Molecular systematics of tribe Rubieae (Rubiaceae): Evolution of major clades, development of leaf-like whorls, and biogeography

Taxon

Volumn 59, Issue 3, 2010, Pages 755-771

  Soza, Valerie L ^a   Olmstead, Richard G ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Biogeography; Chloroplast DNA; Leaf whorls; New world; Phylogeny; Rubieae

Indexed keywords

ADAPTIVE RADIATION; ANCESTRY; BAYESIAN ANALYSIS; BIOLOGICAL DEVELOPMENT; CHEMOTAXONOMY; CHLOROPLAST; CLADISTICS; DICOTYLEDON; DISPERSAL; EVOLUTIONARY BIOLOGY; GEOGRAPHICAL DISTRIBUTION; LEAF; MORPHOLOGY; PARSIMONY ANALYSIS; PHYLOGENY; PHYTOGEOGRAPHY; STEM; TAXONOMY; VEGETATION CLASSIFICATION;

NORTH AMERICA;

EID: 77954551842     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.593008     Document Type: Article

References (62)

1. Andersson, L. & Rova, J.H.E. 1999. The rpsl6 intron and the phylog-eny of the Rubioideae (Rubiaceae). Pl. Syst. Evol. 214: 161-186.
2. Backlund, M. 2005. Phylogenetic studies in the Gentianales: Approaches at different taxonomic levels. Dissertation, Uppsala University, Uppsala.
3. Backlund, M., Bremer, B. & Thullin, M. 2007. Paraphyly of Paederieae, recognition of Putorieae and expansion of Plocama (Rubiaceae-Rubioideae). Taxon 56: 315-328.
4. Baillon, H.E. 1880. Historie desplantes, vol. 7. Paris: Hachette.
5. Behling, H. 1997. Late Quaternary vegetation, climate and fire history from the tropical mountain region of Morro de Itapeva, SE Brazil. Palaeogeogr. Palaeoclimatol. Palaeoecol. 129: 407-422.
6. Bremekamp, C.E.B. 1966. Remarks on the position, the delimitation and the subdivision of the Rubiaceae. ActaBot. Neerl. 15: 1-33.
7. Bremer, B. 1996. Phylogenetic studies within Rubiaceae and relationships to other families based on molecular data. Opera Bot. Belg.7: 33-50.
8. Bremer, B. & Eriksson, T. 1992. Evolution of fruit characters and dispersal modes in the tropical family Rubiaceae. Biol. J. Linn. Soc. 47: 79-95.
9. Bremer, B. & Eriksson, T. 2009. Time tree of Rubiaceae: Phylogeny and dating the family, subfamilies, and tribes. Int. J. Pl. Sci. 170: 766-793.
10. Bremer, B. & Manen, J.-F. 2000. Phylogeny and classification of the subfamily Rubioideae (Rubiaceae). Pl. Syst. Evol. 225: 43-72.
11. Catalàn, P., Kellogg, E.A. & Olmstead, R.G. 1997. Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndhF gene sequences. Molec. Phylog. Evol. 8: 150-166.
12. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Hig-gins, D.G. & Thompson, J.D. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31: 3497-3500.
13. Cox, C.B. & Moore, P.D. 2000. Biogeography: An ecological and evolutionary approach. London: Blackwell.
14. Cronquist, A. 1968. The evolution and classification of flowering plants. Boston: Houghton Mifflin. De Candolle, A.P. 1830. Prodomus systematis naturalis regni vegeta-bilis, vol. 4. Paris: Treuttel et Wiirtz.
15. De Jussieu, A.L. 1789. Genera plantarum secundum ordines naturales disposita. Paris: Herrisant.
16. DeBry, R.W. & Olmstead, R.G. 2000. A simulation study of reducedtree-search effort in bootstrap resampling analysis. Syst. Biol. 49: 171-179.
17. Doyle, J.J. & Doyle, J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19: 11-15.
18. Ehrendorfer, F. 1958. Critical notes on Turkish Rubiaceae. Notes Roy. Bot. Gard. Edinburgh 22: 323-401.
19. Ehrendorfer, F., SchSnbeck-Temesy, E., Puff, C. & Rechinger, W. 2005. Rubiaceae. Part 176 of: Rechinger, K.H., Flora Iranica. Vienna: Verlag des Naturhistorischen Museums Wien.
20. Felsenstein, J. 1985. Confidence limits on phylogenies-an approach using the bootstrap. Evolution 39: 783-791.
