Phylogeny and the inference of evolutionary trajectories

Journal of Experimental Botany

Volumn 65, Issue 13, 2014, Pages 3491-3498

  Hancock, Lillian ^a   Edwards, Erika J ^a  

^a BROWN UNIVERSITY   (United States)

Author keywords

Crassulacean acid metabolism; Evolution; Intermediate phenotypes; Phylogenetic approach; Phylogeny

Indexed keywords

CLASSIFICATION; COMPUTER SIMULATION; EVOLUTION; GENETICS; PHENOTYPE; PHOTOSYNTHESIS; PHYLOGENY; PHYSIOLOGY; THEORETICAL MODEL; TREE;

BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; MODELS, THEORETICAL; PHENOTYPE; PHOTOSYNTHESIS; PHYLOGENY; TREES;

EID: 84922105728     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/eru118     Document Type: Article

References (44)

1. Bender MM. 1971. Variation in 13C/12C ratios of plants in relation to the pathway of photosyntheitic carbon dioxide fxation. Phytochemistry 10, 1239-1344.
2. Bender MM, Ronham I, Vines HM, Black CC. 1973. 13C/12C ratio changes in crassulacean acid metabolism plants. Plant Physiology 53, 427-430.
3. Besnard G, Muasya AM, Russier F, Roalson EH, Salamin N, Christin PA. 2009. Phylogenomics of C4 photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence. Molecular Biology and Evolution 26, 1909-1919.
4. Bollback JP. 2006. SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7, 88.
5. Christin PA, Freckleton RP, Osborne C P. 2010. Can phylogenetics identify C4 origins and reversals? Trends in Ecology and Evolution 25, 403-409.
6. Christin P, Sage TL, Edwards EJ, Ogburn RM, Khoshravesh R, Sage R F. 2011. Complex evolutionary transitions and the signifcance of C 3-C4 intermediate forms of photosynthesis in Molluginaceae. Evolution 65, 643-660.
7. Christin PA, Wallace MJ, Clayton H, Edwards EJ, Furbank RT, Hattersley PW, Sage RF, Macfarlane TD, Lugwid M. 2012. Multiple photosynthetic transitions, polyploidy, and lateral gene transfer in the grass subtribe Neurachninae. Journal of Experimental Botany 63, 6297-6308.
8. Christin PA, Arakaki M, Osborne CP, Brautigam A, Sage RF, Hibberd JM, Kelly S, Covshoff S, Wong GKS, Hancock L, Edwards EJ. 2014. Shared origins of a key enzyme during the evolution of C4 and CAM metabolism. Journal of Experimental Botany 65, 3609-3621.
9. Cushman JC. 2001. Crassulacean acid metabolism. A plastic photosynthetic adaptation to arid environments. Plant Physiology 127, 1439-1448.
10. Dodd AN, Borland AM, Haslam RP, Griffths H, Maxwell K. 2002. Crassulacean acid metabolism: plastic, fantastic. Journal of Experimental Botany 53, 569-580.
11. Edwards EJ, Ogburn RM. 2012. Angiosperm responses to a low-CO2 world: CAM and C4 photosynthesis as parallel evolutionary trajectories. International Journal of Plant Sciences 173, 724-727.
12. Farquhar GD, Ehlerniger JR, Hubick KT. 1989. Carbon isotope discrimination and photosynthesis. Annual Review of Plant Physiology 40, 503-537.
13. Feodorova TA, Voznesenskaya EV, Edwards GE, Roalson EH. 2010. Biogeographic patterns of diversifcation and the origins of C4 in Cleome (Cleomaceae). Systematic Botany 35, 811-826.
14. Guralnick LJ, Jackson MD. 2001. The occurrence and phylogenetics of crassulacean acid metabolism in the Portulacaceae. International Journal of Plant Sciences 162, 257-262.
15. Hattersley PW, Wong SC, Perry S, Roksandic Z. 1986. Comparative ultrastructure and gas-exchange characteristics of the C3-C 4 intermediate Neurachne minor. Plant, Cell and Environment 9, 217-233.
16. Harris FS, Martin CE. 1991. Correlation between CAM-Cycling and photosynthetic gas exchange in fve species of Talinum (Portulacaceae). Plant Physiology 96, 1118-1124.
17. Harmon LJ, Weir JT, Brock CD, Glor RE, Wendell C. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24, 129-131.
18. Heckmann D, Schulze S, Denton A, Gowik U, Westhoff P, Weber APM, Lercher MJ. 2013. Predicting C4 photosynthesis evolution: modular, individually adaptive steps on a Mount Fuji ftness landscape. Cell 153, 1579-1588.
