Rampant non-monophyly of species in Kniphofia moench (Asphodelaceae) suggests a recent Afromontane radiation

Taxon

Volumn 58, Issue 4, 2009, Pages 1141-1152

  Ramdhani, Syd ^a   Barker, Nigel P ^a   Baijnath, Himansu ^b  

^a RHODES UNIVERSITY   (South Africa)

^b UNIVERSITY OF KWAZULU NATAL   (South Africa)

Author keywords

Afromontane; Asphodelaceae; Glacial cycles; Hybridisation; Incomplete lineage sorting; Kniphofia; Non monophyly; nrITS; Radiation; trnT L

Indexed keywords

ADAPTIVE RADIATION; CHLOROPLAST; ENDEMISM; GEOGRAPHICAL DISTRIBUTION; GLACIAL-INTERGLACIAL CYCLE; GRASSLAND; HYPOTHESIS TESTING; INTERGLACIAL; MONOCOTYLEDON; MOUNTAIN ENVIRONMENT; PHYLOGENETICS; PLEISTOCENE; TAXONOMY;

AFRICA; DRAKENSBERG; SOUTHERN AFRICA; SUB-SAHARAN AFRICA;

ASPHODELACEAE; KNIPHOFIA;

EID: 71049151551     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.584008     Document Type: Article

References (90)

