Are Cape floral clades the same age? Contemporaneous origins of two lineages in the genistoids s.l. (Fabaceae)

Molecular Phylogenetics and Evolution

Volumn 45, Issue 3, 2007, Pages 952-970

  Edwards, Dawn ^a,b   Hawkins, Julie A ^a  

^a UNIVERSITY OF READING   (United Kingdom)

^b ROYAL HORTICULTURAL SOCIETY   (United Kingdom)

Author keywords

Cape floral clade; Cape Floristic Region; Crotalarieae; Molecular dating; NPRS; Podalyrieae

Indexed keywords

ARTICLE; CLASSIFICATION; GENETICS; LEGUME; PHYLOGENY; TIME;

FABACEAE; PHYLOGENY; TIME FACTORS;

CROTALARIEAE; FABACEAE; MYA; PODALYRIEAE;

EID: 36049051911     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.09.014     Document Type: Article

References (85)

1. Bakker F.T., Culham A., Marais E.M., and Gibby M. Nested radiation in Cape Pelargonium. In: Bakker F.T., Chatrou L.W., Gravendeel B., and Pelser P.B. (Eds). Plant Species-Level Systematics (2005), A.R.G. Gantner Verlag, Ruggell, Liechtenstein 75-100
2. Barriel V., and Tassy P. Rooting with multiple outgroups: consensus versus parsimony. Cladistics 14 (1998) 193-200
3. Bell C.D., and Donoghue M.J. Dating the dipsacales: comparing models, genes, and evolutionary implications. Am. J. Bot. 92 (2005) 284-296
4. Bremer K. Gondwanan evolution of the grass alliance of families (Poales). Evolution 56 (2002) 1374-1387
5. Caravaca F., Alguacil M.M., Figueroa D., Barea J.M., and Roldan A. Re-establishment of Retama sphaerocarpa as a target species for reclamation of soil physical and biological properties in a semi-arid Mediterranean area. For. Ecol. Manage. 182 (2003) 49-58
6. Chase M.W., and Hills H.H. Silica-gel-an ideal material for field preservation of leaf samples for DNA studies. Taxon 40 (1991) 215-220
7. Cowling R.M. Fire and its role in coexistence and speciation in Gondwanan shrublands. South Afr. J. Sci. 83 (1987) 106-112
8. Crisp M.D., Gilmore S., and Van Wyk B.-E. Molecular phylogeny of the genistoid tribes of papilionoid legumes. In: Herendeen P.S., and Bruneau A. (Eds). Advances in Legume Systematics vol. 9 (2000), Royal Botanic Gardens, Kew 249-276
9. Doyle J.J., and Doyle J.L. A rapid DNA isolation procedure for small amounts of fresh leaf tissue. Phytochem. Bull. 19 (1987) 11-15
10. Doyle J.J., Doyle J.L., Ballenger J.A., Dickson E.E., Kajita T., and Ohashi H. A phylogeny of the chloroplast gene rbcL in the Leguminosae: taxonomic correlations and insights into the evolution of nodulation. Am. J. Bot. 84 (1997) 541-554
11. Duncan R.A., and McDougall I. Linear volcanism in French Polynesia. J. Volcanol. Geotherm. Res. 1 (1976) 197-227
12. Dynesius M., and Jansson R. Evolutionary consequences of changes in species' geographical distributions driven by Milankovitch climate oscillations. Proc. Natl. Acad. Sci. USA 97 (2000) 9115-9120
13. Felsenstein J. Confidence-limits on phylogenies-an approach using the bootstrap. Evolution 39 (1985) 783-791
14. Felsenstein J. Phylogenies from molecular sequences-inference and reliability. Annu. Rev. Genet. 22 (1988) 521-565
15. Flores J., and Jurado E. Are nurse-protege interactions more common among plants from arid environments?. J. Veg. Sci. 14 (2003) 911-916
16. Forest F., Nänni N., Chase M., Crane P., and Hawkins J.A. Diversification of a large genus in a continental biodiversity hotspot: temporal and spatial origin of Muraltia (Polygalaceae) in the Cape of South Africa. Mol. Phylogenet. Evol. 43 (2007) 60-74
17. Goldblatt P. An analysis of the flora of Southern Africa: its characteristics, relationships, and origins. Ann. Mol. Bot. Gard. 65 (1978) 369-546
