Phylogeography of SCHOTIA (Fabaceae): Recent evolutionary processes in an ancient thicket biome lineage

International Journal of Plant Sciences

Volumn 171, Issue 6, 2010, Pages 626-640

  Ramdhani, Syd ^a   Cowling, Richard M ^a   Barker, Nigel P ^b  

^a NELSON MANDELA METROPOLITAN UNIVERSITY   (South Africa)

^b RHODES UNIVERSITY   (South Africa)

Author keywords

Cpdna; Fabaceae; ITS; Leguminosae; Phylogeography; Schotia; Southern Africa; Thicket biome

Indexed keywords

BIOME; CHLOROPLAST; EVOLUTIONARY BIOLOGY; GENETIC MARKER; INTERGLACIAL; LEGUME; PHYLOGENETICS; PHYLOGEOGRAPHY; TAXONOMY;

EASTERN CAPE; SOUTH AFRICA; WESTERN CAPE;

FABACEAE; SCHOTIA;

EID: 77955676712     PISSN: 10585893     EISSN: None     Source Type: Journal    
DOI: 10.1086/653133     Document Type: Article

References (112)

1. Acocks JPH 1953 Veld types of South Africa. Mem Bot Surv S Afr 28:1-128.
2. Aïnouche A-K, RJ Bayer 1999 Phylogenetic relationships in Lupinus (Fabaceae: Papilionoideae) based on internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA. Am J Bot 86:590-607.
3. Allan GJ, JM Porter 2000 Tribal delimitation and phylogenetic relationships of Loteae and Coronilleae (Faboideae: Fabaceae) with special reference to Lotus: evidence from nuclear ribosomal ITS sequences. Am J Bot 87:1871-1881.
4. Aoki K, T Matsumura, T Hattori, N Murakami 2006 Chloroplast DNA phylogeography of Photinia glabra (Rosaceae) in Japan. Am J Bot 93:1852-1858.
5. Barber JC, CC Finch, J Francisco-Ortega, A Santos-Guerra, RK Jansen 2007 Hybridization in Macaronesian Sideritis (Lamiaceae): evidence from incongruence of multiple independent nuclear and chloroplast sequence datasets. Taxon 56:74-88.
6. Barker NP, BD Schrire, J-H Kim 2000 Generic relationships in the tribe Indigofereae (Leguminosae: Papilionoideae) based on sequence data and morphology. Adv Legume Syst 9:311-337.
7. Barker NP, I von Senger, S Howis, C Zachariades, BS Ripley 2005 Plant phylogeography based on nrDNA ITS sequence data: two examples from the Asteraceae. Pages 217-244 in FT Bakker, LW Chatrou, B Gravendeel, PB Pelser, eds. Plant species level systematics: new perspectives on pattern and process. ARG Gantner, Ruggel.
8. Bell CD, DE Soltis, PS Soltis 2005 The age of the angiosperms: a molecular timescale without a clock. Evolution 59:1245-1258.
9. Bello MA, A Bruneau, F Forest, JA Hawkins 2009 Elusive relationships within order Fabales: phylogenetic analyses using matK and rbcL sequence data. Syst Bot 34:102-114.
10. Bennett KD, J Provan 2008 What do we mean by ''refugia''? Quat Sci Rev 27:2449-2455.
11. Bergh N, TA Hedderson, HP Linder, WJ Bond 2007 Palaeoclimateinduced range shifts may explain current patterns of spatial genetic variation in renosterbos (Elytropappus rhinocerotis, Asteraceae). Taxon 56:393-408.
12. Beyra-Matos A, M Lavin 1999 A monograph of Pictetia (Papilionoideae, Leguminosae) and review of the Aeschynomeneae. Syst Bot Monogr 56:1-93.
13. Boucher C, EJ Moll 1980 South African Mediterranean shrublands. Pages 233-248 in F Di Castri, DW Goodall, RL Specht, eds. Mediterranean-type shrublands. Elsevier, Amsterdam.
14. Bruneau A, M Mecure, GP Lewis, PS Herendeen 2008 Phylogenetic patterns and diversification in the caesalpinioid legumes. Botany 86: 697-718.
15. Bryant D, V Moulton 2004 Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Bio Evol 21: 255-265.
16. Bryant D, V Moulton, A Spillner 2007 Consistency of the neighbornet algorithm. Algorithm Mol Biol 2:8, doi:10.1186/1748-7188-2-8. (Pubitemid 47278416)
17. Byrne M 2008 Evidence for multiple refugia at different time scales during Pleistocene climatic oscillations in southern Australia inferred from phylogeography. Quat Sci Rev 27:2576-2585.
