Watching the clock: Studying variation in rates of molecular evolution between species

Trends in Ecology and Evolution

Volumn 25, Issue 9, 2010, Pages 495-503

  Lanfear, Robert ^a   Welch, John J ^b   Bromham, Lindell ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b UNIV MONTPELLIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; EVOLUTIONARY BIOLOGY; GENETIC ANALYSIS; MOLECULAR ECOLOGY; THEORETICAL STUDY;

ANIMAL; BIOLOGICAL MODEL; GENETIC VARIABILITY; MOLECULAR EVOLUTION; SPECIES DIFFERENTIATION; TIME;

ANIMALS; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENETIC VARIATION; MODELS, GENETIC; TIME FACTORS;

EID: 77955657333     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2010.06.007     Document Type: Review

References (80)

1. Nabholz B., et al. Strong variations of mitochondrial mutation rate across mammals - the longevity hypothesis. Mol. Biol. Evol. 2008, 25:120-130.
2. Duffy S., et al. Rates of evolutionary change in viruses: patterns and determinants. Nat. Rev. Genet. 2008, 9:267-276.
3. Smith S.A., Donoghue M.J. Rates of molecular evolution are linked to life history in flowering plants. Science 2008, 322:86-89.
4. Thomas J.A., et al. A generation time effect on the rate of molecular evolution in invertebrates. Mol. Biol. Evol. 2010, 27:1173-1180.
5. Welch J.J., et al. Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evol. Biol. 2008, 8:53.
6. Mooers A.O., Harvey P.H. Metabolic rate, generation time, and the rate of molecular evolution in birds. Mol. Phylogenet. Evol. 1994, 3:344-350.
7. Sarich V.M., Wilson A.C. Generation time and genomic evolution in primates. Science 1973, 179:1144-1147.
8. Bromham L. Molecular clocks in reptiles: Life history influences rate of molecular evolution. Mol. Biol. Evol. 2002, 19:302-309.
9. Pagel M., et al. Large punctuational contribution of speciation to evolutionary divergence at the molecular level. Science 2006, 314:119-121.
10. Davies T.J., et al. Environmental energy and evolutionary rates in flowering plants. Proc. Biol. Sci. 2004, 271:2195-2200.
11. Davies T.J., Savolainen V. Neutral theory, phylogenies, and the relationship between phenotypic change and evolutionary rates. Evolution 2006, 60:476-483.
12. Bromham L., et al. Testing the relationship between morphological and molecular rates of change along phylogenies. Evolution 2002, 56:1921-1930.
13. Martin A.P., Palumbi S.R. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. U. S. A. 1993, 90:4087-4091.
14. Welch J.J., Bromham L. Molecular dating when rates vary. Trends Ecol. Evol. 2005, 20:320-327.
15. Smith A.B., et al. Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata). Mol. Biol. Evol. 2006, 23:1832-1851.
16. Brown J.M., et al. When trees grow too long: Investigating the causes of highly inaccurate Bayesian branch-length estimates. Syst. Biol. 2010, 59:145-161.
17. Ohta T. Population size and rate of evolution. J. Mol. Evol. 1972, 1:305-314.
18. Jones K.E., et al. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 2009, 90:2648-12648.
19. Swofford, D.L. (2002) PAUP. Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4, Sinauer Associates.
20. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
21. Guindon S., et al. PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 2005, 33:W557-559.
22. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
23. Suchard M.A., Rambaut A. Many-core algorithms for statistical phylogenetics. Bioinformatics 2009, 25:1370-1376.
24. Simon C., et al. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Ann. Rev. Ecol. Evol. S. 2006, 37:545-579.
25. Sullivan J., Joyce P. Model selection in phylogenetics. Ann. Rev. Ecol. Evol. S. 2005, 36:445-466.
26. Welch J.J., Waxman D. Calculating independent contrasts for the comparative study of substitution rates. J. Theor. Biol. 2008, 251:667-678.
27. Charlesworth, D. (2010) Don't forget the ancestral polymorphisms. Heredity, [Epub ahead of print]. doi:10.1038/hdy.2010.14.
28. Kimura M. The Neutral Theory of Molecular Evolution 1983, Cambridge University Press.
29. Ho S.Y., Jermiin L. Tracing the decay of the historical signal in biological sequence data. Syst. Biol. 2004, 53:623-637.
30. Lanfear R., et al. Metabolic rate does not calibrate the molecular clock. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:15388-15393.
31. Phillips M.J. Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny. Gene 2009, 441:132-140.
32. Hugall A.F., Lee M.S. The likelihood node density effect and consequences for evolutionary studies of molecular rates. Evolution 2007, 61:2293-2307.
33. Webster A.J., et al. Molecular phylogenies link rates of evolution and speciation. Science 2003, 301:478.
34. Webster A.J., et al. Response to comments on " Molecular phylogenies link rates of evolution and speciation" Science 2004, 303:173.
35. Witt C.C., Brumfield R.T. Comment on " Molecular phylogenies link rates of evolution and speciation" (I). Science 2004, 303:173. author reply 173.
36. Brower A.V. Comment on " Molecular phylogenies link rates of evolution and speciation" (II). Science 2004, 303:173. author reply 173.
