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Publications

Professor Gaut’s CV (pdf)

Recent Publications

  1. Bousios A, Gaut BS. 2016. Mechanistic and evolutionary questions about epigenetic conflicts between transposable elements and their plant hosts. Current opinion in plant biology, 30:123-133
  1. Roessler K, Takuno S, Gaut BS. 2016. CG methylation covaries with differential gene expression between leaf and floral bud tissues of Brachypodium distachyon. Plos One.
  1. Takuno S, Ran JH, Gaut BS. 2016. Evolutionary patterns of genic DNA methylation vary across land plants. Nature Plants, 2:15222.
  1. Diez CM, Gaut BS. 2016. The jury may be out, but it is important that it deliberates: a response to Besnard and Rubio de Casas about olive domestication. New Phytologist, 209:471-473
  1. Rodríguez-Verdugo A, Tenaillon O, Gaut BS. 2016. First-step mutations during adaptation restore the expression of hundreds of genes. Molecular biology and evolution, 33:25-39.
  1. Gaut BS, Díez CM, Morrell PL. 2015 Genomics and the contrasting dynamics of annual and perennial domestication. Trends in Genetics, 31:709-719.
  1. Bousios A, Diez CM, Takuno S, Bystry V, Darzentas N, Gaut BS. 2015. A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response. 2015. Genome Research.
  1. Hug SM, Gaut BS. 2015. The phenotypic signature of adaptation to thermal stress in Escherichia coli. BMC evolutionary biology, 15:1.
  1. Diez CM, Trujillo I, Martinez‐Urdiroz N, Barranco D, Rallo L, Marfil P, Gaut BS. 2015. Olive domestication and diversification in the Mediterranean Basin. New Phytologist, 206:436-447.
  1. Rodriquez-Verdugo A, Carrillo-Cisneros D, González-González A, Gaut BS, Bennett AF. 2014. Different tradeoffs result from alternate genetic adaptations to a common environment. Proc Natl Acac Sci USA, 111:12121-12126.
  1. Gaut BS. 2014. The complex domestication history of the common bean. Nature genetics, 46:663-664.
  1. 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, in press.
  1. Diez CM, Roessler K, Gaut BS. 2013  Epigenetics and Plant Genome Evolution. Current Opinions Plant Biology.
  1. 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.
  1. 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.
  1. 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.
  1. 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.
  1. Hufford MB, Martinez-Meyer E, Gaut BS, Eguiarte LE, Tenaillon MI. Past and Present Distributions in Wild and Domesticated Zea mays: a Chance to Revisit Maize History.  Plos One, 7(11):e47659.
  1. 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, SekhonRS, 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. [Epub ahead of print]
  1. Vonholdt BM, Takuno S, Gaut BS. Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol. 2012 May 15. [Epub ahead of print]
  1. 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).
  1. 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.
  1. 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.
  1. Takuno, S. and B. S. Gaut. 2011. Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol. Biol. Evolution. PMID: 21813466
  1. 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.
  1. DeRose-Wilson and Gaut. 2011. Mapping salinity tolerance during Arabidopsis thaliana germination and seedling growth. Plos One 6(8):e22832.
  1. Yang, L. and B.S. Gaut, 2011. Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol. Biol. Evol. PMID:21389272
  1. 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.
  1. 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.
  1. 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. The basis of rapid genome size change in Arabidopsis. Nature Genetics, in press.
  1. 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(3):1193-203.
  1. Li, Y.H., W. Li, C. Zhang, L. Yang, R.Z. Chang, B.S. Gaut and L.J. Qiu. 2010. Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytol. 188:242-53.
  1. Tenaillon M.I., J.D. Hollister and B.S. Gaut. 2010. A triptych of the evolution of plant transposable elements. Trends Plant Sci. 8:471-478.
  1. Lockton, S. and B. S. Gaut. 2010. The Evolution of Transposable Elements in Natural Populations of Self-Fertilizing Arabidopsis thaliana and its Outcrossing Relative Arabidopsis lyrata.  BMC Evol. Biol. 10:10.
  1. van Heerwaarden, J., J. Ross-Ibarra, J. Doebley, J. Glaubitz, J. Sanchez-Gonzalez, J. de Jesus, B. Gaut and L. Eguiarte.  2010. Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis).  Mol. Ecol. 9(6):1162-1173.
  1. Hollister, J.D., J. Ross-Ibarra and B. S. Gaut  Indel-associated mutation rate varies with mating system in flowering plants. Mol. Biol. Evol., 27:409-416.
  1. Tian, Z., C. Rizzon, J. Du, L. Zhu, J.L. Bennetzen, B.S. Gaut, S.A. Jackson, and J. Ma.  2009.  Do genetic recombination and gene density shape the pattern of DNA elimination in rice LTR-retrotransposons?  Genome Research 19:2221-2230.
  1. Zhang L.B., Zhu Q., Wu Z.Q., Ross-Ibarra J., Gaut B.S., Ge S. and Sang T. 2009. Selection on grain shattering genes and rates of rice domestication. New Phytol, 19(8):1419-28.
  1. Hollister, J and B.S. Gaut.  2009. Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Research, 19(8):1419-28.
  1. Ross-Ibarra, J, M. Tenaillon and B.S. Gaut. 2009. Historical divergence and gene flow in the genus Zea. Genetics, 181(4):1399-413.
  1. Lockton, S. and B.S. Gaut. 2009.  The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana. J. Mol. Evol., 68:80-89.
  1. Ross-Ibarra, J. and B.S. Gaut.  2008.  Multiple domestications do not appear monophyletic. Proc Natl Acad Sci USA.  (Letter, published online)
  1. Lockton, S. J. Ross-Ibarra and B.S. Gaut. 2008. Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata. Proc Natl Acad Sci USA. 105(37):13965-70