Molecular phylogenetics of Haemodoraceae in the Greater Cape and Southwest Australian Floristic Regions

Molecular Phylogenetics and Evolution

Volumn 51, Issue 1, 2009, Pages 19-30

  Hopper, Stephen D ^a,b   Smith, Rhian J ^a   Fay, Michael F ^a   Manning, John C ^c   Chase, Mark W ^a  

^a ROYAL BOTANIC GARDENS   (United Kingdom)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^c SOUTH AFRICAN NATIONAL BIODIVERSITY INSTITUTE   (South Africa)

Author keywords

Diversification; Greater Cape; Haemodoraceae; Lineage turnover; matK; Relictual taxa; Southwestern Australia; SWAFR; trnL intron; trnL F spacer

Indexed keywords

PLANT DNA;

AFRICA; ANGIOSPERM; ARTICLE; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION;

AFRICA, SOUTHERN; ANGIOSPERMS; BAYES THEOREM; DNA, PLANT; EVOLUTION, MOLECULAR; GENETIC SPECIATION; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

HAEMODORACEAE;

EID: 64149105256     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.11.015     Document Type: Article

References (85)

1. Anderson J.M., Anderson H.M., Archangelsky S., Bamford M., Chandra S., Dettmann M., Hill R., McLoughlin S., and Rosler O. Patterns of Gondwana plant colonisation and diversification. J. Afr. Earth Sci. 28 (1999) 145-167
2. Angiosperm Phylogeny Group. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141 (2003) 399-436
3. Born J., Linder H.P., and Desmet P. The Greater Cape Floristic Region. J. Biogeogr. 34 (2007) 147-162
4. Chase, M.W., Fay, M.F., Devey, D.S., Maurin, O., Rønsted, N., Davies, T.J., Pillon, Y., Petersen, G., Seberg, O., Tamura, M.N., Asmussen, C.B., Hilu, K., Borsch, T., Davis, J.I., Stevenson, D.W., Pires, J.C., Givnish, T.J., Sytsma, K.J., McPherson, M.A., Graham, S.W., Rai, H.S. 2006. Multigene analyses of monocot relationships: a summary. In: Columbus, J.T., Friar, E.A., Porter, J.M., Prince, L.M., Simpson, M.G. (Eds.), Monocots. Comparative Biology and Evolution. Aliso 22, pp. 63-75.
5. Chase M.W., and Hills H.G. Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon 40 (1991) 215-220
6. Chase M.W., Soltis D.E., Soltis P.S., Rudall P.J., Fay M.F., Hahn W.H., Sullivan S., Joseph J., Givnish T.J., Sytsma K.J., and Pires C. Higher-level systematics of the monocotyledons: an assessment of current knowledge and a new classification. In: Wilson K.L., and Morrison D.A. (Eds). Systematics and Evolution of Monocots (2000), CSIRO Publishing, Collingwood 3-16
7. Chase M.W., Stevenson W.D.W., Wilkin P., and Rudall P.J. Monocot systematics: a combined analysis. In: Rudall P.J., Cribb P.J., Cutler D.F., and Humphries C.J. (Eds). Monocotyledons: Systematics and Evolution (1995), Royal Botanic Gardens, Kew, UK 685-730
8. Cooper S.J.B., Hinze S., Leys R., Watts C.H.S., and Humphreys W.F. Islands under the desert: molecular systematics and evolutionary origins of stygobitic water beetles (Coleoptera: Dytiscidae) from central Western Australia. Invertebr. Syst. 16 (2002) 589-598
9. Cowling R.M. Fire and its role in coexistence and speciation in Gondwanan shrublands. South Afr. J. Sci. 83 (1987) 106-112
10. Cowling R.M., and Hilton-Taylor C. Phytogeography, flora and endemism. In: Cowling R.M., Richardson D.M., and Pierce S.M. (Eds). Vegetation of Southern Africa (1997), Cambridge University Press 43-61
11. Cowling R.M., and Pierce S. Namaqualand: A Succulent Desert (1999), Fernwood Press, Vlaeberg, South Africa
12. Cowling R.M., Rundel P.W., Lamont B.B., Arroyo M.K., and Arianoutsou M. Plant diversity in mediterranean-climate regions. Trends Ecol. Evol. 11 (1996) 362-366
13. Crawford R.M.M. Plants at the Margin. Ecological Limits and Climate Change (2008), Cambridge University Press, Cambridge
