Life history influences rates of climatic niche evolution in flowering plants

Proceedings of the Royal Society B: Biological Sciences

Volumn 276, Issue 1677, 2009, Pages 4345-4352

  Smith, Stephen A ^a   Beaulieu, Jeremy M ^b  

^a NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

Climatic niche; Life history; Phylogenetics; Rates of evolution

Indexed keywords

HERBACEOUS AGENT;

ANGIOSPERM; BIODIVERSITY; CLIMATE CHANGE; LIFE HISTORY THEORY; PHENOTYPE; PHYLOGENETICS;

ANGIOSPERM; ARTICLE; BIODIVERSITY; CLIMATE; CONSERVATION BIOLOGY; ECOLOGICAL NICHE; GENETIC HETEROGENEITY; LIFE HISTORY; NONHUMAN; PHYLOGENY; PLANT EVOLUTION; PLANT GROWTH; PRIORITY JOURNAL; WOODY PLANT;

MAGNOLIOPHYTA;

EID: 72749117364     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2009.1176     Document Type: Article

References (63)

1. Akaike, H. 1974 A new look at the statistical model identification. IEEE Trans. Autom. Control 19, 716-723. (doi:10.1109/TAC.1974.1100705)
2. Andreasen, K. & Baldwin, B. G. 2001 Unequal evolutionary rates between annual and perennial lineages of checker mallows (Sidalcea, Malvaceae): evidence from 18S-26S rDNA internal and external transcribed spacers. Mol. Biol. Evol. 18, 936-944.
3. Beaulieu, J. M., Leitch, I. J., Patel, S., Pendharkar, A. & Knight, C. A. 2008 Genome size is a strong predictor of cell size and stomatal density in angiosperms. New Phytol. 179, 975-986. (doi:10.1111/j.1469-8137.2008.02528.x)
4. Blomberg, S. P., Garland Jr, T. & Ives, A. R. 2003 Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57, 717-745.
5. Bousquet, J., Strauss, S. H., Doerksen, A. H. & Price, R. A. 1992 Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proc. Natl Acad. Sci. USA 89, 7844-7848. (doi:10.1073/pnas.89.16.7844)
6. Britten, R. J. 1986 Rates of DNA sequence evolution differ between taxonomic groups. Science 231, 1393-1398. (doi:10.1126/science.3082006)
7. Bromham, L., Rambaut, A. & Harvey, P. 1996 Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 43, 610-621. (doi:10.1007/BF02202109)
8. Bromham, L., Woolfit, M., Lee, M. S. Y. & Rambaut, A. 2002 Testing the relationship between morphological and molecular rates of change along phylogenies. Evolution 56, 1921-1930. (Pubitemid 35302004)
9. Butler, M. A. & King, A. A. 2004 Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164, 683-695.
10. Cantino, P. D., Doyle, J. A., Graham, S. W., Judd, W. S., Olmstead, R. G., Soltis, D. E., Soltis, P. S. & Donoghue, M. J. 2007 Toward a phylogenetic nomenclature of Traecheophyta. Taxon 56, 822-846.
11. Cronquist, A. 1988 The evolution and classification of flowering plants. New York, NY: New York Botanical Garden.
12. Davies, T. J. & Savolainen, V. 2006 Neutral theory, phylogenies, and the relationship between phenotypic change and evolutionary rates. Evolution 60, 476-483. (Pubitemid 44804533)
13. Donoghue, M. J. 2008 A phylogenetic perspective on the distribution of plant diversity. Proc. Natl Acad. Sci. USA 105, 11 549-11 555. (doi:10.1073/pnas.0801962105)
14. Donoghue, M. J. & Doyle, J. A. 1989 Phylogenetic analysis of angiosperms and the relationships of Hamamelidae. In Evolution, systematics, and fossil history of the Hamamelidae, vol.1 (eds P. R. Crane & S. Blackmore), pp. 14-45. Oxford, UK: Clarendon.
15. Field, T. S., Arens, N. C., Doyle, J. A., Dawson, T. E. & Donoghue, M. J. 2004 Dark and disturbed: a new image of early angiosperm ecology. Paleobiology 30, 82-107.
16. Friis, E. M., Doyle, J. A., Endress, P. K. & Leng, Q. 2003 Archaefructus: angiosperm precursor or specialized early angiosperm? Trends Plant Sci. 8, 369-373. (doi:10.1016/S1360-1385(03)00161-4)
