Expanded phylogenetic and dating analyses of the apples and their relatives (Pyreae, Rosaceae)

Molecular Phylogenetics and Evolution

Volumn 63, Issue 2, 2012, Pages 230-243

  Lo, Eugenia Y Y ^a   Donoghue, Michael J ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Divergence times; Hybridization; Maloideae; Northern hemisphere disjunctions; Pyreae; Rosaceae; Sorbus

Indexed keywords

PLANT DNA; RIBOSOMAL SPACER DNA;

ARTICLE; BAYES THEOREM; CHLOROPLAST; CLASSIFICATION; GENETICS; MALUS; MITOCHONDRION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

BAYES THEOREM; CHLOROPLASTS; DNA, PLANT; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; GENETIC SPECIATION; LIKELIHOOD FUNCTIONS; MALUS; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; PHYLOGENY;

MALOIDEAE; PSEUDOCYDONIA; ROSACEAE; SORBUS;

EID: 84858074915     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.10.005     Document Type: Article

References (72)

1. Aas G., Maier J., Baltisberger M., Merzger S. Morphology, isozyme variation, cytology, and reproduction of hybrids between Sorbus aria (L.) Crantz and S. torminalis (L.). Crantz. Bot. Helv. 1994, 104:195-214.
2. Aldasoro J.J., Aedo C., Navarro C., Garmendia F.M. The genus Sorbus (Maloideae, Rosaceae) in Europe and in North Africa: morphological analysis and systematics. Syst. Bot. 1998, 23:189-212.
3. Aldasoro J.J., Aedo C., Garmendia F.M., de la Hoz F.P., Navarro C. Revision of Sorbus subgenera Aria and Torminaria (Rosaceae-Maloideae). Syst. Bot. Monogr. 2004, 69:1-148.
4. Baldwin B.G., Sanderson M.J. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proc. Natl. Acad. Sci. USA 1998, 95:9402-9406.
5. Bell C.D., Soltis D.E., Soltis P.S. The age and diversification of the angiosperms re-revisited. Am. J. Bot. 2010, 97:1296-1303.
6. Campbell C.S., Baldwin B.G., Donoghue M.J., Wojciechowski M.F. A phylogeny of the genera of Maloideae (Rosaceae): evidence from Internal Transcribed Spacers of nuclear ribosomal DNA sequences and congruence with morphology. Am. J. Bot. 1995, 82:903-918.
7. Campbell C.S., Evans R.C., Morgan D.R., Dickinson T.A., Arsenault M.P. Phylogeny of subtribe Pyrinae (formerly the Maloideae, Rosaceae): limited resolution of a complex evolutionary history. Plant Syst. Evol. 2007, 266:119-145.
8. Cevallos-Ferriz S.R.S., Stockey R.A. Fruits and seeds from the Princeton chert (Middle Eocene) of British Columbia: Rosaceae (Prunoideae). Bot. Gaz. 1991, 152:369-379.
9. Challice J. Phenolic compounds of the subfamily Pomoideae: a chemotaxonomic survey. Phytochemistry 1973, 12:1095-1101.
10. DeVore M.L., Pigg K.B. A brief review of the fossil history of the family Rosaceae with a focus on the Eocene Okanogan Highlands of eastern Washington State, USA, and British Columbia, Canada. Plant Syst. Evol. 2007, 266:45-57.
11. Dickinson T.A., Lo E.Y.Y., Talent N. Polyploidy, reproductive biology, and Rosaceae: understanding evolution and making classifications. Plant Syst. Evol. 2007, 266:59-78.
12. Donoghue M.J., Bell C.D., Li J.H. Phylogenetic patterns in northern hemisphere plant geography. Int. J. Plant Sci. 2001, 162:S41-S52.
13. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214-223.
14. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughout. Nucl. Acids Res. 2004, 32:1792-1797.
15. Edwards S.V. Is a new and general theory of molecular systematics emerging?. Evolution 2009, 63:1-19.
16. Evans R.C., Dickinson T.A. Floral ontogeny and morphology in subfamily Spiraeoideae Endl. (Rosaceae). Int. J. Plant Sci. 1999, 160:981-1012.
17. Evans R.C., Alice L.A., Campbell C.S., Kellogg E.A., Dickinson T.A. The granule bound starch synthase (GBSSI) gene in Rosaceae: multiple putative loci and phylogenetic utility. Mol. Phylogenet. Evol. 2000, 17:388-400.
