Detecting past positive selection through ongoing negative selection

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 1006-1013

  Bazykin, Georgii A ^a,b   Kondrashov, Alexey S ^a,c  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Allele frequency spectrum; Amino acid substitutions; Divergence; McDonald Kreitman test; Natural selection; Polymorphism

Indexed keywords

DROSOPHILA MELANOGASTER; HOMO SAPIENS;

ADAPTATION; ALLELE; AMINO ACID SUBSTITUTION; ANIMAL; ARTICLE; CODON; DROSOPHILA MELANOGASTER; GENE FREQUENCY; GENETIC DRIFT; GENETIC POLYMORPHISM; GENETIC SCREENING; GENETIC SELECTION; GENETICS; HUMAN; IMMUNOLOGY; METHODOLOGY; MOLECULAR EVOLUTION; MUTATION; PHYLOGENY; SEQUENCE ALIGNMENT;

ADAPTATION, BIOLOGICAL; ALLELES; AMINO ACID SUBSTITUTION; ANIMALS; CODON; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETIC DRIFT; GENETIC TESTING; HUMANS; MUTATION; PHYLOGENY; POLYMORPHISM, GENETIC; SELECTION, GENETIC; SEQUENCE ALIGNMENT;

EID: 84856257886     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr086     Document Type: Article

References (42)

1. Ahn SM, et al. 2009. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 19:1622-1629.
2. Andrews RM, et al. 1999. Reanalysis and revision of the Cambridge reference sequence for humanmitochondrial DNA. NatGenet. 23:147. (Pubitemid 29455385)
3. Asthana S, et al. 2007. Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci U S A. 104:12410-12415. (Pubitemid 47206151)
4. Baxevanis AD. 2008. Searching NCBI databases using Entrez. Curr Protoc Bioinformatics Chapter 1:Unit 1.3.
5. Bazykin GA, Kondrashov FA, Ogurtsov AY, Sunyaev S, Kondrashov AS. 2004. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature 429:558-562. (Pubitemid 38737659)
6. Bazykin GA, et al. 2007. Extensive parallelism in protein evolution. Biol Direct. 2:20.
7. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2009. GenBank. Nucleic Acids Res. 37:D26-D31.
8. Bentley DR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59.
9. Charlesworth J, Eyre-Walker A. 2007. The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations. Proc Natl Acad Sci U S A. 104:16992-16997. (Pubitemid 350210978)
10. Charlesworth J, Eyre-Walker A. 2008. The McDonald-Kreitman test and slightly deleterious mutations. Mol Biol Evol. 25:1007-1015.
11. Drmanac R, et al. 2010. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327:78-81.
12. Eyre-Walker A. 2002. Changing effective population size and the McDonald-Kreitman test. Genetics 162:2017-2024. (Pubitemid 36114681)
13. Eyre-Walker A. 2006. The genomic rate of adaptive evolution. Trends Ecol Evol. 21:569-575. (Pubitemid 44353858)
14. Eyre-Walker A, Keightley PD. 2009. Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol Biol Evol. 26:2097-2108.
15. Grossman SR, et al. 2010. A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327:883-886.
16. Heger A, Ponting CP. 2007. Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res. 17:1837-1849. (Pubitemid 351360007)
17. Hodgkinson A, Ladoukakis E, Eyre-Walker A. 2009. Cryptic variation in the human mutation rate. PLoS Biol. 7:e1000027.
18. Hsu F, et al. 2006. The UCSC known genes. Bioinformatics 22:1036-1046.
19. Huelsenbeck JP, Jain S, Frost SW, Pond SL. 2006. A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proc Natl Acad Sci U S A. 103:6263-6268.
20. Jordan KW, Carbone MA, Yamamoto A, Morgan TJ, Mackay TF. 2007. Quantitative genomics of locomotor behavior in Drosophila melanogaster. Genome Biol. 8:R172.
21. Keightley PD, Eyre-Walker A. 2007. Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177:2251-2261. (Pubitemid 350277004)
22. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
23. Krause J, et al. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464:894-897.
24. Kryazhimskiy S, Bazykin GA, Plotkin J, Dushoff J. 2008. Directionality in the evolution of influenza A haemagglutinin. Proc R Soc B Biol Sci. 275:2455-2464.
25. Kryazhimskiy S, Plotkin JB. 2008. The population genetics of dN/dS. PLoS Genet. 4:e1000304.
26. Kuhn RM, et al. 2009. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 37:D755-D761.
27. Levy S, et al. 2007. The diploid genome sequence of an individual human. PLoS Biol. 5:e254.
28. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654. (Pubitemid 21896661)
29. Mustonen V, Lässig M. 2009. From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation. Trends Genet. 25:111-119.
30. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. 2007. Recent and ongoing selection in the human genome. Nat Rev Genet. 8:857-868. (Pubitemid 47609088)
31. Novembre J, Di Rienzo A. 2009. Spatial patterns of variation due to natural selection in humans. Nat Rev Genet. 10:745-755.
32. Popadin K, Polishchuk LV, Mamirova L, Knorre D, Gunbin K. 2007. Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals. Proc Natl Acad Sci U S A. 104:13390-13395. (Pubitemid 47293955)
33. Ruff CB. 2003. Long bone articular and diaphyseal structure in Old World monkeys and apes. II: estimation of body mass. Am J Phys Anthropol. 120:16-37. (Pubitemid 36019997)
34. Schuster SC, et al. 2010. Complete Khoisan and Bantu genomes from southern Africa. Nature 463:943-947.
35. Smith NG, Eyre-Walker A. 2002. Adaptive protein evolution in Drosophila. Nature 415:1022-1024. (Pubitemid 34193448)
36. Taylor J, Schenck I, Blankenberg D, Nekrutenko A. 2007. Using galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinfor-matics. Chapter 10:Unit 10.5.
37. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTALW: 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)
38. Tweedie S, et al. 2009. FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. 37:D555-D559.
39. Wang J, et al. 2008. The diploid genome sequence of an Asian individual. Nature 456:60-65.
40. Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 7:256-276.
41. Yang Z, Bielawski JP. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 15:496-503.
42. Yang Z, Nielsen R, Hasegawa M. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol. 15:1600-1611. (Pubitemid 28550985)