The Gaut Lab

Brandon’s CV

Recent Publications

121. 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.

120. Diez CM, Roessler K, Gaut BS. 2013  Epigenetics and Plant Genome Evolution.

Current Opinions Plant Biology.  

119.  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. 

118. 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.

117.  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.

116. 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.  

115. 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. 

114. 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]

113. 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]

112. 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).

111. 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


110. 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.

109. Takuno, S. and B. S. Gaut. 2011. Body-methylated genes in Arabidopsis thaliana

are functionally important and evolve slowly. Mol. Biol. Evolution. PMID:


108. 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. 107.DeRose-Wilson and Gaut. 2011. Mapping salinity tolerance during Arabidopsis

         thaliana germination and seedling growth. Plos One 6(8):e22832.

106. Yang, L. and B.S. Gaut, 2011. Factors that contribute to variation in evolutionary

rate among Arabidopsis genes. Mol. Biol. Evol. PMID:21389272

105. 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.

104. 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,


103. 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.

102.  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.

101. 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.

100. 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.

99.  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 lyrataBMC Evol. Biol. 10:10.

98. 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. 

97. 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.

96. 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. 95.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,


  1. 94.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.

93.  Ross-Ibarra, J, M. Tenaillon and B.S. Gaut. 2009. Historical divergence and gene

flow in the genus Zea. Genetics, 181(4):1399-413.

92. 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.

91.  Ross-Ibarra, J. and B.S. Gaut.  2008.  Multiple domestications do not appear

monophyletic. Proc Natl Acad Sci USA.  (Letter, published online)

90.  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.