17. Garland Jr, T. & Ives, A. R. 2000 Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. Am. Nat. 155, 346-364.
18. Garland Jr, T., Dickerman, A. W., Janis, C. M. & Jones, J. A. 1993 Phylogenetic analysis of covariance by computer simulation. Syst. Biol. 42, 265-292.
19. Gaut, B. S., Muse, S. V., Clark, W. D. & Clegg, M. T. 1992 Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. J. Mol. Evol. 35, 292-303. (doi:10.1007/BF00161167)
20. Gaut, B. S., Morton, B. R., McCaig, B. C. & Clegg, M. T. 1996 Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl Acad. Sci. USA 93, 10 274-10 279. (doi:10.1073/pnas.93.19. 10274)
21. Gaut, B. S., Clark, L. G., Wendel, J. F. & Muse, S. V. 1997 Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Mol. Biol. Evol. 14, 769-777.
22. Gillooly, J. F., Allen, A. P., West, G. B. & Brown, J. H. 2005 The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proc. Natl Acad. Sci. USA 102, 140-145. (doi:10.1073/pnas.0407735101)
23. Hamrick, J. L. & Godt, M. J. W. 1996 Effects of life history traits on genetic diversity in plants species. Phil. Trans. R. Soc. Lond. B 351, 1291-1298. (doi:10.1098/rstb.1996.0112)
24. Harmon, L. J., Weir, J. T., Brock, C. D., Glor, R. E. & Challenger, W. 2008 GEIGER: investigating evolutionary radiations. Bioinformatics 24, 129-131. (doi:10.1093/bioinformatics/btm538)
25. Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G. & Jarvis, A. 2005 Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25, 1965-1978. (doi:10.1002/joc.1276)
26. Ho, S. Y. W. 2009 An examination of phylogenetic models of substitution rate variation among lineages. Biol. Lett. 5, 421-424. (doi:10.1098/rsbl.2008. 0729)
27. Kay, K. M., Whittall, J. B. & Hodges, S. A. 2006 A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evol. Biol. 6, 36. (doi:10.1186/1471-2148-6-36)
28. Kimura, M. 1983 The neutral theory of molecular evolution. Cambridge, UK: Cambridge University Press.
29. Kohne, D. E. 1970 Evolution of higher-organism DNA. Q. Rev. Biophys. 3, 327-375. (doi:10.1017/S0033583500004765)
30. Kozak, K. H. & Wiens, J. J. 2006 Does niche conservatism promote speciation? A case study in North American salamanders. Evolution 60, 2604-2621.
31. Laird, C. D., McConaughy, B. L. & McCarthy, B. J. 1969 Rate of fixation of nucleotide substitutions in evolution. Nature 224, 149-154. (doi:10.1038/224149a0)
32. Laroche, J., Peng, L., Maggia, L. & Bousquet, J. 1997 Molecular evolution of angiosperm mitochondrial introns and exons. Proc. Natl Acad. Sci. USA 94, 5722-5727. (doi:10.1073/pnas.94.11.5722)
33. Li, W., Tanimura, M. & Sharp, P. 1987 An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J. Mol. Evol. 25, 330-342. (doi:10.1007/BF02603118)
34. Lynch, M. 2007 The origin of genome architecture. Sunderland, MA: Sinauer Associates, Inc. Publishers.
35. Magallón, S. A. & Sanderson, M. J. 2001 Absolute diversification rates in angiosperm clades. Evolution 55, 1762-1780.
36. Martin, A. P. & Palumbi, S. R. 1993 Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl Acad. Sci. USA 90, 4087-4091. (doi:10.1073/pnas.90.9.4087)
37. 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. Am. Nat. 149, 646-667.
38. Mooers, A. & Harvey, P. 1994 Metabolic rate, generation time, and the rate of molecular evolution in birds. Mol. Phylogenet. Evol. 3, 344-350. (doi:10.1006/mpev.1994.1040)
39. Ohta, T. 1992 The nearly neutral theory of molecular evolution. Ann. Rev. Ecol. Syst. 23, 263-286. (doi:10.1146/annurev.es.23.110192.001403)