18. Goldblatt P., and Manning J. Cape Plants-A Conspectus of the Cape Flora of South Africa (2000), National Botanic Institute, Pretoria
19. Goldblatt P., and Manning J. Plant diversity of the Cape region of southern Africa. Ann. Mol. Bot. Gard. 89 (2002) 281-302
20. Goldblatt P., Savolainen V., Porteous O., Sostaric I., Powell M., Reeves G., Manning J.C., Barraclough T.G., and Chase M.W. Radiation in the Cape flora and the phylogeny of peacock irises Moraea (Iridaceae) based on four plastid DNA regions. Mol. Phylogenet. Evol. 25 (2002) 341-360
21. Good R. The Geography of Flowering Plants (1974), Longman, London
22. Graur D., and Martin W. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20 (2004) 80-86
23. Harris S.A. Systematics and randomly amplified polymorphic DNA in the genus Leucaena (Leguminosae, Mimosoideae). Plant Syst. Evol. 197 (1995) 195-208
24. Hedges S.B., and Kumar S. Precision of molecular time estimates. Trends Genet. 20 (2004) 242-247
25. Herendeen P.S., Crepet W.L., and Dilcher D.L. The fossil history of the Leguminosae: phylogenetic and biogeographic implications. In: Herendeen P.S., and Dilcher D.L. (Eds). Advances in Legume Systematics 4: The Fossil Record (1992), Royal Botanic Gardens, Kew 303-316
26. Herendeen, P.S., Wing, S., 2001. Papilionoid legume fruits and leaves from the Paleocene of northwestern Wyoming. Botany 2001 Abstracts, published by Botanical Society of America. Available from: >http://www.botany2001.org/>.
27. Hu J.M., Lavin M., Wojciechowski M.E., and Sanderson M.J. Phylogenetic analysis of nuclear ribosomal ITS/5.8S sequences in the tribe Millettieae (Fabaceae): Poecilanthe-Cyclolobium, the core Millettieae, and the Callerya group. Syst. Bot. 27 (2002) 722-733
28. Johnson S.D. Pollination, adaptation and speciation models in the Cape flora of South Africa. Taxon 45 (1996) 59-66
29. Kajita T., Ohashi H., Tateishi Y., Bailey C.D., and Doyle J.J. rbcL and legume phylogeny, with particular reference to Phaseoleae, Millettieae, and allies. Syst. Bot. 26 (2001) 515-536
30. Käss E., and Wink M. Phylogenetic relationships in the Papilionoideae (family Leguminosae) based on nucleotide sequences of cpDNA (rbcL) and ncDNA (ITS 1 and 2). Mol. Phylogenet. Evol. 8 (1997) 65-88
31. Kishino H., Thorne J.L., and Bruno W.J. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18 (2001) 352-361
32. Langley C.H., and Fitch W.M. Examination of constancy of rate of molecular evolution. J. Mol. Evol. 3 (1974) 161-177
33. Lavin M., Herendeen P.S., and Wojciechowski M.F. Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the Tertiary. Syst. Biol. 54 (2005) 575-594
34. Lee M.S.Y. Molecular clock calibrations and metazoan divergence dates. J. Mol. Evol. 49 (1999) 385-391
35. Levyns M.R. Migration and origin of the Cape flora. Trans. R. Soc. S. Afr. 37 (1964) 85-107
36. Lewis G., Schrire B., Mackinder B., and Lock M. Legumes of the World (2005), Royal Botanic Gardens, Kew
37. Linder H.P. Gene flow, speciation, and species diversity patterns in a species-rich area: the Cape flora. In: Vrba E.S. (Ed). Species and Speciation (1985), Transvaal Museum, Pretoria 53-57
38. Linder H.P. The radiation of the Cape flora, southern Africa. Biol. Rev. 78 (2003) 597-638
39. Linder H.P. Evolution of diversity. Trends Plant Sci. 10 (2005) 536-541
40. Linder H.P., Eldenas P., and Briggs B.G. Contrasting patterns of radiation in African and Australian Restionaceae. Evolution 57 (2003) 2688-2702
41. Linder H.P., and Hardy C.R. Evolution of the species-rich Cape flora. Philos. Trans. R. Soc. Lond. B 359 (2004) 1623-1632