18. Carine MA, L Robba, R Little, S Russel, AS Guerra 2007 Molecular and morphological evidence for hybridization between endemic Canary Island Convolvulus. Bot J Linn Soc 154:187-204.
19. Chandler GT, RJ Bayer, MD Crisp 2001 A molecular phylogeny of the endemic Australian genus Gastrolobium (Fabaceae: Mirbelieae) and allied genera using chloroplast and nuclear markers. Am J Bot 88:1675-1687.
20. Chase MW, HH Hills 1991 Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon 40:215-220.
21. Church SA, DR Taylor 2005 Speciation and hybridization among Houstonia (Rubiaceae) species: the influence of polyploidy on reticulate evolution. Am J Bot 92:1372-1380.
22. Codd LE 1956 The Schotia species of southern Africa. Bothalia 6: 515-533.
23. Comes HP, RJ Abbott 2001 Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae). Evolution 55:1943-1962.
24. Cowling R, S Pierce 2009 East of the Cape: conserving Eden. Fernwood, Simons Town.
25. Cowling RM 1984 A syntaxonomic and synecological study in the Humansdorp region of the fynbos biome. Bothalia 15:175-227.
26. Cowling RM, MSx Prochesx, JHJ Vlok 2005 On the origin of southern African subtropical thicket vegetation. S Afr J Bot 71:1-23.
27. Cubas P, C Pardo, H Tahiri 2006 Genetic variation and relationships among Ulex (Fabaceae) species in southern Spain and northern Morocco assessed by chloroplast microsatellite (cpSSR) markers. Am J Bot 92:2031-2043.
28. Curtis B, C Mannheimer 2005 Tree atlas of Namibia. National Botanical Research Institute, Windhoek. Davies TJ, TG Barraclough, MW Chase, PS Soltis, DE Soltis, V
29. Savolainen 2004 Darwin's abominable mystery: insights from a supertree of the angiosperms. Proc Natl Acad Sci USA 101: 1904-1909.
30. De Lange PJ, PB Heenan, DJ Keeling, BG Murray, R Smissen, WR Sykes 2008 Biosystematics and conservation: A case study with two enigmatic and uncommon species of Crassula from New Zealand. Ann Bot 101:881-899.
31. Doyle JJ, JL Doyle 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11-15.
32. Drummond AJ, SYW Ho, MJ Phillips, A Rambaut 2006 Relaxed phylogenetics and dating with confidence. PLoS Biol 4:e88, doi: 10.1371/journal.pbio.0040088.
33. Drummond AJ, GK Nicholls, AG Rodrigo, W Solomon 2002 Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320.
34. Drummond AJ, A Rambaut 2007 Bayesian evolutionary analysis sampling trees. Ver 1.4.3. http://beast.bio.ed.ac.uk.
35. Farris JS, M Källersjö, AG Kluge, C Bult 1994 Testing significance of congruence. Cladistics 10:315-319.
36. Fougére-Danezan M, PS Herendeen, S Maumont, A Bruneau 2010 Morphological evolution in the variable resin-producing Detarieae (Fabaceae): do morphological characters retain a phylogenetic signal? Ann Bot 105:311-325.
37. Fougére-Danezan M, S Maumont, A Bruneau 2007 Relationships among resin-producing Detarieae s.l. (Leguminosae) as inferred by molecular data. Syst Bot 32:748-761.
38. Frajman B, B Oxelman 2007 Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences. Mol Phylogenet Evol 43:140-155.
39. Goldblatt P 1978 An analysis of the flora of southern Africa: its characteristics, relationships, and origins. Ann Mo Bot Gard 65: 369-436.
40. Goldman DH, RK Jansen, C van den Berg, IJ Leitch, MF Fay, MW Chase 2004 Molecular and cytological examination of Calopogon (Orchidaceae, Epidendroideae): circumscription, phylogeny, polyploidy, and possible hybrid speciation. Am J Bot 91:707-723.
41. Grimm GW, T Denk 2008 ITS evolution in Platanus (Platanaceae): homoeologues, pseudogenes and ancient hybridization. Ann Bot 101:403-419.
42. Haston EM, GP Lewis, JA Hawkins 2005 A phylogenetic reappraisal of the Peltophorum group (Caesalpinieae: Leguminosae) based on the chloroplast tnL-F, rbcL and rps16 sequence data. Am J Bot 92: 1359-1371.
