Our Publications

— 2017 —

Corbi, J., E. Baack, J.M. Dechaine-Berkas, and J.M. Burke. 2017. Genome-wide analysis of allele frequency change in sunflower crop-wild hybrid populations evolving under natural conditions. Mol. Ecol., in press.

Badouin, H., J. Gouzy, C.J. Grassa, F. Murat, S.E. Staton, L. Cottret, C. Lelandais-Brière, G. Owens, S. Carrrère, B. Mayjonade, L. Legrand, N. Gill, N.C. Kane, J.E. Bowers, S. Hubner, A. Bellec, A. Berard, H. Bergès, N. Blanchet, M.-C. Boniface, B. Dominique, O. Catrice, N. Chaidir, C. Claudel, C. Donnadieu, T. Faraut, G. Fievet, N. Helmstetter, M. King, S.J. Knapp, Z. Lai, M.-C. Le Paslier, Y. Lippi, L. Lorenzon, J.R. Mandel, G. Marage, G. Marchand, E. Marquand, E. Bret-Mestries, E. Morien, S. Nambeesan, T. Nguyen, P. Pegot-Espagnet, N. Pouilly, F. Raftis, E. Sallet, T. Schiex, J. Thomas, C. Vandecasteele, D. Varès, F. Vear, S. Vautrin, M. Crespi, B. Mangin, J.M. Burke, J. Salse, S. Muños, P. Vincourt, L.H. Rieseberg, N.B. Langlade. 2017. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature, online early.

— 2016 —

McAssey, E.V., J. Corbi, and J.M. Burke. 2016. Range-wide phenotypic and genetic differentiation in wild sunflower. BMC Plant Biol. 16: 249. [pdf] [supp]

Niederhuth, C.E., A.J. Bewick, L. Ji, M.A. Alabady, K.D. Kim, Q. Li, N.A. Rohr, A. Rambani, J.M. Burke, J.A. Udall, C. Egesi, J. Schmutz, J. Grimwood, S.A. Jackson, N.M. Springer, and R.J. Schmitz. 2016. Widespread natural variation of DNA methylation within angiosperms. Genome Biol. 17: 194. [pdf]

Bowers, J.E., S.A. Pearl, and J.M. Burke. 2016. Genetic mapping of millions of SNPs in safflower (Carthamus tinctorius L.) via whole genome re-sequencing. G3: Genes, Genomes, Genetics 6: 2203-2211. [pdf]

McAssey, E.V., E.G. Gudger, M.P. Zuellig, and J.M. Burke. 2016. Population genetics of the rubber-producing Russian dandelion (Taraxacum kok-saghyz). PLoS ONE 11: e0146417. [pdf]

— 2015 —

Mason, C.M., C.D.A. Ishibashi, A. Rea, J.R. Mandel, J.M. Burke, and L.A. Donovan. 2015. Environmental requirements trump genetic factors in explaining narrow endemism in two imperiled Florida sunflower. Conserv. Genet. 16: 1277-1293.

Staton, S.E. and J.M. Burke. 2015. Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance. BMC Genomics 16: 623.

Hulke, B.S., C.J. Grassa, J.E. Bowers, J.M. Burke, L. Qi, Z.I. Talukder, and L.H. Rieseberg. 2015. A unified single nucleotide polymorphism map of sunflower (Helianthus annuus L.) derived from current genomic resources. Crop Sci. 55: 1696-1702.

Staton, S.E. and J.M. Burke. 2015. Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads. Bioinformatics 31: 1827-1829.

Nambeesan, S.U., J.R. Mandel, J.E. Bowers, L.F. Marek, D. Ebert, J. Corbi, L.H. Rieseberg, S.J. Knapp, and J.M. Burke. 2015. Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching. BMC Plant Biol. 15:84.