1. Adams, S.P., Leitch, I.J., Bennett, M.D., Chase, M.W. & Leitch, A.R. 2000. Ribosomal DNA evolution and phylogeny in Aloe (Asphodelaceae). Amer. J. Bot. 87: 1578-1583.
2. Aguilar, J.F., Rosselló, J.A. & Feliner, G.N. 1999. Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae). Syst. Biol. 48: 735-754.
3. Ainouche, M.L., Baumel, A., Salmon, A. & Yannic, G. 2003. Hybridization, polyploidy and speciation in Spartina (Poaceae). New Phytol. 161: 165-172.
4. Álvarez, I. & Wendel, J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molec. Phylog. Evol. 29: 417-434.
5. Alzate, F., Mort, M.E. & Ramirez, M. 2008. Phylogenetic analyses of Bomarea (Alstroemeriaceae) based on combined analyses of nrITS DNA, psbA-trbH, rpoB-trnC and matK sequences. Taxon 57: 853-862.
6. Avise, J.C., Ankney, C.D. & Nelson, W.S. 1990. Mitochondrial gene trees and the evolutionary relationships of Mallard and Black ducks. Evolution 44: 1109-1119.
7. Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A. & Saunders, N.C. 1987. Intraspecific phylogeography: the bridge between population genetics and systematics. Annual Rev. Ecol. Syst. 18: 489-522.
8. Baldwin, B.G. & Sanderson, M.J. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proc. Natl. Acad. Sci. U.S.A. 95: 9402-9406.
9. Barber, J.C., Finch, C.C., Francisco-Ortega, J., SantosGuerra, A. & Jansen, R.K. 2007. Hybridization in Macaronesian Sideritis (Lamiaceae): evidence from incongruence of multiple independent nuclear and chloroplast sequence datasets. Taxon 56: 74-88.
10. Barker, N.P., von Senger, I., Howis, S., Zachariades, C. & Ripley, B.S. 2005. Plant phylogeography based on nrDNA ITS sequence data: two examples from the Asteraceae. Pp. 217-244 in: Bakker, F.T., Chatrou, L.W., Gravendeel, B. & Pelser, P.B. (eds.), Plant Species Level Systematics: New Perspectives on Pattern and Process. Gantner, Ruggell.
11. Barrier, M., Baldwin, B.G., Robichaux, R.H. & Purugganan, M.D. 1999. Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications. Molec. Biol. Evol. 16: 1105-1113.
12. Baumel, A., Aniouche, M.L., Bayer, R.J., Aniouche, A.K. & Misset, M.T. 2002. Molecular phylogeny of hybridizing species from the genus Spartina Schreb. (Poaceae). Molec. Phylog. Evol. 22: 303-314.
13. Bentham, G. & Hooker, J.D. 1883. Genera Plantarum, vol. 3, pt. 2. Reeve, London. [Facsimile reprinted by Verlag von J. Cramer, 1965.]
14. Berger, A. 1908. Liliaceae-Asphodeloideae-Aloineae. Pp. 31-72 in: Engler, A. (ed.), Das Pflanzenreich, vol. 30. Engelmann, Leipzig.
15. Beyra-Matos, A. & Lavin, M. 1999. A monograph of Pictetia (Papilionoideae, Leguminosae) and review of the Aeschynomeneae. Syst. Bot. Monogr. 56: 1-93.
16. Brenan, J.P.M. 1978. Some aspects of the phytogeography of tropical Africa. Ann. Missouri Bot. Gard. 65: 437-478.
17. Carine, M.A., Robba, L., Little, R., Russel, S. & Guerra, A.S. 2007. Molecular and morphological evidence for hybridization between endemic Canary Island Convolvulus. Bot. J. Linn. Soc. 154: 187-204.
18. Chase, M.W., De Bruijn, A.Y., Reeves, G., Cox, A.V., Rudall, P.J., Johnson, M.A.T. & Eguiarte, L.E. 2000. Phylogenetics of Asphodelaceae (Asparagales): an analysis of plastid rbcL and trnL-trnF DNA sequences. Ann. Bot. 86: 935-956.
19. Chase, M.W. & Hills, H.H. 1991. Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon 40: 215-220.
20. Chiang, T.-Y., Hung, K.-H., Hsu, T.-W. & Wu, W.-L. 2004. Lineage sorting and phylogeography in Lithocarpus formosanus and L. dodonaeifolius (Fagaceae) from Taiwan. Ann. Missouri Bot. Gard. 91: 207-222.
21. Church, S.A. & Taylor, D.R. 2005. Speciation and hybridisation among Houstonia (Rubiaceae) species: the influence of polyploidy on reticulate evolution. Amer. J. Bot. 92: 1372-1380.
22. Codd, L.E. 1967. The status of the genus Notosceptrum Benth. (Liliaceae). Bot. Not. 120: 41-45.
23. Codd, L.E. 1968. The South African species of Kniphofia. Bothalia 9: 363-513.