43. Hewitt GM 2004 The structure of biodiversity: insights from molecular phylogeography. Front Zool 1:4, doi:10.1186/1742-9994-1-4. (Pubitemid 44969272)
44. Hoare DB, L Mucina, MC Rutherford, JHJ Vlok, DIW Euston-Brown, AR Palmer, LW Powrie, et al 2006 Albany thicket biome. Pages 540-567 in L Mucina, MC Rutherford, eds. The vegetation of South Africa, Lesotho and Swaziland. Tien Wah, Singapore.
45. Hofreiter M 2008 Long DNA sequences and large data sets: investigating the Quaternary via ancient DNA. Quat Sci Rev 27: 2586-2592.
46. Huelsenbeck JP, F Ronquist 2001 MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
47. Hughes CE, DC Bailey, SA Harris 2002 Divergent and reticulate species relationships in Leucaena (Fabaceae) inferred from multiple data sources: insights into polyploid origins and nrDNA polymorphism. Am J Bot 89:1057-1073.
48. Huntley BJ 1984 Characteristics of South African biomes. Pages 1-17 in PV de Booysen, NM Tainton, eds. Ecological effects of fire in South African ecosystems. Springer, Berlin.
49. Huson DH 1998 SplitsTree: a program for analyzing and visualising evolutionary data. Bioinformatics 14:68-73.
50. Huson DH, D Bryant 2006 Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254-267.
51. Javadi F, MF Wojciechowski, H Yamaguchi 2007 Geographical diversification of the genus Cicer (Leguminosae: Papilionoideae) inferred from molecular phylogenetic analyses of chloroplast and nuclear DNA sequences. Bot J Linn Soc 154:175-186.
52. Jü rgens N 1997 Floristic biodiversity and history of African arid regions. Biodiversity and Conservation 6:495-514.
53. Käss E,MWink 1997 Phylogenetic relationships in the Papilionoideae (family Leguminosae) based on nucleotide sequences of cpDNA (rbcL) and nrDNA (ITS 1 and 2). Mol Phylogenet Evol 8:65-88.
54. Kay KM, JB Whittall, SA Hodges 2006 A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evol Biol 6:36, doi:10.1186/1471-2148-6-36. (Pubitemid 43987020)
55. Kenicer GJ, T Kajita, RT Pennington, J Murata 2005 Systematics and biogeography of Lathyrus (Leguminosae) based on internal transcribed and cpDNA sequence data. Am J Bot 92:1199-1209.
56. Killian B, H Ozkan, O Deusch, S Efggen, A Brandolini, J Kohl, W Martin, F Salamini 2007 Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes. Mol Biol Evol 24:217-227.
57. Koch MA, C Kiefer, D Ehrich, J Vogel, C Brochmann, K Mummenhoff 2006 Three times out of Asia Minor: the phylogeography of Arabis alpina L. (Brassiaceae). Mol Ecology 15:825-839.
58. Lavin M, RT Pennington, BB Klitgaard, JI Sprent, HC de Lima, PE Gasson 2001 The Dalbergioid legumes (Fabaceae): delimitation of a pantropical monophyletic clade. Am J Bot 88:503-533.
59. Lewis CA 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.
60. Lubke R 1996 Thicket. Pages 14-18 in AB Low, A Rebelo, eds. Vegetation of South Africa, Lesotho and Swaziland. Department of Environmental Affairs and Tourism, Pretoria.
61. Mackinder B 2005 Detarieae. Pages 68-109 in G Lewis, B Schrire, B Mackinder, M Lock, eds. Legumes of the world. Royal Botanic Gardens, Kew.
62. Maddison WP, DR Maddison 2000 MacClade 4: analysis of phylogeny and character evolution. Sinauer, Sunderland, MA.
63. Magallón S, A Castillo 2009 Angiosperm diversification through time. Am J Bot 96:349-365.
64. Mason-Gamer RJ, EA Kellogg 1996 Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst Biol 45:524-545.
65. McBreen K, PJ Lockhart 2006 Reconstructing reticulate evolutionary histories of plants. Trends Plant Sci 11:398-404.
66. McKenzie RJ, EM Muller, AKW Skinner, PO Karis, NP Barker 2006 Phylogenetic relationships and generic delimitation in subtribe Arctotidinae (Asteraceae: Arctotideae) inferred by DNA sequence data from ITS and five chloroplast regions. Am J Bot 93:1222-1235.