— 2014 —

Pearl, S.A. and J.M. Burke. 2014. Genetic diversity in Carthamus tinctorius (Asteraceae; safflower), an underutilized oilseed crop. Am. J. Bot. 101: 1640-1650. [pdf] [supp]

Owart, B., J. Corbi, J.M. Burke, and J.M. Dechaine. 2014. Selection on crop-derived traits and QTL in sunflower (Helianthus annuus) crop-wild hybrids under water stress. PLoS ONE 9: e102717. [pdf] [supp]

Barb, J.G., J.E. Bowers, S. Renaut, J.I. Rey, S.J. Knapp, L.H. Rieseberg, and J.M. Burke. 2014. Chromosomal evolution and patterns of introgression in Helianthus. Genetics 197: 969-979. [pdf] [supp]

Mandel, J.R., E.V. McAssey, S. Nambeesan, E. Garcia-Navarro, and J.M. Burke. 2014. Molecular evolution of candidate genes for crop-related traits in sunflower (Helianthus annuus L.). PLoS ONE 9: e99620. [pdf] [supp]

Pearl, S.A., J.E. Bowers, S. Reyes Chin-Wo, R.W. Michelmore, and J.M. Burke. 2014. Genetic analysis of safflower domestication. BMC Plant Biol. 14: 43. [pdf] [supp]

Mandel, J.R., R.B. Dikow, V.A. Funk, R.R. Masalia, S.E. Staton, A. Kozik, R.W. Michelmore, L.H. Rieseberg, and J.M. Burke. A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae. Appl. Plant Sci. 2: 1300085. [pdf] [supp]

Hodgins, K.A., Z. Lai, L.O. Oliveira, D.W. Still, M. Scascitelli, M.S. Barker, N.C. Kane, H. Dempewolf, A. Kozik, R.V. Kesseli, J.M. Burke, R.W. Michelmore, and L.H. Rieseberg. 2013. Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives. Mol. Ecol. Resour. 14: 166-177. [pdf] [supp]

— 2013 —

Ziebell, A.L., J.G. Barb, S. Sandhu, B. Moyers, R.W. Sykes, C. Doeppke, K.L. Gracom, M. Carlile, L.F. Marek, M.F. Davis, S.J. Knapp, and J.M. Burke. 2013. Sunflower as a biofuels crop: an analysis of lignocellulosic chemical properties. Biomass Bioenergy 59: 208-217. [pdf] [supp]

Chapman, M.A., J.R. Mandel, and J.M. Burke. 2013. Sequence validation of candidates for selectively important genes in sunflower. PLoS ONE 8: e71941. [pdf] [supp]

McCouch, S.R., G.J. Baute, J. Bradeen, P. Bramel, P.K. Bretting, E. Buckler, J.M. Burke, D. Charest, S. Cloutier, G. Cole, H. Dempewolf, M. Dinhkuhn, C. Feuillet, P. Gepts, D. Grattapaglia, L. Guarino, S. Jackson, S. Knapp, P. Langridge, A. Lawton-Rauh, Q. Lijua, C. Lusty, T. Michael, S. Myles, K. Naito, R.L. Nelson, R. Pontarollo, C.M. Richards, L.H. Rieseberg, J. Ross-Ibarra, S. Rounsley, R. Sackville Hamilton, U. Schurr, N. Stein, N. Tomooka, E. van der Knaap, D. van Tassel, J. Toll, J. Valls, R.K. Varshney, J. Ward, R. Waugh, P. Wenzl, and D. Zamir. 2013. Agriculture: feeding the future. Nature 499: 23-24. [pdf]

Renaut, S., C.J. Grassa, S. Yeaman, B.T. Moyers, Z. Lai, N.C. Kane, J.E. Bowers, J.M. Burke, and L.H. Rieseberg. 2013. Genomic islands of divergence are not affected by geography of speciation in sunflowers. Nat. Commun. 4: 1827. [pdf] [supp]

Mandel, J.R., S. Nambeesan, J.E. Bowers, L.F. Marek, D.P. Ebert, L.H. Rieseberg, S.J. Knapp, and J.M. Burke. 2013. Association mapping and the genomic consequences of selection in sunflower. PLoS Genet. 9: e1003378. [pdf] [supp]

