Multi-gene analysis provides a well-supported phylogeny of Rosales

Molecular Phylogenetics and Evolution

Volumn 60, Issue 1, 2011, Pages 21-28

  Zhang, Shu Dong ^a   Soltis, Douglas E ^b   Yang, Yang ^a   Li, De Zhu ^a   Yi, Ting Shuang ^a  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF FLORIDA   (United States)

Author keywords

Barbeyaceae; Dirachmaceae; Phylogenetics; Rosales

Indexed keywords

ANGIOSPERM; ARTICLE; CLASSIFICATION; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PLANT GENE;

GENES, PLANT; MOLECULAR SEQUENCE DATA; PHYLOGENY; ROSALES;

BARBEYACEAE; CANNABACEAE; DIRACHMACEAE; ELAEAGNACEAE; MAGNOLIOPHYTA; MORACEAE; RHAMNACEAE; ROSACEAE; ULMACEAE; URTICACEAE;

EID: 79956352525     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.04.008     Document Type: Article

References (71)

1. Angiosperm Phylogeny Group (APG), 1998. An ordinal classification for the families of flowering plants. Ann. Mo. Bot. Gard. 85, 531-553.
2. Angiosperm Phylogeny Group (APG), 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141, 399-436.
3. Angiosperm Phylogeny Group (APG), 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 161, 105-121.
4. Baas P., Wheeler E., Chase M. Dicotyledonous wood anatomy and the APG system of angiosperm classification. Bot. J. Linn. Soc. 2000, 134:3-17.
5. Baas P., Jansen S., Smets E. Vegetative anatomy and affinities of Dirachma socotrana (Dirachmaceae). Syst. Bot. 2001, 26:231-241.
6. Boesewinkel F.D., Bouman F. Ovules and seeds of Dirachma socotrana (Dirachmaceae). Plant Syst. Evol. 1997, 205:195-204.
7. Bouman F., Boesewinkel F.D. Ovules and seeds of Barbeya with additional arguments for an urticalean affinity of the Barbeyaceae. Acta Bot. Neerl. 1997, 46:255-261.
8. Brown J.M., Lemmon A.R. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst. Biol. 2007, 56:643-655.
9. Cantino P.D., Doyle J.A., Graham S.W., Judd W.S., Olmstead R.G., Soltis D.E., Soltis P.S., Donoghue M.J. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 2007, 56:822-846.
10. Cronquist A. An integrated system of classification of flowering plants 1981, Columbia University Press, New York.
11. Cronquist A. The evolution and classification of flowering plants 1988, New York Botanical Garden, New York.
12. Cunningham C.W. Can three incongruence tests predict when data should be combined?. Mol. Biol. Evol. 1997, 14:733-740.
13. Dahlgren G. The last Dahlgrenogram, system of classification of the dicotyledons. Plant Taxonomy, Phytogeography and Related Subjects 1989, 249-260. Edinburgh University Press, Edinburgh. K. Tan (Ed.).
14. Darlu P., Lecointre G. When does the incongruence length difference test fail?. Mol. Biol. Evol. 2002, 19:432-437.
15. Dickison W.C., Sweitzer E.M. The morphology and relationships of Barbeya oleoides. Am. J. Bot. 1970, 57:468-476.
16. Engler, A., 1897. Ulmaceae. In: Engler, A., Prantl, K. (Eds.), Die natürlichen Pflanzenfamilien. Nachträge Teil, vol. 3, no.1. Borntraeger, Berlin.
17. Engler A., Diels L. Syllabus der Pflanzenfamilien 1936, Borntraeger, Berlin.
18. Farris J.S., Kallersjo M., Kluge A.G., Bult C. Testing significance of incongruence. Cladistics 1995, 10:315-319.
19. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 1978, 27:401-410.
20. Felsenstein J. Confidence-limits on phylogenies - an approach using the bootstrap. Evolution 1985, 39:783-791.
21. Hadiah J.T., Conn B.J., Quinn C.J. Infra-familial phylogeny of Urticaceae, using chloroplast sequence data. Aust. Syst. Bot. 2008, 21:375-385.
22. Hilu K.W., Borsch T., Müller K., Soltis D.E., Soltis P.S., Savolainen V., Chase M.W., Powell M.P., Alice L.A., Evans R., Sauquet H., Neinhuis C., Slotta T.A.B., Rohwer J.G., Campbell C.S., Chatrou L.W. Angiosperm phylogeny based on matK sequence information. Am. J. Bot. 2003, 90:1758-1776.
