Quantifying adaptive evolution in the Drosophila immune system

PLoS Genetics

Volumn 5, Issue 10, 2009, Pages

  Obbard, Darren J ^a   Welch, John J ^a   Kim, Kang Wook ^a,b   Jiggins, Francis M ^c  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF SHEFFIELD   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DROSOPHILA PROTEIN;

ANIMAL EXPERIMENT; ANTIVIRAL ACTIVITY; ARTICLE; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; EVOLUTIONARY ADAPTATION; FEMALE; GENE; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; HOST PARASITE INTERACTION; IMMUNE SYSTEM; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN; POPULATION STRUCTURE; QUANTITATIVE ANALYSIS; RNA INTERFERENCE; ADAPTATION; ANIMAL; GENETIC SELECTION; GENETICS; IMMUNOLOGY; PARASITOLOGY; PHYSIOLOGY;

DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; DROSOPHILA; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; HOST-PARASITE INTERACTIONS; IMMUNE SYSTEM; SELECTION, GENETIC;

EID: 73449137909     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000698     Document Type: Article

References (59)

1. Sackton TB, Lazzaro BP, Schlenke TA, Evans JD, Hultmark D, et al. (2007) Dynamic evolution of the innate immune system in Drosophila. Nature Genetics 39: 1461-1468.
2. Schlenke TA, Begun DJ (2003) Natural Selection Drives Drosophila Immune System Evolution. Genetics 164: 1471-1480.
3. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, et al. (2005) A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees. PLoS Biology 3: e170. doi:10.1371/journal.pbio.0030170.
4. Begun DJ, Whitley P (2000) Adaptive Evolution of Relish, a Drosophila NF-kB/IkB Protein. Genetics 154: 1231-1238.
5. Lazzaro BP (2005) Elevated Polymorphism and Divergence in the Class C Scavenger Receptors of Drosophila melanogaster and D. simulans. Genetics 169: 2023-2034.
6. Obbard DJ, Jiggins FM, Halligan DL, Little TJ (2006) Natural Selection Drives Extremely Rapid Evolution in Antiviral RNAi Genes. Current Biology 16: 580.
7. Jiggins FM, Kim K-W (2006) Contrasting evolutionary patterns in Drosophila immune receptors. J Mol Evol 63: 769-780.
8. Jiggins FM, Kim KW (2007) A screen for immunity genes evolving under positive selection in Drosophila. Journal of Evolutionary Biology 20: 965-970.
9. Heger A, Ponting CP (2007) Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Research 17: 1837-1849.
10. Eyre-Walker A (2006) The genomic rate of adaptive evolution. Trends in Ecology & Evolution 21: 569-575.
11. McDonald JH, Kreitman M (1991) Adaptive Protein Evolution at the Adh Locus in Drosophila. Nature 351: 652-654.
12. Sawyer SA, Parsch J, Zhang Z, Hartl DL (2007) Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proceedings of the National Academy of Sciences 104: 6504-6510.
13. Shapiro JA, Huang W, Zhang C, Hubisz MJ, Lu J, et al. (2007) Adaptive genic evolution in the Drosophila genomes. Proceedings of the National Academy of Sciences 104: 2271-2276.
14. Parsch J, Zhang Z, Baines JF (2009) The Influence of Demography and Weak Selection on the McDonald-Kreitman Test: An Empirical Study in Drosophila. Mol Biol Evol 26: 691-698.
15. Welch JJ (2006) Estimating the genomewide rate of adaptive protein evolution in Drosophila. Genetics 173: 821-837.
16. Smith NGC, Eyre-Walker A (2002) Adaptive protein evolution in Drosophila. Nature 415: 1022.
17. Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh Y-P, et al. (2007) Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans. PLoS Biol 5: e310. doi:10.1371/journal.pbio.0050310.
18. Eyre-Walker A (2002) Changing Effective Population Size and the McDonald-Kreitman Test. Genetics 162: 2017-2024.
19. Hughes AL (2007) Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level. Heredity 99: 364-373.
20. Harismendy O, Ng P, Strausberg R, Wang X, Stockwell T, et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biology 10: R32.
21. Wilding C, Weetman D, Steen K, Donnelly M (2009) High, clustered, nucleotide diversity in the genome of Anopheles gambiae revealed through pooled-template sequencing: implications for high-throughput genotyping protocols. BMC Genomics 10: 320.
22. Stephan W, Li H (2006) The recent demographic and adaptive history of Drosophila melanogaster. 98: 65-68.
23. Bierne N, Eyre-Walker A (2004) The genomic rate of adaptive amino acid substitution in Drosophila. Molecular Biology and Evolution 21: 1350-1360.
24. Sawyer SA, Hartl DL (1992) Population-Genetics of Polymorphism and Divergence. Genetics 132: 1161-1176.
25. Obbard DJ, Gordon KHJ, Buck AH, Jiggins FM (2009) The evolution of RNAi as a defence against viruses and transposable elements. Philosophical Transactions of the Royal Society B: Biological Sciences 364: 99-115.
26. Lazzaro BP, Clark AG (2003) Molecular population genetics of inducible antibacterial peptide genes in Drosophila melanogaster. Molecular Biology and Evolution 20: 914-923.
27. Jiggins FM, Kim K-W (2005) The Evolution of Antifungal Peptides in Drosophila. Genetics 171: 1847-1859.
