A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

PLoS Genetics

Volumn 9, Issue 8, 2013, Pages

  Capra, John A ^a,d   Hubisz, Melissa J ^b   Kostka, Dennis ^c   Pollard, Katherine S ^a   Siepel, Adam ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^d VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

ALLELE; AMINO ACID SUBSTITUTION; ANIMAL GENETICS; ARTICLE; CHIMPANZEE; CONTROLLED STUDY; GENE CONVERSION; GENOME ANALYSIS; HUMAN; HUMAN GENETICS; HUMAN VERSUS ANIMAL COMPARISON; MATHEMATICAL MODEL; NATURAL SELECTION; NONHUMAN; PREDICTION; PROBABILITY; SEQUENCE ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURE ANALYSIS; ANIMAL; CHROMOSOME MAP; GENETIC RECOMBINATION; GENETIC SELECTION; GENETICS; GENOME; MAMMAL; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PAN TROGLODYTES; PHYLOGENY; SEQUENCE ALIGNMENT; THEORETICAL MODEL;

ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; EVOLUTION, MOLECULAR; GENE CONVERSION; GENOME; HUMANS; MAMMALS; MODELS, THEORETICAL; PAN TROGLODYTES; PHYLOGENY; RECOMBINATION, GENETIC; SELECTION, GENETIC; SEQUENCE ALIGNMENT;

EID: 84884630559     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003684     Document Type: Article

References (54)