24. Codd, L.E. 2005. Kniphofia. Pp. 1-94 in: Germishuizen, G. & Momberg, B.A. (eds.), Flora of Southern Africa, vol. 5. South African National Biodiversity Institute, Pretoria.
25. Comes, H.P. & Abbott, R.J. 2001. Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae). Evolution 55: 1943-1962.
26. Cron, G.V., Balkwill, K. & Knox, E.B. 2008. Phylogenetic evidence for the circumscription of Cineraria L. (Asteraceae-Senecioneae). Taxon 57: 779-798.
27. Cronn, R.C., Small, R.L., Haselkorn, T. & Wendel, J.F. 2002. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. Amer. J. Bot. 89: 707-725.
28. Cronn, R., Small, R.L., Haselkorn, T. & Wendel, J.F. 2003. Cryptic repeated genomic recombination during speciation in Gossypium gossypioides. Evolution 57: 2475-2489.
29. Demissew, S. & Nordal, I. 1997. Kniphofia. Pp. 106-111 in: Edwards, S., Demissew, S. & Hedberg, I. (eds.), Flora of Ethiopia and Eritrea, vol. 6. Educational Materials Production & Distribution Agency (EMPDA), Addis Ababa.
30. Doyle, J.J. & Doyle, J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19: 11-15.
31. Doyle, J.J., Doyle, J.L., Rausher, J.T. & Brown, A.H.D. 2003. Diploid and polyploidy reticulate evolution throughout the history of the perennial soybeans (Glycine subgenus Glycine). New Phytol. 161: 121-132.
32. Farris, J.S., Källersjö, M., Kluge, A.G. & Bult, C. 1994. Testing significance of congruence. Cladistics 10: 315-319.
33. Fjeldså, J. & Lovett, J.C. 1997. Geographical patterns of old and new species in African forest biota: the significance of specific montane areas as evolutionary centres. Biodiv. Cons. 6: 325-346.
34. Galley, C., Bytebier, B., Bellstedt, D.U. & Linder, H.P. 2007. The Cape element in the Afrotemperate flora: from Cape to Cairo. Proc. Roy. Soc. London, Ser. B, Biol. Sci. 274: 535-543.
35. Galley, C. & Linder, H.P. 2006. Geographical affinities of the Cape Flora, South Africa. J. Biogeogr. 33: 236-250.
36. Goldblatt, P. 1978. An analysis of the flora of southern Africa: its characteristics, relationships, and origins. Ann. Missouri Bot. Gard. 65: 369-436.
37. Goldman, D.H., Jansen, R.K., van den Berg, C., Leitch, I.J., Fay, M.F. & Chase, M.W. 2004. Molecular and cytological examination of Calopogon (Orchidaceae, Epidendroideae): circumscription, phylogeny, polyploidy, and possible hybrid speciation. Amer. J. Bot. 91: 707-723.
38. Gravendeel, B., Eurlings, M.C.M., van den Berg, C. & Cribb, P.J. 2004. Phylogeny of Pleione (Orchidaceae) and parentage analysis of its wild hybrids based on plastid and nuclear ribosomal ITS sequences and morphological data. Syst. Bot. 29: 50-63.
39. Harris, D.J., Poulsen, A.D., Frimodt-Møller, C., Preston, J. & Cronk, Q.C.B. 2000. Rapid radiation in Aframomum (Zingiberaceae): evidence from nuclear ribosomal DNA internal transcribed spacer (ITS) sequences. Edinburgh J. Bot. 57: 377-395.
40. Hedberg, O. 1970. Evolution of the Afroapline flora. Biotropica 2: 16-23.
41. Howarth, D.G. & Baum, D.A. 2005. Genealogical evidence of homoploid hybrid speciation in an adaptive radiation of Scaevola (Goodeniaceae) in the Hawaiian Islands. Evolution 59: 948-961.
42. Huelsenbeck, J.P. & Ronquist, F. 2001. MR BAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
43. Käss, E. & Wink, M. 1997. Phylogenetic relationships in the Papilionoideae (family Leguminosae) based on nucleotide sequences of cpDNA (rbcL) and nrDNA (ITS 1 and 2). Molec. Phylog. Evol. 8: 65-88.
44. Kativu, S. 1996. Asphodelaceae of the Flora Zambesiaca area. Kirkia 16: 27-53.
45. Klak, C., Hedderson, T., Linder, P. 2003. A molecular systematic study of the Lampranthus group (Aizoaceae) based on the chloroplast trnL-trnF and nuclear ITS and 5S NTS sequence data. Syst. Bot. 28: 70-85.
46. Knox, E.B. & Palmer, J.D. 1995. Chloroplast DNA variation and the recent radiation of the gaint senecios (Asteraceae) on the tall mountains of eastern Africa. Proc. Natl. Acad. Sci. U.S.A. 92: 10349-10353.
47. Lang, P., Dane, F. & Kubisiak, T.L. 2006. Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data. Tree Genet. Genomes 2: 132-139.