67. McKinnon GE, RE Vaillancourt, HD Jackson, BM Potts 2001 Chloroplast sharing in the Tasmanian eucalypts. Evolution 55:703-711.
68. Midgley JJ, RM Cowling, AHW Seydack, GF van Wyk 1997 Forest. Pages 278-295 in RM Cowling, DM Richardson, SM Pierce, eds. Vegetation of Southern Africa. Cambridge University Press, Cambridge.
69. Moll EJ, F White 1978 The Indian Ocean belt. Pages 561-598 in MJA Werger, ed. Biogeography and ecology of Southern Africa. Junk, The Hague. Mummenhoff K, P Linder, N Friesen, JL Bowman, J-Y Lee, A
70. Franzke 2004 Molecular evidence for bicontinental hybridogenous genomic constitution in Lepidium sensu stricto (Brassicaceae) species from Australia and New Zealand. Am J Bot 91:254-261.
71. Murphy DJ, JT Miller, RJ Bayer, PY Ladiges 2003 Molecular phylogeny of Acacia subgenus Phyllodineae (Mimosoideae: Leguminosae) based on DNA sequences of the internal transcribed spacer region. Aust Syst Bot 16:19-26.
72. Nixon KC 1999 The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15:407-414.
73. Nylander JA 2004 MrModeltest, version 2.2. Uppsala University, Sweden. http://www.abc.se/~nylander/.
74. Page RDM 1996 TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358.
75. Partridge TC, RR Maud 1987 Geomorphical evolution of southern Africa since the Mesozoic. S Afr J Geol 90:179-208.
76. Percy DM, QCB Cronk 2002 Different fates of island brooms: contrasting evolution in Adenocarpus, Genista, and Teline (Genisteae, Fabaceae) in the Canary Islands and Madeira. Am J Bot 89: 854-864.
77. Posada D, KA Crandall 1998 Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
78. Rambaut A, AJ Drummond 2003 Tracer, version 1.3. http://tree .bio.ed.ac.uk/software/tracer/.
79. Ramdhani S, NP Barker, H Baijnath 2009 Rampant non-monophyly of species in Kniphofia Moench (Asphodelaceae) suggests a recent Afromontane radiation. Taxon 58:1141-1152.
80. Ramsay PJ, JAG Cooper 2002 Late Quaternary sea-level change in South Africa. Quat Res 57:82-90.
81. Razafimandimbison SG, EA Kellogg, B Bremer 2004 Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: a case study from the Naucleeae (Rubiaceae). Syst Biol 53:177-192.
82. Ribeiro RA, M Lavin, JP Lemos-Filho, CVM Filho, FRD Santo, MB Lovato 2007 The genus Machaerium (Leguminosae) is more closely related to Aeschynomene Sect. Ochopodium than to Dalbergia: inferences from combined sequence data. Syst Bot 32: 762-771.
83. Ross JH 1977 Flora of southern Africa. Vol 16, pt 2. Botanical Research Institute, Pretoria.
84. Rutherford MC, RH Westfall 1986 Biomes of southern Africa: an objective characterisation. Mem Bot Surv S Afr 54:1-98.
85. Saitou N, M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 6:514-525.
86. Sang T, DJ Crawford, TF Stuessy 1997 Chloroplast DNA phylogeny, reticulate evolution and biogeography of Paeonia (Paeoniaceae). Am J Bot 84:1120-1136.
87. Schnabel A, PE McDonel, JFWendel 2003 Phylogenetic relationships in Gleditsia (Leguminosae) based on ITS sequences. Am J Bot 90: 310-320.
88. Schrire BD, M Lavin, NP Barker, H Cortes-Burns, I von Senger, J-H Kim 2003 Towards a phylogeny of Indigofera (Leguminosae, Papilionoideae): identification of major clades and relative ages. Adv Legume Syst 10:269-302.
89. Schrire BD, M Lavin, GP Lewis 2005 Global distribution patterns of the Leguminosae: insights from recent phylogenies. Biol Skr 55: 375-422.
90. Scott L 1983 Palynological evidence for vegetation patterns in the Transvaal (South Africa) during the Late Pleistocene and Holocene. Bothalia 14:445-449.
