Evolutionary modeling of genotype-phenotype associations, and application to primate coding and non-coding mtDNA rate variation

Evolutionary Bioinformatics

Volumn 2013, Issue 9, 2013, Pages 301-316

  O'Connor, Timothy D ^a   Mundy, Nicholas I ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Generation time hypothesis; Genotype phenotype; Longevity hypothesis; Mitochondria; Primate

Indexed keywords

MITOCHONDRIAL DNA; MITOCHONDRIAL PROTEIN;

ARTICLE; BODY MASS; CODON; CONTROLLED STUDY; EVOLUTIONARY RATE; FEMALE; GENOTYPE PHENOTYPE CORRELATION; LIFE HISTORY; LIFESPAN; LONGEVITY; MALE; MITOCHONDRIAL GENOME; NONHUMAN; PHENOTYPE; PHYLOGENY; PREDICTION; PRIMATE; SEXUAL MATURITY; SIMULATION;

MAMMALIA; PRIMATES;

EID: 84880943147     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S11600     Document Type: Article

References (93)

1. Anisimova M, Liberles DA. The quest for natural selection in the age of comparative genomics. Heredity. 2007;99:567-79.
2. Baer CF, Miyamoto MM, Denver DR. Mutation rate variation in multicellular eukaryotes: causes and consequences. Nature Rev Genet. 2007;8:619-31.
3. Bromham L. Why do species vary in their rate of molecular evolution? Biol Lett. 2009;5:401.
4. Lopez P, Casane D, Philippe H. Heterotachy, an important process of protein evolution. Mol Biol Evol. 2002;19:1-7.
5. Lockhart P, Steel M. A tale of two processes. Syst Biol. 2005;54:948-51.
6. Zhou Y, Rodrigue N, Lartillot N, Philippe H. Evaluation of the models handling heterotachy in phylogenetic inference. BMC Evol Biol. 2007;7:1471-2148.
7. Yang Z. Estimating the pattern of nucleotide substitution. J Mol Evol. 1994;39:105-11.
8. Yang Z. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol. 1996;11:367-72.
9. Welch JJ, Bininda-Emonds ORP, Bromham L. Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evol Biol. 2008;8:53.
10. Nabholz B, Glemin S, Galtier N. Strong variations of mitochondrial mutation rate across mammals-the longevity hypothesis. Mol Biol Evol. 2008; 25:120.
11. Nabholz B, Mauffrey JF, Bazin E, Galtier N, Glemin S. Determination of mitochondrial genetic diversity in mammals. Genetics. 2008;178:351.
12. Nabholz B, Glémin S, Galtier N. The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals. BMC Evol Biol. 2009;9:54.
13. Dorus S, Evans PD, Wyckoff GJ, Choi SS, Lahn BT. Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity. Nature Genet. 2004;36:1326-9.
14. Hurle B, Swanson WJ; NISC Comparative Sequencing Program, Green ED. Comparative sequence analyses reveal rapid and divergent evolutionary changes of the WFDC locus in the primate lineage. Genome Res. 2007;17:276.
15. Ramm SA, Oliver PL, Ponting CP, Stockley P, Emes RD. Sexual selection and the adaptive evolution of mammalian ejaculate proteins. Mol Biol Evol. 2008;25:207.
16. O'Connor TD, Mundy NI. Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate. Bioinformatics. 2009;25:i94-100.
17. Herlyn H, Zischler H. Sequence evolution of the sperm ligand zonadhesin correlates negatively with body weight dimophism in primates. Evolution. 2007;61:289-98.
18. Nadeau NJ, Burke T, Mundy NI. Evolution of an avian pigmentation gene correlates with a measure of sexual selection. Proc R Soc B Lon. 2007;274.
19. Gillooly JF, Allen AP, West GB, Brown JH. The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proc Natl Acad Sci. 2005;102:140-5.
20. Gillman LN, Keeling DJ, Ross HA, Wright SD. Latitude, elevation and the tempo of molecular evolution in mammals. P Roy Soc B-Biol Sci. 2009.
21. Mayrose I, Otto SP. A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution. Mol Biol Evol. 2011;28: 759-70.
22. Pupko T, Galtier N. A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes. Proc R Soc B Lon. 2002;269:1313-6.
23. Galtier N, Jobson RW, Nabholz B, Glémin S, Blier PU. Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution. Biol Lett. 2009;5:413.
24. Pamplona R, Barja G. Highly resistant macromolecular components and low rate of generation of endogenous damage: two key traits of longevity. Ageing Res Rev. 2007;6:189-210.