42. Linder H.P., and Hardy C.R. Species richness in the Cape flora: a macroevolutionary and macroecological perspective. In: Bakker F.T., Chatrou L.W., Gravendeel B., and Pelser P.B. (Eds). Plant Species-Level Systematics (2005), A.R.G. Gantner Verlag, Ruggell, Liechtenstein 47-74
43. Linder H.P., Hardy C.R., and Rutschmann F. Taxon sampling effects in molecular clock dating: an example from the African Restionaceae. Mol. Phylogenet. Evol. 35 (2005) 569-582
44. Linder H.P., and Mann D.M. The phylogeny and biogeography of Thamnochortus (Restionaceae). Bot. J. Linn. Soc. 128 (1998) 319-357
45. Linder H.P., Meadows M.E., and Cowling R.M. History of the Cape flora. In: Cowling R.M. (Ed). Fynbos: Nutrients, Fire and Diversity (1992), Oxford Univ. Press, Cape Town, South Africa 113-134
46. Maddison D.R., and Maddison W.P. MacClade (2001), Sinauer Associates, Inc., Sunderland, MA
47. Magallon S., and Sanderson M.J. Absolute diversification rates in angiosperm clades. Evolution 55 (2001) 1762-1780
48. McDougall I., Embleton B.J.J., and Stone D.B. Origin and evolution of Lord-Howe Island, southwest Pacific Ocean. J. Geol. Soc. Aust. 28 (1981) 155-176
49. Midgley G.F., Hannah L., Roberts R., MacDonald D.J., and Allsopp J. Have Pleistocene climatic cycles influenced species richness patterns in the greater Cape Mediterranean Region?. J. Med. Ecol. 2 (2001) 137-144
50. Mummenhoff K., Al-Shehbaz I.A., Bakker F.T., Linder H.P., and Mühlhausen A. Phylogeny, morphological evolution, and speciation of endemic Brassicaceae genera in the Cape flora of southern Africa. Ann. Mol. Bot. Gard. 92 (2005) 400-424
51. Myers N., Mittermeier R.A., Mittermeier C.G., da Fonseca G.A.B., and Kent J. Biodiversity hotspots for conservation priorities. Nature 403 (2000) 853-858
52. Nielsen R. Mapping mutations on phylogenies. Syst. Biol. 51 (2002) 729-739
53. Nixon K.C. The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15 (1999) 407-414
54. Pennington R.T., Lavin M., Ireland H., Klitgaard B., Preston J., and Hu J.M. Phylogenetic relationships of basal papilionoid legumes based upon sequences of the chloroplast trnL introns. Syst. Bot. 26 (2001) 537-556
55. Polhill R.M. Papilionoideae. In: Polhill R.M., and Raven P.H. (Eds). Advances in Legume Systematics vol. 1 (1981), Royal Botanic Gardens, Kew 191-208
56. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
57. Rambaut, A., Charleston, M., 2002. TreeEdit: an application for organising, viewing and manipulating sets of phylogenetic trees. Published privately, Oxford. Available from: .
58. Reeves G., Chase M.W., Goldblatt P., Rudall P., Fay M.F., Cox A.V., Lejeune B., and Souza-Chies T. Molecular systematics of Iridaceae: evidence from four plastid DNA regions. Am. J. Bot. 88 (2001) 2074-2087
59. Richardson J.E., Weitz F.M., Fay M.F., Cronk Q.C.B., Linder H.P., Reeves G., and Chase M.W. Rapid and recent origin of species richness in the Cape flora of South Africa. Nature 412 (2001) 181-183
60. Rutschmann F. Bayesian Molecular Dating Using PAML/Multidivtime. A Step-by-Step Manual (2005), University of Zurich, Switzerland. Available from:
61. Sanderson M.J. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14 (1997) 1218-1231
62. Sanderson, M.J., 2001. r8s, version 1.0 (beta), User's manual (June 2001). Distributed by the author, University of California, Davis. Available from: .
63. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101-109