48. Larena, B.G., Aguilar, J.F. & Feliner, G.N. 2002. Glacialinduced altitudinal migrations in Armeria (Plumbaginaceae) inferred from patterns of chloroplast DNA haplotype sharing. Molec. Ecol. 11: 1965-1974.
49. Levin, R.A., Watson, K. & Bohs, L. 2005. A four-gene study of evolutionary relationships in Solanum section Acanthophora. Amer. J. Bot. 92: 603-612.
50. Lewis, C.A. 2008. Late Quaternary climatic changes, and associated human responses, during the last ~45 000 yr in the Eastern and adjoining Western Cape, South Africa. Earth Sci. Rev. 88: 167-187.
51. Maddison, D.R. 1991. The discovery and importance of multiple islands of most-parsimonious trees. Syst. Zool. 40: 315-328.
52. Maddison, W.P. & Maddison, D.R. 2000. MacClade 4: Analysis of Phylogeny and Character Evolution. Sinauer, Sunderland.
53. Malcomber, S.T. 2002. Phylogeny of Gaertnera Lam. (Rubiaceae) based on multiple DNA markers: evidence of a rapid radiation in a widespread, morphologically diverse genus. Evolution 56: 42-57.
54. Marais, W. 1973. A revision of the tropical species of Kniphofia (Liliaceae). Kew Bull. 28: 465-483.
55. Mason-Gamer, R.J. 2004. Reticulate evolution, introgression and intertribal gene capture in an allohexaploid grass. Syst. Biol. 53: 25-37.
56. Mast, A.R., Feller, D.M.S., Kelso, S. & Conti, E. 2004. Buzzpollinated Dodecatheon originated from within the heterostylous Primula subgenus Auriculastrum (Primulaceae): a seven-region cpDNA phylogeny and its implications for floral evolution. Amer. J. Bot. 91: 926-942.
57. Mast, A.R. & Givnish, T. 2002. Historical biogeography and the origin of stomatal distributions in Banksia and Dryandra (Proteaceae) based on their cpDNA phylogeny. Amer. J. Bot. 89: 1311-1323.
58. McKinnon, G.E., Steane, D.A., Potts, B.M. & Vaillancourt, R.E. 1999. Incongruence between chloroplast and species phylogeny in Eucalyptus subgenus Monocalyptus (Myrtaceae). Amer. J. Bot. 86: 1038-1046.
59. McKinnon, G.E., Vaillancourt, R.E., Jackson, H.D. & Potts, B.M. 2001.Chloroplast sharing in the Tasmanian Eucalypts. Evolution 55: 703-711.
60. Mummenhoff, K., Brüggemann, H. & Bowman, J.L. 2001. Chloroplast DNA phylogeny and biogeography of Lepidium (Brassicaceae). Amer. J. Bot. 88: 2051-2063.
61. Mummenhoff, K., Linder, P., Friesen, N., Bowman, J.L., Lee, J.-Y. & Franzke, A. 2004. Molecular evidence for bicontinental hybridogenous genomic constitution in Lepidium sensu stricto (Brassicaceae) species from Australia and New Zealand. Amer. J. Bot. 91: 254-261.
62. Nickrent, D.L., Garcia, M.A., Martin, M.P. & Mathiasen, R.L. 2004. A phylogeny of all species of Arceuthobium (Viscaceae) using nuclear and chloroplast DNA sequences. Amer. J. Bot. 91: 125-138.
63. Noyes, R.D. 2006. Intraspecific nuclear ribosomal DNA divergence and reticulation in sexual diploid Erigeron strigosus (Asteraceae). Amer. J. Bot. 93: 470-479.
64. Nylander, J.A. 2004. MrModeltest vers. 2.2. Distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala. Available from http://www.ebc.uu.se/systzoo/staff/nylander.html
65. Okuyama, Y., Fujii, N., Wakabayashi, M., Kawakita, A., Ito, W., Watanabe, M., Murakami, N. & Kato, M. 2005. Nonuniform concerted evolution and chloroplast capture: heterogeneity of observed introgression patterns in three molecular data partition phylogenies of Asian Mitella (Saxifragaceae). Molec. Biol. Evol. 22: 285-296.
66. Oliveira, L.O., Huck, R.B., Gitzendanner, G.A., Judd, W.S., Soltis, D.E. & Soltis, P.S. 2007. Molecular phylogeny, biogeography, and systematics of Dicerandra, a genus endemic to the southeastern United States. Amer. J. Bot. 94: 1017-1027.
67. Page, R.D.M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comput. Applic. Biosci. 12: 357-358.
68. Patterson, T.B. & Givnish, T.J. 2003. Geographic cohesion, chromosomal evolution, parallel adaptive radiations and consequent floral adaptations in Calochortus (Calochortaceae): evidence from a cpDNA phylogeny. New Phytol. 161: 253-264.
