Publications by Petrov Lab Members
Petrov Lab authors are in bold.
2024
Kinsler, G., Li, Y., Sherlock*, G., Petrov, D.A.* (2024) A shift from pleiotropic to modular adaptation revealed by a high-resolution two-step adaptive walk. https://www.biorxiv.org/content/10.1101/2024.04.17.589938v1 Twitter 🧵 *- contributed equally.
Armstrong, E.E., Carey, S.B., Harkess, A., Lazzari, G.Z., Solari, K.A., Maldonado, J.E., Fleischer, R.C., Aziz, N., Walsh, P., Koepfli, K.-P., Eizirik, E., Petrov, D.A.*, Campana, M.G.* (2024) Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees. https://www.biorxiv.org/content/10.1101/2024.04.06.587788v1 (* contributed equally) Twitter 🧵
Hebert, J.D., Xu, H., Tang, Y.J., Tang, Y.J., Ruiz, P.A., Detrick, C., Wang, J., Hughes, N.W., Donosa, O., Andrejka, L., Karmakar, S., Aboilator, I., Cong, L., Sage, J., Petrov, D.A., Winslow, M.M.(2024) Modeling the genomic complexity of human cancer using Cas12a mice. https://www.biorxiv.org/content/10.1101/2024.03.07.583774v1
Hebert, J.D., Tang, Y.J., Andrejka, L., Lopez, S. , Petrov, D.A.#, Boross, G.,#, Winslow, M.M.# (2024) Combinatorial in vivo genome editing identifies widespread epistasis during lung tumorigenesis. https://www.biorxiv.org/content/10.1101/2024.03.07.583981v1 #corrresponding authors
Razo-Mejia, M., Mani, M., Petrov D.A. (2024) Bayesian inference of relative fitness on high-throughput pooled competition assays. Plos Computational Biology 20: e1011937; https://www.biorxiv.org/content/10.1101/2023.10.14.562365v1 Twitter 🧵
2023
Solari, K.A., Morgan, S., Poyarkov, A.D., Weckworth, B., Samelius, G., Sharma, K., Ostrowski, S., Ramakrishnan, U., Kubanychbekov, Z., Kachel, S., Johansson, S., Lkhagvajav, P., Hemmingmoore, H., Alexandrov, D.Y., Bayaraa, M., Grachev, M., Korablev, M.P., Hernandez-Blanco, J.A., Munkhtsog, B., Rosenbaum, B., Rozhnov, V.V., Rajabi, A.M., Noori, H., Armstrong, E.E.*, Petrov, D.A.* (2023). Extreme in every way: exceedingly low genetic diversity in snow leopards due to persistently small population size. (* contributed equally). https://www.biorxiv.org/content/10.1101/2023.12.14.571340v1 Twitter 🧵
Goldman, D.A., Xue, K.S., Parrott, A.B., Jeeda, R.R., Lopez, J.G., Vila, J.C.C., Petrov, D.A., Good, B.H., Relman, D.A., Huang, K.C. (2023). Competition for shared resources increases the impact of propagule size during coalescence of gut microbial communities. https://www.biorxiv.org/content/10.1101/2023.11.29.569120v1
McGee R.S., Kinsler G., Petrov D.A., Tikhonov M. (2023) Improving the accuracy of bulk fitness assays by correcting barcode processing biases. https://www.biorxiv.org/content/10.1101/2023.10.31.565047v1 Twitter 🧵
Blair, L. M., Juan, J. M., Sebastian, L., Tran, V. B., Nie, W., Wall, G. D., Gerceker, M., Lai, I. K., Apilado, E. A., Grenot, G., Amar, D., Foggetti, G., Do Carmo, M., Ugur, Z., Deng, D., Chenchik, A., Paz Zafra, M., Dow, L. E., Politi, K., MacQuitty, J. J., Petrov D. A., Winslow M. M., Rosen M. J., Winters, I. P. (2023). Oncogenic context shapes the fitness landscape of tumor suppression. Nature communications, 14(1), 6422. https://doi.org/10.1038/s41467-023-42156-y; https://www.biorxiv.org/content/10.1101/2022.10.24.511787v1 Twitter 🧵
Xue, K. S., Walton, S. J., Goldman, D. A., Morrison, M. L., Verster, A. J., Parrott, A. B., Yu, F. B., Neff, N. F., Rosenberg, N. A., Ross, B. D., Petrov, D. A., Huang, K. C., Good, B. H., & Relman, D. A. (2023). Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. https://www.biorxiv.org/content/10.1101/2023.09.26.559480v2