Gevaert, S.D., J.R. Mandel, J.M. Burke, and L.A. Donovan. 2013. High genetic diversity and low population structure in Porter’s sunflower (Helianthus porteri). J. Hered. 104: 407-415. [pdf] [supp]

Mandel, J.R., E.F. Milton, L.A. Donovan, S.J. Knapp, and J.M. Burke. 2013. Genetic diversity and population structure in the rare Algodones sunflower (Helianthus niveus ssp. tephrodes) and comparison to related sunflowers. Conserv. Genet. 14: 31-40. [pdf] [supp]

Kane, N.C., J.M. Burke, L.F. Marek, G.J. Seiler, F. Vear, S.J. Knapp, P. Vincourt, and L.H. Rieseberg. 2013. Sunflower genetic, genomic, and ecological resources. Mol. Ecol. Res. 13: 10-20. [pdf] [supp]

— 2012 —

Bowers, J.E., S. Nambeesan, J. Corbi, M.S. Barker, L.H. Rieseberg, S.J. Knapp, and J.M. Burke. 2012. Development of an ultra-dense genetic map of the sunflower genome based on single-feature polymorphisms. PLoS ONE 7: e51360. [pdf] [supp]

Staton, S.E., B. Hartman Bakken, B.K. Blackman, M.A. Chapman, N.C. Kane, S. Tang, M.C. Ungerer, S.J. Knapp, L.H. Rieseberg, and J.M. Burke. 2012. The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements. Plant J. 72: 142-153. [pdf] [supp]

Chapman, M.A. and J.M. Burke. 2012. Evidence of selection on fatty acid biosynthetic genes during the evolution of cultivated sunflower. Theor. Appl. Genet. 125: 897-907. [pdf] [supp]

Bowers, J.E., E. Bachlava, R.L. Brunick, L.H. Rieseberg, S.J. Knapp, and J.M. Burke. 2012. Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. G3: Genes, Genomes, Genetics 2: 721-729. [pdf] [supp]

Chapman, M.A., S. Tang, D. Draeger, S. Nambeesan, H. Shaffer, J.G. Barb, S.J. Knapp, and J.M. Burke. 2012. The genetics of floral symmetry in van Gogh’s sunflowers reveals independent recruitment of CYCLOIDEA genes in the Asteraceae. PLoS Genet. 8: e1002628. [pdf] [supp]

Lai, Z., N.C. Kane, A. Kozik, K.A. Hodgins, K.M. Dlugosch, M.S. Barker, M. Matvienko, Q. Yu, K.G. Turner, S.A. Pearl, G.D.M. Bell, Y. Zou, C. Grassa, A. Guggisberg, K.L. Adams, J.V. Anderson, D.P. Horvath, R.V. Kesseli, J.M. Burke, R.W. Michelmore, and L.H. Rieseberg. 2012. Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. Am. J. Bot. 99: 209-218. [pdf]

Bachlava, E., C.A Taylor, S. Tang, J.E. Bowers, J.R. Mandel, J.M. Burke, and S.J. Knapp. 2012. SNP discovery and development of a high-density genotyping array for sunflower. PLoS ONE 7: e29814. [pdf] [supp]

— 2011 —

Mandel, J.R., J.M. Dechaine, L.F. Marek, and J.M. Burke. 2011. Genetic diversity and population structure in cultivated sunflower and comparison to its wild progenitor Helianthus annuus L. Theor. Appl. Genet. 123: 693-704. [pdf] [supp]

Kane, N.C., N. Gill, M.G. King, J.E. Bowers, H. Bergès, J. Gouzy, E. Bachlava, N.B. Langlade, Z. Lai, M. Stewart, J.M. Burke, P. Vincourt, S.J. Knapp, and L.H. Rieseberg. 2011. Progress towards a reference genome for sunflower. Botany 89: 429-437. [pdf]