18. Evans R.C., Campbell C.S. The origin of the apple subfamily (Rosaceae: Maloideae) is clarified by DNA sequence data from duplicated GBSSI genes. Am. J. Bot. 2002, 89:1478-1484.
19. Evans R.C., Dickinson T.A. Floral ontogeny and morphology in Gillenia (" Spiraeoideae") and subfamily Maloideae C. Weber (Rosaceae). Int. J. Plant Sci. 2005, 166:427-447.
20. Forest, F., Chase, M.W., 2009. Eurosid I. In: Hedges, S.B., Kumar, S. (Eds.), The Timtree of Life. Oxford University Press, pp.188-196.
21. Fryer J., Hylmö B. Cotoneasters: A Comprehensive Guide to Shrubs for Flowers, Fruits, and Foliage 2009, Timber Press Inc.
22. Gabrielian, E., 1978. Rjabiny (Sorbus L.) Zapadnoj Azii i Gimalaev, Yerevan.
23. Goldblatt P. Cytotaxonomic studies in the tribe Quillajeae (Rosaceae). Ann. Mol. Bot. Gard. 1976, 63:200-206.
24. Guo W., Yu Y., Shen R.J., Liao W.B., Chin S.W., Potter D. A phylogeny of Photinia sensu lato (Rosaceae) and related genera based on nrITS and cpDNA analysis. Plant Syst. Evol. 2011, 291:91-102.
25. Huelsenbeck J.P., Ronquist F. Mr. Bayes: a program for the Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755.
26. Iketani H., Ohashi H. Anatomical structure of fruits and evolution of the tribe Sorbeae in the subfamily Maloideae (Rosaceae). J. Jpn. Bot. 1991, 66:319-351.
27. Kalkman C. Rosaceae. Flowering Plants - Dicotyledons: Celastrales, Oxalidales, Rosales, Cornales, Ericales 2004, 343-386. Springer, Berlin. K. Kubitzki (Ed.).
28. Knowles L.L. Statistical phylogeography. Ann. Rev. Ecol. Evol. Syst. 2009, 40:593-612.
29. Kovanda M. Flower and fruit morphology of Sorbus in correlation to the taxonomy of the genus. Preslia 1961, 7:1-16.
30. Kovanda M. On the generic limits in the Maloideae. Preslia 1965, 37:27-34.
31. Liu Z., Pagani M., Zinniker D., DeConto R., Huber M., Brinkhuis H., Sunita R., Shah R., Leckie M., Pearson A. Global cooling during the Eocene-Oligocene climate transition. Science 2009, 27:1187-1190.
32. Lo E.Y.Y., Stefanović S., Dickinson T.A. Molecular reappraisal of relationships between Crataegus and Mespilus (Rosaceae, Pyreae) - two genera or one?. Syst. Bot. 2007, 32:596-616.
33. Lo E.Y.Y., Stefanović S., Christensen K.I., Dickinson T.A. Evidences for genetic association between East Asian and Western North American Crataegus L. (Rosaceae) and rapid divergence of the Eastern North American lineages based on multiple DNA sequences. Mol. Phylogenet. Evol. 2009, 51:157-168.
34. Maddison, W.P., Maddison, D.R., 2008. Mesquite: A Modular System for Evolutionary Analysis. Version 2.71. http://mesquiteproject.org.
35. Magallón S., Castillo A. Angiosperm diversification through time. Am. J. Bot. 2009, 96:349-365.
36. Manchester S.R. Fruits and seeds of the Middle Eocene Nut Beds flora, Clarno Formation, North Central Oregon. Palaeontogr. Am. 1994, 58:1-205.
37. McAllister, H., 2005. The Genus Sorbus - Mountain Ash and Other Rowans. Royal Botanical Gardens, Kew.
38. Milne R.I. Northern hemisphere plant disjunctions: a window on Tertiary land bridges and climate change. Ann. Bot. 2006, 98:465-472.
39. Moore B.R., Donoghue M.J. Correlates of diversification in the plant clade Dipsacales: geographic movement and evolutionary innovations. Am. Nat. 2007, S28-S55.
40. Morgan D.R., Soltis D.E., Robertson K.R. Systematic and evolutionary implications of rbc L sequence variation in Rosaceae. Am. J. Bot. 1994, 81:890-903.
41. Nelson-Jones E.B., Briggs D., Smith A.G. The origin of intermediate species of the genus Sorbus. Theor. Appl. Genet. 2002, 105:953-963.
42. Pamilo P., Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 1988, 5:568-583.