Yousefi, M., Andrejka, L., Szamecz, M., Winslow, M. M., Petrov, D. A., & Boross, G. (2023). Fully accessible fitness landscape of oncogene-negative lung adenocarcinoma. PNAS, 120(38), e2303224120. https://doi.org/10.1073/pnas.2303224120; https://www.biorxiv.org/content/10.1101/2023.01.30.526178v2
Abreu C.I., Mathur S., Petrov D.A. (2023) Strong environmental memory revealed by experimental evolution in static and fluctuating environments. https://www.biorxiv.org/content/10.1101/2023.09.14.557739v2 Twitter 🧵
Kinsler, G., Schmidlin, K., Newell, D., Eder, R., Apodaca, S., Lam, G., Petrov, D.A., & Geiler-Samerotte, K. (2023). Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch. Journal of molecular evolution, 91(3), 293–310. https://doi.org/10.1007/s00239-023-10114-3; https://www.biorxiv.org/content/10.1101/2022.08.25.505320v1
Ebel, E. R., Kim, B. Y., McDew-White, M., Egan, E. S., Anderson, T. J. C., & Petrov, D. A. (2023). Antigenic diversity in malaria parasites is maintained on extrachromosomal DNA. https://www.biorxiv.org/content/10.1101/2023.02.02.526885v1 Twitter 🧵
Lee, M. C., Cai, H., Murray, C. W., Li, C., Shue, Y. T., Andrejka, L., He, A. L., Holzem, A. M. E., Drainas, A. P., Ko, J. H., Coles, G. L., Kong, C., Zhu, S., Zhu, C., Wang, J., van de Rijn, M., Petrov, D. A., Winslow, M. M., & Sage, J. (2023). A multiplexed in vivo approach to identify driver genes in small cell lung cancer. Cell reports, 42(1), 111990. https://doi.org/10.1016/j.celrep.2023.111990
Bitter M.C., Berardi S., Oken H., Huynh A., Schmidt P., Petrov D.A. (2023). Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking. https://www.biorxiv.org/content/10.1101/2023.10.16.562586v1 Twitter 🧵
Kim B.Y., Gellert H.R., Church S.H., Suvorov A., Anderson S.S., Barmina O., Beskid S.G., Comeault A.A., Crown K.N., Diamond S.E., Dorus S., Fujichika T., Hemker J.A., Hrcek J., Kankare M., Katoh T., Magnacca K.N., Martin R.A., Matsunaga T., Medeiros M.J., Miller D.E., Pitnick S., Simoni S., Steenwinkel T.E., Schiffer M., Syed Z.A., Takahashi A., Wei K. H-C. , Yokoyama T., Eisen M.B., Kopp A., Matute D., Obbard D.J., O’Grady P.M., Price D.K., Toda M.J., Werner T., Petrov D.A. (2023) Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. https://www.biorxiv.org/content/10.1101/2023.10.02.560517v1 Twitter 🧵
Armstrong E.E., Mooney J.A., Solari K.A., Kim B.Y., Barsh G.S., Grant V., Greenbaum G., Kaelin C.B., Panchenko K., Pickrell J.K., Rosenberg N., Ryder O.A., Yokoyama T., Ramakrishnan U., Petrov D.A., Hadly E.A. (2023). Unraveling the Genomic Diversity and Evolutionary History of Captive Tigers in the United States. https://www.biorxiv.org/content/10.1101/2023.06.19.545608v1 Twitter 🧵
Chen, V., Johnson, M. S., Hérissant, L., Humphrey, P. T., Yuan, D. C., Li, Y., Agarwala, A., Hoelscher, S. B., Petrov, D. A., Desai, M. M., & Sherlock, G. (2023). Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments. eLife, 12, e92899. https://doi.org/10.7554/eLife.92899; https://www.biorxiv.org/content/10.1101/2023.02.28.530341v1
Tang, R., Shuldiner, E. G., Kelly, M., Murray, C. W., Hebert, J. D., Andrejka, L., Tsai, M. K., Hughes, N. W., Parker, M. I., Cai, H., Li, C., Wahl, G. M., Dunbrack, R. L., Jackson, P. K., Petrov, D. A., & Winslow, M. M. (2023). Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth. Nature Cell Biology, 25(1), 159–169. https://doi.org/10.1038/s41556-022-01049-w
