Addressing the "hardest puzzle in American pomology:" Phylogeny of Prunus sect. Prunocerasus (Rosaceae) based on seven noncoding chloroplast DNA regions

American Journal of Botany

Volumn 91, Issue 6, 2004, Pages 985-996

  Shaw, Joey ^a   Small, Randall L ^a  

^a UNIVERSITY OF TENNESSEE   (United States)

Author keywords

Amygdaloideae; Amygdalus; Chloroplast dna; Euprunus; Plum; Prunocerasus; Prunus; Rosaceae

Indexed keywords

CHLOROPLAST; DNA; PHYLOGENY;

NORTH AMERICA;

AMYGDALOIDEAE; ARMENIACA; PRUNUS; PRUNUS DOMESTICA; PRUNUS SUBCORDATA; PRUNUS TEXANA; ROSACEAE;

EID: 12244264165     PISSN: 00029122     EISSN: 00029122     Source Type: Journal    
DOI: 10.3732/ajb.91.6.985     Document Type: Article

References (63)

1. BADENES, M. L., AND D. E. PARFITT. 1995. Phylogenetic relationships of cultivated Prunus species from an analysis of chloroplast DNA variation. Theoretical and Applied Genetics 90: 1035-1041.
2. BAILEY, L. H. 1892. Prunus hortulana. Garden and Forest 5: 90.
3. BAILEY, L. H., AND E. Z. BAILEY. 1941. Hortus Second: a concise dictionary of gardening, general horticulture, and cultivated plants in North America. Macmillan Company, New York, New York, USA.
4. BAYER, R. J., D. G. GREBER, AND N. H. BAGNALL. 2002. Phylogeny of Australian Gnaphalieae (Asteraceae) based on chloroplast and nuclear sequences, the trnL intron, trnL-trnF intergenic spacer, matK, and ETS. Systematic Botany 27: 801-814.
5. BLACKBURN, B. 1952. Trees and Shrubs in eastern North America: keys to the wild and cultivated woody plants growing in the temperate regions exclusive of conifers. Oxford University Press, New York, New York, USA.
6. BORTIRI, E., S. H. OH, F. Y. GAO, AND D. POTTER. 2002. The phylogenetic utility of nucleotide sequences of sorbitol 6-phosphate dehydrogenase in Prunus (Rosaceae). American Journal of Botany 89: 1697-1708.
7. BORTIRI, E., S. H. OH, J. G. JIANG, S. BAGGETT, A. GRANGER, C. WEEKS, M. BUCKINGHAM, D. POTTER, AND D. E. PARFITT. 2001. Phylogeny and systematics of Prunus (Rosaceae) as determined by sequence analysis of ITS and the chloroplast trnL-trnF spacer DNA. Systematic Botany 26: 797-807.
8. BRETTIN, T. S., R. KARLE, E. L. CROWE, AND A. F. IEZZONI. 2000. Chloroplast inheritance and DNA variation in sweet, sour, and ground cherry. Journal of Heredity 91: 75-79.
9. CORRELL, D. S., AND M. C. JOHNSTON. 1970. Manual of the vascular plants of Texas. Texas Research Foundation, Renner, Texas, USA.
10. CRONN, R. C., R. L. SMALL, T. HASELKORN, AND J. F. WENDEL. 2002. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. American Journal of Botany 89: 707-725.
11. DEMESURE, B., B. COMPS, AND R. PETIT. 1996. Chloroplast DNA phylogeography of the common beech (Fagus sylvatica L.) in Europe. Evolution 50: 2515-2520.
12. DUMOLIN-LAPEGUE, S., M. H. PEMONGE, AND R. J. PETIT. 1997. An enlarged set of consensus primers for the study of organelle DNA in plants. Molecular Ecology 6: 393-397.
13. DUNCAN, W. H., AND M. B. DUNCAN. 1988. Trees of the southeastern United States. University of Georgia Press, Athens, Georgia, USA.
14. DUNN, K. L. 2002. Growing ripe for development: beach plums as a regional crop. Farming: The Journal of Northeast Agriculture September, 19, 30-32. (www.farmingmagazine.com)
15. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17: 368-376.
16. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
17. FERNALD, M. L. 1950. Gray's manual of botany, 8th ed. American Book Company, New York, New York, USA.
