Substitution rate heterogeneity and the male mutation bias

Journal of Molecular Evolution

Volumn 62, Issue 2, 2006, Pages 226-233

  Berlin, Sofia ^a,c   Brandström, Mikael ^a   Backström, Niclas ^a   Axelsson, Erik ^a   Smith, Nick G C ^a,b   Ellegren, Hans ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b LANCASTER UNIVERSITY   (United Kingdom)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Birds; Male mutation bias; Sex chromosomes; Substitution rate variation

Indexed keywords

ANIMAL; ARTICLE; BIRD; EPIDEMIOLOGY; GENETIC HETEROGENEITY; GENETIC SELECTION; GENETICS; MALE; MOLECULAR EVOLUTION; MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEX CHROMOSOME;

ANIMALS; BIAS (EPIDEMIOLOGY); BIRDS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GENETIC HETEROGENEITY; MALE; MUTATION; PHYLOGENY; SELECTION (GENETICS); SEX CHROMOSOMES;

EID: 33748105235     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-005-0103-6     Document Type: Article

References (55)

1. Abajian (1994) Sputnik. Available at: http://abaijan.net/sputnik/index. html
2. Agulnik AI, Bishop CE, Lerner JL, Agulnik SI, Solovyev VV (1997) Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven. Mammal Genome 8:134-138 (Pubitemid 28060721)
3. Axelsson E, Smith NG, Sundstrom H, Berlin S, Ellegren H (2004) Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey. Mol Biol Evol 21:1538-1547 (Pubitemid 38971764)
4. Barnes WM (1992) The fidelity of Taq polymerase catalyzing PCR is improved by an N-terminal deletion. Gene 112:29-35
5. Bartosch-Härlid A, Berlin S, Smith NG, Møller AP, Ellegren H (2003) Life history and the male mutation bias. Evolution 57:2398-2406 (Pubitemid 37388031)
6. Berlin S, Ellegren H (2004) Chicken W: a genetically uniform chromosome in a highly variable genome. Proc Natl Acad Sci USA 101:15967-15969 (Pubitemid 39507910)
7. Bohossian HB, Skaletsky H, Page DC (2000) Unexpectedly similar rates of nucleotide substitution found in male and female hominids. Nature 406:622-625 (Pubitemid 30641047)
8. Carmichael AN, Fridolfsson AK, Halverson J, Ellegren H (2000) Male-biased mutation rates revealed from Z and W chromosome-linked ATP synthase alpha-subunit (ATP5A1) sequences in birds. J Mol Evol 50:443-447 (Pubitemid 30429958)
9. Chamary JV, Hurst LD (2004) Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage. Mol Biol Evol 21:1014-1023
10. Chang BH, Li WH (1995) Estimating the intensity of male-driven evolution in rodents by using X-linked and Y-linked Ube 1 genes and pseudogenes. J Mol Evol 40:70-77
11. Chang BH, Shimmin LC, Shyue SK, Hewett-Emmett D, Li WH (1994) Weak male-driven molecular evolution in rodents. Proc Natl Acad Sci USA 91:827-831 (Pubitemid 24041495)
12. Chicken Genome Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716
13. Crow JF (1997) The high spontaneous mutation rate: is it a health risk? Proc Natl Acad Sci USA 94:8380-8386
14. Dimcheff DE, Drovetski SV, Mindell DP (2002) Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes. Mol Phylogenet Evol 24:203-215 (Pubitemid 34995914)
15. Ebersberger I, Metzler D, Schwarz C, Paabo S (2002) Genomewide Comparison of DNA Sequences between Humans and Chimpanzees. Am J Hum Genet 70:1490-1497 (Pubitemid 34533896)
16. Ellegren H, Fridolfsson AK (1997) Male-driven evolution of DNA sequences in birds. Nat Genet 17:182-184
17. Ellegren H, Fridolfsson AK (2003) Sex-specific mutation rates in salmonid fish. J Mol Evol 56:458-463 (Pubitemid 36390776)
18. Ellegren H, Smith NGC, Webster MT (2003) Mutation rate variation in the mammalian genome. Curr Opin GenetDev 13:562-568 (Pubitemid 37456872)
19. Filatov DA, Charlesworth D (2002) Substitution rates in the X- and Y-linked genes of the plants, Silene latifolia and S. dioica. Mol Biol Evol 19:898-907 (Pubitemid 34602959)
20. Filatov DA (2005) Substitution rates in a new Silene latifolia sex-linked gene, SlssX/Y. 22:402-408
21. Fridolfsson AK, Ellegren H (2000) Molecular evolution of the avian CHD1 genes on the Z and W sex chromosomes. Genetics 155:1903-1912
22. Girard M, Couvert P, Carrie A, Tardieu M, Chelly J, Beldjord C, Bienvenu T (2001) Parental origin of de novo MECP2 mutations in Rett syndrome. Eur J Hum Genet 9:231-236 (Pubitemid 32241774)
23. Haldane JBS (1935) The rate of spontaneous mutation of a human gene. J Genet 31:317-326
24. Handley LJ, Ceplitis H, Ellegren H (2004) Evolutionary strata on the chicken Z chromosome: implications for sex chromosome evolution. Genetics 167:367-76 (Pubitemid 38736394)
25. Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D (2003) Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res 13:13-26
