Locating evolutionary precursors on a phylogenetic tree

Evolution

Volumn 66, Issue 12, 2012, Pages 3918-3930

  Marazzi, Brigitte ^a,b   Ané, Cécile ^c   Simon, Marcelo F ^d   Delgado Salinas, Alfonso ^e   Luckow, Melissa ^f   Sanderson, Michael J ^a  

^a The University of Arizona   (United States)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

^d EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^e UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^f Cornell University ^*  (United States)

Author keywords

Deep homology; Extra floral nectary; Homoplasy; Trait evolution

Indexed keywords

ANT; CRYPSIS; DATA SET; EVOLUTIONARY BIOLOGY; HOMOLOGY; LEGUME; LIFE HISTORY TRAIT; MOLECULAR ANALYSIS; MORPHOLOGY; MUTUALISM; NECTARY; PHYLOGENETICS; PLANT-INSECT INTERACTION; STOCHASTICITY;

ARTICLE; BIOLOGICAL MODEL; FABACEAE; GENETICS; HISTOLOGY; NECTAR; PHYLOGENY;

FABACEAE; MODELS, GENETIC; PHYLOGENY; PLANT NECTAR;

FORMICIDAE;

EID: 84870495664     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2012.01720.x     Document Type: Article

References (72)

1. Aliscioni, S., H. L. Bell, G. Besnard, P.-A. Christin, J. T. Columbus, M. R. Duvall, E. J. Edwards, L. Giussani, K. Hasenstab-Lehman, K. W. Hilu, et al. 2011. New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. New Phytol. 193:304-312.
2. Ané, C., J. G. Burleigh, M. M. McMahon, and M. J. Sanderson. 2005. Covarion structure in plastid genome evolution: a new statistical test. Mol. Biol. Evol. 22:914-924.
3. Barker, D., and M. Pagel. 2005. Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput. Biol. 1:24-31.
4. Bartholmes, C., O. Hidalgo, and S. Gleissberg. 2012. Evolution of the YABBY gene family with emphasis on the basal eudicot Eschscholzia californica (Papaveraceae). Plant Biol. 14:11-23.
5. Beattie, A. J. 1985. The evolutionary ecology of ant-plant mutualisms. Cambridge Univ. Press, Cambridge, U.K.
6. Bernardello, G. 2007. A systematic survey of floral nectaries. Pp. 19-128 in S. W. Nicholson, M. Nepi, and E. Pacini, eds. Nectaries and nectar. Springer Verlag, Dordrecht.
7. Bowman, J. L., and D. R. Smyth. 1999. Crabs claw, a gene that regulates carpel and nectary development in Arabidopsis, encodes a novel protein with zinc finger and helix-loop-helix domains. Development 126:2387-2396.
8. Bronstein, J. L., R. Alarcón, and M. Geber. 2006. The evolution of plant-insect mutualisms. New Phytol. 172:412-428.
9. Brundin, L. 1976. Neocomian chironomid and Podonominae-Aphroteniinae (Diptera) in light of phylogenetics and biogeography. Zool. Scr. 5:139-160.
10. Burnham, K. P., and D. R. Anderson. 2002. Model selection and multi-model inference. Springer, New York.
11. Caspary, R. 1848. De nectariis. Adolphum Marcum, Bonn, Germany.
12. Darwin, C. 1872. On the origin of species. 6th ed. P. F. Collier, New York.
13. Delpino, F. 18681875. Ulteriori osservazioni sulla dicogamia nel regno vegetale. I & ii. Atti della Società Italiana di Scienze Naturali XI, XII.
14. Donoghue, M. J. 2005. Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny. Paleobiology 31:77-93.
15. Doyle, J. J. 2011. Phylogenetic perspectives on the origins of nodulation. Mol. Plant Microbe Interact. 24:1289-1295.
16. Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214. doi:10.1186/1471-2148-7-214.
17. Eastman, J. M., M. E. Alfaro, P. Joyce, A. L. Hipp, and L. J. Harmon. 2011. A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 65:3578-3589.
18. Fahn, A. 1979. Secretory tissues in plants. Academic Press, New York.
19. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Press, Sunderland, MA.
20. Felsenstein, J. 2005. Using the quantitative genetic threshold model for inferences between and within species. Philos. Trans. R. Soc. Lond. B 360:1427-1434.
