Phylogenetic analysis of morphology in Prunus reveals extensive homoplasy

Plant Systematics and Evolution

Volumn 259, Issue 1, 2006, Pages 53-71

  Bortiri, E ^a,b   Heuvel, B Vanden ^a,c   Potter, D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b PLANT GENE EXPRESSION CENTER   (United States)

^c Malik and Seeme Hasan School of Business   (United States)

Author keywords

Evolution; Homoplasy; Likelihood; Morphology; Parsimony; Prunus; Topology tests

Indexed keywords

MADDENIA HYPOLEUCA; PRUNUS; PRUNUS DULCIS; PRUNUS GRAYANA; PYGEUM; ROSACEAE;

EID: 33745631758     PISSN: 03782697     EISSN: 16156110     Source Type: Journal    
DOI: 10.1007/s00606-006-0427-8     Document Type: Article

References (60)

1. H. Akaike 1974 A new look at the statistical model identification criteria IEEE T. Automat. Cont. 19 716 723
2. M. A. Blake 1932 The J. H. Hale peach as a parent in peach crosses P. Am. Soc. Hort. Sci. 29 131 136
3. E. Bortiri S.-H. Oh F.-Y. Gao D. Potter 2002 The phylogenetic utility of nucleotide sequences of sorbitol 6-phosphate dehydrogenase in Prunus (Rosaceae) Amer. J. Bot. 89 1697 1708
4. E. Bortiri S.-H. Oh J. Jiang S. Baggett A. Granger C. Weeks M. Buckingham D. Potter D. E. Parfitt 2001 Phylogeny and systematics of Prunus (Rosaceae) as determined by sequence analysis of ITS and the chloroplast trnL-trnF spacer DNA Syst. Bot. 26 797 807
5. L. Brako J. L. Zarucchi 1993 Catalogue of the flowering plants and gymnosperms of Peru Missouri Botanical Garden St. Louis, USA
6. K. Bremer 1988 The limits of amino acid sequence data in angiosperm phylogenetic reconstruction Evolution 42 795 803
7. K. Browicz D. Zohary 1996 The genus Amygdalus L. (Rosaceae): Species relationships, distribution, and evolution under domestication Genet. Resour. Crop Ev. 43 229 247
8. T. R. Buckley 2002 Model misspecification and probabilistic tests of topology: evidence from empirical data sets Syst. Biol. 51 509 523
9. A. A. Fedorov V. L. Komarov K. F. Kostina N. V. Kovalev A. N. Krishtofovich I. A. Linchevskii A. I. Poyarkova 1971 Rosaceae -Rosoideae, Prunoideae V. L. Komarov Flora of the U.S.S.R, vol 10 Botanical Institute of the Academy of Sciences of the USSR Moscow, Russia 380 448
10. J. Felsenstein 1985 Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 783 791
11. P. Goldblatt 1976 Cytotaxonomic studies in the tribe Quillajeae (Rosaceae) Ann. Missouri. Bot. Gard. 63 200 206
12. N. Goldman J. P. Anderson A. G. Rodrigo 2000 Likelihood-based tests of topologies in phylogenetics Syst. Biol. 49 652 670
13. S. W. Graham P. A. Reeves A. C. E. Burns R. G. Olmstead 2000 Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference Int. J. Pl. Sci. 161 S83 S96
14. V. Grant K. Grant 1965 Flower pollination in the phlox family Columbia University Press New York, USA
15. J. P. Huelsenbeck F. Ronquist 2001 MRBAYES: Bayesian inference of phylogeny Bioinformatics 17 754 755
16. C. Kalkman 1965 The Old World species of Prunus subgenus Laurocerasus including those formerly referred to Pygeum Blumea 13 1 174
17. E. Koehne 1915 Zur Kenntnis von Prunus Grex Calycopadus und Grex Gymnopadus sect. Laurocerasus Bot. Jahrb. 52 279 333
18. G. Krüssmann 1986 Manual of cultivated broad-leaved trees and shrubs, Vol. 3 Timber Press Portland, USA
19. W. Kuitert 1999 Japanese flowering cherries Timber Press Portland, USA
20. S. Lee J. Wen 2001 A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of nuclear ribosomal DNA Amer. J. Bot. 88 150 160
21. N. R. Lersten H. T. Horner 2000 Calcium oxalate crystal types and trends in their distribution patterns in leaves of Prunus (Rosaceae: Prunoideae) Pl. Syst. Evol. 224 83 96
22. P. O. Lewis 2001 A likelihood approach to estimating phylogeny from discrete morphological character data Syst. Biol. 50 913 925
23. F. Lutzoni P. Wagner V. Reeb S. Zoller 2000 Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology Syst. Biol. 49 628 651
24. D. R. Maddison W. P. Maddison 2003 MacClade v. 4.06 Sinauer Associates, Inc Sunderland, USA
25. S. C. Mason 1913 The pubescent-fruited species of Prunus of the Southwestern States J. Agr. Res. 1 147 179
26. R. [tmp] McVaugh 1951 A revision of North American black cherries (Prunus serotina Ehrh and relatives) Brittonia 7 279 315
27. J. N. Moore J. R. Ballington Jr. 1990 Genetic resources of temperate fruit and nut crops International Society for Horticultural Science Wageningen, The Netherlands