25. Bromham L, Rambaut A, Harvey PH. Determinants of rate variation in mammalian DNA sequence evolution. J Mol Evol. 1996;43:610-21.
26. Li WH, Tanimura M, Sharp PM. An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J Mol Evol. 1987;25:330-42.
27. Zuckerkandl E, Pauling L. Evolving Genes and Proteins. In: Bryson V, Vogelch HJ, editors. Evolutionary divergence and convergence in proteins. New York: Academic Press; 1965:97-166.
28. Laird CD, McConaughy BL, McCarthy BJ. Rate of fixation of nucleotide substitutions in evolution. Nature. 1969;224:149-54.
29. Kohne DE. Evolution of higher-organism DNA. Quart Rev Biophys. 1970;3:327-75.
30. Wu CI, Li WH. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc Natl Acad Sci. 1985;82:1741-5.
31. Li WH, Ellsworth DL, Krushkal J, Chang BHJ, Hewett-Emmett D. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol Phylo Evol. 1996;5:182-7.
32. Tëtushkin EY. Rates of molecular evolution of primates. Rus J Genet. 2003;39:721-36.
33. Hayasaka K, Gojobori T, Horai S. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol Biol Evol. 1988;5:626-44.
34. Hasegawa M. Phylogeny and molecular evolution in primates. Jpn J Genet. 1990;65:243-66.
35. Li WH, Tanimura M. The molecular clock runs more slowly in man than in apes and monkeys. Nature. 1987;326:93-6.
36. Steiper ME, Young NM. Primate molecular divergence dates. Mol Phylo Evol. 2006;41:384-94.
37. Hasegawa M, Kishino H, Hayasaka K, Horai S. Mitochondrial DNA evolution in primates: transition rate has been extremely low in the lemur. J Mol Evol. 1990;31:113-21.
38. Galtier N, Blier PU, Nabholz B. Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds. Mitochondrion. 2009;9:51-7.
39. Lartillot N, Poujol R. A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Mol Biol Evol. 2011;28:729-44.
40. Welch JJ, Waxman D. Calculating independent contrasts for the comparative study of substitution rates. J Theor Biol. 2008;251:667-78.
41. Martin AP, Palumbi SR. Body size, metabolic rate, generation time, and the molecular clock. Proc Natl Acad Sci. 1993;90:4087-91.
42. Pagel M, Meade A. A phylogenetic mixture model for detecting patternheterogeneity in gene sequence or character-state data. Syst Biol. 2004;53: 571-81.
43. Pagel M. Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters. P Roy Soc B-Biol Sci. 1994;255:37-45.
44. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci. 1986;17:57-86.
45. Zharkikh A. Estimation of evolutionary distances between nucleotide sequences. J Mol Evol. 1994;39:315-29.
46. Lewis PO. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst Biol. 2001;50:913-25.
47. Yang Z. Computational Molecular Evolution. Oxford University Press, USA; 2006.
48. Silvey SD. Statistical Inference. Chapman & Hall/CRC; 1975.
49. Kendall M, Stuart A. The Advanced Theory of Statistics. Charles Griffn, London; 1979;2.
50. Lindgren BW. Statistical Theory. Chapman & Hall/CRC; 1993.
51. Drummond A, Strimmer K. PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics. 2001;17:662-3.
52. Goodman M, Grossman LI, Wildman DE. Moving primate genomics beyond the chimpanzee genome. Trends Genet. 2005;21:511-7.
53. Horvath JE, Weisrock DW, Embry SL, et al. Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar's lemurs. Genome Res. 2008;18:489.
54. Smith RJ, Jungers WL. Body mass in comparative primatology. J of Human Evol. 1997;32:523-59.
55. Isaac NJB, Jones KE, Gittleman JL, Purvis A. Correlates of species richness in mammals: body size, life history, and ecology. Amer Naturalist. 2005;165:600-7.
56. Magalhães JP, Budovsky A, Lehmann G, et al. The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell. 2009;8:65-72.
57. Magalhães JP, Costa J. A database of vertebrate longevity records and their relation to other life-history traits. J Evol Biol. 2009;22:1770-4.
58. Schwartz S, Kent WJ, Smit A, et al. Human-mouse alignments with BLASTZ. Genome Res. 2003;13:103-7.
59. Blanchette M, Kent WJ, Riemer C, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004;14:708-15.
60. Aquadro CF, Greenberg BD. Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics. 1983;103:287-312.
