Taller plants have lower rates of molecular evolution

Nature Communications

Volumn 4, Issue , 2013, Pages

  Lanfear, Robert ^a,b   Ho, Simon Y W ^c   Jonathan Davies, T ^d   Moles, Angela T ^e   Aarssen, Lonnie ^f   Swenson, Nathan G ^g   Warman, Laura ^e,h   Zanne, Amy E ^i,j   Allen, Andrew P ^k  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

^c UNIVERSITY OF SYDNEY   (Australia)

^d MCGILL UNIVERSITY   (Canada)

^e UNIVERSITY OF NEW SOUTH WALES   (Australia)

^f QUEEN S UNIVERSITY   (Canada)

^g MICHIGAN STATE UNIVERSITY   (United States)

^h USDA FOREST SERVICE   (United States)

ⁱ GEORGE WASHINGTON UNIVERSITY   (United States)

^j MISSOURI BOTANICAL GARDEN   (United States)

^k MACQUARIE UNIVERSITY   (Australia)

more..

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA;

CHLOROPLAST; EVOLUTIONARY BIOLOGY; GENOME; GROWTH FORM; LATITUDE; MOLECULAR ANALYSIS; SPECIES RICHNESS; ULTRAVIOLET RADIATION;

ARTICLE; CHLOROPLAST; HERB; LATITUDE; MITOSIS; MOLECULAR EVOLUTION; PLANT GENOME; PLANT GROWTH; PLANT HEIGHT; SHRUB; TEMPERATURE; TREE; ULTRAVIOLET RADIATION;

AMINO ACID SUBSTITUTION; ANGIOSPERMS; CELL NUCLEUS; CHLOROPLASTS; DATABASES, GENETIC; EVOLUTION, MOLECULAR; LEAST-SQUARES ANALYSIS; PHYLOGENY; PLANTS; REGRESSION ANALYSIS; RNA, RIBOSOMAL; WOOD;

MAGNOLIOPHYTA;

EID: 84878712034     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms2836     Document Type: Article

References (47)

