Testing for ecological limitation of diversification: A case study using parasitic plants

American Naturalist

Volumn 180, Issue 4, 2012, Pages 438-449

  Hardy, Nate B ^a   Cook, Lyn G ^b  

^a CLEVELAND MUSEUM OF NATURAL HISTORY   (United States)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Dated phylogenies; Diversification rates; Ecological limitation; Parasitic plants; Sister taxon comparisons

Indexed keywords

ASYMMETRY; AUTOTROPHY; DICOTYLEDON; ECOLOGICAL APPROACH; PARASITIC PLANT; PHYLOGENETICS; PHYLOGENY; SPECIES DIVERSITY; TAXONOMY;

ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; ERICACEAE; PHYLOGENY; PHYSIOLOGY;

BIODIVERSITY; ERICACEAE; MODELS, BIOLOGICAL; PHYLOGENY;

ARBUTOIDEAE; ERICACEAE; MONOTROPOIDEAE;

EID: 84866324624     PISSN: 00030147     EISSN: None     Source Type: Journal    
DOI: 10.1086/667588     Document Type: Article

References (95)

1. Barkman, T. J., S.-H. Lim, K. M. Salleh, and K. Nais. 2004. Mitochondrial DNA sequences reveal the photosynthetic relatives of Rafflesia, the world's largest flower. Proceedings of the National Academy of Sciences of the USA 101:787-792.
2. Bennett, J. R., and S. Mathews. 2006. Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A. American Journal of Botany 93:1039-1051.
3. Birand, A., A. Vose, and S. Gavrilets. 2012. Patterns of species ranges, speciation and extinction. American Naturalist 179:1-21.
4. Bremer, K., E. Friis, and B. Bremer. 2004. Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification. Systematic Biology 53:496-505.
5. Britton, T., C. L. Anderson, D. Jacquet, S. Lundqvist, and K. Bremer. 2007. Estimating divergence times in large phylogenetic trees. Systematic Biology 56:741-752.
6. Brown, B. J., and R. J. Mitchell. 2001. Competition for pollination: effects of pollen of an invasive plant on seed set of a native congener. Oecologia (Berlin) 129:43-49.
7. Campbell, D. R. 1985. Pollinator sharing and seed set of Stellaria pubera: competition for pollination. Ecology 66:544-553.
8. Chase, M. W., D. E. Soltis, P. S. Soltis, P. J. Rudall, M. F. Fay, W. H. Hahn, S. Sullivan, et al. 2000. Higher-level systematics of the monocotyledons: an assessment of current knowledge and a new classification. Pages 3-16 in K. L. Wilson and D. A. Morrison, eds. Monocots: systematics and evolution. CSIRO, Collingwood.
9. Crisp, M. D., and L. G. Cook. 2009. Explosive radiation or cryptic mass extinction? interpreting signatures in molecular phylogenies. Evolution 63:2257-2265.
10. Davies, T. J., T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, and V. Savolainen. 2003. Darwin's abominable mystery: insights from a supertree of the angiosperms. Proceedings of the National Academy of Sciences of the USA 101:1904-1909.
11. Davis, C. C., M. Latvis, D. L. Nickrent, K. J. Wurdack, and D. A. Baum. 2007. Floral gigantism in Rafflesiaceae. Science 315:1812.
12. Davis, J. I., D. W. Stevenson, G. Petersen, O. Seberg, L. M. Campbell, J. V. Freudenstein, D. H. Goldman, et al. 2004. A phylogeny of the monocots, as inferred from rbcL and atpA sequence variation, and a comparison of methods for calculating jackknife and bootstrap values. Systematic Botany 29:467-510.
13. Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7:214.
14. Eriksson, O., and B. Bremer. 1992. Pollination systems, dispersal modes, life forms, and diversification rates in angiosperm families. Evolution 46:258-266.
15. Fay, M. F., M. W. Chase, N. Rønsted, D. S. Devey, Y. Pillon, J. C. Pires, G. Petersen, O. Seberg, and J. I. Davis. 2006. Phylogenetics of Liliales: summarized evidence from combined analyses of five plastid and one mitochondrial loci. Pages 559-565 in J. T. Columbus, E. A. Friar, J. M. Porter, L. M. Prince, and M. G. Simpson, eds. Monocots: comparative biology and evolution, excluding Poales. Rancho Santa Ana Botanical Garden, Claremont, CA.
16. Forest, F., M. W. Chase, C. Persson, P. R. Crane, and J. A. Hawkins. 2007. The role of biotic and abiotic factors in the evolution of ant dispersal in the milkwort family (Polygalaceae). Evolution 61: 1675-1694.