69. Perret, M., Chautems, A., Spichiger, R., Kite, G. & Savolainen, V. 2003. Systematics and evolution of tribe Sinningieae (Gesneriaceae): evidence from phylogenetic analyses of six plastid DNA regions and nuclear ncpGS. Amer. J. Bot. 90: 445-460.
70. Popp, M. & Oxelman, B. 2007. Origin and evolution of North American polyploid Silene (Caryophyllaceae). Amer. J. Bot. 94: 330-349.
71. Ramdhani, S., Barker, N.P. & Baijnath, H. 2006. Phylogenetics of the genus Kniphofia Moench (Asphodelaceae). Pp. 559-573 in: Ghazanfar, S.A. & Beentje, H.J. (eds.), Taxonomy and Ecology of African Plants: Their Conservation and Sustainable Use. Royal Botanic Gardens, Kew.
72. Ramdhani, S., Barker, N.P. & Baijnath, H. 2008. Exploring the Afromontane centre of endemism: Kniphofia Moench (Asphodelaceae) as a floristic indicator. J. Biogeogr. 35: 2258-2273.
73. Ramsay, P.J. & Cooper, J.A.G. 2002. Late Quaternary sealevel change in South Africa. Quatern. Res. 57: 82-90.
74. Richardson, J.E., Pennington, R.T., Pennington, T.D. & Hollingsworth, P.M. 2001. Rapid diversification of a species rich genus of neotropical rain forest trees. Science 293: 2242-2245.
75. Saltonstall, K. 2002. Cryptic invasion by a non-native genotype of the common reed, Phragmites australis, into North America. Proc. Natl. Acad. Sci. U.S.A. 99: 2445-2449.
76. Sauquet, S., Doyle, J.A., Scharaschkin, T., Borsch, T., Hilu, K.W., Chatrou, L.W. & Thomas, A.L. 2003. Phylogenetic analysis of Magnoliales and Myristicaceae based on multiple data sets: implications for character evolution. Bot. J. Linn. Soc. 142: 125-186.
77. Scott, L. 1983. Palynological evidence for vegetation patterns in the Transvaal (South Africa) during the Late Pleistocene and Holocene. Bothalia 14: 445-449.
78. Scott, L. 2002. Grassland development under glacial and interglacial conditions in southern Africa: review of pollen, phytolith and isotope evidence. Palaeogeogr. Palaeoclimatol. Palaeoecol. 177: 47-57.
79. Scott, L., Anderson, H.M. & Anderson, J.M. 1997. Vegetation history. Pp. 62-84 in: Cowling, R.M., Richardson, D.M. & Pierce, S.M. (eds.), Vegetation of Southern Africa. Cambridge University Press, Cambridge.
80. Shaw, J., Lickey, E.B., Beck, J.T., Farmer, S.B., Lui, W., Miller, J., Siripun, K.C., Winder, C.T., Schilling, E.E. & Small, R.L. 2005. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Amer. J. Bot. 92: 142-166.
81. Swofford, D.L. 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), version 4.0b10. Sinauer, Sunderland.
82. Taberlet, P., Gielly, L., Pautou, G. & Bouvet, J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Pl. Molec. Biol. 17: 1105-1109.
83. Taylor, J. 1985. Kniphofia a survey. Plantsman 7: 129-160.
84. Treutlein, J., Smith, G.F., van Wyk, B.-E. & Wink, M. 2003. Phylogenetic relationships in Asphodelaceae (subfamily Alooideae) inferred from chloroplast DNA sequences (rbcL, matK) and from genomic fingerprinting (ISSR). Taxon 52: 193-207.
85. Vogel, J.C. 1983. Isotopic evidence for the past climates and vegetation of southern Africa. Bothalia 14: 391-394.
86. Vriesendorp, B. & Bakker, F.T. 2005. Reconstructing patterns of reticulate evolution in angiosperms: what can we do? Taxon 54: 593-604.
87. Warwick, S.I., Al-Shehbaz, I.A., Sauder, C.A., Murray, D.F. & Mummenhoff, K. 2004. Phylogeny of Smelowskia and related genera (Brassicaceae) based on nuclear ITS DNA and chloroplast trnL intron DNA sequences. Ann. Missouri Bot. Gard. 91: 99-123.
88. White, T.J., Bruns, T., Lee, S. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pp. 315-324 in: Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J. (eds.), PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego.
89. Whitehouse, C. 2002. Asphodelaceae. Pp. 1-19 in: Beentje, H.J. (ed.), Flora of Tropical East Africa. Balkema, Rotterdam.
90. Zinderen Bakker E.M. van. 1983. The Late Quaternary history of climate and vegetation in East and southern Africa. Bothalia 14: 369-375.