18. FLORY, W. S. 1938. Cross sterility in hybrid plum varieties. Proceedings of the American Society for Horticultural Science, Contribution No. 409: 43-46.
19. FOGLE, H. W. 1978. Plum improvement in the United States. Acta Horticulturae 74: 35-40.
20. GENE CODES. 1998. Sequencher, version 3.1.1. Gene Codes, Ann Arbor, Michigan, USA.
21. GLEASON, H. A. 1952. The new Britton and Brown illustrated flora of the United States and adjacent Canada, vol. 2. Lancaster Press, Lancaster, Pennsylvania, USA.
22. GLEASON, H. A., AND A. CRONQUIST. 1991. Manual of vascular plants of northeastern United States and adjacent Canada, 2nd ed. New York Botanical Garden, Bronx, New York, USA.
23. GODFREY, R. K. 1988. Trees, shrubs, and woody vines of northeastern Florida and adjacent Georgia and Alabama. The University of Georgia Press, Athens, Georgia, USA.
24. GOLDBLATT, P., V. SAVOLAINEN, O. PORTEOUS, I. SOSTARIC, M. POWELL, G. REEVES, J. C. MANNING, T. C. BARRACLOUGH, AND M. W. CHASE. 2002. Radiation in the Cape flora and the phylogeny of peacock irises Moraea (Iridaceae) based on four plastid DNA regions. Molecular Phylogenetics and Evolution 25: 341-360.
25. HARTMANN, S., J. D. NASON, AND D. BHATTACHARYA. 2002. Phylogenetic origins of Lophocereus (Cactaceae) and the Senita Cactus-Senita Moth pollination mutualism. American Journal of Botany 89: 1085-1092.
26. HEDRICK, U. P., W. H. ALDERMAN, M. J. DORSEY, O. M. TAYLOR, AND R. WELLINGTON. 1911. The plums of New York. J. B. Lyon Company State Printers, Albany, New York, USA.
27. HUELSENBECK, J. P., AND F. RONQUIST. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
28. JUNG, Y. H., S. H. HAN, AND M. Y. OH. 2002. Phylogenetic analysis of Korean Prunus (Rosaceae) based on ITS sequences of nuclear ribosomal DNA. Korean Journal of Genetics 24: 247-258.
29. KARP, D. 2003. The beach plums: hard to tame, but growers don't give up. The New York Times website: http://www.nytimes.com/2003/09/03/dining/03PLUM. html.
30. KUSUMI, J., Y. TSUMURA, H. YOSHIMARU, AND H. TACHIDA. 2000. Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences. American Journal of Botany 87: 1480-1488.
31. LEE, S., AND J. WEN. 2001. A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of nuclear ribosomal DNA. American Journal of Botany 88: 150-60.
32. MASON, S. C. 1913. The pubescent-fruited species of Prunus of the Southwestern States. Journal of Agricultural Research 1: 147-179.
33. MCCAULEY, D. E. 1995. The use of chloroplast DNA polymorphism in studies of gene flow in plants. Trends in Ecology and Evolution 10: 198-202.
34. MOHANTY, A., J. P. MARTÍN, AND I. AGUINAGALDE. 2000. Chloroplast DNA diversity within and among populations of the allotetraploid Prunus spinosa L. Theoretical and Applied Genetics 100: 1304-1310.
35. MOWREY, B. D., AND D. J. WERNER. 1990. Phylogenetic relationships among species of Prunus as inferred by isozyme markers. Theoretical and Applied Genetics 80: 129-133.
36. NYLANDER, J. A. A. 2002. Testing models of evolution - MrModeltest version 1.1b. Computer program and documentation distributed by author, website: http://www.ebc.uu.se/systzoo/staff/nylander.html.
37. OHSAKO, T., AND O. OHNISHI. 2000. Intra- and interspecific phylogeny of wild Fagopyrum (Polygonaceae) species based on nucleotide sequences of noncoding regions in chloroplast DNA. American Journal of Botany 87: 573-582.
38. OXELMAN, B., M. LIDÉN, AND D. BERGLUND. 1997. Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant Systematics and Evolution 206: 393-410.
