Male-driven evolution

Current Opinion in Genetics and Development

Volumn 12, Issue 6, 2002, Pages 650-656

  Li, Wen Hsiung ^a   Yi, Soojin ^a   Makova, Kateryna ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME 3; GENE MUTATION; GENETIC CODE; GENETIC VARIABILITY; GENOME; HUMAN; MALE; METHYLATION; MOLECULAR EVOLUTION; MUTATION RATE; PRIMATE; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; SEQUENCE HOMOLOGY; SEX DIFFERENCE; SEX RATIO; Y CHROMOSOME; ANIMAL; DNA METHYLATION; EVOLUTION; MUTATION;

HOMO; PRIMATES;

ANIMALS; DNA METHYLATION; EVOLUTION; HUMANS; MALE; MUTATION;

EID: 0036889392     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(02)00354-4     Document Type: Review

References (60)

1. Haldane J.B.S. The rate of spontaneous mutation of a human gene. J Genet. 31:1935;317-326.
2. Miyata T., Hayashida H., Kuma K., Mitsuyasu K., Yasunaga T. Male-driven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harb Symp Quant Biol. 52:1987;863-867.
3. Chang B.H., Shimmin L.C., Shyue S.K., Hewett-Emmett D., Li W.H. Weak male-driven molecular evolution in rodents. Proc Natl Acad Sci USA. 91:1994;827-831.
4. Li W.H., Ellsworth D.L., Krushkal J., Chang B.H.J., Hewett-Emmett D. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol Phyl Evol. 5:1996;182-187.
5. Olderburg J., Schwaab R., Grimm T., Zerres K., Hakenberg P., Brackmann H.H., Olek K. Direct and indirect estimation of the sex ratio of mutation frequencies in hemophilia A. Am J Hum Genet. 53:1993;1229-1238.
6. Hurst L.D., Ellegren H. Sex biases in the mutation rate. Trends Genet. 14:1998;446-452.
7. McVean G.T., Hurst L.D. Evidence for a selectively favourable reduction in the mutation rate of the X chromosome. Nature. 386:1997;388-392.
8. Ellegren H., Fridolfsson A.K. Male-driven evolution of DNA sequences in birds. Nat Genet. 17:1997;182-184.
9. Kahn N.W., Quinn T.W. Male-driven evolution among Eoaves? A test of the replicative division hypothesis in a heterogametic female (ZW) system. J Mol Evol. 49:1999;750-759.
10. Carmichael A.N., Fridolfsson A.K., Halverson J., Ellegren H. Male-driven evolution rates revealed from Z and W chromosome-linked ATP synthase α-subunit (ATP5A1) sequences in birds. J Mol Evol. 50:2000;443-447.
11. Slattery J., O'Brien S.J. Patterns of Y and X chromosome DNA sequence divergence during the Felidae radiation. Genetics. 148:1998;1245-1255.
12. Lawson L.J., Hewitt G.M. Comparison of substitution rates in ZFX and ZFY introns of sheep and goat related species supports the hypothesis of male-biased mutation rates. J Mol Evol. 54:2002;54-61.
13. Bohossian H.B., Skaletsky H., Page D.C. Unexpectedly similar rates of nucleotide substitution found in male and female hominids. Nature. 406:2000;622-625.
14. Makova K.D., Li W.H. Strong male-driven evolution of DNA sequences in humans and apes. Nature. 416:2002;624-626. The first study that used homologous noncoding regions in an autosome (chromosome 3) and chromosome Y to estimate the sex ratio of mutation rate. As this study does not involve any X-linked sequence, it avoids the possibility that the low mutation rate in X-linked sequences is caused by a reduced mutation rate favored by natural selection rather than as a result of sex differences. It also points out that closely related species are not suitable for estimating the sex ratio of mutation rate.
15. International Human Genome Sequencing Consortium . Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
16. Monk M. Epigenetic programming of differential gene expression in development and evolution. Dev Genet. 17:1995;188-197.
17. Chang B.H., Hewett-Emmett D., Li W.H. Male-to-female ratios of mutation rate in higher primates estimated from intron sequences. Zool Studies. 35:1996;36-48.
18. Filipski J. Why the rate of silent codon substitutions is variable within a vertebrate genome. J Theor Biol. 34:1988;159-164.
19. Wolfe K.H., Sharp P.M., Li W.H. Mutation rates differ among regions of the mammalian genome. Nature. 337:1989;283-285.
20. Casane D., Boissinot S., Chang B.H.J., Shimmin L.C., Li W.H. Mutation pattern variation among regions of the primate genome. J Mol Evol. 45:1997;216-226.
