Publications

(After 2010)

  • Roessler, K, A Bousios, E Meca and BS Gaut. 2018. Modeling interactions between transposable elements and the plant epigenetic response: a surprising reliance on element retention. Genome Biology and Evolution 10(3):803-815.
  • Gaut, BS. 2017. A convergent outcome: Small genomes in mangroves. New Phytologist DOI: 10.1111/nph.14906
  • Zhou, Y, M Massonnet, J Sanjak, DCantu and BS Gaut.. The Evolutionary Genomics of Grape (Vitis vinifera ssp. vinifera) Domestication, Proc Natl Acad. Sci, 114(44):11715-11720.
  • Rebollar, EA, E Sandoval-Castellanos,KRoessler,BS Gaut, LD Alcaraz, M Benítez and AE Escalante. Seasonal changes in a maize-based polyculture of central Mexico reshape the co-occurrence networks of soil bacterial communities in soil. Frontiers Microbiology 8:2478.
  • Gaut, BS. 2017 Natural Rubber and the Russian Dandelion Genome. National Science Review.
  • González-González, A, SM Hug, A Rodríguez-Verdugo, JS Patel, and BS Gaut. Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects on Escherichia coli gene expression. MBE,34(11):2839-2855.
  • Aguirre-Liguori, JA, MI Tenaillon, A Vázquez-Lobo, BS Gaut, JP Jaramillo-Correa, S Montes, V Souza, LE Eguiarte. Connecting genomic patterns of local adaptation and niche suitability in teosintes, Molecular Ecology, 6(16):4226-4240.
  • Minio, A, J Lin, BS Gaut and D Cantu. 2017. How single molecule real-time sequencing and haplotype phasing have enabled reference-grade diploid genome assembly of wine grapes. Frontiers in Plant Science, 8:826-832.
  • Takuno, S, DK Seymour, BS Gaut. 2017. The evolutionary dynamics of orthologs that shift in gene body methylation between Arabidopsis species. Mol. Biol. Evol. 34:1479-1491.
  • Bousios, A., BS Gaut and N Darzentas. 2017. Considerations and complications of mapping high-throughput small RNA data to transposable elements. Mobile DNA, 8:3-16.
  • Liu, Q, Y. Zhang, P. Morrell, BS Gaut. 2017. Deleterious variants in Asian rice and the potential cost of domestication. Mol. Biol. Evol. 34:908-924.
  • Bousios, A and BS Gaut. 2016. Open questions about ongoing conflicts between transposable elements and their plant hosts. Current Opinions in Plant Biology 30:123-133.
  • Roessler, K, S Takuno and BS Gaut. 2016. CG methylation covaries with differential gene expression between leaf and floral bud tissues of Brachypodium distachyon, Plos One, 11(3):e0150002.
  • Takuno, S., J-H Ran and BS Gaut. 2016. Evolutionary patterns of genic DNA methylation vary across Land Plants. Nature Plants, 30:123-133.
  • Bousios, A, CM Diez, S Takuno, V Bystry, N Darzentas and BS Gaut. 2016. Palindromic structures in maize Sirevirus LTRs are central to the interplay between transposable element evolution and the host epigenetic response. Genome Research, 26(2):226-37.
  • Diez, CM and BS Gaut. 2015. The jury may be out, but it is important that it deliberates: a response to Besnard and Rubio de Casas. New Phytologist, 209(2):471-3. (Peer reviewed letter)
  • Gaut, BS, CM Diez and PL Morrell. 2015. Genomics and the contrasting dynamics of annual and perennial domestication. Trends in Genetics (12):709-19
  • Rodriguez-Verdugo, A, O Tenaillon and BS Gaut. 2016. First-step Mutations during Adaptation to Thermal Stress Shift the Expression of Thousands of Genes Back toward the Pre-stressed State. Mol. Biol. Evol 33(1):25-39.
  • Hug, SM and BS Gaut. 2015. The phenotypic signature of adaptation to thermal stress in Escherichia coli. BMC Evolutionary Biology, 15:177.
  • Gaut, B.S. 2015. Evolution is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution. Mol. Biol. Evol., 32(7):1661-71.
  • Diez, CM, I Trujillo, N Martinez-Urdiroz, D Barranco, L Rallo, P Marfil, BS Gaut. 2015. Olive domestication and diversification in the Meditteranean Basin. New Phytologist, 206:436-447.
  • Gaut, BS. 2014. The complex domestication history of the common bean. Nature Genetics 46:663-664. (News and Views; not refereed).
  • Rodriguez-Verdugo A, Gonzalez-Gonzalez A, Carrillo-Cisneros D, Gaut BS and Bennett AF. 2014. Different trade-offs result from alternate genetic adaptations to a common environment. Proc. Natl. Acad. Sci. USA, 111:12121-12126.