28. Watson FL, Puttmann-Holgado R, Thomas F, Lamar DL, Hughes M, et al. (2005) Extensive Diversity of Ig-Superfamily Proteins in the Immune System of Insects. Science 309: 1874-1878.
29. Schmucker D, Chen B (2009) Dscam and DSCAM: complex genes in simple animals, complex animals yet simple genes. Genes & Development 23: 147-156.
30. Levine MT, Begun DJ (2007) Comparative Population Genetics of the Immunity Gene Relish: Is Adaptive Evolution Idiosyncratic? PLoS ONE 2: e442. doi:10.1371/journal.pone.0000442.
31. Bergelson J, Kreitman M, Stahl EA, Tian D (2001) Evolutionary Dynamics of Plant R-Genes. Science 292: 2281-2285.
32. Hughes AL, Nei M (1988) Pattern of Nucleotide Substitution at Major Histocompatibility Complex Class-I Loci Reveals Overdominant Selection. Nature 335: 167-170.
33. Kraaijeveld AR, Godfray HCJ (1999) Geographic Patterns in the Evolution of Resistance and Virulence in Drosophila and Its Parasitoids. The American Naturalist 153: S61-S74.
34. Corby-Harris V, Pontaroli AC, Shimkets LJ, Bennetzen JL, Habel KE, et al. (2007) Geographical Distribution and Diversity of Bacteria Associated with Natural Populations of Drosophila melanogaster Appl Environ Microbiol 73: 3470-3479.
35. Carpenter JA, Obbard DJ, Maside X, Jiggins FM (2007) The recent spread of a vertically transmitted virus through populations of Drosophila melanogaster. Molecular Ecology 16: 3947-3954.
36. Brun G, Plus N (1980) The viruses of Drosophila. In: Ashburner M, Wright TRF, eds. The genetics and biology of Drosophila. New York: Academic Press. pp 625-702.
37. Johnson KN, Christian PD (1999) Molecular Characterization of Drosophila C Virus Isolates. Journal of Invertebrate Pathology 73: 248-254.
38. Kelly John K (2006) Geographical Variation in Selection, from Phenotypes to Molecules. The American Naturalist 167: 481-495.
39. Woolhouse MEJ, Webster JP, Domingo E, Charlesworth B, Levin BR (2002) Biological and biomedical implications of the coevolution of pathogens and their hosts. Nature Genetics 32: 569-577.
40. Thoetkiattikul H, Beck MH, Strand MR (2005) Inhibitor kappa B-like proteins from a polydnavirus inhibit NF-kappa B activation and suppress the insect immune response. Proceedings Of The National Academy Of Sciences Of The United States Of America 102: 11426-11431.
41. Lemaitre B, Nicolas E, Michaut L, Reichhart J-M, Hoffmann JA (1996) The Dorsoventral Regulatory Gene Cassette spatzle/Toll/cactus Controls the Potent Antifungal Response in Drosophila Adults. Cell 86: 973-983.
42. Tennessen JA (2005) Molecular evolution of animal antimicrobial peptides: widespread moderate positive selection. Journal of Evolutionary Biology 18: 1387-1394.
43. Wagner A (2002) Selection and gene duplication: a view from the genome. Genome Biology 3.
44. Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, et al. (2008) An endogenous small interfering RNA pathway in Drosophila. 453: 798-802.
45. Chung W-J, Okamura K, Martin R, Lai EC (2008) Endogenous RNA Interference Provides a Somatic Defense against Drosophila Transposons. 18: 795-802.
46. Zambon RA, Vikram VN, Wu LP (2006) RNAi is an antiviral immune response against a dsRNA virus in Drosophila melanogaster. Cellular Microbiology 8: 880-889.
47. Klattenhoff C, Xi H, Li C, Lee S, Xu J, et al. (2009) The Drosophila HP1 Homolog Rhino Is Required for Transposon Silencing and piRNA Production by Dual-Strand Clusters. Cell In Press, Corrected Proof.
48. Vermaak D, Henikoff S, Malik HS (2005) Positive Selection Drives the Evolution of rhino a Member of the Heterochromatin Protein 1 Family in Drosophila. PLoS Gen 1: e9. doi:10.1371/journal.pgen.0010009.
49. Swanson WJ, Vacquier VD (2002) The rapid evolution of reproductive proteins. Nature Reviews Genetics 3: 137-144.
50. Presgraves DC (2007) Does genetic conflict drive rapid molecular evolution of nuclear transport genes in Drosophila? BioEssays 29: 386-391.
51. Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18: 1851-1858.
52. Fay JC, Wyckoff GJ, Wu CI (2001) Positive and negative selection on the human genome. Genetics 158: 1227-1234.
53. Charlesworth J, Eyre-Walker A (2008) The McDonald-Kreitman Test and Slightly Deleterious Mutations. Mol Biol Evol 25: 1007-1015.
54. Begun DJ, Aquadro CF (1992) Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356: 519-520.
55. Singh ND, Arndt PF, Petrov DA (2005) Genomic Heterogeneity of Background Substitutional Patterns in Drosophila melanogaster. Genetics 169: 709-722.
56. Burnham KP, Anderson DR (1998) Model Selection and Inference: A Practical Information-Theoretic Approach. New York: Springer-Verlag.
57. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences 13: 555-556.
58. Watterson GA (1975) On the number of segregating sites in models without recombination. Theor Popn Biol 7: 256-276.
59. Pannell JR, Charlesworth B (2000) Effects of metapopulation processes on measures of genetic diversity. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences 355: 1851-1864.