91. Scott L, HM Anderson, JM Anderson 1997 Vegetation history. Pages 62-84 in RM Cowling, DM Richardson, SM Pierce, eds. Vegetation of southern Africa. Cambridge University Press, Cambridge.
92. Seigler DS, JE Ebinger, JT Miller 2006 The genus Senegalia (Fabaceae: Mimosoideae) from the New World. Phytologia 88: 38-90.
93. Shaw J, EB Lickey, JT Beck, SB Farmer, W Lui, J Miller, KC Siripun, CT Winder, EE Schilling, RL Small 2005 The tortoise and the hare. II. Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92:142-166.
94. Sigwela AM 2005 Animal seed interactions in the thicket biome: consequences of faunal replacements and land use for seed dynamics. PhD diss. University of Port Elizabeth, Eastern Cape.
95. Sikes DS, PO Lewis 2001 PAUPRat: version 1: PAUP* implementation of the parsimony ratchet. http://users.iab.uaf.edu/;derek-sikes/ software2.htm.
96. Sotuyo S, A Delgado-Salinas, MW Chase, GP Lewis, K Oyama 2007 Cryptic speciation in the Caesalpinia hintonii complex (Leguminosae: Caesalpinioideae) in a seasonally dry Mexican forest. Ann Bot 100:1307-1314.
97. Swofford DL 2002 PAUP*: phylogenetic analysis using parsimony (*and other methods). Ver 4.0 beta 10. Sinauer, Sunderland, MA.
98. Taberlet P, L Geilly, G Pautou, J Bouvet 1991 Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105-1109.
99. Torke BM, BA Schaal 2008 Molecular phylogenetics of the speciesrich neotropical genus Swartzia (Leguminosae, Papilionoideae) and related genera of the swartzioid clade. Am J Bot 95:215-228.
100. van Wyk AE, GF Smith 2001 Regions of florsitic endemism in southern Africa: a review with emphasis on succulents. Umdaus, Pretoria.
101. van Zinderen Bakker EM 1983 The Late Quaternary history of climate and vegetation in east and southern Africa. Bothalia 14: 369-375.
102. Vlok JHJ, DIW Easton-Brown, RM Cowling 2003 Acocks' Valley Bushveld 50 years on: new perspectives on the delimitation, characterisation and origin of subtropical thicket vegetation. S Afr J Bot 69:27-51.
103. Vogel JC 1983 Isotopic evidence for the past climates and vegetation of southern Africa. Bothalia 14:391-394.
104. Vriesendorp B, FT Bakker 2005 Reconstructing patterns of reticulate evolution in angiosperms: what can we do? Taxon 54:593-604.
105. Waltari E, RJ Hijmans, AT Peterson, A ́ S Nyá ri, SL Perkins, RP Guralnick 2007 Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS One 2: e563, doi:10.1371/journal.pone.0000563. (Pubitemid 351279859)
106. Watanabe K, TOhi-Toma, JMurata 2008 Multiple hybridization in the Aristolochia kaempferi group (Aristolochiaceae): evidence from reproductive isolation and molecular phylogeny. Am J Bot 95:885-896.
107. Weiss-Schneeweiss H, K Tremetsberger, GM Schneeweiss, JS Parker, TF Stuessy 2008 Karyotype diversification and evolution in diploid and polyploid South American Hypochaeris (Asteraceae) inferred from rDNA localization and genetic fingerprint data. Ann Bot 101: 909-918.
108. White TJ, T Bruns, S Lee, J Taylor 1990 Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pages 315-324 in M Innis, DH Gelfand, JJ Sninsky, TJ White, eds. PCR protocols: a guide to methods and applications. Academic Press, San Diego, CA.
109. Whithead JB, PJ Lockhart 2007 Deciphering ancient rapid radiations. Trends Ecol Evol 22:258-265.
110. Wikström N, V Savolainen, MW Chase 2001 Evolution of the angiosperms: calibrating the family tree. Proc R Soc B 268:2211-2220.
111. - 2003 Angiosperm divergence times: congruence and incongruence between fossils and sequence divergence estimates. Pages 142-165 in PCJ Donoghue, MP Smith, eds. Telling the evolutionary time: molecular clocks and the fossil record. Taylor & Francis, London.
112. Wojciechowski MF, M Lavin, MJ Sanderson 2004 A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family. Am J Bot 91:1846-1862.