21. Matassi G., Sharp P.M., Gautier C. Chromosomal location effects on gene sequences evolution in mammals. Curr Biol. 9:1999;786-791.
22. Gu Z., Wang H., Nekrutenko A., Li W.H. Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence. Gene. 259:2000;81-88.
23. s values. However, the correlation in the mouse-rat comparisons was weaker, suggesting that the human and rodent genomes differ in their local patterns of mutation or selection on synonymous sites. Further, the local similarity in evolutionary rates extends over whole mouse chomosomes.
24. Castresana J. Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content. Nucleic Acids Res. 8:2002;1751-1756.
25. Ebersberger I., Metzler D., Schawarts C., Pääbo S. Genomewide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet. 70:2002;1490-1497. The authors obtained almost 2 million bases of nonrepetitive chimpanzee sequences by sequencing randomly sheared genomic DNA. Comparisons with their human counterparts revealed the patterns of substitutions that are dependent on both the genomic regions and the times spent in the two different germlines.
26. Ticher A., Graur D. Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes. J Mol Evol. 28:1989;286-298.
27. Wolfe K.H., Sharp P.M. Mammalian gene evolution: nucleotide sequence divergence between mouse and rat. J Mol Evol. 37:1993;441-456.
28. Bernardi G., Mouchiroud D., Gautier C. Silent substitutions in mammalian genomes and their evolutionary implications. J Mol Evol. 37:1993;583-589.
29. Bielawski J.P., Dunn K.A., Yang Z. Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics. 156:2000;1299-1350.
30. Hurst L.D., Williams E.J.B. Covariation of GC content and the silent site substitution rate in rodents: implications for methodology and for the evolution of isochores. Gene. 261:2000;107-114.
31. Lercher M.J., Hurst L.D. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18:2002;337-340. Using regression analyses, the authors demonstrate a positive correlation between recombination rate and nucleotide diversity in the human genome, and show that at least part of the correlation appears to be mediated by regional differences in mutation rate.
32. Yi S, Ellsworth DL, Li WH: Slow molecular clocks in old world monkeys, apes and humans. Mol Biol Evol 2002, in press.
33. Perry J., Ashworth A. Evolutionary rate of a gene affected by chromosomal position. Curr Biol. 9:1999;987-989.
34. Strathern J., Shafer B., McGill C. DNA synthesis errors associated with double-strand-break repair. Genetics. 140:1995;965-972.
35. Papavasiliou F.N., Schatz D.G. Cell-cycle-regulated DNA double-strand breaks in somatic hypermutation of immunoglobulin genes. Nature. 408:2000;216-220.
36. Eyre-Walker A. Recombination and mammalian genome evolution. Proc R Soc Lond Ser B. 252:1993;237-243.
37. Fullerton S.M., Bernardo Carvalho A., Clark A.G. Local rates of recombination are positively correlated with GC content in the human genome. Mol Biol Evol. 18:2001;1139-1142. The first study to show that GC content and recombination are correlated within intron sequences. The authors suggest that local recombination rate is an important indicator of compositional heterogeneity in the human genome.
38. Marais G., Mouchiroud D., Duret L. Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci USA. 98:2001;5688-5692. The authors analyzed the pattern of codon usage in the C. elegans and D. melanogaster genomes and showed a positive correlation between recombination rate and the frequency of optimal codons. The authors claimed that this effect is as a result of a mutational bias toward G and C in regions of high recombination rate, possibly as a direct consequence of the recombination process. This is one of the first studies to contrast the mutationist hypothesis and the selectionist hypothesis to explain the genomic scale codon usage. However, see [59] for additional analyses and critiques.
39. Brown T.C., Jiricny J. Different base/base mispairs are corrected with different efficiencies and specificities in monkey kidney cells. Cell. 54:1988;705-711.
40. Takano-Shimizu T. Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes. Mol Biol Evol. 18:2001;606-619.