Blackman, B.K., D.A. Rasmussen, J.L. Strasburg, A.R. Raduski, J.M. Burke, S.J. Knapp, S.D. Michaels, and L.H. Rieseberg. 2011. Contributions of flowering time genes to sunflower domestication and improvement. Genetics 187: 271-287. [pdf] [supp]

— 2010 —

Wills, D.M., Abdel-Haleem, H., S.J. Knapp, and J.M. Burke. 2010. Genetic architecture of novel traits in the Hopi sunflower. J. Hered. 101: 727-736. [pdf]

Dechaine, J.M., J.C. Burger, and J.M. Burke. 2010. Ecological patterns and genetic analysis of post-dispersal seed predation in sunflower (Helianthus annuus) crop-wild hybrids. Mol. Ecol. 19: 3477-3488. [pdf] [supp]

Chapman, M.A, J. Hvala, J. Strever, and J.M. Burke. 2010. Population genetic analysis of safflower (Carthamus tinctorius L.; Asteraceae) reveals a Near-Eastern origin and five centers of diversity. Am. J. Bot. 97: 831-840. [pdf] [supp]

Shi, J., S. Wolf, J.M. Burke, G. Presting, J. Ross-Ibarra, and R.K. Dawe. 2010. Widespread gene conversion in centromere cores. PLoS Biol. 8: e1000327. [pdf] [supp]

— 2009 —

Chapman, M.A, J. Hvala, J. Strever, M. Matvienko, A. Kozik, R.W. Michelmore, S. Tang, S.J. Knapp, and J.M. Burke. 2009. Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.). Theor. Appl. Genet. 120: 85-91. [pdf] [supp]

Heesacker, A., R.L. Brunick, L.H. Rieseberg, J.M. Burke, S.J. Knapp. 2009. Karyotypic evolution of the common and silverleaf sunflower genomes. Plant Genome 2: 233-246. [pdf] [supp]

Sherman, N.A. and J.M. Burke. 2009. Population genetic analysis reveals a homoploid hybrid origin of Stephanomeria diegensis (Asteraceae). Mol. Ecol. 18: 4049-4060. [pdf] [supp]

Baskauf, C.J. and J.M. Burke. 2009. Population genetics of Astragalus bibullatus (Fabaceae) using AFLPs. J. Hered. 100: 424-431. [pdf]

Dechaine, J.M., J.C. Burger, M.A. Chapman, G.J. Seiler, R. Brunick, S.J. Knapp, and J.M. Burke. 2009. Fitness effects and genetic architecture of plant-herbivore interactions in sunflower crop-wild hybrids. New Phytol. 184: 828-841. [pdf] [supp]

— 2008 —

Chapman, M.A., C.H. Pashley, J. Wenzler, J. Hvala, S. Tang, S.J. Knapp, and J.M. Burke. 2008. A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus L.). Plant Cell 20: 2931-2945. [pdf] [supp]

Chapman, M.A., J.L. Leebens-Mack, and J.M. Burke. 2008. Positive selection and expression divergence following gene duplication in the sunflower CYCLOIDEA family. Mol. Biol. Evol. 25: 1260-1273. [pdf]

Rieseberg, L.H. and J.M. Burke. 2008. Molecular evidence and the origin of cultivated sunflower. Proc. Natl. Acad. Sci. USA 105: E46. [pdf]

Burger, J.C., M.A. Chapman, and J.M. Burke. 2008. Molecular insights into the evolution of crop plants. Am. J. Bot. 95: 113-122. [pdf]

Baack, E.J., Y. Sapir, M.A. Chapman, J.M. Burke, and L.H. Rieseberg. 2008. Selection on domestication traits and quantitative trait loci in crop-wild sunflower hybrids. Mol. Ecol. 17: 666-677. [pdf]

— 2007 —

Burke, J.M., J.C. Burger, and M.A. Chapman. 2007. Crop evolution: from genetics to genomics. Curr. Opin. Genet. Dev. 17: 525-532. [pdf]