61. Cann RL, Brown WM, Wilson AC. Polymorphic sites and the mechanism of evolution in human mitochondrial DNA. Genetics. 1984;106:479-99.
62. Loytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci. 2005;102:10557-62.
63. Loytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science. 2008;320:1632.
64. Fletcher W, Yang Z. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol. 2010;27:2257-67.
65. Shoemaker BA, Panchenko AR. Deciphering protein-protein interactions. Part I: Experimental techniques and databases. PLoS Comput Biol. 2007;3:e42.
66. Shoemaker BA, Panchenko AR. Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol. 2007;3:e43.
67. Wong WSW, Yang Z, Goldman N, Nielsen R. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics. 2004;168:1041-51.
68. Felsenstein J. Phylogenies and the comparative method. American Naturalist. 1985;125:1.
69. Pagel M. Inferring evolutionary processes from phylogenies. Zoologica Scripta. 1997;26:331-48.
70. Pagel M. Inferring the historical patterns of biological evolution. Nature. 1999;401:877-84.
71. Freckleton RP, Harvey PH, Pagel M. Phylogenetic analysis and comparative data: a test and review of evidence. Am Nat. 2002;160:712-26.
72. Wlasiuk G, Nachman MW. Promiscuity and the rate of molecular evolutionat primate immunity genes. Evolution. 2010;64:2204-20.
73. Tsantes C, Steiper ME. Age at first reproduction explains rate variation in the strepsirrhine molecular clock. Proc Natl Acad Sci. 2009;106: 18165-70.
74. Schwartz RS, Mueller RL. Variation in DNA substitution rates among lineages erroneously inferred from simulated clock-like data. PLoS ONE. 2010;5:e9649.
75. Ives AR, Garland T Jr. Phylogenetic logistic regression for binary dependent variables. Syst Biol. 2010;59:9-26.
76. Moritz C, Dowling TE, Brown WM. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu Rev Ecol Evol Syst. 1987;18:269-92.
77. Pamilo P, O'Neill RJW. Evolution of the sry genes. Mol Biol Evol. 1997;14: 49-55.
78. Clark NL, Swanson WJ. Pervasive adaptive evolution in primate seminal proteins. PLoS Genet. 2005;1:e35.
79. Thomas JA, Welch JJ, Lanfear R, Bromham L. A generation time effect on the rate of molecular evolution in invertebrates. Mol Biol Evol. 2010;27: 1173-80.
80. Ohta T. An examination of the generation-time effect on molecular evolution. Proc Natl Acad Sci. 1993;90:10676-80.
81. Mooers AØ, Harvey PH. Metabolic rate, generation time, and the rate of molecular evolution in birds. Mol Phylo Evol. 1994;3:344-50.
82. Nikolaev SI, Montoya-Burgos JI, Popadin K, Parand L, Margulies EH, Antonarakis SE. Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. Proc Natl Acad Sci. 2007; 104:20443.
83. Jones KE, Bielby J, Cardillo M, et al. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology. 2009;90:2648.
84. Millar JS. Adaptive features of mammalian reproduction. Evolution. 1977; 31:370-86.
85. Blueweiss L, Fox H, Kudzma V, Nakashima D, Peters R, Sams S. Relationships between body size and some life history parameters. Oecologia. 1978;37:257-72.
86. Millar RM. Life histories of mammals: an analysis of life tables. Ecology. 1983;64:631-5.
87. Peters RH. The Ecological Significance of Body Size. Cambridge University Press, Cambridge, UK; 1983.
88. Calder WAL. Size, Function and Life History. Harvard University Press, Cambridge, MA, USA; 1984.
89. Gillooly JF, Brown JH, West GB, Savage VM, Charnov EL. Effects of size and temperature on metabolic rate. Science. 2001;293:2248.
90. Bleiweiss R. Relative-rate tests and biological causes of molecular evolution in hummingbirds. Mol Biol Evol. 1998;15:481-91.
91. Lanfear R, Thomas JA, Welch JJ, Brey T, Bromham L. Metabolic rate does not calibrate the molecular clock. Proc Natl Acad Sci. 2007;104:15388.
92. Thomas JA, Welch JJ, Woolfit M, Bromham L. There is no universal molecular clock for invertebrates, but rate variation does not scale with body size. Proc Natl Acad Sci. 2006;103:7366.
93. Grossman LI, Wildman DE, Schmidt TR, Goodman M. Accelerated evolution of the electron transport chain in anthropoid primates. Trends Genet. 2004;20:578-85.