Impact of genetic architecture on the relative rates of X versus autosomal adaptive substitution

Molecular Biology and Evolution

Volumn 29, Issue 8, 2012, Pages 1933-1942

  Connallon, Tim ^a   Singh, Nadia D ^b   Clark, Andrew G ^a  

^a Department of Obstetrics Gynecology   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

dominance; epistasis; genetics of adaptation; molecular evolution; soft sweeps

Indexed keywords

ARTICLE; AUTOSOMAL ADAPTIVE SUBSTITUTION; AUTOSOMAL INHERITANCE; CHROMOSOME ANALYSIS; CONCEPTUAL FRAMEWORK; DNA SEQUENCE; EFFECTIVE POPULATION SIZE; GENE FREQUENCY; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; MOLECULAR EVOLUTION; MUTATIONAL ANALYSIS; PREDICTIVE VALUE; PROBABILITY; QUANTITATIVE ANALYSIS; X LINKED ADAPTIVE SUBSTITUTION;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; CHROMOSOMES, HUMAN, X; EVOLUTION, MOLECULAR; GENES; HUMANS; MODELS, GENETIC; MUTATION; PHYLOGENY; POPULATION DENSITY; X CHROMOSOME;

EID: 84864655409     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss057     Document Type: Article

References (69)

1. Arendt J, Reznick D. 2008. Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? Trends Ecol Evol. 23:26-32.
2. Barton NH. 1989. The divergence of a polygenic system subject to stabilizing selection, mutation and drift. Genet Res. 54:59-77.
3. Bazykin GA, Kondrashov AS. 2011. Detecting past positive selection through ongoing negative selection. Genome Biol Evol. 3:1006-1013.
4. Bollback JP, Huelsenbeck JP. 2009. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics 181:225-234.
5. Bull JJ. 1983. Evolution of sex determination mechanisms. Menlo Park (CA): Benjamin/Cummings. p. 316.
6. Charlesworth B. 2009. Effective population size and patterns of molecular evolution and variation. Nat Rev Genet. 10:195-205.
7. Charlesworth B, Coyne JA, Barton NH. 1987. The relative rates of evolution of sex chromosomes and autosomes. Am Nat. 130:113-146.
8. Christin PA, Salamin N, Muasya AM, Roalson EH, Russier F, Besnard G. 2008. Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis. Mol Biol Evol. 25:2361-2368.
9. Christin PA, Samaritani E, Petitpierre B, Salami N, Besnard G. 2009. Evolutionary insights on C4 photosynthetic subtypes in grasses from genomics and phylogenetics. Genome Biol Evol. 1:221-230.
10. Christin PA, Weinreich DM, Besnard G. 2010. Causes and evolutionary significance of genetic convergence. Trends Genet. 26:400-405.
11. Colosimo PF, Hosemann KE, Balabhadra S, Villarreal G, Dickson M, Grimwood J, Schmutz J, Myers RM, Schluter D, Kingsley DM. 2005. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307:1928-1933.
12. Cresko WA, Amores A, Wilson C, Murphy J, Currey M, Phillips P, Bell MA, Kimmel CB, Postlethwait JH. 2004. Parallel genetic basis for repeated evolution of armor loss in Alaskan threespine stickleback populations. Proc Natl Acad Sci U S A. 101:6050-6055.
13. Ellegren H. 2011. Sex chromosome evolution: recent progress and the influence of male and female heterogamety. Nat Rev Genet. 12:157-166.
14. Elmer KR, Meyer A. 2011. Adaptation in the age of ecological genomics: insights from parallelism and convergence. Trends Ecol Evol. 26:298-306.
15. Eyre-Walker A. 2006. The genomic rate of adaptive evolution. Trends Ecol Evol. 21:569-575.
16. Fay JC, Wyckoff GJ, Wu CI. 2001. Positive and negative selection on the human genome. Genetics 158:1227-1234.
17. Fisher RA. 1958. The genetical theory of natural selection. 2nd ed. New York: Dover Publications Inc. p. 291.
18. Gillespie JH. 1984. Molecular evolution over the mutational landscape. Evolution 38:1116-1129.
19. Gillespie JH. 1991. The causes of molecular evolution. New York: Oxford University Press. p. 352.
20. Gillespie JH. 2004. Why k 5 4Nus is silly. In: Singh RS, Uyenoyama MK, editors. The evolution of population biology. Cambridge: Cambridge University Press. p. 178-192.
21. Gompel N, Prud'Homme B. 2009. The causes of repeated genetic evolution. Dev Biol. 332:36-47.
22. Hermisson J, Pennings PS. 2005. Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169:2335-2352.
23. Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, Sella G, Przeworski M. 2011. Classic selective sweeps were rare in recent human evolution. Science 331:920-924.
24. Hurst LD, Pal C, Lercher MJ. 2004. The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet. 5:299-310.
25. Karasov T, Messer PW, Petrov DA. 2010. Evidence that adaptation in Drosophila is not limited by mutation at single sites. PLoS Genet. 6:e1000924.
26. Kimura M. 1971. Theoretical foundation of population genetics at the molecular level. Theor Popul Biol. 2:174-208.
27. Kimura M. 1979. Model of effectively neutral mutations in which selective constraint is incorporated. Proc Natl Acad Sci U S A. 76:3440-3444.
28. Kimura M, Ohta T. 1971a. On the rate of molecular evolution. J Mol Evol. 1:1-17.
29. Kimura M, Ohta T. 1971b. Protein polymorphism as a phase of molecular evolution. Nature 229:467-469.