17. Freudenstein, J. V., M. B. Broe, and E. R. Feldenkris. 2010. Resolving relationships at the base of Ericaceae: how do the leafless members fit in? Paper presented at Botany 2010, Providence, RI, July 31-August 4.
18. 13C natural abundance of autotrophic and myco-heterotrophic orchids provides insight into nitrogen and carbon gain from fungal association. New Phytologist 160:209-223.
19. Gibson, C. C., and A. R. Watkinson. 1989. The host range and selectivity of a parasitic plant: Rhinanthus minor L. Oecologia (Berlin) 78:401-406.
20. Gilinsky, N. L. 1994. Volatility and the Phanerozoic decline of background extinction intensity. Paleobiology 20:445-458.
21. Goldblatt, P., A. Rodriguez, M. P. Powell, T. J. Davies, J. C. Manning, M. van der Bank, and V. Savolainen. 2008. Iridaceae "out of Australia"? phylogeny, biogeography, and divergence time based on plastid DNA sequences. Systematic Botany 33:495-508.
22. Graham, S. A., J. Hall, K. Sytsma, and S.-H. Shi. 2005. Phylogenetic analysis of the Lythraceae based on four gene regions and morphology. International Journal of Plant Sciences 166:995-1017.
23. Guyer, C., and J. B. Slowinski. 1993. Adaptive radiation and the topology of large phylogenies. Evolution 47:253-263.
24. Hardy, N. B., and L. G. Cook. 2010. Gall-induction in insects: evolutionary dead-end or speciation driver? BMC Evolutionary Biology 10:257.
25. Harmon, L. J., J. A. Shulte, A. Larson, and J. B. Losos. 2003. Tempo and mode of evolutionary radiation in iguanian lizards. Science 301:961-964.
26. Hedges, S. B., J. Dudley, and S. Kumar. 2006. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22:2971-2972.
27. Hey, J. 1992. Using phylogenetic trees to study speciation and extinction. Evolution 46:627-640.
28. Janssen, T., and K. Bremer. 2004. The age of major monocot groups inferred from 800_ rbcL sequences. Botanical Journal of the Linnean Society 146:385-398.
29. Jones, K. E., O. R. P. Bininda-Emonds, and J. L. Gittleman. 2005. Bats, clocks, and rocks: diversification patterns in Chiroptera. Evolution 59:2243-2255.
30. Katoh, T. 2008. Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9:286-298.
31. Kelch, D. G. 1998. Phylogeny of Podocarpaceae: comparison of evidence from morphology and 18S rDNA. American Journal of Botany 85:986-996.
32. Kobe, R. K. 1999. Light gradient partitioning among topical tree species through differential seedling mortality and growth. Ecology 80:187-201.
33. Kron, K. A., W. S. Judd, P. F. Stevens, D. M. Crayn, A. A. Anderberg, P. A. Gadek, C. J. Quinn, and J. L. Luteyn. 2002. A phylogenetic classification of Ericaceae: molecular and morphological evidence. Botanical Review 68:335-423.
34. Lengyel, S., A. D. Gove, A. M. Latimer, J. D. Majer, and R. R. Dunn. 2009. Ants sow the seeds of global diversification in flowering plants. PLoS One 4:e5480.
35. Losos, J. B., and D. Schluter. 2000. Analysis of an evolutionary species-area relationship. Nature 408:847-850.
36. Maddison, W. P., and D. R. Maddison. 2012. Mesquite: a modular system for evolutionary analysis. Version 2.73. http:// mesquiteproject.org.
37. Magallón, S., and A. Castillo. 2009. Angiosperm diversification through time. American Journal of Botany 96:349-365.
38. Magallón, S. M., and M. J. Sanderson. 2001. Absolute diversification rates in angiosperm clades. Evolution 55:1762-1780.
39. McPeek, M. A. 2008. The ecological dynamics of clade diversification and community assembly. American Naturalist 172:E270-E284.
40. Merckx, V., and J. V. Freudenstein. 2010. Evolution of mycoheterotrophy in plants: a phylogenetic perspective. New Phytologist 185: 605-609.
41. Mitter, C., B. Farrell, and B. Wiegmann. 1988. The phylogenetic study of adaptive zones: has phytophagy promoted insect diversification? American Naturalist 132:107-128.
42. Moore, T. E., G. A. Verboom, and F. Forest. 2010. Phylogenetics and biogeography of the parasitic genus Thesium (Santalaceae), with an emphasis on the Cape of South Africa. Botanical Journal of the Linnean Society 162:435-452.
