7

Publications from the Petrov Lab

78. Singh, N.D., Benssasson, D. and D. A. Petrov. Evolution of genome size in grasshoppers. Mol. Biol. Evol., (in preparation).

77. Messer, P., and Petrov, D.A. Population genetics of parallel bottlenecks. Genetics, (in preparation).

76. Aminetzach, Y.T., Macpherson, J.M., and D. A. Petrov. Parallel evolution at the pesticide resistance locus CHKov1 in Drosophila. Mol. Biol. Evol., (in preparation).

75. Petrov, D.A., Fiston-Lavier, A.-S., Lenkov, K., Lipatov, M., and Gonzalez, J. Genome-wide assessment of the population dynamics of transposable elements in D. melanogaster. Genome Research, (in preparation).

74. Aminetzach, Y.T.*, Karasov, T.L.*, and D. A. Petrov. Pesticide resistance by exaptation: adaptive evolution at CHKov1 predates the use of pesticides. Mol. Biol. Evol., (in preparation). (*these authors contributed equally).

73. Hershberg, R. and D.A. Petrov. Selection drives nucleotide content variation in bacteria. PloS Biology, (submitted).

72. Karasov, T., Messer, P., and D.A. Petrov. Evidence that adaptation in Drosophila is not limited by mutation at single sites. Science, (submitted).

71. González, J., Karasov, T., Messer, P.W., and D. A. Petrov. Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genetics, (in review).  

70. Cai,. J., Borenstein, E. and D.A. Petrov. Consistent network properties of genes involved in human disease. Genome Research, (in preparation).

69. Cai, J. and D. A. Petrov. Stronger purifying selection and lower rates of adaptation in the evolutionary persistent genes. Gen. Biol. and Evol., (in review).

68. Markova, P. and Petrov, D.A. The choice of aligner significantly impacts estimates of positive selection in Drosophila. Genome Research , (in review)

67. Chan, Y.F., Marks, M.E., Jones, F.C., Villarreal, G., Shapiro, M.D.,  Fisher, S., Southwick, A.M., Absher, D.M., Grimwood, J., Schmutz, J., Myers, R., Petrov, D., Jónsson, B., Schluter, D., Bell, M.B., and D. M. Kingsley. (2009). Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science, (in review).

66. González, J. and D.A. Petrov. (2009). MITEs - the ultimate parasites. Science, 325, 1352-53. doi:10.1126/science.1179556.

65. Hershberg, R. and D.A. Petrov. (2009). Global rules for optimal codon choice. PLoS Genetics, 5, e1000556; doi:10.1371/journal.pgen.1000556.

64. González, J. and D.A. Petrov. (2009). The adaptive role of transposable elements in the Drosophila genome. Gene, doi:10.1016/j.gene.2009.06.008.

63. Messer, P. (2009). Measuring rates and patterns of spontaneous mutation from deep and large-scale polymorphism data. Genetics, 182, 1219-1232; doi:10.1534/genetics.109.105692.

62. Sella, G., Petrov, D.A., Przeworski, M. and P. Andolfatto. (2009). Pervasive natural selection in the Drosophila genome? PLoS Genetics, 5, e1000495; doi:10.1371/journal.pgen.1000495.

61. Cai, J., Borenstein, E., Chen, R., and D. A. Petrov. (2009). Strong purifying selection acts on Mendelian- and complex-disease genes of all evolutionary ages. Gen. Biol. Evol., 0, 131; doi: 10.1093/gbe/evp013.

60. González, J., Macpherson, J.M., and D.A. Petrov. (2009). A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster. Mol. Biol. Evol., 26, 513-526; doi:10.1093/molbev/msn270. 

59. Li, V.C, Davis, J.C, Lenkov, K., Bolival, B., Fuller, M.T. and D. A. Petrov. (2009). Rapid and correlated evolution of the testis TAFs in Drosophila due to low constraint and high rates of positive selection. Mol. Biol. Evol., 26, 1103-1116; doi:10.1093/molbev/msp030.

