A Gradient of Silent Substitution Rate in the Human Pseudoautosomal Region

Molecular Biology and Evolution

Volumn 21, Issue 2, 2004, Pages 410-417

  Filatov, Dmitry A ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

Human; Mutation rate; Pseudoautosomal region; Recombination; Silent substitution rate

Indexed keywords

ADENINE; CYTOSINE; DINUCLEOTIDE; GUANINE; THYMINE;

ARTICLE; AUTOSOME; CHIMPANZEE; GENE; GENE CONVERSION; GORILLA; HUMAN; METHYLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORANG UTAN; POLYMERASE CHAIN REACTION; TELOMERE;

ANIMALS; GENOME, HUMAN; HOMINIDAE; HUMANS; POINT MUTATION; RECOMBINATION, GENETIC; SPECIES SPECIFICITY;

PAN TROGLODYTES; PONGO PYGMAEUS; RICKETTSIA SP. PAR;

EID: 1542347027     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh032     Document Type: Article

References (54)

1. Bielawski, J. P., K. A. Dunn, and Z. Yang. 2000. Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics 156:1299-1308.
2. Birdsell, J. A. 2002. Integrating genomics, bioinformatics and classical genetics to study the effect of recombination on genome evolution. Mol. Biol. Evol. 19:1181-1197.
3. Boulton, A., R. S. Myers, and R. J. Redfield. 1997. The hotspot conversion paradox and the evolution of meiotic recombination. Proc. Natl. Acad. Sci. USA 94:8058-8063.
4. Brown, W. R. A. 1988. A physical map of the human pseudoautosomal region. EMBO J. 7:2377-2385.
5. Brown, T. C., and J. Jiricny. 1988. Different base/base mispairs are corrected with different efficiencies and specificities in monkey kidney cells. Cell 54:705-711.
6. Burgoyne, P. S., S. K. Mahadevaiah, M. J. Sutcliffe, and S. J. Palmer. 1992. Fertility in mice requires X-Y pairing and a Y-chromosomal spermiogenesis gene mapping to the long arm. Cell 71:391-398.
7. Chen, F.-C., and W.-H. Li. 2001. Genomic divergence between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68:444-456.
8. Ciccodicola, A., M. D'Esposito, T. Esposito et al. (21 co-authors). 2000. Differentially regulated and evolved genes in the fully sequenced Xq/Yq pseudoautosomal region. Hum. Mol. Genet. 9:395-401.
9. Cooke, H. J., W. R. Brown, and G. A. Rappold. 1985. Hypervariable telomeric sequences from the human sex chromosomes are pseudoautosomal. Nature 317:687-692.
10. Coyne, J. A., W. Meyers, A. Crittenden, and P. Sniegowski. 1993. The fertility effects of pericentric inversions in Drosophila melanogaster. Genetics 134:487-496.
11. Duret, L., and N. Galtier. 2000. The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artefact. Mol. Biol. Evol. 17:1620-1625.
12. Ellis, N., and P. N. Goodfellow. 1989. The mammalian pseudoautosomal region. Trends Genet. 5:406-410.
13. Ellis, N., P. Yen, K. Neiswanger, L. J. Shapiro, and P. N. Goodfellow. 1990. Evolution of the pseudoautosomal boundary in the old world monkeys and great apes. Cell 63:977-986.
14. Eyre-Walker, A. 1993. Recombination and mammalian genome evolution. Proc. R. Soc. Lond. Ser. B Biol. Sci. 252:237-243.
15. Eyre-Walker, A., and M. Bulmer. 1995. Synonymous substitution rates in enterobacteria. Genetics 140:1407-1412.
16. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
17. Filatov, D. A. 2002. ProSeq: a software for preparation and evolutionary analysis of DNA sequence data sets. Mol. Ecol. Notes 2:621-624.
18. Filatov, D. A., and D. Charlesworth. 2002. Substitution rates in the X- and Y-linked genes of the plants, Silene latifolia and S. dioica. Mol. Biol. Evol. 19:898-907.
19. Filatov, D. A., and D. T. Gerrard. 2003. High mutation rates in human and ape pseudoautosomal genes. Gene 317:67-77.
20. Freije, D., C. Helms, M. S. Watson, and H. Donis-Keller. 1992. Identification of a second pseudoautosomal region near the Xq and Yq telomeres. Science 258:1784-1787.
21. Fullerton, S. M., A. B. Carvalho, and A. G. Clark. 2001. Local rates of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 18:1339-1142.
22. Glaser, B., D. Myrtek, Y. Rumpler, K. Schiebel, M. Hauwy, G. A. Rappold, and W. Schempp. 1999. Transposition of SRY into ancestral pseudoautosomal region creates a new pseudoautosomal boundary in a progenitor of simian primates. Hum. Mol. Genet. 8:2071-2078.
23. Goodman, M., C. A. Porter, J. Czelusniak, S. L. Page, H. Schneider, J. Shoshani, G. Gunnell, and C. P. Groves. 1998. Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Pol. Phylogenet. Evol. 9:585-598.
