Publications from the Petrov Lab

84. Markova, P. and D.A. Petrov. Regions encoding disordered proteins are the primary source of alignment ambiguities and indels in Drosophila proteins. Mol Biol. Evol, (submitted).

83. Hershberg, R. and D.A. Petrov. On the limitations of using ribosomal genes as references for the study of codon usage: A rebuttal. PLoS ONE, (in review).

82. Zhu, Y.,  Bergland, A.O.,  González, J., and Petrov, D.A. One lane, one population: empirical validation of pooled whole genome population re-sequencing. Genetics, (in review).

81. González, J. and D. A. Petrov. (2012). Evolution of genome content: population dynamics of transposable elements in flies and humans. Evolutionary Genomics: statistical and computationla methods. Springer-Humana, ed. Maria Anisimova (in press).

81. Rabinowitz, M, Ryan, R., Gemelos, G., Hill, M., Baner, J., Cinnioglu, C., Banjevic, M., Potter, D., Petrov, D.A., and Demko, Z. (2012). Origins and rates of aneuploidy in human blastomeres. Fertility and Sterility, 97, 395-401.

79. Sellis, D., Callahan, B.J., Petrov, D.A and P.W. Messer. (2011). Heterozygote advantage as a natural consequence of adaptation in diploids. Proc. Natl. Acad. Sci., 108: 20666-20671. Short description on our blog.

78. Lawrie, D., Petrov, D.A, and P.W. Messer. (2011). Faster than neutral evolution of constrained sequences: the complex interplay of mutational biases and weak selection. Gen. Biol. Evol., 3:383–395. doi:10.1093/gbe/evr032 Short description on our blog.

77. Markova, P. and D. A. Petrov. (2011). High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes. Genome Research, doi:10.1101/gr.115949.110. Short description on our blog.

76. Petrov, D.A., Fiston-Lavier, A.-S., Lipatov, M., Lenkov, K., and J. Gonzalez. (2011). Population genomics of transposable elements in Drosophila melanogaster. Mol. Biol. Evol., 28: 1633-1644. doi: 10.1093/molbev/msq337 Short description on our blog.

75. Fiston-Lavier, A-S., Carrigan, M., Petrov, D.A., J. Gonzalez. (2011). T-lex: A program for fast and accurate assessment of transposable element presence using next-generation sequencing data. Nuc. Acids. Res., 39, e36 doi:10.1093/nar/gkq1291 Short description on our blog.

74. Cai,. J., Borenstein, E. and D.A. Petrov. (2010). Broker genes in human disease Gen. Biol. Evol., 2: 815-825. doi: 10.1093/gbe/evq064 Short description on our blog.

73. Hershberg, R. and D.A. Petrov.(2010). Evidence that mutation is universally biased towards AT in bacteria. PLoS Genetics, 6: e1001115; doi:10.1371/journal.pgen.1001115 Short description on our blog.

72. Cai, J. and D. A. Petrov. (2010). Stronger purifying selection and lower rates of adaptation in the evolutionary persistent genes. Gen. Biol. and Evol., 2:393–409. doi:10.1093/gbe/evq019. Short description on our blog.

71. Fiston-Lavier*, A.-S., Singh*, N.D., Lipatov, M., and D. A. Petrov. (2010). Drosophila melanogaster recombination rate calculator. Gene, doi:10.1016/j.gene.2010.04.015. (*these authors contributed equally). Short description on our blog.

70. Karasov*, T., Messer*, P., and D.A. Petrov. (2010). Evidence that adaptation in Drosophila is not limited by mutation at single sites. PLoS Genetics, 6(6): e1000924. doi:10.1371/journal.pgen.1000924.(*these authors contributed equally). Short description on our blog.

69. González, J., Karasov, T., Messer, P.W., and D. A. Petrov. (2010). Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genetics, 6, e1000905.doi:10.1371/journal.pgen.1000905. Short description on our blog.

68. 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. (2010). Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science, 32, 302-305. doi:10.1126/science.11182213.

67. D. E. Krane, V. Bahn, D. Balding, B. Barlow, H. Cash, B. L. Desportes, P. D'Eustachio, K. Devlin, T. E. Doom, I. Dror, S. Ford, C. Funk, J. Gilder, G. Hampikian, K. Inman, A. Jamieson, P. E. Kent, R. Koppl, I. Kornfield, S. Krimsky, J. Mnookin, L. Mueller, E. Murphy, D. R. Paoletti, D. A. Petrov, M. Raymer, D. M. Risinger, A. Roth, N. Rudin, W. Shields, J. A. Siegel, M. Slatkin, Y. S. Song, T. Speed, C. Spiegelman, P. Sullivan, A. R. Swienton, T. Tarpey, W. C. Thompson, E. Ungvarsky, and S. Zabell. (2009). Time for DNA disclosure. Science, 326, 1631-1632. DOI: 10.1126/science.326.5960.1631

66. González, J. and D.A. Petrov. (2009). MITEs - the ultimate parasites. Science, 325, 1352-53. Short description on our blog.

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

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. Short description on our blog.

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. Short description on our blog.

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. Short description on our blog.

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. Short description on our blog.

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. Short description on our blog.

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). Short description on our blog.

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). Short description on our blog.

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. Short description on our blog.

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.