Chapman, M.A. and J.M. Burke. 2007. DNA sequence diversity and the origin of cultivated safflower (Carthamus tinctorius L.; Asteraceae). BMC Plant Biol. 7: 60. [pdf]

Kolkman, J.M., S.T. Berry, A.J. Leon, M.B. Slabaugh, S. Tang, W. Gao, D.K. Shintani, J.M. Burke, and S.J. Knapp. 2007. Single nucleotide polymorphisms and linkage disequilibrium in sunflower. Genetics 177: 457-468. [pdf]

Wills, D.M. and J.M. Burke. 2007. QTL analysis of the early domestication of sunflower. Genetics 176: 2589-2599. [pdf]

Chapman, M.A., J.-C. Chang, D. Weisman, R.V. Kesseli, and J.M. Burke. 2007. Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae). Theor. Appl. Genet. 115: 747-755. [pdf] [supp]

Chapman, M.A. and J.M. Burke. 2007. Genetic divergence and hybrid speciation. Evolution 61: 1773-1780. [pdf]

Ellis, J.R. and J.M. Burke. 2007. EST-SSRs as a resource for population genetic analyses. Heredity 99: 125-132. [pdf]

— 2006 —

Liu, A. and J.M. Burke. 2006. Patterns of nucleotide diversity in wild and cultivated sunflower. Genetics 173: 321-330. [pdf]

Ellis, J.R., C.H. Pashley, J.M. Burke, and D.E. McCauley. 2006. High genetic diversity in a rare and endangered sunflower as compared to a common congener. Mol. Ecol. 15: 2345-2355. [pdf]

Chapman, M.A. and J.M. Burke. 2006. Radishes gone wild. Heredity 97: 379-380. [pdf]

Chapman, M.A. and J.M. Burke. 2006. Letting the gene out of the bottle: the population genetics of GM crops. New Phytol. (Tansley Review) 170: 429-443. [pdf]

Pashley, C.H., J.R. Ellis, D.E. McCauley, and J.M. Burke. 2006. EST databases as a source for molecular markers: lessons from Helianthus. J. Hered. 97: 381-388. [pdf] [supp]

Wills, D.M. and J.M. Burke. 2006. Chloroplast DNA variation confirms a single origin of domesticated sunflower (Helianthus annuus L.). J. Hered. 97: 403-408. [pdf]

Arnold, M.L. and J.M. Burke. 2006. Natural hybridization. In C.W. Fox and J.B. Wolf, eds. Pp. 399-413 in Evolutionary Genetics: Concepts and Case Studies. Oxford University Press.

— 2005 —

Burke, J.M., S.J. Knapp, and L.H. Rieseberg. 2005. Genetic consequences of selection during the evolution of cultivated sunflower. Genetics 171: 1933-1940. [pdf]

Lai, Z., T. Nakazato, M. Salmaso, J.M. Burke, S. Tang, S.J. Knapp, and L.H. Rieseberg. 2005. Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species. Genetics 171: 291-303. [pdf] [supp]

Wills, D.M., M.L. Hester, A. Liu and J.M. Burke. 2005. Chloroplast SSR polymorphisms in the Compositae and the mode of organellar inheritance in Helianthus annuus. Theor. Appl. Genet. 110: 941-947. [pdf]

Wood, T.E., J.M. Burke and L.H. Rieseberg. 2005. Parallel genotypic adaptation: when evolution repeats itself. Genetica 123: 157-170. [pdf]

— 2004 —

Cornman, R.S., J.M. Burke, R.A. Wesselingh and M.L. Arnold. 2004. Contrasting genetic structure of adults and progeny in a Louisiana iris hybrid population. Evolution 58: 2669-2681. [pdf]

Burke, J.M. 2004. When good plants go bad… Evolution 58:1637-1638. [pdf]

