Intraspecific variability and timing in ancestral ecology reconstruction: A test case from the Cape flora

Systematic Biology

Volumn 54, Issue 2, 2005, Pages 299-316

  Hardy, Christopher R ^a,b   Linder, H Peter ^a  

^a Institute of Systematic Botany   (Switzerland)

^b MILLERSVILLE UNIVERSITY   (United States)

Author keywords

Ancestor reconstruction; Cape flora; Evolutionary ecology; Generalized frequency coding; Macroecology; Optimization; Restionaceae; Thamnochortus

Indexed keywords

PRIMER DNA;

ANGIOSPERM; ARTICLE; CLASSIFICATION; CLIMATE; COMPARATIVE STUDY; DNA SEQUENCE; ECOLOGY; ENVIRONMENT; GENE; GENETICS; HISTOLOGY; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYSIOLOGY; PLASTID; SOUTH AFRICA; SPECIES DIFFERENCE;

ANGIOSPERMS; BASE SEQUENCE; CLASSIFICATION; CLIMATE; DNA PRIMERS; ECOLOGY; ENVIRONMENT; GENES, PLANT; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASTIDS; SEQUENCE ANALYSIS, DNA; SOUTH AFRICA; SPECIES SPECIFICITY;

RESTIONACEAE; THAMNOCHORTUS;

EID: 19144372984     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150590923317     Document Type: Article

References (87)