19. Kadereit G, Freitag H. 2011. Molecular phylogeny of Camphorosmeae (Camphorosmoideae, Chenopodiaceae): implications for biogeography, evolution of C4-photosynthesis and taxonomy. Taxon 60, 51-78.
20. Kellogg EA. 1999. Phylogenetic aspects of the evolution of C4 photosynthesis. In: Sage FR, Monson RK, eds, C4 plant biology. San Diego: Academic Press. pp 411-44.
21. Kennedy RA, Laetsch WM. 1974. Plant species intermediate for C 3, C4 photosynthesis. Science 184, 1087-1089.
22. Lüttge U. 2004. Ecophysiology of crassulacean acid metabolism (CAM). Annals of Botany 93, 629-652.
23. Marshall DM, Muhaidat R, Brown N, Liu Z, Stanley S, Griffths H, Sage R, Hibberd J. 2007. Cleome, a genus closely related to Arabidopsis, contains species spanning a developmental progression from C3 to C4 photosynthesis. The Plant Journal 51, 886-896.
24. McKown AD, Moncalvo JM, Dengler NG. 2005. Phylogeny of Flaveria (Asteraceae) and inference of C4 photosynthesis evolution. American Journal of Botany 92, 1911-1928.
25. Monson R. 1989. On the evolutionary pathways resulting in C4 photosynthesis and crassulacean acid metabolism (CAM). Advances in Ecological Research 19, 57-110.
26. Monson RK, Moore BD. 1989. On the signifcance of C3-C 4 intermediate photosynthesis to the evolution of C4 photosynthesis. Plant, Cell and Environment 12, 689-699.
27. Mooers AO, Harmon LJ, Blum MGB, Wong DHJ, Heard SB. 2007. Some models of phylogenetic tree shape. In: Gascuel O, Steel M, eds, Reconstucting evolution: new mathematical and computational advances. Oxford: Oxford University Press, pp 149-170.
28. Ocampo G, Koteyeva NK, Voznesenskaya EV, Edwards GE, Sage TL, Sage RF, Columbus JT. 2013. Evolution of leaf anatomy and photosynthetic pathways in Portulacaceae. American Journal of Botany 100, 1-15.
29. O'Leary MH. 1988. Carbon isotopes in photosynthesis. BioScience 38, 328-336.
30. Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289-290.
31. Powell AM. 1978. Systematics of Flaveria (Flaveriinae Asteraceae). Annals of the Missouri Botanical Garden 65, 590-636.
32. R Development Core Team. 2008. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
33. Roalson EH. 2011. C4 photosynthesis origins in the monocots: a review and reanalysis. In: Raghavendra AS, Sage RF, eds, C4 photosynthesis and related CO2 concentrating mechanisms. Dordrecht, The Netherlands: Kluwer. pp 319-338.
34. Smith JAC, Winter K. 1996. Taxonomic distribution of crassulacean acid metabolism. In: Winter K, Smith JAC, eds, Crassulacean acid metabolism. Biochemistry, ecophysiology and evolution. Berlin Heidelberg: Springer. pp 427-436.
35. Sage RF. 2002. Are crassulacean acid metabolism and C-4 photosynthesis incompatible? Functional Plant Biology 29, 775-785.
36. Sage R F. 2004. The evolution of C4 photosynthesis. New Phytologist 161, 341-470.
37. Sage RF, Sage TL, Kocacinar F. 2012. Photorespiration and the evolution of C4 photosynthesis. Annual Review of Plant Biology 63, 19-47.
38. Silvera K, Neubig K, Whitten W, Williams N, Winter K, Cushman J. 2010. Evolution along the crassulacean acid metabolism continuum. Functional Plant Biology 37: 995-1010.
39. Sternberg L, Deniro MJ. 1983. Isotopic composition of cellulose from C3, C4, and CAM plants growing near one another. Science 220, 947-949.
40. Sternberg L, Deniro MJ, Johnson HB. 1984. Isotope ratios of cellulose from plants having different photosynthetic pathways. Plant Physiology 74, 557-561.
41. Ting I P. 1985. Crassulacean acid metabolism. Annual Review of Plant Physiology 36, 595-622.
42. Vogan PJ, Frohlich MW, Sage RF. 2007. The functional signifcance of C3-C4 intermediate traits in Heliotiopium L. (Boraginaceae): gas exchange perspectives. Plant, Cell and Environment 30, 1337-1345.
43. Williams BP, Johnston IG, Covshoff S, Hibberd JM. 2013. Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis. eLife 2, e00961.
44. Winter K, Garcia M, Holtum M. 2008. On the nature of facultative and constitutive CAM: environmental and developmental control of CAM expression during early growth of Clusia, Kalanchöe, and Opuntia. Journal of Experimental Botany 59, 1829-1840.