43. Morales, C., and A. Traveset. 2008. Interspecific pollen transfer: magnitude, prevalence and consequences for plant fitness. Critical Reviews in Plant Sciences 27:221-238.
44. Nee, S., A. Mooers, and P. H. Harvey. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proceedings of the National Academy of Sciences of the USA 89:8322-8326.
45. Neyland, R. 2002. A phylogeny inferred from large-subunit (26S) ribosomal DNA sequences suggests that Burmanniales are polyphyletic. Australian Systematic Botany 15:19-28.
46. Nickrent, D. L., A. Blarer, Y.-L. Qiu, D. E. Soltis, P. S. Soltis, and M. Zanis. 2002. Molecular data place Hydnoraceae with Aristolochiaceae. American Journal of Botany 89:1809-1817.
47. Nickrent, D. L., A. Blarer, Y.-L. Qiu, V. Vidal-Russel, and F. E. Anderson. 2004. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evolutionary Biology 4:40.
48. Nickrent, D. L., J. P. Der, and F. E. Anderson. 2005. Discovery of the photosynthetic relatives of the "Maltese mushroom" Cynomorium. BMC Evolutionary Biology 5:38.
49. Nickrent, D. L., V. Malécot, R. Vidal-Russel, and J. P. Der. 2010. A revised classification of Santalales. Taxon 59:538-558.
50. Niklas, K. J. 1997. The evolutionary biology of plants. University of Chicago Press, Chicago.
51. Norton, D. A., and M. A. Carpenter. 1998. Mistletoes as parasites: host specificity and speciation. Trends in Ecology & Evolution 13: 101-105.
52. Ollerton, J., A. Stott, E. Allnutt, S. Shove, C. Taylor, and E. Lamborn. 2006. Pollination niche overlap between a parasitic plant and its host. Oecologia (Berlin) 151:473-485.
53. Olmstead, R. G., and D. Ferguson. 2001. A molecular phylogeny of the Boraginaceae/Hydrophyllaceae. Paper presented at Botany 2001, Albuquerque, NM, August 12-16.
54. Oxelman, B., P. Kornhall, R. G. Olmstead, and B. Bremer. 2005. Further disintegration of Scrophulariaceae. Taxon 54:411-425.
55. Paradis, E. 2011a. Shift in diversification in sister-clade comparisons: a more powerful test. Evolution 66:288-295.
56. Paradis, E. 2011b. Time-dependent speciation and extinction from phylogenies: a least squares approach. Evolution 65:661-672.
57. Paradis, E., J. Claude, and K. Strimmer. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290.
58. Phillimore, A. B., R. P. Freckleton, C. D. L. Orme, and I. P. F. Owens. 2006. Ecology predicts large-scale patterns of phylogenetic diversification in birds. American Naturalist 168:220-229.
59. Price, M. N., P. S. Dehal, and A. P. Arkin. 2010. FastTree 2: approximately maximum-likelihood trees for large alignments. PLoSONE 5:e9490.
60. Pybus, O. G., and P. H. Harvey. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society B: Biological Sciences 267:2267-2272.
61. Quental, T. B., and C. R. Marshall. 2009. Extinction during evolutionary radiations: reconciling fossil record with molecular phylogenies. Evolution 63:3158-3167.
62. Quental, T. B., and C. R. Marshall. 2010. Diversity dynamics: molecular phylogenies need the fossil record. Trends in Ecology & Evolution 25:434-441.
63. Rabosky, D. L. 2006. LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evolutionary Bioinformatics 2:247-250.
64. Rabosky, D. L. 2009a. Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecology Letters 12:735-743.
65. Rabosky, D. L. 2009b. Ecological limits on clade diversification in higher taxa. American Naturalist 173:662-674.
66. Rabosky, D. L. 2010. Extinction rates should not be estimated from molecular phylogenies. Evolution 64:1816-1824.
67. Rabosky, D. L., and R. E. Glor. 2010. Equilibrium speciation in a model adaptive radiation of island lizards. Proceedings of the National Academy of Sciences of the USA 107:22178-22183.
68. Rabosky, D. L., and I. J. Lovette. 2008. Density-dependent diversification in North American wood warblers. Proceedings of the Royal Society B: Biological Sciences 275:2363-2371.
69. Raup, D. 1972. Taxonomic diversity during the Phanerozoic. Science 177:1065-1071.