Foggetti G., Li C., Cai H., Petrov D. A., Winslow M. M. & Politi K. (2023) Tumor suppressor pathways shape EGFR-driven lung tumor progression and response to treatment, Molecular & Cellular Oncology, 9:1, DOI: 10.1080/23723556.2021.1994328
Tilk S., Frydman J., Curtis C., Petrov D.A. (2023) Cancers adapt to their mutational load by buffering protein misfolding stress; Elife https://doi.org/10.7554/eLife.87301.1 https://www.biorxiv.org/content/10.1101/2022.06.08.495407v2 Twitter 🧵
2022
Armstrong, E. E., Campana, M. G., Solari, K. A., Morgan, S. R., Ryder, O. A., Naude, V. N., Samelius, G., Sharma, K., Hadly, E. A., & Petrov, D. A. (2022). Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris). G3 12(12), jkac277, https://doi.org/10.1093/g3journal/jkac277; https://www.biorxiv.org/content/10.1101/2022.04.26.489474v1
Yousefi, M.*, Boross, G.*, Weiss, C., Murray, C.W., Hebert, J., Cai, H., Ashkin, E.L., Karmakar, S., Andrejka, L., Chen, L., Wang, M., Tsai, M.K., Lin, W.-Y., Li, C., Yakhchalian, P., Colón, C.I., Chew, S.-K, Chu, P., Swanton, C., Kunder, C.A., Petrov, D.A., and Winslow, M.M. (2022) Combinatorial Inactivation of Tumor Suppressors Efficiently Initiates Lung Adenocarcinoma with Therapeutic Vulnerabilities. Cancer Res 82: 1589–1602. https://doi.org/10.1158/0008-5472.CAN-22-0059; https://www.biorxiv.org/content/10.1101/2021.10.20.464849v1 (* contributed equally).
Tang, R.*, Shuldiner, E.G.*, Kelly, M., Murray, C.W., Hebert, J.D., Andrejka, L., Tsai, M., Cai, H., Li, Y.-C., Wahl, G.M., Jackson, P.K., Petrov, D.A., Winslow, M.M. Multiplexed identification of RAS paralog imbalance as a driver of lung cancer growth. Nature Cell Biology 25, 159-169; https://www.biorxiv.org/content/10.1101/2021.07.08.451571v1 (* contributed equally).
Rudman, S.M.*, Greenblum, S.I.*, Rajpurohit, S.*, Betancourt, N.J., Hanna, J., Tilk, S., Yokoyama, T., Petrov, D.A, Schmidt, P. Direct observation of adaptive tracking on ecological timescales in Drosophila. (2022) Science 375, eabj7484; doi:10.1126/science.abj7484; https://www.biorxiv.org/content/10.1101/2021.04.27.441526v1
Tilk, S., Curtis, C., Petrov, D.A.*, McFarland, C.D.* (2022) Most cancers carry a substantial deleterious load due to Hill-Robertson interference. eLife 11, e67790; https://www.biorxiv.org/content/10.1101/764340v2. Twitter 🧵
2021
Ebel, E.R., Uricchio, L.H., Petrov, D. A. and Egan, E.S. (2021). Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy. Trends in Parasitology, 38: 290-301.
Cerca, J., Armstrong, E.E., Vizueta, J., Fernández, R., Dimitrov, D., Petersen, B., Prost, S., Rozas, J., Petrov, D.A., Gillespie, R.J. (2021). The Tetragnatha kauaiensis genome sheds light on the origins of genomic novelty in spiders. Genome Biology and Evolution, evab262
Suvorov, A., Kim, B.Y, Wang, J.R, Armstrong, E.E., Peede, D., D’Agostino, E.R.R., Price, D.K., Wadell , P., Lang , M., Courtier-Orgogozo, V., David, J.R,, Petrov, D.A., Matute, D.R.*, Schrider, D.R.*, Comeault, A.A.*. (2021). Widespread introgression across a phylogeny of 155 Drosophila genomes. Current Biology. https://www.biorxiv.org/content/10.1101/2020.12.14.422758v1.full (* contributed equally)
Bergelson*, J., Kreitman*, M., Petrov*, D.A., Sanchez*, A., Tikhonov*, M. (2021). Functional biology in its natural context: A search for emergent simplicity. Elife, 10, e67646; (* - contributed equally).