23. Hipp A.L., Hall J.C., Sytsma K.J. Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test. Syst. Biol. 2004, 53:81-89.
24. Holmgren P.K., Holmgren N.H., Barnett L.C. Index herbariorum. Part 1. The herbaria of world. Regnum vegetable 1990, New York Botanical Garden, Bronx, New York.
25. Huelsenbeck J.P. Is the Felsenstein zone a fly trap?. Syst. Biol. 1997, 46:69-74.
26. Hutchinson J. The families of flowering plants. Dicotyledons 1959, vol. 1. Clarendon Press, Oxford.
27. Jansen S., Piesschaert F., Smets E. Wood anatomy of Elaeagnaceae, with comments on vestured pits, helical thickenings, and systematic relationships. Am. J. Bot. 2000, 87:20-28.
28. Jian S., Soltis P.S., Gitzendanner M.A., Moore M.J., Li R., Hendry T.A., Qiu Y.L., Dhingra A., Bell C.D., Soltis D.E. Resolving an ancient, rapid radiation in Saxifragales. Syst. Biol. 2008, 57:38-57.
29. Johnson L.A., Soltis D.E. Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using matK sequences. Ann. Mo. Bot. Gard. 1995, 82:149-175.
30. Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl. Acids Res. 2002, 30:3059-3066.
31. Link D.A. Dirachma somalensis D. A. Link sp. nov. A new species of a remarkable and highly endangered monogeneric family. Bull. Jard. Bot. Natl. Belg. 1991, 61:3-13.
32. Melchior, H., 1964. Ulmaceae. In: Melchior, H. (Ed.), A. Engler's Syllabus der Pflanzenfamilien, 12th ed. Borntraeger, Berlin, pp. 52-54.
33. Mishima M., Ohmido N., Fukui K., Yahara T. Trends in site-number change of rDNA loci during polyploid evolution in Sanguisorba (Rosaceae). Chromosoma 2002, 110:550-558.
34. Nickrent D.L., Der J.P., Anderson F.E. Discovery of the photosynthetic relatives of the " Maltese mushroom" Cynomorium. BMC Evol. Biol. 2005, 5:38-48.
35. Olmstead R.G., Sweere J.A. Combining data in phylogenetic systematics - an empirical-approach using 3 molecular-data sets in the Solanaceae. Syst. Biol. 1994, 43:467-481.
36. Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst. Biol. 2004, 53:793-808.
37. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
38. Potter D., Eriksson T., Evans R.C., Oh S., Smedmark J.E.E., Morgan D.R., Kerr M., Robertson K.R., Arsenault M., Dickinson T.A., Campbell C.S. Phylogeny and classification of Rosaceae. Plant Syst. Evol. 2007, 266:5-43.
39. Rambaut, A., 2002. Se-Al Sequence Alignment Editor. http://evolve.zoo.ac.uk.
40. Ravi V., Khurana J.P., Tyagi A.K., Khurana P. Rosales sister to Fabales: towards resolving the rosid puzzle. Mol. Phylogenet. Evol. 2007, 44:488-493.
41. Richardson J.E., Fay M.F., Cronk Q.C.B., Bowman D., Chase M.W. A phylogenetic analysis of Rhamnaceae using rbcL and trnL-F plastid DNA sequences. Am. J. Bot. 2000, 87:1309-1324.
42. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
43. Ronse De Craene L.P., Miller A.G. Floral development and anatomy of Dirachma socotrana, (Dirachmaceae), a controversial member of the Rosales. Plant Syst. Evol. 2004, 249:111-127.
44. Savolainen V., Chase M.W., Hoot S.B., Morton C.M., Soltis D.E., Bayer C., Fay M.F., de Bruijn A.Y., Sullivan S., Qiu Y.L. Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst. Biol. 2000, 49:306-362.
45. Savolainen V., Fay M.F., Albach D.C., Backlund A., van der Bank M., Cameron K.M., Johnson S.A., Lledó M.D., Pintaud J.C., Powell M., Sheahan M.C., Soltis D.E., Soltis P.S., Weston P., Whitten W.M., Wurdack K.J., Chase M.W. Phylogeny of the eudicots: a nearly complete familial analysis based on rbcL gene sequences. Kew Bull. 2000, 55:257-309.
46. Schweinfurth G. Barbeya Schwf. gen. nov. Urticacearum. Malpighia 1891, 5:332-340.
47. Soltis D.E., Soltis P.S., Morgan D.R., Swensen S.M., Mullin B.C., Dowd J.M., Martin P.G. Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen-fixation in angiosperms. Proc. Natl. Acad. Sci. USA 1995, 92:2647-2651.
