Publications by Petrov Lab Members (lab authors in bold)

157. Machado, H.E., Lawrie, D.S., and D. A. Petrov. (2019). Pervasive strong selection at the level of codon usage bias in D. melanogaster. Genetics, 214, 511–528; http://biorxiv.org/content/biorxiv/early/2017/02/09/106476.full.pdf

156. Tilk, S., Bergland, A.O., Goodman, A., Schmidt, P., Petrov, D.A., Greenblum, S. (2019). Accurate allele frequencies from ultra-low coverage pool-seq samples in evolve-and-resequence experiments. G3, 9, 4159-4168; https://www.biorxiv.org/content/early/2018/01/11/244004

155. Rudman, S.M., Greenblum, S., Hughes, R.C., Rajpurohit, S., Kiratli, O.,Lowder, D.B., Lemmon, S.G, Petrov, D.A, Chaston, J.M., Schmidt, P. (2019) Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster. Proc. Natl. Acad. of Sci., 116, 20035-20032; https://www.biorxiv.org/content/10.1101/632257v1

154. Li, Y., Petrov, D.A.* and Sherlock, G.* (2019). Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation. Nature Ecology and Evolution, 3, 1539-1551. (* - contributed equally).

153. Feder, A.F., Pennings,P.S, Hermisson, J. and Petrov, D.A. (2019) Evolutionary dynamics in structured populations under strong population genetic force. G3, 9, 3395-3407; https://www.biorxiv.org/content/10.1101/579854v1

152. Uricchio, L.H., Petrov, D.A., and Enard, D. (2019). Exploiting selection at linked sites to infer the rate and strength of adaptation. Nature Ecol. and Evol., 3, 977–984; originally posted on https://www.biorxiv.org/content/early/2018/09/26/427633

151. Natesh, M.#, Taylor, R.W#, Truelove, N., Hadly, E.A., Palumbi, S., Petrov, D.A* and Ramakrishnan, U.* (2019). Empowering conservation science and practice with efficient and economical genotyping from poor quality samples. Methods in Ecology and Evolution,00:1-7; (* and #- contributed equally); originally posted at https://www.biorxiv.org/content/early/2018/06/20/349472

 

150. Rech, G.E., Bogaerts-Marquez, M., Barron, M.G, Merenciano, M., Villanueva-Canas, J.L., Horvath, V., Fiston-Lavier, A.-F., Luyten, I., Venkataram, S., Quesneville, H., Petrov, D.A.*, and Gonzalez, J.* (2019). Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLoS Genetics, 15, e1007900; https://www.biorxiv.org/content/early/2018/07/30/380618 (* - contributed equally).

 

149. Combs, P.A., Krupp, J.J., Khosla, N.M., Bua, D., Petrov, D.A., Levine, J.D.,  Fraser, H.B. Tissue-specific cis-regulatory divergence implicates eloF in inhibiting interspecies mating in Drosophila. Current Biology, 28, 1-7.

148. Armstrong, E.E., Taylor,R.W., Prost,S., Blinston, P., van der Meer, E., Madzikanda, H., Mufute, O., Mandisodza, R., Stuelpnagel, J., Sillero-Zubiri, C., and Petrov, D.A. Cost-effective assembly of the African wild dog genome using linked long reads. GIGAScience; originally posted at https://www.biorxiv.org/content/biorxiv/early/2017/09/27/195180.full.pdf

147. Enard, D. and Petrov, D.A. (2018) Evidence that RNA viruses drove adaptive introgressions between Neanderthals and modern humans. Cell 175: 360-371; http://biorxiv.org/content/early/2017/03/24/120477

 

146. Theys, K., Feder, A.F., Gelbart, M., Hart,l M., Stern, A., Pennings, P.S. (2018) Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV. PLoS Genetics 14: e1007420

145. Rajpurohit, S., Gefen, E., Bergland, A.O., Petrov, D.A., Gibbs, A.G., and Schmidt, P.S. Spatiotemporal patterns of desiccation tolerance in natural populations of Drosophila melanogaster. (2018). Mol. Ecol., 27: 3525-3540; http://biorxiv.org/content/early/2016/10/07/079616

144. McCoy, R.C., Newnham, L.J., Ottolini, C., Hoffmann, E., Chatzimeletiou, K. Cornejo, O.E., Zhan, Q.Zaninovic, N., Rosenwaks, Z., Petrov, D.A., Demko, Z.P., Sigurjonsson S., Handyside, A.H. (2018). Tripolar mitosis drives the association between maternal genotypes of PLK4 and aneuploidy in human preimplantation embryos. Human Molecular Genetics, ddy147; http://www.biorxiv.org/content/early/2017/08/29/182303

143. Rogers*, Z.N., McFarland*, C.D., Winters, I.P., Seoane, J.A., Brady, J.J., Yoon, S., Curtis, C., Petrov, D.A#. and Winslow, M.M.# (2018). The fitness landscape of tumor suppression in lung adenocarcinoma in vivo. Nature Genetics, 50, 483–486. (* and # - contributed equally).