21. Fukuda, Y. 1988. Phyllotaxis in two species of Rubia, R. akane and R. sikkimensis. Bot. Mag. (Tokyo) 101: 25-38.
22. Govaerts, R.(ed.) 2006. World checklist of selected plant families. In: Bisby, F.A., Roskov, Y.R., Ruggiero, M.A., Orrell, T.M., Pa-glinawan, L.E., Brewer, P.W., Bailly, N. & van Hertum, J. (eds.), Species 2000 & ITIS catalogue of life: 2007 annual checklist. Digital resource at www.catalogueoflife.org/annual-checklist/2007/. Reading, U.K.: Species 2000.
23. Graham, A. 2009. Fossil record of the Rubiaceae. Ann. Missouri Bot. Gard. 96: 90-108.
24. Hooker, J.D. 1873. Rubiaceae. Pp. 7-151 in: Bentham, G. & Hooker, J.D., Genera plantarum, vol. 2. London: Lovell Reeve & Co., Williams & Norgate.
25. Huelsenbeck, J.P. & Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
26. Huysmans, S., Dessein, S., Smets, E. & Robbrecht, E. 2003. Pollen morphology of NW European representatives confirms monophyly of Rubieae (Rubiaceae). Rev. Paleobot. Palynol. 127: 219-240.
27. Jansen, S., Dessein, S., Piesschaert, F., Robbrecht, E. & Smets, E. 2000. Aluminum accumulation in leaves of Rubiaceae: Systematic and phylogenetic implications. Ann. Bot. (Oxford) 85: 91-101.
28. Jeune, B. 1980. Croissance des feuilles et stipules du Galium palustre L. subsp. elongatum (Presl) Lange et valeur phylogenique de ces données de morphogénèse. Adansonia 19: 451-465.
29. Kårehed, J., Groeninckx, I., Dessein, S., Motley, T.J. & Bremer, B. 2008. The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae. Molec. Phylog. Evol. 49: 843-866.
30. Kumar, S., Mishra, R.K., Kumar, A., Srivastava, S. & Chaudhary, S. 2009. Regulation of stipule development by COCHLEATA and STIPULE-REDUCED genes in pea Pisum sativum. Planta 230: 449-458.
31. Latorre, C., Betancourt, J.L., Rylander, K.A., Quade, J. & Matthei, O. 2003. A vegetation history from the arid prepuna of northern Chile (22-23 °S) over the last 13,500 years. Palaeogeogr. Palaeo-climatol. Palaeoecol. 194: 223-246.
32. Lozano-Garcfa, M.S., Ortega-Guerrero, B. & Sosa-Nájera, S. 2002. Mid- to late-Wisconsin pollen record of San Felipe Basin, Baja California. Quatern. Res. 58: 84-92.
33. Maddison, D.R. & Maddison, W.P. 2000. MacClade 4: Analysis of phylogeny and character evolution, version 4.0. Sinauer, Massachusetts: Sinauer.
34. Maddison, W.P. & Maddison, D.R. 2009. Mesquite: A modular system for evolutionary analysis, version 2.6. http://mesquiteproject.org.
35. Manen, J.-F. & Natali, A. 1995. Comparison of the evolution of ribu-lose-1,5-biphosphate carboxylase (rbcL) and atpB-rbcL noncod-ing spacer sequences in a recent plant group, the tribe Rubieae (Rubiaceae). J. Molec. Evol. 41: 920-927.
36. Manen, J.-F., Natali, A. & Ehrendorfer, F. 1994. Phylogeny of Rubi-aceae-Rubieae inferred from the sequence of a cpDNA intergene region. Pl. Syst. Evol. 190: 195-211.
37. Mort, M.E., Archibald, J.K., Randle, C.P., Levsen, N.D., O'Leary, T.R., Topalov, K., Wiegand, C.M. & Crawford, D.J. 2007. Inferring phylogeny at low taxonomic levels: Utility of rapidly evolving cpDNA and nuclear ITS loci. Amer. J. Bot. 94: 173-183.
38. Natali, A., Manen, J.-F. & Ehrendorfer, F. 1995. Phylogeny of the Rubiaceae-Rubioideae, in particular the tribe Rubieae: Evidence from a non-coding chloroplast DNA sequence. Ann. Missouri Bot. Gard. 82: 428-439.
39. Natali, A., Manen, J.-F., Kiehn, M. & Ehrendorfer, F. 1996. Tribal, generic and specific relationships in the Rubioideae-Rubieae (Ru-biaceae) based on sequence data of a cpDNA intergene region. Opera Bot. Belg. 7: 193-203.
