylogeny and systematics of Pinus. Pp. 49-68 in Ecology and Biogeography of Pinus, ed. D. M. Richardson. Cambridge: Cambridge University Press.
36. RICHMOND, T. A. and C. R. SOMERVILLE. 2000. The cellulose synthase superfamily. Plant Physiology 124: 495-498.
37. ROSENBERG, N. A. 2003. The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57: 1465-1477.
38. _, 2007. Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution 61: 317-323.
39. RZEDOWSKI, J. and L. VELA. 1966. Pinus strobus var. chiapensis en la Sierra Madre del Sur de México. Ciencia 24: 211-216.
40. SHARP, A. J. 1953. Notes on the flora of Mexico: World distribution of the woody dicotyledonous families and the origin of the modern vegetation. Journal of Ecology 41: 374-380.
41. SHAW, J., E. B. LICKEY, J. T. BECK, S. B. FARMER, W. LIU, J. MILLER, K. C. SIRIPUN, C. T. WINDER, E. E. SCHILLING, and R. L. SMALL. 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.
42. SLOWINSKI, J. B. and R. D. M. PAGE. 1999. How should species phylogenies be inferred from sequence data? Systematic Biology 48: 814-825.
43. SMALL, R. L., R. C. CRONN, and J. F. WENDEL. 2004. Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany 17: 145-170.
44. SMITH, J. M. 1992. Analyzing the mosaic structure of genes. Journal of Molecular Evolution 34: 126-129.
45. SORENSON, F. C. 1999. Relationship between self-fertility, allocation of growth, and inbreeding depression in three coniferous species. Evolution 53: 417-425.
46. SORENSEN, F. C. 2001. Effect of population outcrossing rate on inbreeding depression in Pinus contorta var murrayana seedlings. Scandanavian Journal of Forest Resources 16: 391-403.
47. STEINHOFF, R. J., D. G. JOYCE, and L. FINS. 1983. Isozyme variation in Pinus monticola. Canadian Journal of Forest Resources 13: 1122-1132.
48. SWOFFORD, D. L. 2002. PAUP* Phylogenetic analysis using parsimony (* and other methods), 4.0 beta 10. Sunderland: Sinauer Associates.
49. SYRING, J., A. WILLYARD, R. CRONN, and A. LISTON. 2005. Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. American Journal of Botany 92: 2086-2100.
50. _, K. FARRELL, R. BUSINSKÝ, R. CRONN, and A. LISTON. 2007. Widespread genealogical nonmonophyly in species of Pinus subgenus Strobus. Systematic Biology 56: 1-19.
51. TAJIMA, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
52. TEMPLETON, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37: 221-244.
53. UNITED STATES GEOLOGICAL SURVEY. 1999. Digital representation of Atlas of United States Trees by Elbert L. Little, Jr. URL: http://esp.cr.usgs.gov/data/atlas/little/.
54. WILLIAMS, C. G. and O. SAVOLAINEN. 1996. Inbreeding depression in conifers: implications for breeding strategy. Forest Science 42: 102-117.
55. WRIGHT, J. A., A. M. MARIN V, and W. S. DVORAK. 1996. Conservation and use of the Pinus chiapensis genetic resource in Columbia. Forest Ecology and Management 88: 283-288.
56. ZHANG, Y., G. BROWN, R. WHETTEN, C. A. LOOPSTRA, D. NEALE, M. J. KIELISZEWSKI, and R. R. SEDEROFF. 2003. An arabinogalactan protein associated with secondary cell wall formation in differentiating xylem of loblolly pine. Plant Molecular Biology 52: 91-102.