 

142. Li, Y.*, Venkataram, S.*, Agarwala, A*., Dunn, B., Petrov, D.A#, Sherlock, G.#, Fisher, D.S.# (2018). Hidden complexity of yeast adaptation under
“simple” evolutionary conditions. Current Biology, 28, 1–11. (* - contributed equally; # - corresponding authors).

141. Behrman, E.L., Howick, V.M., Kapun, M., Staubach, F., Bergland, A.O., Petrov, D.A., Lazzaro, B.P., Schmidt, P.S. (2018). Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster. Proc. Royal Soc. B., 285: 20172599; http://www.biorxiv.org/content/early/2017/09/10/186882

 

140. Winters, I.P., Chiou, S.-H., Paulk,N.K., McFarland,C.D., Lalgudi, P.V., Ma, R.K., Lisowski, L., Connolly, A.J., Petrov, D.A., Kay, M.K., and Winslow, M.M. (2017). Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity. Nature Communications, 8: 2053.

139. Ebel, E.R., Tellis, N., Venkataram, S., Petrov, D.A.*, and Enard, D.* (2017). Accelerated evolution of mammalian proteins that interact with Plasmodium and related parasites. PLoS Genetics, 13: e1007023; originally posted at http://biorxiv.org/content/early/2016/10/17/081216.

138. Sherlock, G. and Petrov, D. A. (2017). Seeking Goldilocks during evolution of drug resistance. PLoS Biology, 15: e2001872.

137. Wittman, M. J., Bergland, A.O., Feldman, M.W., Schmidt, P.S., and D. A. Petrov. (2017). Segregation lift: A general mechanism for the maintenance of polygenic variation under seasonally fluctuating selection. Proc. Natl. Acad. Sci., 114: E9932-E9941; originally posted at http://biorxiv.org/content/biorxiv/early/2017/03/09/115444.full.pdf

136. Rogers, Z.N.*, McFarland, C.D.*, Winters*, I.P., Naranjo, S., Chuang, C.-H., Petrov, D.A., and Winslow, M. (2017). Tuba-seq: a quantitative and multiplexed approach to uncover the fitness landscape of tumor suppression in vivo. Nature Methods, doi:10.1038/nmeth.4297; (* - contributed equally)

135. Feder, A.F., Kline,C., Polacino,P., Cottrell,M., Kashuba A.D.M., Keele,B.F., Hu,S.-L., Petrov, D.A., Pennings,P.S., and Ambrose, Z. (2017) High resolution spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host. PLOS Pathogens, 13(5): e1006358; http://biorxiv.org/content/early/2017/01/04/097980

134. Assaf, Z.J., Tilk, S., Park,J., Siegal, M.L., and Petrov, D.A. (2017). Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations. Genome Research, doi:10.1101/gr.219956.116; http://biorxiv.org/content/early/2016/12/19/095182

133. Wilson, B.A, Pennings, P.S. and Petrov, D.A. (2017). Soft selective sweeps in evolutionary rescue. Genetics, 205: 1573-1586; http://biorxiv.org/content/early/2016/05/12/052993

132. Akhund-Zade, J., Bergland, A.O., Crowe, S. O., and R. L. Unckless. (2017). The genetic basis of natural variation in Drosophila (Diptera: Drosophilidae) virgin egg retention. J.of Insect Sci. 17: 1–9.

131. Zhu, Y., Sherlock, G. and Petrov, D. A. (2017). Extremely rare polymorphisms recapitulate AT-biased mutational spectrum of the mutation-accumulation estimates in yeast. PLoS Genetics, 13: e10064

130. Rajpurohit, S., Hanus, R., Vrkoslav V., Behrman E.L., Bergland A.O., Petrov D.A., Cvacka J., and P.S. Schmidt. (2017). Adaptive dynamics of cuticular hydrocarbons in Drosophila. Journal of Evolutionary Biology, 30:66-80.