14. Creeth J.M., and Denborough M.A. The use of equilibrium-density-gradient methods for the preparation and characterization of blood-group-specific glycoproteins. Biochem. J. 117 (1970) 879-891
15. Crisp M., Cook L., and Steane D. Radiation of the Australian flora: what can comparisons of molecular phylogenies across multiple taxa tell us about the evolution of diversity in present-day communities?. Philos. Trans. R. Soc. B 359 (2004) 1551-1571
16. Dahlgren R. A revised system of classification of the angiosperms. Bot. J. Linn. Soc. 80 (1980) 91-124
17. Dodson J.R., and Macphail M.K. Palynological evidence for aridity events and vegetation change during the Middle Pliocene, a warm period in Southwestern Australia. Glob. Planet. Change 41 (2004) 285-307
18. Dodson J.R., Robinson M., and Tardy C. Two fine-resolution Pliocene charcoal records and their bearing on pre-human fire frequency in south-western Australia. Austral Ecol. 30 (2005) 592-599
19. Doyle J.J., and Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19 (1987) 11-15
20. Drummond A.J., and Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7 (2007) 214
21. Drummond A.J., Ho S.Y.W., Phillips M.J., and Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4 (2006) e88 10.1371/journal.pbio.0040088
22. Dynesius M., and Jansson R. Evolutionary consequences of changes in species' geographical distributions driven by Milankovitch climate oscillations. Proc. Nat. Acad. Sci. 97 (2000) 9115-9120
23. Edwards D., and Hawkins J.A. Are Cape floral clades the same age? Contemporaneous origins of two lineages in the genistoids s.l. (Fabaceae). Mol. Phylogenet. Evol. 45 (2007) 952-970
24. Ellis A., Weis A., and Gaut B. Evolutionary radiation of ''stone plants'' in the genus Argyroderma (Aizoaceae): unravelling the effects of landscape, habitat, and flowering time. Evolution 60 (2006) 39-55
25. Fitch W.M. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20 (1971) 406-416
26. Frakes L.A. Evolution of Australian Environments. Flora of Australia. second ed. vol. 1 (1999), Commonwealth Scientific and Industrial Research Organisation (CSIRO) publishing, Victoria and Australian Biological Resources Study, Canberra pp. 163-203
27. Gallagher K., and Brown R. Denudation and uplift at passive margins: the record on the Atlantic Margin of southern Africa. Phil. Trans. R. Soc. Lond. A 357 (1999) 835-859
28. Galley C., and Linder H.P. Geographical affinities of the Cape flora, South Africa. J. Biogeogr. 33 (2006) 236-250
29. Goldblatt P. An analysis of the flora of Southern Africa: its characteristics, relationships, and origins. Ann. Missouri. Bot. Gard. 65 (1978) 369-546
30. Goldblatt P. Floristic diversity in the Cape Flora of South Africa. Biodivers. Conserv. 6 (1997) 359-377
31. Goldblatt P., and Manning J.C. Cape Plants. A Conspectus of the Cape Flora of South Africa. Strelitzia 9 (2000) 1-743
32. Goldblatt P., and Manning J.C. Plant diversity of the Cape Region of Southern Africa. Ann. Missouri Bot. Gard. 89 (2002) 281-302
33. Graham S.W., Olmstead R.G., and Barrett S.C.H. Rooting phylogenetic trees with distant outgroups: a case study from the Commelinoid monocots. Mol. Biol. Evol. 19 (2002) 1769-1781
34. Hopper S.D. Biogeographical aspects of speciation in the south west Australian flora. Annu. Rev. Ecol. Syst. 10 (1979) 399-422
35. Hopper S.D. Patterns of diversity at the population and species levels in south-west Australian mediterranean ecosystems. In: Hobbs R.J. (Ed). Biodiversity of Mediterranean Ecosystems in Australia (1992), Surrey Beattey & Sons, Sydney 27-46