1. Andersson, L. 1990. The driving force: Species concepts and ecology. Taxon 39:375-382.
2. Archie, J. W. 1985. Methods for coding variable morphological features for numerical taxonomic analysis. Syst. Zool. 34:326-345.
3. Asmussen, C. B., and M. W. Chase. 2001. Coding and noncoding plastid DNA in palm systematics. Am. J. Bot. 88:1103-1117.
4. Butler, M. A., and J. B. Losos. 1997. Testing for unequal amounts of evolution in a continuous character on different branches of a phylogenetic tree using linear and squared-change parsimony: An example using Lesser Antillean Anolis lizards. Evolution 51:1623-1635.
5. Campbell, B. M. 1983. Montane plant environments in the Fynbos Biome. Bothalia 14:283-298.
6. Change, V., and E. N. Smith. 2001. FastMorphologyGFC version 1.0. http://www3.uta.edu/faculty/ensmith.
7. Chase, M. W., and V. A. Albert. 1998. A perspective on the contribution of plastid rbcL DNA sequences to angiosperm phylogenetics. Pages 488-507 in Molecular systematics of plants II: DNA sequencing (D. E. Soltis, P. S. Soltis, and J. J. Doyle, eds.). Kluwer Academic Publishers, Boston, Massachusetts.
8. Cowling, R. M. 1987. Fire and its role in coexistence and speciation in Gondwanan shrublands. S. African J. Sci. 83:106-112.
9. Cowling, R. M., P. W. Rundel, B. B. Lamont, M. K. Arroyo, and M. Arianoutsou. 1996. Plant diversity in Mediterranean-climate regions. Trends Ecol. Evol. 11:362-366.
10. Cunningham, C. W. 1999. Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses. Syst. Biol. 48:665-674.
11. Cunningham, C. W., K. E. Omland, and T. H. Oakley. 1998. Reconstructing ancestral character states: A critical reappraisal. Trends Ecol. Evol. 13:361-366.
12. Donoghue, M. J., and D. D. Ackerly. 1996. Phylogenetic uncertainties and sensitivity analysis in comparative biology. Philos. Trans. R. Soc. Lond. B 351:1241-1249.
13. Ehrlich, P. R., and P. H. Raven. 1969. Differentiation in populations: Gene flow seems to be less important in speciation than the neo-Darwinians thought. Science 165:1228-1232.
14. Eldenäs, P. K., and H. P. Linder. 2000. Congruence and complementarity of morphological and trnL-trnF sequence data and the phylogeny of the African Restionaceae. Syst. Bot. 25:692-707.
15. Farris, J. S. 1970. Methods for computing Wagner trees. Syst. Zool. 19:83-92.
16. Felsenstein, J. 1979. Alternative methods of phylogenetic inference and their interrelationship. Syst. Zool. 28:49-62.
17. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
18. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
19. Felsenstein, J. 1989. PHYLIP phylogeny inference package. Cladistics 5:164-166.
20. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
21. Fitch, W. 1971. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20:406-416.
22. Frumhoff, P. C., and H. K. Reeve. 1994. Using phylogenies to test hypotheses of adaptation: A critique of some current proposals. Evolution 48:172-180.
23. Goldblatt, P. 1978. An analysis of the flora of southern Africa: Its characteristics, relationships, and origins. Ann. MO. Bot. Gard. 65:369-436.
24. Goldblatt, P., and J. C. Manning. 2000. Cape plants: A conspectus of the Cape flora of South Africa. National Botanical Institute of South Africa, Pretoria, South Africa, and MBG Press, St. Louis, Missouri, USA.
25. Goloboff, P. 1993. NONA, version 1.6. Distributed by the author, Buenos Aires, Argentina.
26. Graham, C. H., S. R. Ron, J. C. Santos, C. J. Schneider, and C. Moritz. 2004. Integrating phylogenetics and environmental niche models to explore speciation mechanisms in dendrobatid frogs. Evolution 58:1781-1793.
27. Graybeal, A. 1994. Evaluating the phylogenetic utility of genes: A search for genes informative about deep divergences among vertebrates. Syst. Biol. 43:174-193.
28. Hilu, K. W., and H. Liang. 1997. The matK gene: Sequence variation and application in plant systematics. Am. J. Bot. 84:830-839.
29. Housworth, E. A., E. P. Martins, and M. Lynch. 2004. The phylogenetic mixed model. Am. Nat. 163:84-96.
30. Huelsenbeck, J. P., R. Nielsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Syst. Biol. 53:131-158.
31. Kocyan, A., Y.-L. Qiu, P. K. Endress, and E. Conti. 2004. A phylogenetic analysis of Apostasioideae (Orchidaceae) based on ITS, trnL-F and matK sequences. Plant Syst. Evol. 247:203-213.
32. Lambrechts, J. J. N. 1979. Geology, geomorphology and soils. Pages 16-26 in Fynbos ecology: A preliminary synthesis (J. Day, W. R. Siegfried, G. N. Louw, and M. L. Jarman, eds.). Council for Scientific and Industrial Research, Pretoria, South Africa.
33. Levin, D. A. 2000. The origin, expansion, and demise of plant species. Oxford University Press, New York.
34. Levin, D. A. 2003. Ecological speciation: Lessons from invasive species. Syst. Bot. 28:643-650.
35. Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50:913-925.
36. Linder, H. P. 1984. A phylogenetic classification of the genera of the African Restionaceae. Bothalia 15:11-76.
37. Linder, H. P. 1985. Gene flow, speciation, and species diversity patterns in a species-rich area: The Cape flora. Pages 53-57 in Species and speciation (E. S. Vrba, ed.). Transvaal Museum Monograph 4, South Africa.
38. Linder, H. P. 1991. A review of the southern African Restionaceae. Contr. Bolus Herb. 13:209-264.
39. Linder, H. P. 2002. The African Restionaceae: An IntKey identification and description system, version 2. Contr. Bol. Herb. 20. Available at http://www.systbot.unizh.ch/datenbanken/restionaceae/index.htm.
40. Linder, H. P. 2003. The radiation of the Cape flora, southern Africa. Biol. Rev. 78:597-638.
41. Linder, H. P., B. G. Briggs, and L. A. S. Johnson. 2000. Restionaceae: A morphological phylogeny. Pages 653-660 in Monocots: Systematics and evolution (K. L. Wilson and D. A. Morrison, eds.). CSIRO Publishing, Collingwood, Victoria, Australia.
42. Linder, H. P., and C. R. Hardy. In press. Speciation in the Cape flora: A macroevolutionary and macroecological perspective. In Plant species-level systematics: New perspectives on pattern and process (F. T. Bakker, L. W. Chatrou, B. Gravendeel, and P. B. Pelser, eds.). Koeltz, Königstein.
43. Losos, J. B. 1999. Uncertainty in the reconstruction of ancestral character states and limitations on the use of phylogenetic comparative methods. Anim. Behav. 58:1319-1324.
44. Maddison, W. P. 1991. Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree. Syst. Zool. 40:304-314.