40. Nie, Z.-L., Wen, J., Sun, H. & Bartholomew, B. 2005. Monophyly of Kelloggia Torrey ex Benth. (Rubiaceae) and evolution of its intercontinental disjunction between western North America and eastern Asia. Amer. J. Bot. 92: 642-652.
41. Niklas, K.J. 1998. Light harvesting "fitness landscapes" for vertical shoots with different phyllotactic patterns. Pp. 759-773 in: Jean, V. & Barabe, D. (eds.), Symmetry in plants. River Edge: World Scientific Publishing Co.
42. Nylander, J.A.A., Wilgenbusch, J.C., Warren, D.L. & Swofford, D.L. 2008. AWTY (are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24: 581-583.
43. Posada, D. & Crandall, K.A. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14: 817-818.
44. Pötter, U. & Klopfer, K. 1987. Untersuchungen zur Blatt-und Blüten-entwicklung bei Galium aparine L. (Rubiaceae). Flora 179: 305314.
45. Richard, M.A. 1829. Mémoire sur la famille des Rubiacées. Paris: J. Tastu.
46. Robbrecht, E. 1988. Tropical woody Rubiaceae. Opera Bot. Belg. 1: 1-171.
47. Robbrecht, E. & Manen, J.-F. 2006. The major evolutionary lineages of the coffee family (Rubiaceae, angiosperms). Combined analysis (nDNA and cpDNA) to infer the position of Coptosapelta and Luculia, and supertree construction based on rbcL, rps16, trnL-trnF and atpB-rbcL data. A new classification in two subfamilies, Cinchonoideae and Rubioideae. Syst. & Geogr. Pl. 76: 85-146.
48. Ronquist, F. & Huelsenbeck, J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
49. Rutishauser, R. 1999. Polymerous leaf whorls in vascular plants: Developmental morphology and fuzziness of organ identities. Int. J. Pl. Sci. 160 (6 Suppl.): S81-S103.
50. Rydin, C., Kainulainen, K., Razafimandimbison, S.G., Smedmark, J.E.E. 2009 Deep divergences in the coffee family and the systematic position of Acranthera. Pl. Syst. Evol. 278: 101-123.
51. Rydin, C., Razafimandimbison, S.G., Khodabandeh, A. & Bremer, B. 2009b. Evolutionary relationships in the Spermacoceae alliance (Rubiaceae) using information from six molecular loci: Insights into systematic affinities of Neohymenopogon andMouretia. Taxon 58: 793-810.
52. Sambrook, J., Fritsch, E.F. & Maniatus, T. 1989. Molecular cloning:A laboratoy manual, 2nd ed, vol. 2. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.
53. Schischkin, B.K. (ed.). 2000. Flora of the U.S.S.R., vol. 23. Delhra Dunn, India: Bishen Singh Mahendra Pal Singh; Koenigstein: Koeltz Scientific Books.
54. Schoute, J.C. 1938. On whorled phyllotaxis IV. Early binding whorls. Recueil Trav. Bot. Neerl. 35: 415-558.
55. Schumann, K. 1897. Rubiaceae. Pp. 1-156 in: Engler, A. & Prantl, K. (eds.), Die naturlichen Pflanzenfamilien, Teil IV, Abt. 4. Leipzig: Engelmann.
56. Shaw, J., Lickey, E.B., Beck, J.T., Farmer, S.B., Liu, 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.
57. Shaw, J., Lickey, E.B., Schilling, E.E. & Small, R.L. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III. Amer. J. Bot. 94: 275-288.
58. Swofford, D.L. 2002. PAUP : Phylogenetic analysis using parsimony (*and other methods), version 4.0. Sunderland, Massachusetts: Sinauer.
59. 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.
60. Takeda, H. 1916. Some points in the morphology of the stipules in the Stellatae, with special reference to Galium. Ann. Bot. (Oxford) 30: 197-214.
61. Thompson, R.S. 1990. Late Quaternary vegetation and climate in the Great Basin. Pp. 200-239 in: Betancourt, J.L., van Devender, T.R.n & Martin, P.S. (eds.), PackratMiddens: The last 40,000 years of biotic changes. Tucson: Univ. of Arizona Press.
62. White, J.M. & Ager, T.A. 1994. Palynology, paleoclimatology and correlation of middle Miocene beds from Porcupine River (locality 90-1), Alaska. Quatern. Int. 22/23: 43-77.