58. Cai, J., Macpherson, J.M., Sella, G.*, and D.A., Petrov*. (2009). Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genetics, 5, e1000336. (*co-senior authors).

57. González, J. *, Macpherson, J.M. *, Messer, P.W. *, and D. A. Petrov. (2009). Inferring the strength of selection in Drosophila under complex demographic models. Mol. Biol. Evol., 26, 513-526. (*these authors contributed equally and are listed alphabetically).

56. Hershberg*, R., Lipatov*, M., Small, P., Sheffer, H., Niemann, S., Homolka, S., Roach, J.C., Kremer, K., Petrov, D.A., Feldman, M.W., and S., Gagneaux. (2008). High functional diversity in M. tuberculosis driven by genetic drift and human demography. PLoS Biology, 6(12), e311. (*these authors contributed equally).

55. Hershberg, R. and D.A., Petrov. Selection on codon bias. (2008). Annu. Rev. Genet., 42, 287-299.

54. González, J., Lenkov, K., Lipatov, M., Macpherson, J.M., and D.A. Petrov.(2008). High rate of recent TE-induced adaptations in Drosophila melanogaster. PLoS Biology 6(10): e251.

53. Dean, J., Davis, J.C., Davis, R.W., and D.A. Petrov. (2008). Pervasive redundancy and little new functionality among duplicated genes in yeast. PLoS Genetics, July; 4(7): e1000113.

52. Macpherson, J.M., Gonzalez, J., Witten, D., Davis, J.C., Rosenberg, N., Hirsh, A.E., and D. A. Petrov. (2008). Nonadaptive explanations for signatures of partial selective sweeps in Drosophila. Mol. Biol. Evol. 25(6):1025-42.

51. Macpherson, J.M. *, Sella, G. *, Davis, J.C., and D. A. Petrov. (2007) Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics, 177, 2083-2099. (*these authors contributed equally).

50. Singh, N.D., Macpherson, M.J., Jensen, J., and D.A. Petrov. (2007). Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster. BMC Evol. Biol., 7, 202.

49. Hershberg, R., Tang, H., and D.A. Petrov. (2007). Reduced selection leads to accelerated gene loss in Shigella. Genome Biology, 8, R164.

48. Oliver, M.J., Petrov, D.A., Ackerly, D., Falkowski, P.G., and O.M. Schofield. (2007). The mode and tempo of genome size evolution in eukaryotes. Genome Research, 17, 594-601.

47. Singh, N.D. and D. A. Petrov. (2007). Evolution of gene function on the X chromosome versus the autosomes. Genome Dynamics issue "Gene and Protein Evolution", ed. J.N.,Volff. (in press).

46. Singh, N.D., Arndt, P.F., and D.A. Petrov. (2006). Minor shift in background substitution patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences. BMC Biology, 4, 37.

45. Boissinot, S.*, Davis, J.C*, Entezam, A.*, Petrov, D.A and Furano, A.V. (2006). Fitness cost of LINE-1 (L1) activity in humans. Proc. Natl. Acad. Sci., 103, 9590-9594. (*these authors contributed equally).

44. Lipatov, M., Arndt, P.F., Hwa, T., and D.A. Petrov. (2006). A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution. J. Mol. Evol., 62: 168-175.

43. Lipatov, M., Lenkov, K., D.A. Petrov, and C.Bergman. (2005). Gene-transposable element chimeras in Drosophila: bioinformatic and population genetic analyses. BMC Evol. Biol., 3, 24.

42. Davis, J.C. and D.A. Petrov. (2005). Do disparate mechanisms of duplication add similar genes to the genome? Trends in Genetics, 21, 548-555.

41. Singh, N.D. Davis, J.C., and D.A. Petrov. (2005). Codon bias and GC content on the X chromosome in Drosophila correlate negatively with recombination rate. J. Mol. Evol., 61, 315-324.