21. Felsenstein, J. 2012. A comparative method for both discrete and continuous characters using the threshold model. Am. Nat. 179:145-156.
22. Fourquin, C., M. Vinauger-Douard, B. Fogliani, C. Dumas, and C. P. Scutt. 2005. Evidence that CRABS CLAW and TOUSLED have conserved their roles in carpel development since the ancestor of the extant angiosperms. Proc. Natl. Acad. Sci. USA 102:4649-4654.
23. Friedman, J., and S. C. H. Barrett. 2008. A phylogenetic analysis of the evolution of wind pollination in the angiosperms. Int. J. Plant Sci. 169:49-58.
24. Giannini, N. P., and P. A. Goloboff. 2010. Delayed-response phylogenetic correlation: An optimization-based method to test covariation of continuous characters. Evolution 64:1885-1898.
25. Gill, P. E., W. Murray, and M. H. Wright. 1981. Practical optimization. Academic Press, London, New York.
26. Gómez-Acevedo, S., L. Rico-Arce, A. Delgado-Salinas, S. Magallon, and L. E. Eguiarte. 2010. Neotropical mutualism between Acacia and Pseudomyrmex: phylogeny and divergence times. Mol. Phylog. Evol. 56:393-408.
27. Harvey, P. H., and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford Univ. Press, Oxford, U.K.
28. Hennig, W. 1966. Phylogenetic systematics. University of Illinois Press, Chicago.
29. Huelsenbeck, J. P., R. Nielsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Syst. Biol. 52:131-158.
30. Irish, V. F. 2009. Evolution of petal identity. J. Exp. Bot. 60:2517-2527.
31. Janzen, D.H. 1966. Coevolution of mutualism between ants and acacias in Central America. Evolution 20:249-275.
32. Keeler, K. H. 2011. World list of plants with extrafloral nectaries. Available at http://bsweb.unl.edu/Emeriti/keeler/extrafloral/Cover.htm.
33. Kitching, I. J., P. L. Forey, C. J. Humphries, and D. Williams. 1998. Cladistics: The theory and practice of parsimony analysis. Oxford Univ. Press, New York.
34. Koptur, S. 1992. Extrafloral nectary-mediated interactions between insects and plants. Pp. 81-129 in E. Bernays, ed. Insect-plant interactions. CRC Press, London.
35. Lee, J. Y., S. F. Baum, J. Alvarez, A. Patel, D. H. Chitwood, and J. L. Bowman. 2005a. Activation of crabs claw in the nectaries and carpels of Arabidopsis. Plant Cell 17:25-36.
36. Lee, J. Y., S. F. Baum, S. H. Oh, C. Z. Jiang, J. C. Chen, and J. L. Bowman. 2005b. Recruitment of crabs claw to promote nectary development within the eudicot clade. Development 132:5021-5032.
37. Lewis, G., B. Schrire, B. Mackinder, and M. Lock. 2005. Legumes of the world. Royal Botanic Gardens, Kew.
38. Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50:913-925.
39. Maddison, W. P., and D. R. Maddison. 2010. Mesquite: a modular system for evolutionary analysis. Available at http://mesquiteproject.org.
40. Marazzi, B., M. M. McMahon, M. Lanan, J. L. Bronstein. 2011. Diversity and evolution of extrafloral nectaries in Sonoran desert plants. Abstract book of the XVII International Botanical Conference, Melbourne, Australia. Abstract number P0882, p. 616.
41. Marazzi, B., and M. J. Sanderson. 2010. Large-scale patterns of diversification in the widespread legume genus Senna and the evolutionary role of extrafloral nectaries. Evolution 64:3570-3592.
42. Markmann, K., and M. Parniske. 2009. Evolution of root endosymbiosis with bacteria: how novel are nodules? Trends Plant Sci. 14:77-86.
43. McKey, D. 1989. Interactions between ants and leguminous plants. Monogr. Syst. Bot. Missouri Bot. Gard. 29:673-718.
44. Melo Y., S. R. Machado, and M. Alves. 2010. Anatomy of extrafloral nectaries in Fabaceae from dry seasonal forest in Brazil. Bot. J. Linn. Soc. 163:87-98.
45. Meng, X. L. 1994. Posterior predictive p-values. Ann. Stat. 22:1142-1160.
46. Minin, V. N., and M. A. Suchard. 2008. Fast, accurate and simulation-free stochastic mapping. Philos. Trans. R. Soc. Lond. B 363:3985-3995.