43. Phipps J.B., Robertson K.R., Smith P.G., Rohrer J.R. A checklist of the subfamily Maloideae (Rosaceae). Can. J. Bot. 1990, 68:2209-2269.
44. Phipps J.B., Robertson K.R., Rohrer J.R., Smith P.G. Origins and evolution of subfamily Maloideae (Rosaceae). Syst. Bot. 1991, 16:303-332.
45. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
46. Potter D., Eriksson T., Evans R.C., Oh S.H., Smedmark J.E.E., Morgan D.R., Kerr M., Robertson K.R., Arsenault M.P., Dickinson T.A., Campbell C.S. Phylogeny and classification of Rosaceae. Plant Syst. Evol. 2007, 266:5-43.
47. Rabosky D.L. Extinction rates should not be estimated from molecular phylogenies. Evolution 2009, 64:1816-1824.
48. Rambaut, A., 2002. Se-Al Sequence Alignment Editor v2.0a11. University of Oxford, Oxford.
49. Rambaut, A., Drummond, A.J., 2003. Tracer. http://beast.bio.ed.ac.uk/tracer.
50. Rehder A. Manual of Cultivated Trees and Shrubs Hardy in North America Exclusive of the Subtropical and Warmer Temperate Regions 1940, MacMillan, New York. second ed.
51. Ricklefs R.E. Estimating diversification rates from phylogenetic information. Trends Ecol. Evol. 2007, 22:601-610.
52. Robertson K.R., Phipps J.B., Rohrer J.R. A synopsis of genera in Maloideae (Rosaceae). Syst. Bot. 1991, 16:376-394.
53. Robertson K.R., Phipps J.B., Rohrer J.R. Summary of leaves in the genera of Maloideae (Rosaceae). Ann. Mol. Bot. Gard. 1992, 79:81-94.
54. Rohrer J.R., Robertson K.R., Phipps J.B. Floral morphology of Maloideae (Rosaceae) and its systematic relevance. Am. J. Bot. 1994, 81:574-581.
55. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
56. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 2002, 19:101-109.
57. Sanderson M.J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 2003, 19:301-302.
58. Sanderson M.J., Doyle J.A. Sources of error and confidence intervals in estimating the age of angiosperms from rbc L and 18S rDNA data. Am. J. Bot. 2001, 88:1499-1516.
59. Savile D.B.O. Fungi as aids in higher plant classification. Bot. Rev. 1979, 45:380-495.
60. Sax K. The origin and relationships of the Pomoideae. J. Arnold Arbor. 1931, 12:3-22.
61. Shaw J., Lickey E.B., Beck J.T., Farmer S.B., Liu W.S., Miller J., Siripun K.C., Winder C.T., Schilling E.E., Small R.L. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am. J. Bot. 2005, 92:142-166.
62. Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
63. Smith S.A., Dunn C.W. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 2008, 24:715-716.
64. Stamatakis A., Ludwig T., Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005, 21:456-463.
65. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 2008, 57:758-771.
66. Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods), Version 40b10. Sinauer Associates, Sunderland.
67. Tiffney B.H. Perspectives on the origin of the floristic similarity between eastern Asia and eastern North America. J. Arnold Arbor. 1985, 66:73-94.
68. Tiffney B.H. The Eocene North Atlantic land bridge: its importance in Tertiary and modern phylogeography of the Northern Hemisphere. J. Arnold Arbor. 1985, 66:243-273.
69. Wikstrom N., Savolainen V., Chase M.W. Evolution of the angiosperms: calibrating the family tree. Proc. Roy. Soc. Biol. Sci. B 2001, 268:2211-2220.
70. Wolfe J.A., Wehr W. Rosaceous Chamaebatiaria-like foliage from the paleogene of western North America. Aliso 1988, 12:177-200.
71. Yu T. Rosaceae-Prunoideae and Connaraceae - Flora Republicae Popularis Sinicae, vol. 36 1974, Science, Beijing.
72. White T.J., Bruns T., Lee S., Taylor J. Amplification and direct sequencing of fungal ribosomal genes for phylogenies. PCR Protocols: A Guide to Methods and Applications 1990, 315-322. Academic Press, San Diego. M. Innis, D. Gelfand, J. Sninsky, T. White (Eds.).