Kapun, M., Nunez, J. C.B., Bogaerts-Márquez, M., Murga-Moreno, J., Paris, M., Outten, J., Coronado-Zamora, M., Tern, C., Rota-Stabelli, O., García Guerreiro M. P., Casillas, S., Orengo, D. J., Puerma, E., Kankare, M., Ometto, L., Loeschcke, V., Onder, B. S., Abbott, J. K., Schaeffer, S. W., Rajpurohit, S., Behrman, E. L., Schou, M. F., Merritt, T. J.S., Lazzaro, B. P., Glaser-Schmitt, A., Argyridou, E., Staubach, F., Wang, Y., Tauber, E., Serga, S. V., Fabian, D. K., Dyer, K. A., Wheat, C. W., Parsch, J., Grath, S., Savic Veselinovic, M., Stamenkovic-Radak, M., Jelic, M., Buendía-Ruíz, A. J., Gómez-Julián, M. J., Espinosa-Jimenez, M. L., Gallardo-Jiménez, F. D., Patenkovic, A., Eric, K., Tanaskovic, M., Ullastres, A., Guio, L., Merenciano M., Guirao-Rico, S., Horváth, V., Obbard, D. J., Pasyukova, E., Alatortsev, V. E., Vieira, C. P., Vieira, J., Torres, J. R., Kozeretska, I., Maistrenko, O., Montchamp-Moreau, C., Mukha, D. V., Machado, H. E., Barbadilla, A., Petrov, D.A, Schmidt, P., Gonzalez, J., Flatt, T., Bergland, A. O. (2021). Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource. Molecular Biiology and Evolution, msab259; https://www.biorxiv.org/content/10.1101/2021.02.01.428994v1; correction: https://digital.csic.es/handle/10261/270563
Chaikovsky, A.C., Li, C., Jeng, E. E., Loebell, S., Lee, M.C., Murray, C.W., Cheng, R. Demeter, J., Swaney, D.L., Chen, S., Newton, B.W., Johnson, J.R., Drainas, A.P., Shue, Y.T., Seoane, J.A., Srinivasan, P., He, A., Yoshida, A., Hipkins, S.Q. McCrea, E., Poltorack, C., Krogan, N.J., Diehl, J.A., Kong, C., Jackson, P.K., Curtis, C., Petrov, D.A., Bassik, C., Winslow, M.M., Sage, J. (2021). The AMBRA1 E3 ligase adaptor regulates Cyclin D protein stability. Nature, 592, 794–798.
Kim, B.Y,* Wang, J.R,* Miller, D.E, Barmina, O., Delaney, E., Thompson, A., Comeault, A.A., Peede, D. D’Agostino, E.R.R., Pelaez, J., Aguilar, J.M, Haji, D., Matsunaga, T., Armstrong, E.E., Zych, M., Ogawa, Y., Stamenković-Radak, M, Jelić, M, Veselinović, M.S., Tanasković, M., Erić, P., Gao, J.J, Takehiro, T.K., Katoh, Masanori J. Toda, Watabe, H., Watada, M., Davis, J.S., Moyle, L.C., Manoli, G., Bertolini, E., Košťál, V., Hawley, R.S., Takahashi, A., Jones, C.D., Price, D.K., Whiteman, N., Kopp, A., Matute, D.R.#, Petrov, D.A.# (2021). Highly contiguous assemblies of 101 drosophilid genomes. https://www.biorxiv.org/content/10.1101/2020.12.14.422775v1 (* and # - contributed equally). Elife, 10: e66405; correction: https://elifesciences.org/articles/78579
Weiss, C.V., Harshman, L., Inoue, F., Fraser, H.B, Petrov, D.A.*, Ahituv, N.*, Gokhman, D.* (2021). The cis-regulatory effects of modern human-specific variants. Elife, 10: e63713, (*corresponding authors); https://www.biorxiv.org/content/10.1101/2020.10.07.330761v1.
Ebel, E.R., Kuypers, F., Lin, C., Petrov, D. A.* and Egan, E.S.*. (2021). Common host variation drives malaria parasite fitness in healthy human red cells. Elife, 10: e69808,(*corresponding authors); https://www.biorxiv.org/content/10.1101/2020.10.08.332494v1. (*-co-corresponding authors)
Ebel, E.R., Reis, F., Petrov, D.A., and Beleza, S. (2021). Shifts in antimalarial drug policy since 2006 have rapidly selected P. falciparum resistance alleles in Angola. Malaria Journal, 20: 175; https://www.biorxiv.org/content/10.1101/2020.09.29.310706v1.abstract.