26. Hare MP, Palumbi SR (2003) High intron sequence conservation across three mammalian orders suggests functional constraints. Mol Biol Evol 20:969-978 (Pubitemid 36578724)
27. Ibarguchi G, Gissing GJ, Gaston AJ, Boag PT, Friesen VL (2004) Male-biased mutation rates and the overestimation of extrapair paternity: problem, solution, and illustration using thick-billed murres (Uria lomvia, Alcidae). J Hered 95:209-216 (Pubitemid 38924754)
28. Kahn NW, Quinn TW (1999) Male-driven evolution among Eoaves? A test of the replicative division hypothesis in a heterogametic female (ZW) system. J Mol Evol 49:750-759 (Pubitemid 32250302)
29. Kirkpatrick M, Hall DW (2004) Male-biased mutation, sex linkage, and the rate of adaptive evolution. Evol Int J Org Evol 58:437-440 (Pubitemid 38362388)
30. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245 (Pubitemid 33735359)
31. Lercher MJ, Williams EJ, Hurst LD (2001) Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias. Mol Biol Evol 18:2032-2039 (Pubitemid 33026774)
32. Li WH, Yi S, Makova K (2002) Male-driven evolution. Curr Opin Genet Dev 12:650-656 (Pubitemid 35335982)
33. Lu J, Wu CI (2005) Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc Natl Acad Sci USA 102:4063-4067 (Pubitemid 40388555)
34. Ludwig MZ (2002) Functional evolution of noncoding DNA. Curr Opin Genet Dev 12:634-639
35. Lundberg KS, Shoemaker DD, Adams MW, Short JM, Sorge JA, Mathur EJ (1991) High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene 108:1-6
36. Malcom CM, Wyckoff GJ, Lahn BT (2003) Genic mutation rates in mammals: local similarity, chromosomal heterogeneity, and X-versus-autosome disparity. Mol Biol Evol 20:1633-1641 (Pubitemid 41070825)
37. Makova KD, Li WH (2002) Strong male-driven evolution of DNA sequences in humans and apes. Nature 416:624-626 (Pubitemid 34406760)
38. Makova KD, Yang S, Chiaromonte F (2004) Insertions and deletions are male biased too: a whole-genome analysis in rodents. Genome Res 14:567-573 (Pubitemid 38500227)
39. McVean GT, Hurst LD (1997) Evidence for a selectively favourable reduction in the mutation rate of the X chromosome. Nature 386:388-392 (Pubitemid 27154477)
40. Miyata T, Hayashida H, Kuma K, Mitsuyasu K, Yasunaga T (1987) Male-driven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harbor Symp Quant Biol 52:863-867 (Pubitemid 18262395)
41. Nachman MW (2002) Variation in recombination rate across the genome: evidence and implications. Curr Opin Genet Dev 12:657-663
42. Sachidanandam R, Weissman D, Schmidt SC, et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933 (Pubitemid 32165347)
43. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W (2000) PipMaker - a web server for aligning two genomic DNA sequences. Genome Res 10:577-586 (Pubitemid 30259089)
44. Shimmin LC, Chang BH, Li WH (1993a) Male-driven evolution of DNA sequences. Nature 362:745-747 (Pubitemid 23125976)
45. Shimmin LC, Chang BH, Hewett-Emmett D, Li WH (1993b) Potential problems in estimating the male-to-female mutation rate ratio from DNA sequence data. J Mol Evol 37:160-166 (Pubitemid 23215688)
46. Smith NGC, Eyre-Walker A (2003) Partitioning the variation in mammalian substitution rates. Mol Biol Evol 20:10-17 (Pubitemid 36077893)
47. Smith NGC, Webster MT, Ellegren H (2002) Deterministic mutation rate variation in the human genome. Genome Res 12:1350-1356
48. Sokal RR, Rohlf FJ (2000) Biometry - the principles and practice of statistics ion biological research. W.H. Freeman, New York,
49. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526 (Pubitemid 23157236)
50. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680 (Pubitemid 24354800)
51. Trappe R, Laccone F, Cobilanschi J, Meins M, Huppke P, Hanefeld F, Engel W (2001) MECP2 mutations in sporadic cases of Rett syndrome are almost exclusively of paternal origin. Am J Hum Genet 68:1093-1101 (Pubitemid 32424408)
52. Waterston RH, Lindblad-Toh K, Birney E et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562 (Pubitemid 35477048)
53. Whittle CA, Johnston MO (2002) Male-driven evolution of mitochondrial and chloroplastidial DNA sequences in plants. Mol Biol Evol 19:938-949
54. Wilkin DJ, Szabo JK, Cameron R, Henderson S, Bellus GA, Mack ML, Kaitila I, Loughlin J, Munnich A, Sykes B, Bonaventure J, Francomano CA (1998) Mutations in fibroblast growth-factor receptor 3 in sporadic cases of achondroplasia occur exclusively on the paternally derived chromosome. Am J Hum Genet 63:711-716 (Pubitemid 30422670)
55. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556