Reconstructing ancestral ecologies: Challenges and possible solutions

Diversity and Distributions

Volumn 12, Issue 1, 2006, Pages 7-19

  Hardy, Christopher R ^a,b  

^a Institute for Systematic Botany   (Switzerland)

^b MILLERSVILLE UNIVERSITY   (United States)

Author keywords

Ancestor reconstruction; Cape Floristic Region; Darwin's finches; Historical ecology; Macroecology; Optimization; South Africa

Indexed keywords

EVOLUTIONARY BIOLOGY; EVOLUTIONARY THEORY; HISTORICAL ECOLOGY; MACROECOLOGY; MAXIMUM LIKELIHOOD ANALYSIS; PHYLOGENY;

FRINGILLIDAE;

EID: 33645025874     PISSN: 13669516     EISSN: 14724642     Source Type: Journal    
DOI: 10.1111/j.1366-9516.2006.00207.x     Document Type: Review

References (63)

1. Akaike H. 1974 A new look at the statistical model identification IEBE Transactions on Automatic Control 19 716 723
2. Cunningham C.W. 1999 Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses Systematic Biology 48 665 674
3. Cunningham C.W. Omland K.E. Oakley T.H. 1998 Reconstructing ancestral character states: a critical reappraisal Trends in Ecology and Evolution 13 361 366
4. Donoghue M.J. Ackerly D.D. 1996 Phylogenetic uncertainties and sensitivity analysis in comparative biology Philosophical Transactions of the Royal Society of LondonSeries B, Biological Sciences 351 1241 1249
5. Doughty P. 1996 Statistical analysis of natural experiments in evolutionary biology: comments on recent criticisms of the use of comparative methods to study adaptation American Naturalist 148 943 956
6. Farris J.S. 1970 Methods for computing Wagner trees Systematic Zoology 19 83 92
7. Felsenstein J. 1985 Phylogenies and the comparative method American Naturalist 125 1 15
8. Fitch W. 1971 Toward defining the course of evolution: minimum change for a specific tree topology Systematic Zoology 20 406 416
9. Frumhoff P.C. Reeve H.K. 1994 Using phylogenies to test hypotheses of adaptation: a critique of some current proposals Evolution 48 172 180
10. Givnish T.J. Sytsma K.J. 1997 Molecular evolution and adaptive radiation Cambridge University Press Cambridge
11. Goloboff P. Farris J.S. Nixon K.C. 2004 tnt : Tree searching using New Technology Program available from. (Last accessed 9 September 2004)
12. Graham C.H. Ron S.R. Santos J.C. Schneider C.J. Moritz C. 2004 Integrating phylogenetics and environmental niche models to explore speciation mechanisms in dendrobatid frogs Evolution 58 1781 1793
13. Hansen T.F. Martins E.P. 1996 Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data Evolution 50 1404 1417
14. Hardy C.R. Linder H.P. 2005a Intraspecific variability and timing in ancestral ecology reconstruction: a test case from the Cape flora Systematic Biology 54 299 316
15. Hardy C.R. Linder H.P. 2005b ) Phylogeny and historical ecology in Rhodocoma (Restionaceae) from the Cape Floristic Region. Monocots: systematics and evolution. Proceedings of the 3rd International Conference on the Comparative Biology of the Monocotyledons Rancho Santa Ana Botanic Garden Claremont, CA, USA
16. Harvey P.H. Pagel M.D. 1991 The comparative method in evolutionary biology Oxford University Press Oxford, UK
17. Huelsenbeck J.P. Rannala B. Masly J.P. 2000 Accommodating phylogenetic uncertainty in evolutionary studies Science 288 2349 2350
18. Huey R.B. Bennett A.F. 1987 Phylogenetic studies of coadaptation: preferred temperatures versus optimal performance temperatures of lizards Evolution 41 1098 1115
19. Johnson S.D. 1996 Pollination, adaptation and speciation models in the Cape flora of South Africa Taxon 45 59 66
20. Johnson S.D. Linder H.P. Steiner K.E. 1998 Phylogeny and radiation of pollination systems in Disa (Orchidaceae) American Journal of Botany 85 402 411
21. Kurzweil H. Linder H.P. Chesselet P. 1991 The phylogeny and evolution of the Pterygodium-Corycium complex (Coryciinae, Orchidaceae) Plant Systematics and Evolution 175 161 223
22. Linder H.P. 2003 The radiation of the Cape flora, southern Africa Biological Reviews 78 597 638
23. Linder H.P. Hardy C.R. 2005 Speciation in the Cape flora: a macroevolutionary and macroecological perspective Plant species-level systematics: new perspectives on pattern and process (ed. by Bakker F.T. Chatrou L.W. Gravendeel B. Pelser P.B. Koeltz Königstein, Germany
24. Linder H.P. Hardy C.R. Rutschmann F. 2005 Taxon sampling effects in molecular clock dating: an example from the African Restionaceae Molecular Phylogenetics and Evolution 35 569 582
25. Linder H.P. Vlok J.H. 1991 The morphology, taxonomy and evolution of Rhodocoma (Restionaceae) Plant Systematics and Evolution 175 139 160
26. Losos J.B. 1999 Uncertainty in the reconstruction of ancestral character states and limitations on the use of phylogenetic comparative methods Animal Behavior 58 1319 1324
27. Lutzoni F. Pagel M. Reeb V. 2001 Major fungal lineages derived from lichen-symbiotic ancestors Nature 411 937 940
28. Maddison W.P. 1989 Reconstructing character evolution on polytomous cladograms Cladistics 5 365 377
29. Maddison W.P. 1991 Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree Systematic Zoology 40 304 314