Garud, N., Messer, P.W., Petrov, D.A. (2021). Detection of hard and soft sweeps from Drosophila melanogaster genomic data. PLoS Genetics,17: e1009373; https://www.biorxiv.org/content/10.1101/2020.06.20.163261v1.
Foggetti, G., Li, C., Cai, H., Hellyer, J., Ayeni, D., Hastings, K., Choi, J., Wurtz, A., Andrejka, L., Maghini, D., Rashleigh, N., Levy, S., Homer, R., Gettinger, S., Diehn, M., Wakelee, H., Petrov, D.A., Winslow, M.M., Politi, K. (2021). Genetic determinants of EGFR-driven lung cancer growth and therapeutic response in vivo. Cancer Discovery, 11: 1736–53; https://www.biorxiv.org/content/10.1101/2020.04.13.036921v1.abstract.
Cai, H.*, Chew, S.-K.*, Li, C.*, Tsai, M., Andrejka, L., Murray, C., Hughes, N., Shuldiner, E., Tang, E., Hung, K., Chen, L., Lee, C., Yousefi, M., McFarland, C.M., Lin, W.-Y., Kunder, C., Cong, L., Petrov, D.A.#, Swanton, C.#, and Winslow, M.M.#. (2021). A functional taxonomy of tumour suppression in oncogenic KRAS-driven lung cancer. (* - contributed equally; # corresponding authors); Cancer Discovery, 11: 1754–73. Twitter 🧵
Li, C., Lin,W.-Y., Rizvi, H., Cai, H., McFarland, C.M., Rogers, Z.N., Yousefi, M., Winters, I.P., Rudin,C.M., Petrov,D.A., and Winslow, M.M. (2021). Quantitative in vivo analyses reveal a complex pharmacogenomic landscape in lung adenocarcinoma. Cancer Discovery, 81: 4570–80; https://www.biorxiv.org/content/10.1101/2020.01.28.923912v1. Twitter 🧵
Machado*, H.E., Bergland*, A.O., Taylor, R., Tilk, S., Behrman, E., Dyer, K., Fabian, D.K, Flatt, T., Gonzalez, J., Karasov, T.L., Kozeretska, I., Lazzaro B.P., Merritt, T.J.S., O'Brien, K., Rajpurohit, S., Roy, P.R., Schaeffer, S.W., Schmidt, P.# and D. A. Petrov#. (2021). Broad geographic sampling reveals predictable and pervasive seasonal adaptation in Drosophila. Elife, 10: e67577; (* and # - contributed equally); https://www.biorxiv.org/content/10.1101/337543v3
Armstrong, E.E., Khan, A., Taylor, R.W., Gouy, A., Greenbaum, G., Thiery, A., Kang, J.T.L., Redondo, S.A., Prost, S., Barsh, G., Kaelin, C., Phalke, S., Chugani, A., Gilbert, M., Miquelle, D., Zachariah, A., Borthakur, U., Reddy, A., Louis, E., Ryder, O., Jhala, Y., Petrov, D.A., Excoffier, L., Hadly, E.A., and Ramakrishnan, U. (2021). Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection; Molecular Biology and Evolution, 38: 2366–2379; https://www.biorxiv.org/content/10.1101/696146v1.abstract.
Zhu, X., Zhou, B., Pattni, R., Gleason, K., Tan, C., Kalinowski, A., Sloan, S., Fiston-Lavier, A.-F., Mariani, J., Petrov, D.A., Barrres, B., Duncan, L, Abyzov, A., Vogel, H., Brain Somatic Mosaicism Network, Moran, J.V., Vaccarino, F.M., Tamminga, C., Levinson, D.F., Urban, A.E. (2021). Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia. Nature Neuroscience, 24, 186-196; correction: https://www.nature.com/articles/s41593-023-01438-w
Feder, A.F., Pennings,P.S, and Petrov, D.A. (2021). The clarifying role of time series data in the population genetics of HIV. PLoS Genetics, 17: e1009050; https://www.biorxiv.org/content/early/2018/12/29/495275
Harpak, A., Garud, N., Rosenberg, N.A., Petrov, D.A, Combs, N., Pennings, P.S, Munshi-South, J. (2021). Genetic adaptation in New York City rats. Genome Biology and Evolution, 13, evaa247; https://www.biorxiv.org/content/10.1101/2020.02.07.938969v1
Gokhman, D., Agoglia, R.M., Kinnebrew, M., Sun, D., Gordon, W., Bajpai, V.K., Naqvi, S., Chan, A., Chen, C., Petrov, D.A., Zhang, H., Mishina, Y., Ahituv, N., Wysocka, J., Rohatgi, R., Fraser, H.B . (2021). Human-chimpanzee hybrid cells reveal gene regulatory evolution underlying skeletal divergence. Nature Genetics, 53, 467-476.