64. Schrire B.D., Lavin M., Barker N.P., Cortes-Burns H., von Senger I., and Kim J.-H. Towards a phylogeny of Indigofera (Leguminosae-Papilionoideae): identification of major clades and relative-ages. In: Klitgaard B.B., and Bruneau A. (Eds). Advances in Legume Systematics 10: Higher Level Systematics (2003), Royal Botanic Gardens, Kew 269-302
65. Schutte A.L., and Van Wyk B.-E. Evolutionary relationships in the Podalyrieae and Liparieae (Fabaceae) based on morphological, cytological, and chemical evidence. Plant Syst. Evol. 209 (1998) 1-31
66. Sequeira A.S., Lanteri A.A., Scataglini M.A., Confalonieri V.A., and Farrell B.D. Are flightless Galapaganus weevils older than the Galapagos Islands they inhabit?. Heredity 85 (2000) 20-29
67. Shapiro B., Sibthorpe D., Rambaut A., Austin J., Wragg G.M., Bininda-Emonds O.R.P., Lee P.L.M., and Cooper A. Flight of the dodo. Science 295 (2002) 1683
68. * implementation of the parsimony ratchet. Distributed by the authors. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, USA.
69. Sprent J.I. Nodulation in Legumes (2001), Royal Botanic Gardens, Kew
70. Sun Y., Skinner D.Z., Liang G.H., and Hulbert S.H. Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA. Theor. Appl. Genet. 89 (1994) 26-32
71. *. Phylogenetic Analysis Using Parsimony (* and other methods) (2002), Sinauer Associates, Inc., Sunderland, MA
72. Takhtajan A.L. Floristic Regions of the World (1986), Shiva Offset Press, India
73. Thompson J.D., Higgins D.G., and Gibson T.J. Clustal-W-improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
74. Thorne J.L., and Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51 (2002) 689-702
75. Thorne J.L., Kishino H., and Painter I.S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15 (1998) 1647-1657
76. Van der Bank M., Chase M.W., Van Wyk B.-E., Fay M.F., Van der Bank F.H., Reeves G., and Hulme A. Systematics of the tribe Podalyrieae (Fabaceae) based on DNA, morphological and chemical data. Bot. J. Linn. Soc. 139 (2002) 159-170
77. Verboom G.A., Linder H.P., and Stock W.D. Phylogenetics of the grass genus Ehrharta: evidence for radiation in the summer-arid zone of the South African Cape. Evolution 57 (2003) 1008-1021
78. White T.J., Bruns T., Lee S., and Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.A., Gelfand D.H., Sninsky J.J., and White T.J. (Eds). PCR Protocols: A Guide to Methods and Application (1990), Academic Press, San Diego 315-322
79. Wikström N., Savolainen V., and Chase M.W. Evolution of the angiosperms: calibrating the family tree. Proc. R. Soc. Lond. B 268 (2001) 2211-2220
80. Wikström N., Savolainen V., and Chase M.W. Angiosperm divergence times: congruence and incongruence between fossils and sequence divergence estimates. In: Smith P.C.J., and Donoghue M.P. (Eds). Telling the Evolutionary Time: Molecular Clocks and the Fossil Record (2004), Taylor and Francis, London 142-165
81. Wojciechowski M.F. Reconstructing the phylogeny of legumes: an early 21st century perspective. In: Klitgaard B.B., and Bruneau A. (Eds). Advances in Legume Systematics 10: Higher Level Systematics (2003), Royal Botanic Gardens, Kew 5-35
82. Wojciechowski M.F., Lavin M., and Sanderson M.J. A phylogeny of legumes (Leguminosae) based on analyses of the plastid matK gene resolves many well-supported subclades within the family. Am. J. Bot. 91 (2004) 1846-1862
83. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. BioSci. 13 (1997) 555-556
84. Yoder A.D., and Yang Z.H. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17 (2000) 1081-1090
85. Zachos J., Pagani M., Sloan L., Thomas E., and Billups K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292 (2001) 686-693