30. Maddison D.R. 1994 Phylogenetic methods for inferring the evolutionary history and processes of change in discretely valued characters Annual Review of Entomology 39 267 292
31. Maddison W.P. 1995 Calculating the probability distributions of ancestral states reconstructed by parsimony on phylogenetic trees Systematic Biology 44 474 481
32. Maddison W.P. Maddison D.R. 1987 ) macclade version 2.1. Analysis of phylogeny and character evolution. Available by anonymous FTP from Indiana University. ftp://ftp.bio.indiana. edu/molbio/mac/. (Last accessed 15 September 2005)
33. Maddison W.P. Maddison D.R. 1992 macclade version 3: analysis of phylogeny and character evolution Sinauer Associates, Inc., Sunderland, Massachusetts
34. Maddison W.P. Maddison D.R. 2003 mesquite : a modular system for evolutionary analysis, version 10 Available at. (Last accessed 9 September 2004)
35. Manning J.C. Linder H.P. 1992 Pollinators and evolution in Disperis (Orchidaceae), or why are there so many species? South African Journal of Science 88 38 49
36. Martins E.P. 1999 Estimation of ancestral states of continuous characters: a computer simulation study Systematic Biology 48 642 650
37. Martins E.P. 2004 compare, version 46Computer programs for the statistical analysis of comparative data Distributed by the author at Department of Biology, Indiana University Bloomington Indiana
38. Martins E.P. Diniz J.A.F. Housworth E.A. 2002 Adaptive constraints and the phylogenetic comparative method: a computer simulation test Evolution 56 1 13
39. Martins E.P. Hansen T.F. 1997 Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data American Naturalist 149 646 667
40. Michevich M.F. Mitter C. 1981 Treating polymorphic characters in systematics: a phylogenetic treatment of electrophoretic data Advances in cladistics: proceedings of the first meeting of the Willi Hennig Society (ed. by Funk V.A. Brooks D.R. pp 45 48 The New York Botanical Garden press New York
41. Mickevich M.F. Johnson M.F. 1976 Congruence between morphological and allozyme data in evolutionary inference and character evolution Systematic Zoology 25 260 270
42. Mooers A.O. Schluter D. 1999 Reconstructing ancestor states with maximum likelihood: support for one- and two-rate models Systematic Biology 48 623 633
43. Nixon K.C. 2002 ) winclada, version 1.00.08. Published by the author Ithaca, New York
44. Pagel M. 1994 Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters Proceedings of the Royal Society of LondonSeries B, Biological Sciences 255 37 45
45. Pagel M. 1997 Inferring evolutionary processes from phylogenies Zoologica Scripta 26 331 348
46. Pagel M. 1999a Inferring the historical patterns of biological evolution Nature 401 877 884
47. Pagel M. 1999b The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies Systematic Biology 48 612 622
48. Pagel M. Lutzoni F. 2002 Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation Biological evolution and statistical physics (ed. by Lässig M. Valleriani A. pp 148 161 Springer-Verlag Berlin
49. Pagel M. Meade A. Barker D. 2004 Bayesian estimation of ancestral character states on phylogenies Systematic Biology 53 673 684
50. Ronquist F. 1996 diva version 11. Computer program and manual available by anonymous FTP from Uppsala University ftp.uu.se or ftp.systbot.uu.se. (Last accessed 7 November 2002)
51. Ronquist F. 2004 Bayesian inference of character evolution Trends in Ecology and Evolution 19 475 481
52. Salisbury B.A. Kim J. 2001 Ancestral state estimation and taxon sampling density Systematic Biology 50 557 564
53. Schluter D. 1997 ancestorml A program for the estimation of ancestral states and standard errors for continuous characters using maximum likelihood Available from the author at. (Last accessed 9 September 2004)
54. Schluter D. Price T. Mooers A.O. Ludwig D. 1997 Likelihood of ancestor states in adaptive radiation Evolution 51 1699 1711
55. Schutte A.L. Vlok J.H.J. vanWyk B.E. 1995 Fire survival strategy: a character of taxonomic, ecological and evolutionary importance in fynbos legumes Plant Systematics and Evolution 195 243 259
56. 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
57. Smith E.N. Gutberlet R.L. 2001 Generalized frequency coding: a method of preparing polymorphic multistate characters for phylogenetic analysis Systematic Biology 50 156 169
58. Sterelny K. 1999 Species as ecological mosaics Species: new interdisciplinary essays (ed. by Wilson R.A. pp 119 138 Massachusetts Institute of Technology Boston
59. Svenning J.C. 2003 Deterministic Plio-Pleistocene extinctions in the European cool-temperate tree flora Ecology Letters 6 646 653
60. Swofford D.L. 2002 ) paup * version 4.0 Sinauer Associates, Inc.
61. Swofford D.L. Maddison W.P. 1987 Reconstructing ancestral character states under Wagner parsimony Mathematical Biosciences 87 199 229
62. Thorne J.L. Kishino H. Painter I.S. 1998 Estimating the rate correction of the rate of molecular evolution Molecular Biology and Evolution 15 1647 1657
63. Zwickl D.J. Hillis D.M. 2002 Increase taxon sampling greatly reduces phylogenetic error Systematic Biology 51 588 598