28. D. R. Morgan D. E. Soltis K. R. Robertson 1994 Systematic and evolutionary implications of rbcL sequence variation in Rosaceae Amer. J. Bot. 81 890 903
29. B. D. Mowrey D. J. Werner 1990 Phylogenetic relationships among species of Prunus as inferred by isozyme markers Theor. Appl. Genet. 80 129 133
30. J. A. A. Nylander F. Ronquist J. P. Huelsenbeck J. L. Nieves-Aldrey 2004 Bayesian phylogenetic analysis of combined data Syst. Biol. 53 47 67
31. S.-H. Oh D. Potter 2004 Molecular phylogenetic systematics and biogeography of tribe Neillieae (Rosaceae) using DNA sequences of cpDNA, rDNA, and leafy Amer. J Bot. 92 179 192
32. D. Posada T. R. Buckley 2004 Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests Syst. Biol. 53 793 808
33. D. Posada K. A. Crandall 2001 Selecting the best-fit model of nucleotide substitution Syst. Biol. 50 580 601
34. D. Posada K. A. Crandall 1998 Modeltest: testing the model of DNA substitution Bioinformatics 14 817 818
35. D. Potter F. Gao E. Bortiri S.-H. Oh S. Baggett 2002 Phylogenetic relationships in Rosaceae from chloroplast matK and trnL-trnF nucleotide sequence data Pl. Syst. Evol. 231 77 89
36. Rambaut A. (2001) Sequence Alignment Editor 2.0. Available from the author at: http://evolve.zoo.ox.ac.uk
37. P. H. Raven 1972 Plant species disjunctions: a summary Ann. Missouri Bot. Gard. 59 234 246
38. A. Rehder 1940 Manual of cultivated trees and shrubs hardy in North America. 2nd edn Macmillan New York, USA
39. M. J. Roemer 1847 Familiarum naturalium regni vegetabilis synopses monographicae 4 Weimar Germany
40. Schulze-Menz G. K. (1964) Rosaceae. In: Melchior H. (ed.) Engler's Syllabus der Pflanzenfamilien II Gebrüder Borntraeger, Berlin, Germany, pp. 209-218
41. J. Shaw R. Small 2004 Addressing the ''hardest puzzle in American pomology:'' Phylogeny of Prunus sect. Prunocerasus (Rosaceae) based on seven noncoding chloroplast DNA regions Amer. J. Bot. 91 985 996
42. H. Shimodaira M. Hasegawa 1999 Multiple comparison of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol. 16 1114 1116
43. M. P. Simmons H. Ochoterena T. G. Carr 2001 Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses Syst. Biol. 50 454 462
44. M. D. Sorenson 1999 TreeRot, version 2 Boston University Boston, USA
45. C. Sterling 1964 Comparative morphology of the carpel in the Rosaceae. II. Amygdaloideae: Maddenia, Pygeum, Osmaronia Amer. J. Bot. 51 354 360
46. P. F. Stevens 1991 Character states, morphological variation, and phylogenetic analysis: a review Syst. Bot. 16 553 583
47. D. L. Swofford 2001 PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4 Sinauer, Sunderland Massachusetts, USA
48. A. Takhtajan 1997 Diversity and classification of flowering plants Columbia University Press New York, USA
49. K. Tamura M. Nei 1996 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees Molec. Biol. Evol. 10 512 526
50. A. R. Templeton 1983 Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes Evolution 37 221 244
51. J. D. Thompson T. J. Gibson F. Plewniak F. Jeanmougin D. G. Higgins 1997 The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 25 4876 4882
52. Wen J. (1999) Evolution of eastern Asian and eastern North American disjunct distribution in flowering plants. Annual. Rev. Ecol. Syst. 421-455.
53. W. F. Wight 1915 Native American species of Prunus B. U.S. Dep. Agr. 179 1 75
54. P. Wilf 1997 When are leaves good thermometers? A new case for Leaf Margin Analysis Paleobiology 23 373 390
55. D. H. Wilken 1993 Prunus J. C. Hickman The Jepson manual: higher plants of California University of California Press Berkeley, USA 969 970
56. M. F. Wojciechowski M. J. Sanderson J.-M. Hu 1999 Evidence on the monophyly of Astragalus (Fabaceae) and its major subgroups based on nuclear ribosomal DNA ITS and chloroplast DNA trnL intron data Syst. Bot. 24 409 437
57. R. Wyatt 1983 Pollinator-plant interactions and the evolution of breeding systems L. Real Pollination Biology Academic Press Inc London, UK 51 95
58. T. T. Yü L. T. Lu T. C. Ku C. L. Li S. X. Chen 1986 Rosaceae (3), Amygdaloideae. Flora Reipublicae Popularis Sinicae, vol. 38 Science Press Beijing, China
59. Zhang S.-Y. (1992a) Systematic wood anatomy of the Rosaceae. Blumea 37: 81-158.
60. Zhang S.-Y. (1992b) Wood anatomy of trees and shrubs from China. III. Rosaceae. IAWA 13: 21-91.