2020
Kinsler, G., Geiler-Samerotte, K., Petrov, D.A. A genotype-phenotype-fitness map reveals local modularity and global pleiotropy of adaptation. Elife, 9, e61271; https://www.biorxiv.org/content/10.1101/2020.06.25.172197v1 Twitter 🧵
Enard, D. and Petrov, D.A. (2020). Ancient epidemics through the lens of recent adaptation in human genomes. Phil. Trans. B, 375, 20190575; https://www.biorxiv.org/content/10.1101/2020.03.18.997346v1
Armstrong, E.E., Taylor, R.W., Miller, D.E., Kaelin,C., Barsh,G., Hadly E.A., Petrov. D.A. (2020). Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, HiC, and long read data. BMC Biology, 18: 3. http://biorxiv.org/cgi/content/short/705483v1
2019
Kolodny, O., McLaren, M.R., Greenbaum, G., Ramakrishnan, U., Feldman, M.W., Petrov, D.A., Taylor, R.W. Reconsidering the management paradigm of fragmented populations. https://www.biorxiv.org/content/10.1101/649129v1
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
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
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
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).
Commentary in Nature Ecology and Evolution by Danna Gifford
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
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
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
Stanford Report Article about this work
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).
2018
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.
Commentary in Current Biology by Coughlan and Matute
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
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
NY Times article by Carl Zimmer
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
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
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
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).
Stanford Report Article about this work
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).
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
2017
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.
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.
Sherlock, G. and Petrov, D. A. (2017). Seeking Goldilocks during evolution of drug resistance. PLoS Biology, 15: e2001872.
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
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)
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
Video Abstract by Alison Feder
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
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
Video Abstract by Pleuni Pennings
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.
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
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.
2016
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).
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.
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).
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
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
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.
Elife Commentary: At the mercy of viruses by Wilke and Sawyer
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.
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.
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).
Video Abstract by Alison Feder
This paper won the 2017 Ommen Prize for the best paper in Evolutionary Medicine!
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.
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 .
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.
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
News and Views in Molecular Ecology: Genomics of clinal variation in Drosophila:
disentangling the interactions of selection and demography by T. Flatt
2015
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
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.
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.
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
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).
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.
Perspective in Science: Aneuploidy and mother’s genes
Article in the Scientist: A Benefit of Failed Pregnancy? By Ruth Williams
Article in The Conversation: Chromosome errors cause many pregnancies to end before they are even detected. By Rajiv McCoy and Dmitri Petrov
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
Research Highlight at Haldanessieve.org
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
Find T-lex2 at http://petrov.stanford.edu/cgi-bin/Tlex.html
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).
News and Views by David Gresham: Evolution: Fitness tracking for adapting populations
2014
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
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
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.
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.
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
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.
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.
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
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.
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
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
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.
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.
2013
Venkataram, S., Sellis, D., and Petrov, D.A. (2023) Backward predictability of evolution in the diploid Fisher's geometric model; https://www.biorxiv.org/content/10.1101/001016v5
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.
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
Pennings, PS. (2013). HIV Drug resistance: Problems and Perspectives. Infectious Disease Reports, 5: 21-25.
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).
Research Highlight at Haldanessieve.org.
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)
Research Highlight at Haldanessieve.org
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)
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
Research Highlight of the arxiv post of this paper is at Haldanessieve.org
The most viewed item in November 2012
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.
2012
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
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.
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.
Research Highlight in Nature Review Genetics by Hannah Stower
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.
Messer, P.W. and Neher, R.A. (2012). Estimating the strength of selective sweeps from deep population diversity data. Genetics, 191, 593-605.