1. Gaut, B., Yang, L., Takuno, S. & Eguiarte, L. E. The patterns and causes of variation in plant nucleotide substitution rates. Annu. Rev. Ecol. Evol. S 42, 245-266 (2011)
2. Wright, S., Keeling, J. & Gillman, L. The road from Santa Rosalia: a faster tempo of evolution in tropical climates. Pro. Natl Acad. Sci. USA 103, 7718-7722 (2006)
3. Davies, T. J., Savolainen, V., Chase, M. W., Moat, J. & Barraclough, T. G. Environmental energy and evolutionary rates in flowering plants. Proc. Biol. Sci. 271, 2195-2200 (2004)
4. Barraclough, T. G. & Savolainen, V. Evolutionary rates and species diversity in flowering plants. Evolution 55, 677-683 (2001) (Pubitemid 32464091)
5. Goldie, X., Gillman, L., Crisp, M. & Wright, S. Evolutionary speed limited by water in arid Australia. Pro. R. Soc. B 277, 2645-2653 (2010)
6. Smith, S. A. & Donoghue, M. J. Rates of molecular evolution are linked to life history in flowering plants. Science 322, 86-89 (2008)
7. Reich, P. B., Tjoelker, M. G., Machado, J.-L. & Oleksyn, J. Universal scaling of respiratory metabolism, size and nitrogen in plants. Nature 439, 457-461 (2006) (Pubitemid 43152834)
8. Westoby, M. A leaf-height-seed (LHS) plant ecology strategy scheme. Plant Soil 199, 213-227 (1998) (Pubitemid 28205458)
9. Enquist, B., West, G., Charnov, E. & Brown, J. Allometric scaling of production and life-history variation in vascular plants. Nature 408, 907-911 (1999)
10. Bromham, L. The genome as a life-history character: why rate of molecular evolution varies between mammal species. Philos. Trans. R. Soc. B 366, 2503-2513 (2011)
11. Lanfear, R., Welch, J. J. & Bromham, L. Watching the clock: studying variation in rates of molecular evolution between species. Trends Ecol. Evol. 25, 495-503 (2010)
12. Burleigh, J. G., Hilu, K. W. & Soltis, D. E. Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms. BMC Evol. Biol. 9, 61 (2009)
13. Moles, A. T. et al. Global patterns in plant height. J. Ecol. 97, 923-932 (2009)
14. Li, W. H., Ellsworth, D. L., Krushkal, J., Chang, B. H. & Hewett-Emmett, D. Rates of nucleotide substitution in primates and rodents and the generationtime effect hypothesis. Mol. Phylogenet. Evol. 5, 182-187 (1996) (Pubitemid 126317003)
15. Petit, R. J. & Hampe, A. Some evolutionary consequences of being a tree. Annu. Rev. Ecol. Evol. S 37, 187-214 (2006) (Pubitemid 44907617)
16. Thomas, J. A., Welch, J. J., Lanfear, R. & Bromham, L. A generation time effect on the rate of molecular evolution in invertebrates. Mol. Biol. Evol. 27, 1173-1180 (2010)
17. Nabholz, B., Gle'min, S. & Galtier, N. Strong variations of mitochondrial mutation rate across mammals-the longevity hypothesis. Mol. Biol. Evol. 25, 120-130 (2008)
18. Welch, J. J., Bininda-Emonds, O. R. P. & Bromham, L. Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evol. Biol. 8, 53 (2008)
19. Gaut, B. S., Clark, L. G., Wendel, J. F. & Muse, S. V. Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Mol. Biol. Evol. 14, 769-777 (1997) (Pubitemid 27287298)
20. Whittle, C. -A. & Johnston, M. O. Broad-scale analysis contradicts the theory that generation time affects molecular evolutionary rates in plants. J. Mol. Evol. 56, 223-233 (2003) (Pubitemid 36169690)
21. Verdu, M., Pausas, J. G., Segarra-Moragues, J. G. & Ojeda, F. Burning phylogenies: fire, molecular evolutionary rates, and diversification. Evolution 61, 2195-2204 (2007) (Pubitemid 47340768)
22. Martin, A. P. & Palumbi, S. R. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl Acad. Sci. USA 90, 4087-4091 (1993) (Pubitemid 23134171)
23. Niklas, K. J. & Enquist, B. J. Invariant scaling relationships for interspecific plant biomass production rates and body size. Proc. Natl Acad. Sci. USA 98, 2922-2927 (2001) (Pubitemid 32209585)
24. Lanfear, R., Thomas, J. A., Welch, J. J., Brey, T. & Bromham, L. Metabolic rate does not calibrate the molecular clock. Proc. Natl Acad. Sci. USA 104, 15388-15393 (2007) (Pubitemid 47502927)
25. Santos, J. C. Fast molecular evolution associated with high active metabolic rates in poison frogs. Mol. Biol. Evol. 29, 2001-2018 (2012)
26. Lourenço, J. M., Gle'min, S., Chiari, Y. & Galtier, N. The determinants of the molecular substitution process in turtles. J. Evol. Biol. 26, 38-50 (2013)
27. Hoffmann, S., Spitkovsky, D., Radicella, J., Epe, B. & Wiesner, R. Reactive oxygen species derived from the mitochondrial respiratory chain are not responsible for the basal levels of oxidative base modifications observed in nuclear DNA of mammalian cells. Free Radical Bio. Med. 36, 765-773 (2004) (Pubitemid 38264419)
28. Joyner-Matos, J., Bean, L. C., Richardson, H. L., Sammeli, T. & Baer, C. F. No evidence of elevated germline mutation accumulation under oxidative stress in Caenorhabditis elegans. Genetics 189, 1439-1447 (2011)
29. Woolfit, M. Effective population size and the rate and pattern of nucleotide substitutions. Biol. Lett. 5, 417-420 (2009)
30. Klekowski, E. J. J. Genetic load and its causes in long-lived plants. Trees-Struct. Funct. 2, 195-203 (1988)
31. Klekowski, E. J. & Godfrey, P. J. Ageing and mutation in plants. Nature 3, 389-391 (1989)
32. Kimura, M. The Neutral Theory of Molecular Evolution (Cambridge University Press, 1985)
33. Gleeson, S. & Tilman, D. Plant allocation, growth-rate and successional status. Funct. Ecol. 8, 543-550 (1994) (Pubitemid 2117002)
34. Grime, J. & Hunt, R. Relative growth-rate: its range and adaptive significance in a local flora. J. Ecol. 63, 393-422 (1975)
35. Korall, P., Schuettpelz, E. & Pryer, K. M. Abrupt deceleration of molecular evolution linked to the origin of arborescence in ferns. Evolution 64, 2786-2792 (2010)
36. Bromham, L. Why do species vary in their rate of molecular evolution? Biol. Lett. 5, 401-404 (2009)
37. Willi, Y. & Hoffmann, A. A. Demographic factors and genetic variation influence population persistence under environmental change. J. Evol. Biol. 22, 124-133 (2009)
38. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690 (2006) (Pubitemid 44642609)
39. AGP. II An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141, 399-436 (2003)
40. Hugall, A. F. & Lee, M. S. Y. The likelihood node density effect and consequences for evolutionary studies of molecular rates. Evolution 61, 2293-2307 (2007) (Pubitemid 47512219)
41. Pond, S. L., Frost, S. D. & Muse, S. V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21, 676-679 (2005) (Pubitemid 40424796)
42. Sanderson, M. J. r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301-302 (2003) (Pubitemid 36181923)
43. Magallon, S. & Castillo, A. Angiosperm diversification through time. Am. J. Bot. 96, 349-365 (2009)
44. Welch, J. J. & Waxman, D. Calculating independent contrasts for the comparative study of substitution rates. J. Theor. Biol. 251, 667-678 (2008)
45. Freckleton, R., Harvey, P. & Pagel, M. Phylogenetic analysis and comparative data: a test and review of evidence. Am. Nat. 160, 712-726 (2002)
46. Garland, T., Harvey, P. & Ives, A. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Syst. Biol. 41, 18-32 (1992)
47. R Development Core Team R. A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2012).