  • Diez CM, Meca E, Tenaillon MI, Gaut BS. 2014. Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome. Plos Genetics 17:10(4):e1004298.
  • Diez CM, Roessler K, Gaut BS. 2014. Epigenetics and Plant Genome Evolution. Current Opinions Plant Biology 18:1-8.
  • Diez CM, Gaut BS, Meca E, Scheinvar E, Montes-Hernandez S, Eguiarte LE, Tenaillon MI. 2013. Genome size variation in wild and cultivated maize along altitudinal gradients. New Phytologist, 199:264-276.
  • Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F, Guo Y, Steige K, Platts AE, Escobar JS, Newmam JK, Wang W, Mandákova T, Vello E, Smith LM, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu TT, Blanchette M, Clark RM, Quesneville H, Nordborg M, Gaut BS, Lysak MA, Jenkins J, Grimwood J, Prochnick S, Shu S, Rokhsar D, Schmutz J, Weigel D, Wright SI. 2013. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature Genetics, 45:831-835.
  • Rodriquez-Verdugo A, Gaut BS, Tenaillon O. 2013. Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress. BMC Evolutionary Biology, 13:50-61.
  • Takuno S, Gaut BS. 2013. Gene-body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc Natl Acac Sci USA, 10:1797-1802.
  • Hufford MB, Martinez-Meyer E, Gaut BS, Eguiarte LE, Tenaillon MI. 2012. Past and Present Distributions in Wild and Domesticated Zea mays: a chance to Revisit Maize History. Plos One, 7(11):e47659.
  • Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ,Gaut B, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhäjärvi T, Rong T, Sekhon RS, Sun Q, Tenaillon MI, Tian F, Wang J, Xu X, Zhang Z, Kaeppler SM, Ross-Ibarra J, McMullen MD, Buckler ES, Zhang G, Xu Y, Ware D. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics Jun 3. doi: 10.1038/ng.2313.
  • Vonholdt BM, Takuno S, Gaut BS. 2012. Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol. 2012 May 15.
  • Gaut, B.S. 2012. Arabidopsis as a model system to study the genetics of local adaptation. Nature Genetics, 44(2):115-6. (News and Views; not refereed).
  • Tenaillon, O., A. Rodriguez-, R.L. Gaut, P. McDonald, A.F. Bennett, T.D. Long and B.S. Gaut. 2012. The molecular diversity of adaptive convergence. Science 335(6067):457-61.
  • Sakai, H., H. Mizuno, Y. Kawahara, H. Wakimoto, H. Ikawa, H. Kawahigashi, H. Kanamori, T. Matsumoto, T. Itoh and B.S. Gaut. 2011. Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes. Genome Biol. Evol. PMID:22042334.
  • Takuno, S. and B. S. Gaut. 2011. Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol. Biol. Evolution. PMID:21813466.
  • Gaut, B.S., L. Yang, S. Takuno and L.E. Eguiarte. 2011. The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates. Annual Reviews of Ecology, Evolution and Systematics, 42:245–66.
  • DeRose-Wilson and Gaut. 2011. Mapping salinity tolerance during Arabidopsis thaliana germination and seedling growth. Plos One 6(8):e22832.
  • Yang, L. and B.S. Gaut, 2011. Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol. Biol. Evol. 28(8):2359-69
  • Tenaillon, M., M. Hufford, B.S. Gaut and J. Ross-Ibarra. 2011. Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians. Genome Biol. Evol., 3:219-29.
  • Hollister, J., L. Smith, Y-L. Guo, F. Ott, D. Weigel and B.S. Gaut. 2011. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata, Proc. Natl. Acad. Sci. USA, 108(6):2322-7.
  • Hu, T. T., P. Pattyn, G. E. Bakker, J. Cao, J.-F. Chen, R. M. Clark, N. Fahlgren, J. A. Fawcett, J. Grimwood, H. Gundlach, G. Haberer, J. D. Hollister, S. Ossowski, R. P. Ottilar, A. A. Salamov, K. Schneeberger, M. Spannagl, X. Wang, L. Yang, M. E. Nasrallah, J. Bergelson, J. C. Carrington, B. S. Gaut, J. Schmutz, K. F. X. Mayer, Y. Van de Peer, I. V. Grigoriev, M. Nordborg, D. Weigel, and Y.-L. Guo. 2011.The basis of rapid genome size change in Arabidopsis. Nature Genetics, 43(5):476-81.
  • Yang, L., S. Takuno, E. Waters, and B.S. Gaut. 2011. Lowly-expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degradation. Mol. Biol. Evol., 28:1193-203.