Burke, J.M., Z. Lai, M. Salmaso, T. Nakazato, S. Tang, A. Heesacker, S.J. Knapp and L.H. Rieseberg. 2004. Comparative mapping and rapid karyotypic evolution in the genus Helianthus. Genetics 167: 449-457. [pdf] [supp]

— 2003 —

Burke, J.M. and L. H. Rieseberg. 2003. Fitness effects of transgenic disease resistance in sunflowers. Science 300: 1250. [pdf]

Rieseberg, L.H., A. Widmer, A.M. Arntz and J.M. Burke. 2003. The genetic architecture necessary for transgressive segregation is common in both natural and domesticated populations. Phil. Trans. R. Soc. London B 358: 1141-1147. [pdf]

— 2002 —

Rieseberg, L.H., A. Widmer, A.M. Arntz and J.M. Burke. 2002. Directional selection is the primary cause of phenotypic diversification. Proc. Natl. Acad. Sci. USA 99: 12242-12245. [pdf] [supp]

Burke, J.M., K.A. Gardner and L.H. Rieseberg. 2002. The potential for gene flow between cultivated and wild sunflower (Helianthus annuus) in the United States. Am. J. Bot. 89: 1550-1552. [pdf]

Burke, J.M., S. Tang, S.J. Knapp and L.H. Rieseberg. 2002 Genetic analysis of sunflower domestication. Genetics 161: 1257-1267. [pdf]

Burke, J.M. and J.L. Hamrick. 2002. Genetic variation and evidence of hybridization in the genus Rhus (Anacardiaceae). J. Hered. 93: 37-41. [pdf]

— 2001 —

Rieseberg, L.H. and J.M. Burke. 2001. A genic view of species integration. J. Evol. Biol. 14: 883-886. [pdf]

Burke, J.M. and M.L. Arnold. 2001. Genetics and the fitness of hybrids. Annu. Rev. Genet. 35: 31-52. [pdf]

Rieseberg, L.H. and J.M. Burke. 2001. The biological reality of species: gene flow, selection, and collective evolution. Taxon 50: 47-67. [pdf]

— 2000 —

Burke, J.M. and L.H. Rieseberg. 2000. Hybrids and hybridization. R. Robinson, ed. Plant Sciences for Students, Macmillan Reference USA, New York. [pdf]

Burke, J.M., C.W. DePamphilis, R. Wyatt, and M.L. Arnold. 2000. Nectar characteristics of interspecific hybrids and their parents in Aesculus (Hippocastanaceae) and Iris (Iridaceae). J. Torrey Bot. Soc. 127: 200-206. [pdf]

Burke, J.M., M.R. Bulger, R.A. Wesselingh, and M.L. Arnold. 2000. Frequency and spatial patterning of clonal reproduction in Louisiana iris hybrid populations. Evolution 54:137-144. [pdf]

— 1999 —

Allen, E.S., J.M. Burke, M.E. Welch, and L.H. Rieseberg. 1999. Reliability of science on the web. Nature 402: 722. [pdf]

Burke, J.M. and M.L. Arnold. 1999. Isolation and characterization of microsatellites in Iris. Mol. Ecol. 8: 1091-1092. [pdf]

Arnold, M.L., M.R. Bulger, J.M. Burke, A.L. Hempel, and J.H. Williams. 1999. Natural hybridization: how low can you go (and still be important)? Ecology 80: 371-381. [pdf]

— 1998 —

Burke, J.M., T.J. Voss, and M.L. Arnold. 1998. Genetic interactions and natural selection in Louisiana iris hybrids. Evolution 52: 1304-1310. [pdf]

Burke, J.M., S.E. Carney, and M.L. Arnold. 1998. Hybrid fitness in the Louisiana irises: analysis of parental and F1 performance. Evolution 52: 37-43. [pdf]

— 1996 —

Hodges, S.A., J.M. Burke, and M.L. Arnold. 1996. Natural formation of Iris hybrids: experimental evidence on the establishment of hybrid zones. Evolution 50: 2504- 2509. [pdf]