40. O'Meara, B. C., Ané, C., Sanderson, M. J. & Wainwright, P. C. 2006 Testing for different rates of continuous trait evolution using likelihood. Evolution 60, 922-933.
41. Petit,R. J. & Hampe, A. 2006 Some evolutionary consequences of being a tree. Annu. Rev. Ecol. Evol. Syst. 37, 187-214. (doi:10.1146/annurev.ecolsys. 37.091305.110215)
42. R Development Core Team 2009 R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. http://www.R-project.org
43. Revell, L. J. In press. Size-correction and principal components for interspecific comparative studies. Evolution (doi:10.1111/j.1558-5646.2009. 00804.x)
44. Revell, L. J. & Collar, D. C. 2009 Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution 63, 1090-1100. (doi:10.1111/j.1558-5646.2009.00616.x)
45. Rohlf, F. J. 2001 Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55, 2143-2160.
46. Sarich, V. M. & Wilson, A. C. 1973 Generation time and genomic evolution in primates. Science 179, 1144-1147. (doi:10.1126/science.179.4078. 1144)
47. Schluter, D., Price, T., Mooers, A. Ø & Ludwig, D. 1997 Likelihood of ancestral states in adaptive radiation. Evolution 51, 1699-1711. (doi:10.2307/2410994)
48. Sibley, C. G. & Ahlquist, J. E. 1984 The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization. J. Mol. Evol. 20, 2-15. (doi:10.1007/BF02101980)
49. Simpson, G. G. 1944 Tempo and mode of evolution. New York, NY: Columbia University Press.
50. Sinnott, E. W. 1916 Rapidity of evolution in various plant types. Am. Nat. 50, 466-478. (doi:10.1086/279557)
51. Smith, S. A. & Donoghue, M. J. 2008 Rates of molecular evolution are linked to life history in flowering plants. Science 322, 86-89. (doi:10.1126/science.1163197)
52. Smith, S. A., Beaulieu, J. M. & Donoghue, M. J. 2009 Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol. Biol. 9, 37. (doi:10.1186/1471-2148-9-37)
53. Stebbins, G. L. 1965 The probable growth habit of the earliest flowering plants. Ann. Mo. Bot. Gard. 52, 457-468. (doi:10.2307/2394810)
54. Sturtevant, A. H. 1965 A history of genetics. New York, NY: Harper and Row.
55. Sugiura, N. 1978 Further analysis of the data by Akaike's information criterion and the finite corrections. Commun. Stat. Theory Methods A7, 13-26.
56. Sun, G., Ji, Q., Dilcher, D. L., Zheng, S., Nixon, K. C. & Weng, X. 2002 Archaefructaceae, a new basal angiosperm family. Science 296, 899-904. (doi:10.1126/science.1069439) (Pubitemid 34464893)
57. Taylor, D. W. & Hickey, L. J. 1992 Phylogenetic evidence for the herbaceous origin of angiosperms. Plant Syst. Evol. 180, 137-156. (doi:10.1007/BF00941148)
58. Verdú, M. 2002 Age at maturity and diversification in woody angiosperms. Evolution 56, 1352-1361. (Pubitemid 34890494)
59. Wiens, J. J. 2004 Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species. Evolution 58, 193-197.
60. Wiens, J. J. & Donoghue, M. J. 2004 Historical biogeography, ecology, and species richness. Trends Ecol. Evol. 19, 639-644. (doi:10.1016/j.tree.2004. 09.011)
61. Wiens, J. J. & Graham, C. H. 2005 Niche conservatism: integrating evolution, ecology, and conservation biology. Annu. Rev. Ecol. Syst. 36, 519-539.
62. Wu, C. I. & Li, W. 1985 Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl Acad. Sci. USA 82, 1741-1745. (doi:10.1073/pnas.82.6.1741)
63. Xiang, Q. Y., Thorne, J. L., Seo, T. K., Zhang, W. H., Thomas, D. T. & Ricklefs, R. E. 2008 Rates of nucleotide substitution in Cornaceae (Cornales) - pattern of variation and underlying causal factors. Mol. Phylogenet. Evol. 49, 327-342. (doi:10.1016/j.ympev.2008.07.010)