36. Hopper S.D. An evolutionary perspective on south-west Western Australian landscapes, biodiversity and fire: a review and management implications. In: Abbott I., and Burrows N. (Eds). Fire in Ecosystems of South-west Western Australia: Impacts and management (2003), Backhuys Publishers, Leiden 9-35
37. Hopper, S.D., Chase, M.W., Fay, M.F., 2006. A molecular phylogenetic study of generic and subgeneric relationships in the south-west Australian endemics Conostylis and Blancoa (Haemodoraceae). In: Columbus, J.T., Friar, E.A., Porter, J.M., Prince, L.M., Simpson, M.G. (Eds.), Monocots: Comparative Biology and Evolution, Aliso 22, 527-538.
38. Hopper S.D., Fay M.F., Rossetto M., and Chase M.W. A molecular phylogenetic analysis of the bloodroot and kangaroo paw family, Haemodoraceae: taxonomic, biogeographic and conservation implications. Bot. J. Linn. Soc. 131 (1999) 285-299
39. Hopper S.D., and Gioia P. The Southwest Australian Floristic Region: evolution and conservation of a global hot spot of biodiversity. Annu. Rev. Ecol. Syst. 35 (2004) 623-650
40. Hopper S.D., Harvey M.S., Chappill J.A., Main A.R., and Main B.Y. The Western Australian biota as Gondwanan Heritage-a review. In: Hopper S.D., Chappill J.A., Harvey M.S., and George A.S. (Eds). Gondwanan Heritage: Past, Present and Future of the Western Australian Biota (1996), Surrey Beatty & Sons, Chipping Norton, New South Wales 1-46
41. Hopper S.D., Purdie R.W., George A.S., and Patrick S.J. Conostylis. Flora Aust. 45 (1987) 57-110
42. Ihlenfeldt H.D. Diversification in an arid world: the Mesembryanthemaceae. Ann. Rev. Ecol. Syst. 25 (1994) 521-546
43. James S.H. Cytoevolutionary patterns, genetic systems and the phytogeography of Australia. In: Keast A. (Ed). Ecological Biogeography of Australia (1981), Dr. W. Junk, The Hague/Boston/London 763-782
44. James S.H. Inbreeding, self-fertilization, lethal genes and genomic coalescence. Heredity 68 (1992) 449-456
45. Janssen T., and Bremer K. The age of major monocot groups inferred from 800+ rbcL sequences. Bot. J. Linn. Soc. 146 (2004) 385-398
46. Jansson R. Global patterns in endemism explained by past climate change. Proc. R. Soc. Lond. B. 270 (2003) 583-590
47. Jansson R., and Davies T.J. Global variation in diversification rates of flowering plants : energy vs. Climate change. Ecol. Lett. 11 (2008) 173-183
48. Jaramillo C., Rueda M.J., and Mora G. Cenozoic Plant Diversity in the Neotropics. Science 311 (2006) 1893-1896
49. Jennings W.B., Pianka E.R., and Donnellan S. Systematics of the lizard family Pygopodidae with implications for the diversification of Australian temperate biotas. Syst. Biol. 52 (2003) 757-780
50. Johnson S.D. Pollination, adaptation and speciation models in the Cape flora of South Africa. Taxon 45 (1996) 59-66
51. Kelchner S.A. The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann. Missouri Bot. Gard. 87 (2000) 482-498
52. Kershaw A.P., Clark J.S., Gill A.M., and D'Costa D.M. A history of fire in Australia. In: Bradstock R.A., Williams J.E., and Gill M.A. (Eds). Flammable Australia (2002), Cambridge University Press, Cambridge 3-25
53. Kershaw P., Moss P., and van der Kaars S. Causes and consequences of long-term climatic variability on the Australian continent. Freshwater Biol. 48 (2003) 1274-1283
54. Klak C., Reeves G., and Hedderson T. Unmatched tempo of evolution in Southern African semi-desert ice plants. Nature 427 (2004) 63-65
55. Krajewski C., Wroe S., and Westerman M. Molecular evidence for the pattern and timing of cladogenesis in dasyurid marsupials. Zool. J. Linn. Soc. Lond. 130 (2000) 375-404