41. Gerton J.L., DeRisi J., Shroff R., Lichten M., Brown P.O., Petes T.D. Inaugural article: global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 97:2000;11383-11390.
42. Smith N.G.C., Hurst L.D. The causes of synonymous rate variation in the rodent genome: can substitution rates be used to estimate the sex bias in mutation rate? Genetics. 152:1999;661-673.
43. Gu X., Li W.H. Higher rates of amino acid substitution in rodents than in humans. Mol Phylogenet Evol. 1:1992;211-214.
44. Mimault C., Giraud G., Courtois V., Cailloux F., Boire J.V., Dastugue B., Boespflug-Tanguy O. Brain Dysmeylinating Disease: Proteolipoprotein gene analysis in 82 patients with sporadic Pelizaeus-Merzbacher Disease: duplications, the major cause of the disease, originate more frequently in male germ cells, but point mutations do not. The Clinical European Network on Brain Dysmyelinating Disease. Am J Hum Genet. 65:1999;360-369.
45. Girad M., Couvert P., Carrié A., Tardieu M., Chelly J., Beldjord C., Bienvenu T. Parental origin of de novo MECP2 mutations in Rett syndrome. Eur J Hum Genet. 9:2001;231-236.
46. Trappe R., Laccone F., Cobilanschi J., Meins M., Huppke P., Hanefeld F., Engel W. MECP2 mutations in sporadic cases of Rett syndrome are almost exclusively of paternal origin. Am J Hum Genet. 68:2001;1093-1101.
47. Wilkin D., Szabo J.K., Cameron R., Henderson S., Bellus G.A., Mack M.L., Kaitila I., Loughlin J., Munnich A., Sykes B., et al. Mutations in fibroblast growth-factor receptor 3 in sporadic cases of Achondroplasia occur exclusively on the paternally derived chromosome. Am J Hum Genet. 63:1998;711-716.
48. Moloney D.M., Slaney S.F., Oldridge M., Wall S.A., Sahlin P., Stenman G., Wilkie A.O.M. Exclusive paternal origin of new mutations in Apert syndrome. Nat Genet. 13:1996;48-53.
49. Glaser R.L., Jiang W., Boyadjiev S.A., Tran A.K., Zachary A.A., Maldergem L.V., Johnson D., Walsh S., Oldridge M., Wall S.A., et al. Paternal origin of FGFR2 mutations in sporadic cases of Couzon syndrome and Pfeiffer syndrome. Am J Hum Genet. 66:2000;768-777.
50. Nordenskjöld A., Friedman E., Anvret M. WT1 mutations in patients with Denys-Drash syndrome: a novel mutation in exon 8 and paternal allele origin. Hum Genet. 93:1994;115-120.
51. Yin L., Seri M., Barone V., Tocco T., Scaranari M., Romeo G. Prevalence and parental origin of de novo RET mutations in Hirschsprung's disease. Eur J Hum Genet. 4:1996;356-358.
52. Shuffenecker I., Ginet N., Goldgar D., Eng C., Chambe B., Boneu A., Houdent C., Pallo D., Schlumberger M., Thivolet C., Lenoir G.M. Prevalence and parental origin of de novo RET mutations in multiple endocrine neoplasia type 2A and familial medullary thyroid carcinoma. Le Groupe D'Étude des Tumeur À Calcitonine. Am J Hum Genet. 60:1997;233-237.
53. Carson K.M., Dou S., Chi D., Scavarda N., Toshima K., Jackson C.E., Wells S.A., Goodfellow P.J., Donis-Keller H. Single missense mutation in the tyrosine kinase catalytic domain of the RET protooncogene is associated with multiple endocrine neoplasia type 2B. Proc Natl Acad Sci USA. 91:1994;1579-1583.
54. Kluwe L., Mauntner V., Parry D.M., Jacoby L.B., Baser M., Gusella J., Davis K., Stavrou D., MacCollin M. The parental origin of new mutations in neurofibromatosis 2. Neurogenet. 3:2000;17-24.
55. Richards F., Payne S.J., Zbar B., Affara N.A., Ferguson-Smith A., Maher E.R. Molecular analysis of de novo germline mutations in the von Hippel-Lindau disease gene. Hum Mol Genet. 4:1995;2139-2143.
56. Huang W., Chang B.H., Gu X., Hewett-Emmett D., Li W. Sex differences in mutation rate in higher primates estimated from AMG intron sequences. J Mol Evol. 44:1997;463-465.
57. Shimmin L.C., Chang B.H., Li W.H. Male-driven evolution of DNA sequences. Nature. 362:1993;745-747.
58. Chang B.H., Li W.H. Estimating the intensity of male-driven evolution in rodents by using X-linked and Y-linked Ube 1 genes and pseudogenes. J Mol Evol. 40:1995;70-77.
59. Hey J., Kliman R.M. Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics. 160:2002;595-608.
60. Li W.H. Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics. 85:1977;331-337.