40. Singh, N.D., Davis, J.C., and D.A. Petrov. (2005). Increase in codon bias on the X chromosome in eukaryotes. Genetics, 171, 145-155.

39. Aminetzach, Y.T., M. J., Macpherson, and D.A. Petrov. (2005). Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila. Science, 309, 764-767

 

38. Arndt, P.F., Hwa, T., and Petrov, D.A.(2005).Substantial regional variation in substitution rates in the human genome: importance of GC Content, gene density, and telomere-specific effects. J. Mol. Evol., 60, 748-763.

37. Petrov, D.A. and J. F. Wendel. Evolution of eukaryotic genome structure. (2005). In “Evolutionary Genetics: Concepts and Case Studies”, Oxford University Press, edited by C.W. Fox and J. B. Wolf (in press).

36. Davis, J.C.*, Brandman, O.*, and D. A. Petrov. (2005). Protein evolution in the context of Drosophila development. J. Mol. Evol., (in press).(* these authors made equal contributions to the paper).

35. Gu, Z., David, L., Petrov, D.A., Jones, T., Davis, R.W., Steinmetz, L.W. (2005). Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci., 102, 1092-1097.

 

34. Singh, N.D., Arndt, P.F., and D. A. Petrov. (2005). Effect of recombination on patterns of substitution in Drosophila. Genetics,169, 709-722.

33. Knight, C. A., Molinari, N., and D.A. Petrov.(2005). The large genome constraint hypothesis: evolution, ecology, and phenotype. Annals of Botany, 95, 177-190.

32. Morris, J.R, Petrov, D.A, Lee, A.M., and C.-Ting Wu. (2004). Enhancer choice in cis and trans: role of the promoter. Genetics, 167, 1739-1747.

31. Davis, J.C and D. A. Petrov. (2004). Preferential duplication of conserved proteins in eukaryotic genomes. PLOS Biology, 2, 318-326.

30. Singh, N.D. and D. A. Petrov. (2004). Dramatic sequence turnover at an intergenic locus in Drosophila. Mol. Biol. Evol., 21, 670-680.

29. Bensasson, D., Feldman, M. W., and D. A. Petrov (2003). High rates of DNA duplication and mitochondrial DNA insertion in the human genome. J. Mol. Evol., 57, 343-354.

28. Arndt, P.F., Petrov, D.A., and Hwa, T. (2003). A sharp shift in the pattern of substitution at the time of mammalian radiation. Mol. Biol. Evol., 20, 1887-1896.

27. Petrov, D.A, Aminetzach, Y.T., Davis, J.C., Bensasson, D.,& Hirsh, A.E. (2003). Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol. Biol. Evol., 20, 880-892.

26. Nuzhdin, S.V. and D. A. Petrov (2003). Transposable elements in clonal lineages: lethal hangover from sex. Biol. J. Linn. Soc., 79, 33-41.

25. Ptak, S. and D. A. Petrov. (2002). How intron splicing affects the deletion and insertion profile in D. melanogaster. Genetics, 162, 1233-1244.

24. D. A. Petrov. (2002). Mutational equilibrium model of genome size evolution. Theor. Pop. Biol., 61, 531-543.

23. Sakharkar, M.K., Kangueane P., Petrov, D.A., Kolaskar, A.S., & Subbiah, S. A. (2002). Database on "Intron-less/single exonic" genes from eukaryotes (SEGE). Bioinformatics, 18, 1266-1267.

22. D. A. Petrov. (2002). Evolution of genome size. Encyclopedia of Evolution. Ed. Mark Pagel, Oxford University Press.

21. D.A. Petrov. (2002). DNA loss and evolution of genome size in Drosophila. Genetica, 115, 81-91.

20. Walbot, V. and D.A. Petrov. (2001). Gene galaxies in the maize genome. Proc. Natl. Acad. Sci. USA, 98, 8163-8164.

19. D. A. Petrov. (2001). Evolution of genome size: new approaches to an old problem. Trends in Genetics, 17, 23-28.

18. Bensasson, D., Petrov, D.A., Zhang, D.-X., Hartl, D.L., Hewitt, G. (2001). Genomic Gigantism: DNA loss is slow in mountain grasshoppers. Mol. Biol. Evol., 18, 246-253.