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.
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.
2011
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.
Faculty 1000 evaluation (and here is pdf)
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.
Faculty 1000 evaluation (and here is pdf)
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.
2 x Faculty 1000 evaluations (and here is pdf)
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.
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.
2010
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.
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.
Faculty 1000 evaluation (and here is pdf)
Commentary to our paper in PLoS Genetics
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.
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.
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.
Faculty 1000 evaluation (and here is pdf)
Commentary to our paper in PLoS Genetics by Nick Barton
Commentary in Nature Review Genetics by Mary Muers
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.
Faculty 1000 evaluation (and here is pdf)
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.
Faculty 1000 evaluation (and here is pdf)
2009
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
González, J. and D.A. Petrov. (2009). MITEs - the ultimate parasites. Science, 325, 1352-53. Short description on our blog.
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.
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.
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.
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.
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.
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.
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.
Stanford Report: Adaptation is key in human evolution
Science Daily: Adaptation plays significant role in human adaptation
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.
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).
2008
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.
Science Editors choice: Of Migrations and Variations
Hershberg, R. and D.A., Petrov. Selection on codon bias. (2008). Annu. Rev. Genet., 42, 287-299.
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.
Faculty 1000 evaluation (and here is pdf)
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.
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.
2007
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).
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.
Hershberg, R., Tang, H., and D.A. Petrov. (2007). Reduced selection leads to accelerated gene loss in Shigella. Genome Biology, 8, R164.
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.
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).
2006
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.
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).
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.
2005
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.
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.
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.
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.
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
Faculty 1000 evaluation (and here is pdf)
Science Editorial: Rogue Fly Dna Offers Protection from Pesticides
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.
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).
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).
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.
Singh, N.D., Arndt, P.F., and D. A. Petrov. (2005). Effect of recombination on patterns of substitution in Drosophila. Genetics,169, 709-722.
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.
2004
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.
Davis, J.C. and D. A. Petrov. (2004). Preferential duplication of conserved proteins in eukaryotic genomes. PLOS Biology, 2, 318-326.
Singh, N.D. and D. A. Petrov. (2004). Dramatic sequence turnover at an intergenic locus in Drosophila. Mol. Biol. Evol., 21, 670-680.
2003
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.
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.
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.
Nuzhdin, S.V. and D. A. Petrov (2003). Transposable elements in clonal lineages: lethal hangover from sex. Biol. J. Linn. Soc., 79, 33-41.
2002
Ptak, S. and D. A. Petrov. (2002). How intron splicing affects the deletion and insertion profile in D. melanogaster. Genetics, 162, 1233-1244.
D. A. Petrov. (2002). Mutational equilibrium model of genome size evolution. Theor. Pop. Biol., 61, 531-543.
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.
D. A. Petrov. (2002). Evolution of genome size. Encyclopedia of Evolution. Ed. Mark Pagel, Oxford University Press.
D.A. Petrov. (2002). DNA loss and evolution of genome size in Drosophila. Genetica, 115, 81-91.
2001
Walbot, V. and D.A. Petrov. (2001). Gene galaxies in the maize genome. Proc. Natl. Acad. Sci. USA, 98, 8163-8164.
D. A. Petrov. (2001). Evolution of genome size: new approaches to an old problem. Trends in Genetics, 17, 23-28.
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.
2000 and before
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).
Petrov, D.A. & Hartl, D. L. (2000). Pseudogene evolution and natural selection for a compact genome. J. of Heredity, 91, 221-227.
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.
Petrov, D.A. & Hartl, D. L. (1999). Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc. Natl. Acad. Sci. USA, 96, 1475-1479.
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.
Moriyama, E.N., Petrov, D.A., & Hartl, D.L. (1998). Genome size and intron size in Drosophila. Mol. Biol. Evol., 15, 770-773.
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.
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.
Petrov, D.A. (1997). Slow but steady: genome reduction through spontaneous mutation. The Plant Cell, 9, 1900-1901.
Petrov, D.A., Lozovskaya, E. R., & Hartl, D. L. (1996). High intrinsic rate of DNA loss in Drosophila. Nature, 384, 346-349.
Siegal, M. L., Petrov, D. A., & Deaguiar, D. (1996). Triple-ligation strategy with advantages over directional cloning. Biotechniques, 21, 614-619.
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.
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.
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.
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.
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.
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.