37. Venditti C., et al. Detecting the node-density artifact in phylogeny reconstruction. Syst. Biol. 2006, 55:637-643.
38. Venditti C., Pagel M. Model misspecification not the node-density artifact. Evolution 2008, 62:2125-2126.
39. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 2002, 19:101-109.
40. Nabholz B., et al. The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals. BMC Evol. Biol. 2009, 9:54.
41. Ho S.Y. An examination of phylogenetic models of substitution rate variation among lineages. Biol. Lett. 2009, 5:421-424.
42. Cutler D.J. Understanding the overdispersed molecular clock. Genetics 2000, 154:1403-1417.
43. Harvey P.H., Pagel M.D. The Comparative Method in Evolutionary Biology 1991, Oxford University Press.
44. Freckleton R.P. The seven deadly sins of comparative analysis. J. Evol. Biol. 2009, 22:1367-1375.
45. Garland T., et al. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Syst. Biol. 1992, 41:18-32.
46. Felsenstein J. Phylogenies and the comparative method. Am. Nat. 1985, 125:1-15.
47. Freckleton R.P., et al. Phylogenetic analysis and comparative data: a test and review of evidence. Am. Nat. 2002, 160:712-726.
48. Grafen A. The phylogenetic regression. Philos. Trans. R. Soc. Lond. B Biol. Sci. 1989, 326:119-157.
49. Freckleton R.P., Harvey P.H. Detecting non-Brownian trait evolution in adaptive radiations. PLoS Biol. 2006, 4:e373.
50. Lanfear R., Bromham L. Statistical tests between competing hypotheses of Hox cluster evolution. Syst. Biol. 2008, 57:1-11.
51. Freckleton R.P. Phylogenetic tests of ecological and evolutionary hypotheses: checking for phylogenetic independence. Funct. Ecol. 2000, 14:129-134.
52. Pagel M. Inferring evolutionary processes from phylogenies. Zool. Scr. 1998, 26:331-348.
53. Huelsenbeck J.P., Rannala B. Detecting correlation between characters in a comparative analysis with uncertain phylogeny. Evolution 2003, 57:1237-1247.
54. O'Connor T.D., Mundy N.I. Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate. Bioinformatics 2009, 25:i94-100.
55. Oakley T.H., Cunningham C.W. Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution 2000, 54:397-405.
56. Laird C.D., et al. Rate of fixation of nucleotide substitutions in evolution. Nature 1969, 224:149-154.
57. Wu C.I., Li W.H. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. U. S. A. 1985, 82:1741-1745.
58. Gillooly J.F., et al. The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:140-145.
59. Bromham L., et al. Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 1996, 43:610-621.
60. Gruber J., et al. The mitochondrial free radical theory of ageing--where do we stand?. Front. Biosci. 2008, 13:6554-6579.
61. Galtier N., et al. Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution. Biol. Lett. 2009, 5:413-416.
62. Bromham L. Why do species vary in their rate of molecular evolution?. Biol. Lett. 2009, 5:401-404.
63. Chamary J.V., et al. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat. Rev. Genet. 2006, 7:98-108.
64. Eyre-Walker A., Keightley P.D. The distribution of fitness effects of new mutations. Nat. Rev. Genet. 2007, 8:610-618.
65. Woolfit M. Effective population size and the rate and pattern of nucleotide substitutions. Biol. Lett. 2009, 5:417-420.
66. Bromham L., Leys R. Sociality and the rate of molecular evolution. Mol. Biol. Evol. 2005, 22:1393-1402.
67. Woolfit M., Bromham L. Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes. Mol. Biol. Evol. 2003, 20:1545-1555.
68. Pond S.L., et al. HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005, 21:676-679.
69. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.
70. Aris-Brosou S., Bielawski J.P. Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation. Gene 2006, 378:58-64.
71. Anisimova M., Kosiol C. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol. Biol. Evol. 2009, 26:255-271.
72. Bierne N., Eyre-Walker A. The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias. Genetics 2003, 165:1587-1597.
73. Pond S.K., Muse S.V. Site-to-site variation of synonymous substitution rates. Mol. Biol. Evol. 2005, 22:2375-2385.
74. Paradis E., et al. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 2004, 20:289-290.
75. R Development Core Team (2009). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org.
76. Freckleton R.P., et al. Bergmann's rule and body size in mammals. Am. Nat. 2003, 161:821-825.
77. Martins E.P., Hansen T.F. Phylogenies and the comparative method: A general approach to incorporating phylogenetic information into the analysis of interspecific data. Am. Nat. 1997, 149:646-667.
78. Woolfit M., Bromham L. Population size and molecular evolution on islands. Proc. Biol. Sci. 2005, 272:2277-2282.
79. Wright S., et al. The road from Santa Rosalia: a faster tempo of evolution in tropical climates. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:7718-7722.
80. Ives A.R., Garland T. Phylogenetic logistic regression for binary dependent variables. Syst. Biol. 2010, 59:9-26.