1. Chen JM, Cooper DN, Chuzhanova N, Ferec C, Patrinos GP, (2007) Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet 8: 762-775.
2. Marais G, (2003) Biased gene conversion: implications for genome and sex evolution. Trends Genet 19: 330-338.
3. Duret L, Galtier N, (2009) Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genom Hum G 10: 285-311.
4. Lamb BC, (1984) The properties of meiotic gene conversion important in its effects on evolution. Heredity (Edinb) 53 (Pt 1):: 113-138.
5. Brown TC, Jiricny J, (1988) Different base/base mispairs are corrected with different efficiencies and specificities in monkey kidney cells. Cell 54: 705-711.
6. Galtier N, Duret L, (2007) Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet 23: 273-277.
7. Berglund J, Pollard KS, Webster MT, (2009) Hotspots of biased nucleotide substitutions in human genes. PLoS Biol 27: e26.
8. Galtier N, Duret L, Glémin S, Ranwez V, (2009) GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet 25: 1-5.
9. Ratnakumar A, Mousset S, Glemin S, Berglund J, Galtier N, et al. (2010) Detecting positive selection within genomes: the problem of biased gene conversion. Philos Trans R Soc Lond B Biol Sci 365: 2571-2580.
10. Glémin S, (July 2010) Surprising fitness consequences of GC-biased gene conversion: I. mutation load and inbreeding depression. Genetics 185: 939-959.
11. Necşulea A, Popa A, Cooper DN, Stenson PD, Mouchiroud D, et al. (2011) Meiotic recombination favors the spreading of deleterious mutations in human populations. Hum Mutat 32: 198-206.
12. Capra JA, Pollard KS, (2011) Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biology and Evolution 3: 516-527.
13. Kostka D, Hubisz MJ, Siepel A, Pollard KS, (2012) The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol 29: 1047-1057.
14. Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM, (2008) High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454: 479-485.
15. Dreszer TR, Wall GD, Haussler D, Pollard KS, (2007) Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res 17: 1420-1430.
16. Duret L, Arndt PF, (2008) The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet 4: e1000071.
17. Katzman S, Capra JA, Haussler D, Pollard KS, (2011) Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biology and Evolution 3: 614-626.
18. Nagylaki T, (1983) Evolution of a finite population under gene conversion. Proc Natl Acad Sci USA 80: 6278-6281.
19. Lartillot N, (2013) Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes. Molecular Biology and Evolution 30: 489-502.
20. Jeffreys AJ, Murray J, Neumann R, (1998) High-resolution mapping of crossovers in human sperm defines a minisatellite-associated recombination hotspot. Mol Cell 2: 267-273.
21. Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, et al. (2010) Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467: 1099-1103.
22. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P, (2005) A fine-scale map of recombination rates and hotspots across the human genome. Science 310: 321-324.
23. Ptak SE, Hinds DA, Koehler K, Nickel B, Patil N, et al. (2005) Fine-scale recombination patterns differ between chimpanzees and humans. Nat Genet 37: 429-434.
24. Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, et al. (2005) Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308: 107-111.
25. Auton A, Fledel-Alon A, Pfeifer S, Venn O, Segurel L, et al. (2012) A fine-scale chimpanzee genetic map from population sequencing. Science 336: 193-198.
26. Hubisz MJ, Pollard KS, Siepel A, (2011) PHAST and RPHAST: phylogenetic analysis with space/time models. Briefings in Bioinformatics 12: 41-51.
27. Siepel A, Haussler D (2005) Phylogenetic hidden Markov models. In: Nielsen R, editor, Statistical Methods in Molecular Evolution, New York: Springer. pp. 325-351.
28. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
29. Webb AJ, Berg IL, Jeffreys A, (2008) Sperm cross-over activity in regions of the human genome showing extreme breakdown of marker association. Proc Natl Acad Sci USA 105: 10471-10476.
30. Romiguier J, Ranwez V, Douzery EJ, Galtier N, (2010) Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes. Genome Research 20: 1001-1009.
31. IJdo JW, Baldini A, Ward DC, Reeders ST, Wells RA, (1991) Origin of human chromosome 2: an ancestral telomere-telomere fusion. Proceedings of the National Academy of Sciences 88: 9051-9055.
32. International Hapmap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 339: 851-861.
33. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
34. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Research 29: 308-311.
35. Stenson P, Mort M, Ball E, Howells K, Phillips A, et al. (2009) The Human Gene Mutation Database: 2008 update. Genome Med 1: 13.
36. Zhang Y, De S, Garner J, Smith K, Wang SA, et al. (2010) Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information. BMC Medical Genomics 3: 1.
37. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, et al. (2012) Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 22: 1790-1797.
38. Pollard K, Salama S, King B, Kern A, Dreszer T, et al. (2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genet 2: e168.
39. Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D, (2010) GC-biased evolution near human accelerated regions. PLoS Genet 6: e1000960.
40. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, et al. (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478: 476-482.
41. Kosiol C, Vinar T, da Fonseca R, Hubisz M, Bustamante C, et al. (2008) Patterns of positive selection in six mammalian genomes. PLoS Genet 4: e1000144.
42. George RD, McVicker G, Diederich R, Ng SB, MacKenzie AP, et al. (2011) Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Research 21: 1686-1694.
43. Mugal CF, Arndt PF, Ellegren H, (2013) Twisted Signatures of GC-Biased Gene Conversion Embedded in an Evolutionary Stable Karyotype. Molecular Biology and Evolution [epub ahead of print] doi:10.1093/molbev/mst067.
44. Navarro A, Barton NH, (2003) Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes. Science 300: 321-324.
45. Myers S, Freeman C, Auton A, Donnelly P, McVean G, (2008) A common sequence motif associated with recombination hot spots and genome instability in humans. Nat Genet 40: 1124-1129.
46. Spencer CC, Deloukas P, Hunt S, Mullikin J, Myers S, et al. (2006) The influence of recombination on human genetic diversity. PLoS Genet 2: e148.
47. Siepel A, Pollard K, Haussler D (2006) New methods for detecting lineage-specific selection. In: Proc. 10th Int'l Conf. on Research in Computational Molecular Biology. Berlin: Springer-Verlag, pp. 190-205.
48. Hasegawa M, Kishino H, Yano T, (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
49. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, et al. (2013) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 41: D64-69.
50. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14: 708-715.
51. Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2011) Ensembl 2011. Nucleic Acids Research 39: D800-D806.
52. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, et al. (2012) Gencode: The reference human genome annotation for the encode project. Genome Research 22: 1760-1774.
53. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, et al. (2004) The UCSC table browser data retrieval tool. Nucleic Acids Research 32: D493-D496.
54. Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, et al. (2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet 45: 723-729.