24. Hardison R. C., K. M. Roskin, S. Yang et al. (18 co-authors) 2003. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13:13-26.
25. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
26. Hellmann, I., I. Ebersberger, S. E. Ptak, S. Paabo, and M. Przeworski. 2003. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72:1527-1535.
27. Hudson, R. R., M. Kreitman, and M. Aguade. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
28. Kim, H. S., and O. Takenaka. 1996. A comparison of TSPY genes from Y-chromosomal DNA of the great apes and humans: sequence, evolution, and phylogeny. Am. J. Phys. Anthropol. 100:301-309.
29. Kondrashov, A. S. 2002. Direct estimates of human per nucleotide mutation rates at 20 loci causing mendelian diseases. Hum. Mutat. 21:12-27.
30. Kong, A., D. F. Gudbjartsson, J. Sainz et al. (17 co-authors), 2002. A high-resolution recombination map of the human genome. Nat. Genet. 31:241-247.
31. Lamb, B. C. 1986. Gene conversion disparity-factors influencing its direction and extent, with tests of assumptions and predictions in its evolutionary effects. Genetics 114:611-632.
32. Lercher, M. J., and L. D. Hurst. 2002. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18:337-340.
33. Li, W.-H. 1997. Molecular evolution. Sinauer Associates. Sunderland, Mass.
34. Lien, S., J. Szyda, B. Schechinger, G. Rappold, and N. Arnheim. 2000. Evidence for heterogeneity in recombination in the human pseudoautosomal region: high resolution analysis by sperm typing and radiation-hybrid mapping. Am. J. Hum. Genet. 66:557-566.
35. Makova, K. D., and W.-H. Li. 2002. Strong male-driven evolution of DNA sequences in humans and apes. Nature 416:624-626.
36. May, C. A., A. C. Shone, L. Kalaydjieva, A. Sajantila, and A. J. Jeffreys. 2002. Crossover clustering and rapid decay of linkage disequilibrium in the Xp/Yp pseudoautosomal gene SHOX. Nat. Genet. 31:272-275.
37. Muse, S. V., and B. S. Weir. 1992. Testing for equality of evolutionary rates. Genetics 132:269-276.
38. Nachman, M. W., and S. Crowell. 2000. Estimates of the mutation rate per nucleotide in humans. Genetics 156:297-304.
39. Nagylaki, T. 1983. Evolution of a finite population under gene conversion. Proc. Natl. Acad. Sci. USA 80:6278-6281.
40. Novitski, E., and G. Braver. 1954. An analysis of crossing over within a heterozygous inversion in Drosophila melanogaster. Genetics 39:197-209.
41. Perry, J., and A. Ashworth. 1999. Evolutionary rate of a gene affected by chromosomal position. Curr. Biol. 9:987-989.
42. Petit, C., J. Levilliers, and J. Weissenbach. 1988. Physical mapping of the human pseudoautosomal region; comparison with the genetic linkage map. EMBO J. 7:2369-2376.
43. Robertson, K. D., and A. P. Wolffe. 2000. DNA methylation in health and disease. Nat. Rev. Genet. 1:11-19.
44. Schiebel, K., J. Meder, A. Rump, A. Rosenthal, M. Winkelmann, C. Fischer, T. Bonk, A. Humeny, and G. Rappold. 2000. Elevated DNA sequence diversity in the genomic region of the phosphatase PPP2R3L gene in the human pseudoautosomal region. Cytogenet. Cell Genet. 91:224-230.
45. Shimmin, L.C., B. H. J. Chang, and W.-H. Li. 1993. Male-driven evolution of DNA sequences. Nature 362:745-747.
46. Sokal, R. R., and F. J. Rohlf. 1995. Biometry, 3rd edition. W. H. Freeman, San Francisco.
47. Soriano P., E. A. Keitges, D. F. Schorderet, K. Harbers, S. M. Gartler, and R. Jaenisch. 1987. High-rate of recombination and double crossovers in the mouse pseudoautosomal region during male meiosis. Proc. Natl. Acad. Sci. USA 84:7218-7220.
48. Strathem, J. N., B. K. Shafer, and C. B. McGill. 1995. DNA synthesis errors associated with double-strand-break repair. Genetics 140:965-972.
49. Takano-Shimizu, T. 2001. Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes. Mol. Biol. Evol. 18:606-619.
50. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
51. Waterston, R. H., K. Lindblad-Toh, E. Bimey, J. Rogers, J. F. Abril et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
52. Yang, Z. 1994. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.
53. -. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood CABIOS 13:555-556.
54. Yi, S., D. L. Ellsworth, and W.-H. Li. 2002. Slow molecular clocks in old world monkeys, apes, and humans. Mol. Biol. Evol. 19:2191-2198.