17. Petrov, D.A., Sangster, T.A., Johnston, J. S., Hartl, D.L., & Shaw, K.L. (2000). Evidence for DNA loss as a determinant of genome size. Science, 287, 1060-1062 (see comments Science, 287, 985-986).

16. Petrov, D.A. & Hartl, D. L. (2000). Pseudogene evolution and natural selection for a compact genome. J. of Heredity, 91, 221-227.

15. Lozovskaya, E.R., Nurminsky, D.I., Petrov, D.A., & Hartl, D.L. (1999). Genome size as a mutation-selection-drift process. Genes and Genet. Syst., 74, 201-207.

14. Petrov, D.A. & Hartl, D. L. (1999). Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc. Natl. Acad. Sci. USA, 96, 1475-1479.

13. Petrov, D.A., Chao, Y.-C., Stephenson, E.C., & Hartl, D. L. (1998). Pseudogene evolution in Drosophila suggests a high rate of DNA loss. Mol. Biol. Evol., 15, 1562-1567.

12. Moriyama, E.N., Petrov, D.A., & Hartl, D.L. (1998). Genome size and intron size in Drosophila. Mol. Biol. Evol., 15, 770-773.

11. Petrov, D.A. & Hartl, D. L. (1998). High rate of DNA loss in the D. melanogaster and D. virilis species groups. Mol. Biol. Evol., 15, 293-302.

10. Petrov, D.A. & Hartl, D. L. (1997). Trash DNA is what gets thrown away: High rate of DNA loss in Drosophila. Gene, 205, 279-289.

9. Petrov, D.A. (1997). Slow but steady: genome reduction through spontaneous mutation. The Plant Cell, 9, 1900-1901.

8. Petrov, D.A., Lozovskaya, E. R., & Hartl, D. L. (1996). High intrinsic rate of DNA loss in Drosophila. Nature, 384, 346-349.

7. Siegal, M. L., Petrov, D. A., & Deaguiar, D. (1996). Triple-ligation strategy with advantages over directional cloning. Biotechniques, 21, 614-619.

6. Lozovskaya, E. R., Hartl, D. L., & Petrov, D. A. (1995). Genomic regulation of transposable elements in Drosophila. Cur. Opin. in Gen. and Dev., 5, 768-773.

5. Petrov, D. A., Schutzman, J. L., Hartl, D. L., & Lozovskaya, E. R. (1995). Diverse transposable elements are mobilized in hybrid dysgenesis in Drosophila virilis. Proc. Natl. Acad. Sci. USA, 92, 8050-8054.

4. Lozovskaya, E. R., Petrov, D. A., & Hartl, D. L. (1993). A combined molecular and cytogenetic approach to genome evolution in Drosophila using large-fragment DNA cloning. Chromosoma, 102, 253-266.

3. Krane, D. E., Allen, R. W., Sawyer, S. A., Petrov, D. A., & Hartl, D. L. (1992). Genetic differences at four DNA typing loci in Finnish, Italian, and mixed Caucasian populations. Proc. Natl. Acad. Sci. USA, 89, 10583-10587.

2. Danilevskaya, O. N., Petrov, D. A., Pavlova, M. N., Koga, A., Kurenova, E. V., & Hartl, D. L. (1992). A repetitive DNA element, associated with telomeric sequences in Drosophila melanogaster, contains open reading frames. Chromosoma, 102, 32-40.

1. Smoller, D. A., Petrov, D.A., & Hartl, D. L. (1991). Characterization of bacteriophage P1 library containing inserts of Drosophila DNA of 75-100 kilobase pairs. Chromosoma, 100, 487-494.