 

129. Venkataram, S.*, Dunn, B.*, Li, Y., Argawala, A., Chang, J., Ebel, E., Geiler-Samerotte, K., Herrisant, L., Blundell, J., Levy, S.F., Fisher, D., Sherlock, G.*, and D.A.Petrov*. (2016). A comprehensive genotype-fitness map for adaptation-driving mutations in yeast. Cell, 167, 1–12 (* contributed equally).

128. Lou, D., Kim, E., Meyerson, N., Pancholi, N., Mohni, K., Enard, D., Petrov, D., Weller, S., Weitzman, M., and S. Sawyer. (2016). An intrinsically disordered region of Nbs1 constitutes a species-specific barrier to Herpes Simplex Virus 1 in primates. Cell Host Microbe, 20, 178–188.

127. Zhu, Y., Sherlock, G.* and Petrov, D. A.* (2016). Population structure and origins of clinical Saccharomyces cerevisiae strains. G3, 6, 2421–2434. http://biorxiv.org/content/early/2016/03/21/044958; (* contributed equally).

126. Sellis, D., Kvitek, D.J., Dunn, B., Schwartz, K., Sherlock, G., and Petrov, D.A. (2016). Empirical evidence for heterozygote advantage in adapting diploid populations of Saccharomyces cerevisiae.  Genetics, 203: 1401-1413; posted originally on biorxiv http://biorxiv.org/content/early/2015/12/02/033563

125. Garud, N. and Petrov, D.A. (2016). Elevation of linkage disequilibrium above neutral expectations in ancestral and derived populations of Drosophila melanogaster.Genetics, 203: 863–880; posted on bioRxiv at http://biorxiv.org/content/early/2015/10/27/029942

124. Enard, D., Cai, L., Gwennap, C., and Petrov, D.A. Viruses are a dominant driver of protein adaptation in mammals. (2016). Elife, 5:e12469; first appeared at biorXiv http://biorxiv.org/content/early/2015/10/18/029397.

123. Demko, Z.P., Simon, A.L., McCoy, R. C., Petrov, D. A., Rabinowitz, M. Ph.D. (2016). Effects of maternal age on euploidy in a large cohort of embryos analyzed with 24-chromosome single-nucleotide polymorphism-based preimplantation genetic screening. Fertility and Sterility, pii: S0015-0282(16)00066-2. doi: 10.1016/j.fertnstert.2016.01.025.

122. Zhao, X., Behrman, E.L., Bergland, A.O., Gregory B.D., D.A. Petrov and P.S. Schmidt. (2016). Global transcriptional profiling of diapause and climatic adaptation in Drosophila melanogaster. Mol. Biol. and Evol., 33:707–720.

121. Feder, A.F., Rhee, S.Y., Holmes, S.P., Shafer, R.W., Petrov, D.A.*, and Pennings, P.S.*. (2016). More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1. ELife, 5, e10670. (* contributed equally).

120. Tuttle,E. M.*, Bergland, A.O.,* Korody, M.L., Brewer, M.S., Newhouse, D.J., Minx, P., Stager, M., Betuel, A., Cheviron, Z.A., Warren, W.C., Gonser, R.A., and C.N. Balakrishnan. (2016). Divergence and functionald degradation of a sex chromosome-like supergene. Current Biology, 26, 1–7.

119. Wilson, B., Garud, N.R., Feder, A.F., Assaf, Z.J., and Pennings, P.S. (2016). The population genetics of drug resistance evolution in natural populations of viral, bacterial, and eukaryotic pathogens. Mol. Ecol., 25, 42–66 .

118. Machado, H.E., Bergland, A.O., O’Brien, K.R., Behrman, E.L., Schmidt, P.S. and D. A. Petrov. (2016). Comparative population genomics of latitudinal variation in D. simulans and D. melanogaster. Mol. Ecol., 10.1111/mec.13446.