30. Kimura M, Ohta T. 1971c. Theoretical aspects of population genetics. Princeton (NJ): Princeton University Press. p. 219.
31. Kirkpatrick M, Hall DW. 2004. Male-biased mutation, sex-linkage, and the rate of adaptive evolution. Evolution 58:437-440.
32. Kopp M, Hermisson J. 2007. Adaptation of a quantitative trait to a moving optimum. Am Nat. 176:715-719.
33. Kopp M, Hermisson J. 2009. The genetic basis of phenotypic adaptation II: the distribution of adaptive substitutions in the moving optimum model. Genetics 183:1453-1476.
34. Lee JM, Sonnhammer ELL. 2003. Genomic gene clustering analysis of pathways in eukaryotes. Genome Res. 13:875-882.
35. Losos JB. 2011. Convergence, adaptation, and constraint. Evolution 65:1827-1840.
36. Manceau M, Domingues VS, Linnen CR, Rosenblum EB, Hoekstra HE. 2010. Convergence in pigmentation at multiple levels: mutations, genes and function. Philos Trans R Soc B. 365:2439-2450.
37. Mank JE. 2009. Sex chromosomes and the evolution of sexual dimorphism: lessons from the genome. Am Nat. 73:141-150.
38. Mank JE, Nam K, Ellegren H. 2010a. Faster-Z evolution is predominantly due to genetic drift. Mol Biol Evol. 27:661-670.
39. Mank JE, Vicoso B, Berlin S, Charlesworth B. 2010b. Effective population size and the faster-X effect: empirical results and their interpretation. Evolution 64:663-674.
40. Michalak P. 2008. Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 91:243-248.
41. Orr HA. 1998. The population genetics of adaptation: the distribution of factors fixed during adaptive evolution. Evolution 52:935-949.
42. Orr HA. 2002. The population genetics of adaptation: the adaptation of DNA sequences. Evolution 56:13117-21330.
43. Orr HA. 2005a. The genetic theory of adaptation: a brief history. Nat Rev Genet. 6:119-127.
44. Orr HA. 2005b. Theories of adaptation: what they do and don't say. Genetica 123:3-13.
45. Orr HA. 2005c. The probability of parallel evolution. Evolution 59:216-220.
46. Orr HA. 2010. The population genetics of beneficial mutations. Philos Trans R Soc B. 365:1195-1201.
47. Orr HA, Betancourt AJ. 2001. Haldane's Sieve and adaptation from the standing genetic variation. Genetics 157:875-884.
48. Presgraves DC. 2008. Sex chromosomes and speciation in Drosophila. Trends Genet. 24:336-343.
49. Pritchard JK, Di Rienzo A. 2010. Adaptation: not by sweeps along. Nat Rev Genet. 11:665-667.
50. Pritchard JK, Pickrell JK, Coop G. 2010. The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Curr Biol. 20:R208-R215.
51. Protas ME, Hersey C, Kochanek D, Zhou Y, Wilkens H, Jeffery WR, Zon LI, Borowsky R, Tabin CJ. 2006. Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism. Nat Genet. 38:107-111.
52. Reed RD, Papa R, Martin A, et al. (13 co-authors). 2011. optix drives the repeated convergent evolution of butterfly wing pattern mimicry. Science 333:1137-1141.
53. Rokyta DR, Abdo Z, Wichman HA. 2009. The genetics of adaptation for eight microvirid bacteriophages. J Mol Evol. 69:229-239.
54. Sattath S, Elyashiv E, Kolodny O, Rinott Y, Sella G. 2011. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans. PLoS Genet. 7:e1001302.
55. Sawyer SA, Kulathinal RJ, Bustamante CD, Hartl DL. 2003. Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. J Mol Evol. 57:S154-S164.
56. Shapiro MD, Marks ME, Peichel CL, Blackman BK, Nereng KS, Jonsson B, Schluter D, Kingsley DM. 2004. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 428:717-723.
57. Smith NGC, Eyre-Walker A. 2002. Adaptive protein evolution in Drosophila. Nature 415:1022-1024.
58. Stern DL, Orgogozo V. 2009. Is genetic evolution predictable? Science 323:746-751.
59. Sucena E, Delon I, Jones I, Payre F, Stern DL. 2003. Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism. Nature 424:935-938.
60. Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, et al. (19 co-authors). 2007. Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet. 39:31-40.
61. Unckless RL, Orr HA. 2009. The population genetics of adaptation: multiple substitutions on a smooth fitness landscape. Genetics 183:1079-1086.
62. Vicoso B, Charlesworth B. 2006. Evolution on the X chromosome: unusual patterns and processes. Nat Rev Genet. 7:645-653.
63. Vicoso B, Charlesworth B. 2009. Effective population size and the faster-X effect: an extended model. Evolution 63:2413-2426.
64. Weinreich DM, Delaney NF, DePristo MA, Hartl DL. 2006. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312:111-114.
65. Welch JJ. 2006. Estimating the genomewide rate of adaptive protein evolution in Drosophila. Genetics 173:821-837.
66. White MJD. 1973. Animal cytology and evolution. London: Cambridge University Press. p. 961.
67. Wood TE, Burke JM, Rieseberg LH. 2005. Parallel genotypic adaptation: when evolution repeats itself. Genetica 123:157-170.
68. Yokoyama S, Radlwimmer FB. 2001. The molecular genetics and evolution of red and green color vision in vertebrates. Genetics 158:1697-1710.
69. Zhang J. 2006. Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys. Nat Genet. 38:819-823.