48. Soltis D.E., Soltis P.S., Chase M.W., Mort M.E., Albach D.C., Zanis M., Savolainen V., Hahn W.H., Hoot S.B., Fay M.F., Axtell M., Swensen S.M., Prince L.M., Kress W.J., Nixon K.C., Farris J.S. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc. 2000, 133:381-461.
49. Soltis D.E., Albert V.A., Savolainen V., Hilu K., Qiu Y.L., Chase M.W., Farris J.S., Stefanović S., Rice D.W., Palmer J.D., Soltis P.S. Genome-scale data, angiosperm relationships, and 'ending incongruence': a cautionary tale in phylogenetics. Trends Plant Sci. 2004, 9:477-483.
50. Soltis D.E., Soltis P.S., Endress P.K., Chase M.W. Phylogeny and Evolution of the Angiosperms 2005, Sinauer, Sunderland, Massachusetts.
51. Soltis D.E., Gitzendanner M.A., Soltis P.S. A 567-taxon data set for angiosperms: the challenges posed by bayesian analyses of large data sets. Int. J. Plant Sci. 2007, 168:137-157.
52. Song B.H., Wang X.Q., Li F.Z., Hong D.Y. Further evidence for paraphyly of the Celtidaceae from the chloroplast gene matK. Plant Syst. Evol. 2001, 228:107-115.
53. Souza-Chies T.T., Bittar G., Nadot S., Carter L., Besin E., Lejeune B. Phylogenetic analysis of Iridaceae with parsimony and distance methods using the plastid gene rps4. Plant Syst. Evol. 1997, 204:109-123.
54. Stefanović S., Rice D.W., Palmer J.D. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?. BMC Evol. Biol. 2004, 4:35-53.
55. Stevens, P.F. 2001. Angiosperm Phylogeny Website. Version 9 (February 2011).
56. Swensen S.M. The evolution of actinorhizal symbioses: evidence for multiple origins of the symbiotic association. Am. J. Bot. 1996, 83:1503-1512.
57. Swofford, D.L., 2003. PAUP*: phylogenetic Analysis using Parsimony (and Other Methods), Version 4.0b10. Sinauer Associates, Sunderland, Massachusetts.
58. Sytsma K.J., Morawetz J., Pires J.C., Nepokroeff M., Conti E., Zjhra M., Hall J.C., Chase M.W. Urticalean rosids: circumscription, rosid ancestry, and phylogenetics based on rbcL, trnL-F, and ndhF sequences. Am. J. Bot. 2002, 89:1531-1546.
59. Takhtajan A. Outline of the classification of flowering plants (Magnoliophyta). Bot. Rev. 1980, 46:225-359.
60. Takhtajan A. Systema Magnoliophytorum 1987, Nauka, Leningrad.
61. Takhtajan A. Diversity and Classification of Flowering Plants 1997, Columbia University Press, New York.
62. Thorne R.F. Classification and geography of flowering plants. Bot. Rev. 1992, 58:225-348.
63. Thorne R.F., Reveal J.L. An updated classification of the class magnoliopsida (" Angiospermae" ). Bot. Rev. 2007, 73:67-181.
64. Thulin M., Bremer B., Richardson J., Niklasson J., Fay M.F., Chase M.W. Family relationships of the enigmatic rosid genera Barbeya and Dirachma from the Horn of Africa region. Plant Syst. Evol. 1998, 213:103-119.
65. Tobe H., Takahashi M. Trichome and pollen morphology of Barbeya (Barbeyaceae) and its relationships. Taxon 1990, 39:561-567.
66. Wang H.C., Moore M.J., Soltis P.S., Bell C.D., Brockington S.F., Alexandre R., Davis C.C., Latvis M., Manchester S.R., Soltis D.E. Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc. Natl. Acad. Sci. USA 2009, 106:3853-3858.
67. Wiegrefe S.J., Sytsma K.J., Guries R.P. The Ulmaceae, one family or two? Evidence from chloroplast DNA restriction site mapping. Plant Syst. Evol. 1998, 210:249-270.
68. Wu Z.Y., Lu A.M., Tang Y.C., Chen Z.D., Li D.Z. The Families and Genera of ANGIOSPERMS in China - A Comprehensive Analysis 2003, Science Press, Beijing.
69. Zerega N.J.C., Clement W.L., Datwyler S.L., Weiblen G.D. Biogeography and divergence times in the mulberry family (Moraceae). Mol. Phylogenet. Evol. 2005, 37:402-416.
70. Zhang Z.H., Li C.Q., Li J.H. Phylogenetic placement of Cynomorium in Rosales inferred from sequences of the inverted repeat region of the chloroplast genome. J. Syst. Evol. 2009, 47:297-304.
71. Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion. Ph.D. Dissertation, The University of Texas at Austin.