117. Bergland, A.O., Tobler, R., González, J., Schmidt, P., and Petrov, D.A. (2016). Secondary contact has contributed to genome-wide patterns of clinal variation in North American and Australian populations of Drosophila melanogaster. Mol. Ecol., doi:10.1111/mec.13455; posted on bioRxiv at http://biorxiv.org/content/early/2015/01/06/009084

116. McCoy, R. C., Demko, Z., Ryan, A., Banjevic, M., Hill, M., Sigurjonsson, S., Rabinowitz, M., Petrov, D. A. (2015). Evidence of selection against complex mitotic-origin aneuploidy during preimplantation development. PLoS Genetics, 11: e1005601. doi:10.1371/journal.pgen.1005601

115. Glemin, S., Arndt, P.F., Messer, P.W., Petrov, D.A., Galtier, N., and L. Duret. (2015). Quantification of GC-biased gene conversion in the human genome. Genome Research, 25:1215-1228.

114. Garud, N. and Rosenberg, N.A. (2015). Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps. Theor. Pop. Biology., 102: 94-101.

113. Moreno-Gamez, S., Hill, A.L, Rosenbloom, D. I. S., Petrov, D.A., Nowak, M.A., and P. Pennings. (2015). Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multi-drug resistance. Proc. Natl. Acad. Sci., doi: 10.1073/pnas.1424184112; posted on bioRxiv at http://biorxiv.org/content/early/2014/12/19/013003

112. Assaf, Z.J., Petrov, D.A.* and Blundell, J.R.*. (2015). The obstruction of adaptation in diploids by recessive deleterious alleles. Proc. Natl. Acad. Sci. USA, www.pnas.org/cgi/doi/10.1073/pnas.1424949112; (* contributed equally).

111. McCoy, R. C., Demko, Z., Ryan, A., Banjevic, M., Hill, M., Sigurjonsson, S., Rabinowitz, M., Fraser, H. B., Petrov, D. A. (2015). Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos. Science, 348: 235-238.

110. Garud, N., Messer, P.W., Buzbas, E., and Petrov, D.A. (2015). Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLoS Genetics, 11: e1005004. doi:10.1371/journal.pgen.1005004; originally posted on http://arxiv.org/abs/1303.0906

109. Fiston-Lavier, A.-S, Barrón, M.G., Petrov, D.A., González, J. (2015). T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data. Nucleic Acids Research, 43, e22 doi: 10.1093/nar/gku1250; originally posted at http://biorxiv.org/content/early/2014/09/16/002964

108. Levy, S.*, Blundell, J.R.*, Venkataram, S., Petrov, D.A., Fisher, D.S., and Sherlock, G. (2015). Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature, doi:10.1038/nature14279. (* authors contributed equally).

 

107. Adrion, J.R., Kousathanas, A., Pascual, M., Burrack, H.J., Haddad, N.M., Bergland, A.O., Machado, H., Sackton, T., Schlenke, T.A., Watada, M., Wegmann, D. and N. D. Singh. (2014). Drosophila suzukii: the genetic footprint of a recent, worldwide invasion. Mol. Biol. Evol., 31:3148–3163

106. Sellis, D. and Longo, M.D. (2014). Patterns of variation during adaptation in functionally linked loci. Evolution, 69:75-89; doi: 10.1111/evo.12548

105. Paaby, A.B., Bergland, A.O., Behrman, E., and Schmidt, P. (2014). A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life history adaptation. Evolution, 68:3395–3409.

104. Barrón, M.G., Fiston-Lavier, A.-S., Petrov, D.A., and González-Perez, J. (2014). Population genomics of transposable elements in Drosophila. Annual Review of Genetics, 48:561–81.

103. Bergland, A.O, Behrman, E.L., O’Brien, K.R., Schmidt, P.S., and Petrov, D.A. (2014). Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila. PLoS Genet 10: e1004775; originally posted at http://arxiv.org/abs/1303.5044

102. Kelley, J.L., Peyton, J.T., Fiston-Lavier, A.-S., Teets N.M., Yee, M.-C., Johnston, J.C., Bustamante, C.D., Lee, R.E., Denlinger, D.L. (2014). Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nature Communications, 5, #4611, doi:10.1038/ncomms5611.

101.  Zhu, Y., Siegal, M.L., Hall, D.W., and Petrov, D.A. (2014). Reply to Chen and Zhang: On interpreting genome-wide trends from yeast mutation accumulation data. Proc. Natl. Acad. Sci., 111, E4063.

100. Wilson, B., Petrov, D.A, and Messer, P.W. (2014). Soft selective sweeps in complex demographic scenarios. Genetics, 198, 669-684; originally posted on http://biorxiv.org/content/early/2014/04/23/004424

99. Zhu, Y.,  Siegal, M.L., Hall, D.W., and Petrov, D.A. (2014). Precise estimates of mutation rate and spectrum in yeast. Proc. Natl. Acad. Sci., 111, E2310-E2318. doi:10.1073/pnas.1323011111.