56. Levyns M.R. Some evidence bearing on the past history of the Cape Flora. Trans. R. Soc. S. Afr. 26 (1938) 401-424
57. Levyns M.R. Migration and origin of the Cape flora. Trans. R. Soc. S. Afr. 37 (1964) 85-107
58. Linder, H.P., 1985. Gene flow, speciation and species diversity patterns in a species-rich area: the Cape Flora. In: Vrba, E.S. (Ed.), Species and Speciation. Transvaal Museum Monograph 4, 53-57.
59. Linder H.P. The radiation of the Cape flora, southern Africa. Biol. Rev. 78 (2003) 597-638
60. Linder H.P. Evolution of diversity: the Cape flora. Trends Plant Sci. 10 (2005) 536-702
61. Linder H.P. Plant species radiations: where, when, why?. Philos. Trans. R. Soc. B 363 (2008) 3097-3105
62. 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
63. McLoughlin S. The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism. Aust. J. Bot. 49 (2001) 271-300
64. 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
65. Mulch A., and Chamberlain C.P. The rise and growth of Tibet. Nature 439 (2006) 670-671
66. Nylander J.A.A. MrModeltest v2. Program distributed by the author (2004), Evolutionary Biology Centre, Uppsala University
67. Pybus O.G., and Rambaut A. GENIE: estimating demographic history from molecular phylogenies. Bioinformatics 18 10 (2002) 1404-1405
68. Rambaut, A., 2008. FigTree v1.1.2. A graphical viewer of phylogenetic trees. Available from: .
69. Rambaut, A., Charleston, M., 2002. TreeEdit v1.0 alpha 10. Phylogenetic tree editor. Available from: .
70. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. Available from: .
71. Rambaut, A., Drummond, A.J., 2008a. LogCombiner v1.4.7. MCMC output combiner. Available from: .
72. Rambaut, A. Drummond, A.J., 2008b. Tree Annotator. MCMC output analysis. Available from: .
73. Robert C., Diester-Haass L., and PaturelClay J. Mineral assemblages, siliciclastic input and paleoproductivity at ODP Site 1085 off Southwest Africa: A late Miocene-early Pliocene history of Orange river discharges and Benguela current activity, and their relation to global sea level change. Mar. Geol. 216 (2005) 221-238
74. Ronquist, F., 1996. DIVA (dispersal-vicariance analysis). Ver. 1.1. Software available via www.ebc.uu.se/systzoo/research/diva/diva.html. Uppsala University, Uppsala.
75. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
76. Scher H.D., and Martin E.E. Timing and climatic consequences of the opening of Drake Passage. Science 312 (2006) 428-430
77. Scott L., Anderson H.M., and Anderson J.M. Vegetation history. In: Cowling R.M., Richardson D.M., and Pierce S.M. (Eds). Vegetation of Southern Africa (1997), Cambridge University Press 62-84
78. Shepherd K.A., Waycott M., and Calladine A. Radiation of the Australian Salicornioideae (Chenopodiaceae)-based on evidence from nuclear and chloroplast DNA sequences. Am. J. Bot. 91 (2004) 1387-1397
79. Simpson M.G. Phylogeny and classification of the Haemodoraceae. Ann. Mo. Bot. Gard. 77 (1990) 722-784
80. Simpson M.G. Reversal in ovary position from inferior to superior in the Haemodoraceae: evidence from floral ontogeny. Int. J. Plant Sci. 159 (1998) 466-479
81. Sun H., McLewin W., and Fay M.F. Molecular phylogeny of Helleborus (Ranunculaceae), with an emphasis on the East Asia-Mediterranean disjunction. Taxon 50 (2001) 1001-1018
82. * and other methods) (2001), Sinauer Associates, Sunderland, Massachusetts
83. Taberlet P., Gielly L., Pautou G., and Bouvet J. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17 (1991) 1105-1109
84. Yang Z. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39 (1994) 105-111
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