39. PORTER, T. C. 1877. Prunus alleghaniensis n. sp. Coulter's Botanical Gazette 2: 85.
40. POSADA, D., AND K. A. KRANDALL. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
41. RADFORD, A. E., H. E. AHLES, AND C. R. BELL. 1968. Manual of the vascular flora of the Carolinas. The University of North Carolina Press, Chapel Hill, North Carolina, USA.
42. REHDER, A. 1940. Manual of cultivated trees and shrubs hardy in North America, exclusive of the subtropical and warmer temperate regions, 2nd revised and enlarged edition. Macmillan, New York, New York, USA.
43. REID, W., AND K. L. B. GAST. 1993. The potential for domestication and utilization of native plums in Kansas. In J. Janick and J. E. Simon [eds.], New crops, 520-523. Wiley, New York, New York, USA.
44. ROBERTSON, K. R. 1974. The genera of Rosaceae in the southeastern United States. Journal of the Arnold Arboretum 55: 654-662.
45. ROHRER, J. R. 2000. The sand cherry in Wisconsin and neighboring states. Michigan Botanist 39: 59-69.
46. SARGENT, C. S. 1902. Texas, Louisiana, and Arkansas [P. tarda]. Botanical Gazette 33: 108.
47. SCHÖNENBERGER, J., AND E. CONTI. 2003. Molecular phylogeny and floral evolution of the Peneaceae, Olinaceae, Rhynchocalycaceae, and Alzateaceae (Myrtales). American Journal of Botany 90: 293-309.
48. SMALL, J. K. 1898. Studies in the botany of the southern United States-XIII. Bulletin of the Torrey Botanical Club 25: 134-151.
49. SMALL, J. K. 1933. Manual of the southeastern flora. Published by the author, The Science Press Printing Company, Lancaster, Pennsylvania, USA.
50. SMALL, R. L., J. A. RYBURN, R. C. CRONN, T. SEELANAN, AND J. F. WENDEL. 1998. The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogenetic reconstruction in a recently diverged plant group. American Journal of Botany 85: 1301-1315.
51. SMITH, E. B. 1994. Keys to the flora of Arkansas. University of Arkansas Press, Fayetteville, Arkansas, USA.
52. STEYERMARK, J. A. 1963. Flora of Missouri. Iowa State University Press, Ames, Iowa, USA.
53. SWOFFORD, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods) version 4.0b10. Sinauer Associates, Sunderland, Massachusetts, USA.
54. TABERLET, P., L. GIELLY, G. PAUTOU, AND J. BOUVET. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17: 1105-1109.
55. THOMPSON, J. D., T. J. GIBSON, F. PLEWNIAK, F. JEANMOUGIN, AND D. G. HIGGINS. 2001. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876-4882.
56. WATKINS, R. 1976. Cherry, plum, peach, apricot, and almond. In N. W. Simmons [ed.], Evolution of crop plants, 242-247. Longman, London, UK.
57. WAUGH, F. A. 1899. The pollination of plums. Vermont Agricultural Experimentation Station, Annual Report 12: 189-209.
58. WAUGH, F. A. 1901. Plums and plum culture. Orange Judd, New York, New York, USA.
59. WIGHT, W. F. 1913. North American species of the genus Amygdalus. Dudley Memorial Volume. Leland Stanford Junior University Publications, University Series, California, USA.
60. WIGHT, W. F. 1915. Native American species of Prunus. Bulletin of the U.S. Department of Agriculture 179: 1-75.
61. WOFFORD, B. E., AND E. W. CHESTER. 2002. Guide to the trees, shrubs, and woody vines of Tennessee. The University of Tennessee Press, Knoxville, Tennessee, USA.
62. WUNDERLIN, R. P. 1988. Guide to the vascular plants of Florida. University of Florida Press, Gainesville, Florida, USA.
63. YAMANE, K., Y. YASUI, AND O. OHNISHI. 2003. Intraspecific cpDNA variations of diploid and tetraploid perennial buckwheat, Fagopyrum cymosum (Polygonaceae). American Journal of Botany 90: 339-346.