98. McCoy, R.C., Taylor, R.W., Blauwkamp, T.A., Kelley, J.L., Kertesz, M., Pushkarev, D., Petrov, D.A., Fiston-Lavier, A.-S. (2014). Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements. PLoS ONE 9: e106689. doi:10.1371/journal.pone.0106689; originally posted at http://biorxiv.org/content/early/2014/01/21/001834

97. Enard, D., Messer, P.W., and Petrov, D.A. (2014). Genome wide signals of pervasive positive selection in human evolution. Genome Research, 24, 885-895. doi:10.1101/gr.164822.113; posted at http://arxiv.org/abs/1308.4951

96. Lawrie, D.S., and Petrov, D.A. (2014). Comparative population genomics: power and principles for the inference of functionality. Trends in Genetics, 30, 133–139.

95. McCoy, R.C., Garud, N.R., Kelley, J.K., Boggs, C.L., and Petrov, D.A. (2014). Demographic inference accurately times recent bottleneck in an introduced butterfly population. Mol. Ecology, 23, 136-150.

 

94. Petrov, D.A. (2013). Searching for adaptation in the genome. Princeton Guide to Evolution, Princeton University Press, Losos, J.B., editor in chief, ISBN: 9780691149776.

93. Messer, P.W. and Petrov, D.A. (2013). Population genomics of rapid adaptation by soft selective sweeps. Trends in Ecology and Evolution, 28, 659-669. http://dx.doi.org/10.1016/j.tree.2013.08.003

92. Pennings, PS. (2013). HIV Drug resistance: Problems and Perspectives. Infectious Disease Reports, 5: 21-25.

91. Staubach, F., Baines, J.F., Kuenzel, S., Bik, E.K., and D.A. Petrov. (2013). Bacterial diversity associated with Drosophila in the laboratory and in the natural environment. PLoS ONE 8: e70749. doi:10.1371/journal.pone.0070749 (previous version at http://arXiv:1211.3367).

90. Messer, P.W. SLiM: simulating evolution with selection and linkage. (2013). Genetics 194, 1037-1039. (early access 0.1534/genetics.113.152181; arXiv version http://arXiv:1301.3109)

89. Lawrie, D. S., Messer, P.W., Hershberg, R., and Petrov, D. (2013). Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genetics, 9: e1003527. doi:10.1371/journal.pgen.1003527 (originally http://arxiv.org/abs/1301.3325)

88. Messer, P.W. and Petrov, D.A (2013).  McDonald-Kreitman test under frequent adaptation: problems and solutions. PNAS, 110: 8615-8620www.pnas.org/cgi/doi/10.1073/pnas.1220835110

87. Losos, J.B, Arnold, S.J., Bejerano, G., Brodie, E.D., Hibbett, D., Hoekstra, H.E., Mindell, D.P., Monteiro, A., Moritz, C., Orr, H.A., Petrov, D.A., Renner, S.S., Ricklefs, R.E., Soltis, P.S., and Turner, T.L. (2013). Evolutionary Biology for the 21st Century. PLoS Biology, 11: e1001466. doi:10.1371/journal.pbio.1001466.

 

86. Feder, A.F., Petrov, D.A., and A.O. Bergland. (2012).  LDx: maximum likelihood estimation of linkage disequilibrium from high-throughput pooled resequencing data. PLoS ONE 7: e48588. doi:10.1371/journal.pone.0048588; original submission arXiv:1210.2363

85. Hershberg, R. and D.A. Petrov. (2012). On the limitations of using ribosomal genes as a reference for the study of codon usage: A rebuttal. PLoS ONE, 7:
e49060. doi:10.1371/journal.pone.0049060.

84. Staubach, F., Lorenc, A., Messer, P., Tang, K., Petrov, D.A. and Tautz, D. (2012). Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genetics, 8: e1002891. doi:10.1371/journal.pgen.1002891.

83. Zhu, Y.,  Bergland, A.O.,  González, J., and Petrov, D.A. (2012). Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster. PLoS One, 7: e41901. doi:10.1371/journal.pone.0041901.

82. Messer, P.W. and Neher, R.A. (2012). Estimating the strength of selective sweeps from deep population diversity data. Genetics, 191, 593-605.

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. Methods in Molecular Biology, 855, 361-383.

80. 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.