45. Maddison, W. P. 1995. Calculating the probability distributions of ancestral states reconstructed by parsimony on phylogenetic trees. Syst. Biol. 44:474-481.
46. Maddison, W. P., and D. R. Maddison. 1987. MacClade version 2.1. Distributed by the authors, Cambridge, Massachusetts.
47. Maddison, W. P. and D. R. Maddison. 1992. MacClade version 3: Analysis of phylogeny and character evolution. Sinauer Associates, Sunderland, Massachusetts.
48. Maddison, W. P., and D. R. Maddison. 2003. Mesquite: A modular system for evolutionary analysis, version 1.0. Available at: http://mesquiteproject.org.
49. Maddison, W. P., and M. Slatkin. 1990. Parsimony reconstructions of ancestral states do not depend on the relative distances between linearly-ordered character states. Syst. Zool. 39:175-178.
50. Manen, J., A. Natali, and F. Ehrendorfer. 1994. Phylogeny of Rubiaceae-Rubieae inferred from the sequence of a cpDNA intergene region. Pl. Syst. Evol. 190:195-211.
51. Marloth, R. 1904. Results of experiments on Table Mountain for ascertaining the amount of moisture deposited from the southeast clouds. Trans. S. Afr. Phil. Soc. 14:403-408.
52. Martins, E. P. 1999. Estimation of ancestral states of continuous characters: A computer simulation study. Syst. Biol. 48:642-650.
53. Martins, E. P. 2003. COMPARE, version 4.5. Computer programs for the statistical analysis of comparative data. Distributed by the author at http://compare.bio.indiana.edu/. Department of Biology, Indiana University, Bloomington, Indiana.
54. Martins, E. P., J. A. Diniz-Filho, and E. A. Housworth. 2002. Adaptation and the phylogenetic comparative method. Evolution 21:317-340.
55. Martins, E. P., and T. F. Hansen. 1997. Phylogenies and the comparative method: A general approach to incorporating phylogenetic information into the analysis of interspecific data. Am. Nat. 149:646-667.
56. Mickevich, M. F., and M. F. Johnson. 1976. Congruence between morphological and allozyme data in evolutionary inference and character evolution. Syst. Zool. 25:260-270.
57. Mickevich, M. F., and C. Mitter. 1981. Treating polymorphic characters in systematics: A phylogenetic treatment of electrophoretic data. Pages 45-58 in Advances in cladistics: Proceedings of the first meeting of the Willi Hennig Society (V. A. Funk and D. R. Brooks, eds.). New York Botanical Garden Press, New York.
58. Nixon, K. C. 2002. WinClada ver. 1.00.08. Published by the author, Ithaca, New York.
59. Nixon, K. C., and J. I. Davis. 1991. Polymorphic taxa, missing values and cladistic analysis. Cladistics 7:233-241.
60. Nixon, K. C., and Q. D. Wheeler. 1990. An amplification of the phylogenetic species concept. Cladistics 6:211-223.
61. Omland, K. E. 1999. The assumptions and challenges of ancestral state reconstructions. Syst. Biol. 48:604-611.
62. Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12:357-358.
63. Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884.
64. Posada, D., and K. A. Crandall. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:917-818.
65. Rae, T. 1998. The logical basis for the use of continuous characters in phylogenetic systematics. Cladistics 14:221-228.
66. Rice, N. H., E. Martínez-Meyer, and A. T. Peterson. 2003. Ecological niche differentiation in the Aphelocoma jays: A phylogenetic perspective. Biol. J. Linn. Soc. 80:369-383.
67. Ronquist, F. 1996. DIVA version 1.1. Computer program and manual available by anonymous FTP from Uppsala University (ftp.uu.se or ftp.systbot.uu.se).
68. Sanderson, M. J. 2002a. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
69. Sanderson, M. J. 2002b. r8s, version 1.5. Computer program distributed by the author, http://ginger.ucdavis.edu/r8s.
70. Sankoff, D., and P. Rousseau. 1975. Locating the vertices of a Steiner tree in arbitrary space. Math. Program. 9:240-246.
71. Schluter, D. T. 2000. The ecology of adaptive radiation. Oxford University Press, New York.
72. Schluter, D., T. Price, A. Ø. Mooers, and D. Ludwig. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711.
73. Schutte, A. L., J. H. J. Vlok, and B. W. Van Wyk. 1995. Fire survival strategy: A character of taxonomic, ecological and evolutionary importance in fynbos legumes. Pl. Syst. Evol. 195:243-259.
74. Sharkey, M. J. 1999. Transition confidence and modified mean values: Confidence measures for hypotheses of character state transition between nodes and ancestral state optimizations. Cladistics 15:113-120.
75. Simmons, M. P., and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49:369-381.
76. Smith, E. N., and R. L. Gutberlet. 2001. Generalized frequency coding: A method of preparing polymorphic multistate characters for phylogenetic analysis. Syst. Biol. 50:156-169.
77. Sterelny, K. 1999. Species as ecological mosaics. Pages 119-138 in Species: New interdisciplinary essays (R. A. Wilson, ed.). Massachusetts Institute of Technology, Cambridge, Massachusetts.
78. Swofford, D. L. 2002. PAUP* version 4.0. Sinauer Associates, Sunderland, MA, USA.
79. Swofford, D. L., and S. H. Berlocher. 1987. Inferring evolutionary trees from gene frequency data under the principle of maximum parsimony. Syst. Zool. 36:293-325.
80. Swofford, D. L., and W. P. Maddison. 1987. Reconstructing ancestral character states under Wagner parsimony. Math. Biosci. 87:199-229.
81. Swofford, D. L., and W. P. Maddison. 1992. Parsimony, characterstate reconstructions, and evolutionary inferences. Pages 187-223 in Systematics, historical ecology, and North American freshwater fishes (R. L. Mayden, ed.). Stanford University Press, Stanford, California.
82. Taberlet, P., L. Gielly, G. Pautou, and J. Bouvet. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Pl. Mol. Bio. 17:1105-1109.
83. Thiele, K. 1993. The holy grail of the perfect character: The cladistic treatment of morphometric data. Cladistics 9:275-304.
84. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
85. van Wilgen, B. W. 1987. Fire regimes in the Fynbos biome. Pages 6-14 in Disturbance and dynamics of fynbos biome communities (R. M. Cowling, C. D. Le Maitre, B. McKenzie, R. P. Prys-Jones, and B. W. Van Wilgen, eds.). South African National Scientific Programmes, Pretoria, South Africa, report number 135.
86. Wiens, J. J. 1995. Polymorphic characters in phylogenetic systematics. Syst. Biol. 47:482-500.
87. Young, N. D., and J. Healy. 2001. GapCoder: A computer program for including indels in phylogenetic analysis. Available from the authors at http://www.home.cr.duq.edu/~youngnd/GapCoder.