47. Nepi, M. 2007. Nectary structure and ultrastructure. Pp. 129-166 in S. W. Nicholson, M. Nepi, and E. Pacini, eds. Nectaries and nectar. Springer Verlag, Dordrecht.
48. O'Meara, B. C., C. Ané, M. J. Sanderson, and P. C. Wainwright. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922-933.
49. Pagel, M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol. 48:612-622.
50. Pagel, M., A. Meade, and D. Barker. 2004. Bayesian estimation of ancestral character states on phylogenies. Syst. Biol. 53:673-684.
51. Pascal, L. M., E. F. Motte-Florac, D. B. McKey. 2000. Secretory structures on leaf rachis of Caesalpinieae and Mimosoideae (Leguminosae): implications for the evolution of nectary glands. Am. J. Bot. 87:327-338.
52. Press, W. H., B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling. 1988. Numerical recipes in C. Cambridge Univ. Press, New York.
53. Preston, J. C., L. C. Hileman, and P. Cubas. 2009. Reduce, reuse, and recycle: developmental evolution of trait diversification. Am. J. Bot. 98:397-403.
54. Pupko, T., I. Pe'er, R. Shamir, and D. Graur. 2000. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol. Biol. Evol. 17:890-896.
55. Rajakumar, R., D. S. Mauro, M. B. Dijkstra, M. H. Huang, D. E. Wheeler, F. Hiou-Tim, A. Khila, M. Cournoyea, and E. Abouheif. 2012. Ancestral developmental potential facilitates parallel evolution in ants. Science 335:79-82.
56. Rasmussen, F. N. 1983. On apomorphic tendencies and phylogenetic inference-commentary. Syst. Bot. 8:334-337.
57. Sanderson, M. J. 1991. In search of homoplastic tendencies: statistical inference of topological patterns in homoplasy. Evolution 45:351-358.
58. Sanderson, M. J. 1993. Reversibility in evolution-a maximum-likelihood approach to character gain loss bias in phylogenies. Evolution 47:236-252.
59. Sanderson, M. J. 2003. R8s: inferring absolute rates of evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302.
60. Sanderson, M., and L. Hufford, eds. 1996. Homoplasy: the recurrence of similarity in evolution. Academic Press, New York.
61. Schmid, R. 1988. Reproductive versus extra-reproductive nectaries-historical perspective and terminological recommendations. Bot. Rev. 54:179-232.
62. Scotland, R. W. 2010. Deep homology: a view from systematics. BioEssays 32:438-449.
63. Shubin, N., C. Tabin, and S. Carroll. 1997. Fossils, genes and the evolution of animal limbs. Nature 388:639-648.
64. Shubin, N., C. Tabin, and S. Carroll 2009. Deep homology and the origins of evolutionary novelty. Nature 457:818-823.
65. Simon, M. F., R. Grether, L. P. de Queiroz, C. Skema, R. T. Pennington, and C. E. Hughes. 2009. Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire. Proc. Natl. Acad. Sci. USA 106:20359-20364.
66. Soltis, D. E., P. S. Soltis, D. R. Morgan, S. M. Swensen, B. C. Mullin, J. M. Dowd, and P. G. Martin. 1995. Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen-fixation in angiosperms. Proc. Natl. Acad. Sci. USA 92:2647-2651.
67. Tuffley, C., and M. Steel. 1998. Modeling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147:63-91.
68. Vavilov, N. I. 1922. The law of homologous series in variation. J. Genetics 12:47-89.
69. Vogel, S. 1997. Remarkable nectaries: structure, ecology, organophyletic perspectives. I. Substitutive nectaries. Flora 192:305-333.
70. Wake, D. B., M. H. Wake, and C. D. Specht. 2011. Homoplasy: from detecting pattern to determining process and mechanism of evolution. Science 331:1032-1035.
71. Wiens, J. J. 2011. Re-evolution of lost mandibular teeth in frogs after more than 200 million years, and re-evaluating Dollo's law. Evolution 65:1283-1296.
72. Zimmerman, J. G. 1932. Über die extrafloralen nektarien der angiospermen. Beihefte zum Botanischen Zentralblatt 49:99-196.