70. Reynolds, H. L., A. Packer, J. D. Bever, and K. Clay. 2003. Grassroots ecology: plant-microbe-soil interactions as drivers of plant community structure and dynamics. Ecology 84:2281-2291.
71. Ricklefs, R. E. 2006. Global variation in the diversification rate of passerine birds. Ecology 87:2468-2478.
72. Ricklefs, R. E., J. B. Losos, and T. M. Townsend. 2007. Evolutionary diversification of clades of squamate reptiles. Journal of Evolutionary Biology 20:1751-1762.
73. Rohwer, J. G., and B. Rudolph. 2005. Jumping genera: the phylogenetic position of Cassytha, Hypodaphnis, and Neocinnamomum (Lauraceae) based on different analyses of trnK intron sequences. Annals of the Missouri Botanical Garden 92:153-178.
74. Sanderson, M. J., D. Boss, D. Chen, K. A. Cranston, and A. Wehe. 2008. The PhyLoTA browser: processing GenBank for molecular phylogenetic research. Systematic Biology 57:335-346.
75. Sanderson, M. J., and M. J. Donoghue. 1994. Shifts in diversification rate with origin of angiosperms. Science 264:1590-1593.
76. Rabosky, D. L. 1996. Reconstructing shifts in diversification rates on phylogenetic trees. Trends in Ecology & Evolution 11:15-20.
77. Schluter, D. 2000. The ecology of adaptive radiation. Oxford University Press, New York.
78. Sepkoski, J. J. 1978. A kinetic model of Phanerozoic taxonomic diversity. I. Analysis of marine orders. Paleobiology 4:223-251.
79. Shimodaira, H., and M. Hasagawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16:1114-1116.
80. Smith, R. A., and C. W. dePamphilis. 1998. Phylogenetic placement of the holoparasitic family Lennoaceae: preliminary molecular evidence. American Journal of Botany 65:157.
81. Smith, R. A., D. M. Ferguson, T. J. Barkman, and C.W. dePamphilis. 2000. Molecular phylogenetic evidence for the origin of Lennoaceae: a case of adelphoparasitism in the angiosperms? American Journal of Botany 87(suppl.):158.
82. Smith, S. E., and D. J. Read. 1997. Mycorrhizal symbiosis. 2nd ed. Academic Press, San Diego, CA.
83. Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
84. Stefanovic, S., D. F. Austin, and R. G. Olmstead. 2003. Classification of Convolvulaceae: a phylogenetic approach. Systematic Botany 28:791-806.
85. Talavera, G., and J. Castresana. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56:564-577.
86. Thorogood, C., and S. Hiscock. 2010. Specific developmental pathways underlie host specificity in the parasitic plant Orobanche. Plant Signaling and Behavior 5:275-277.
87. Vamosi, S. M., and J. C. Vamosi. 2005. Endless tests: guidelines for analyzing non-nested sister-group comparisons. Evolutionary Ecology Research 7:567-579.
88. Walker, T. D., and J. W. Valentine. 1984. Equilibrium models of evolutionary species diversity and the number of empty niches. American Naturalist 124:887-899.
89. Weir, J. T. 2006. Divergent timing and patterns of species accumulation in lowland and highland Neotropical birds. Evolution 60: 842-855.
90. Westwood, J. H., J. I. Yoder, M. P. Timko, and C. W. dePamphilis. 2010. The evolution of parasitism in plants. Trends in Plant Science 15:227-235.
91. Wiegmann, B. M., C. Mitter, and B. Farrell. 1993. Diversification of carnivorous parasitic insects: extraordinary radiation or specialized dead end? American Naturalist 142:737-754.
92. Wiens, J. 2011. The causes of species richness patterns across space, time, and clades and the role of "ecological limits. " Quarterly Review of Biology 86:75-96.
93. Wolfe, A. D., C. P. Randle, L. Liu, and K. E. Steiner. 2005. Phylogeny and biogeography of Orobanchaceae. Folia Geobotanica 40:115-134.
94. Wolfe, J. A. 1964. Miocene floras from Fingerrock wash, southwestern Nevada. U.S. Geological Survey Professional Paper 454-N:1-31.
95. Young, N. D., K. E. Steiner, and C. W. dePamphilis. 1999. The evolution of parasitism in Scrophulariaceae/Orobanchaceae: plastid gene sequences refute an evolutionary transition series. Annals of the Missouri Botanical Garden 86:876-893.