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Ecological Genomics Institute

2014 Publications

Alexander, H.M., Mauck, K.E., Whitfield, A.E., Garrett K.A. and C.M. Malmstrom. 2014. Plant-virus interactions and the agro-ecological interfaceEuropean Journal of Plant Pathology 138:529-547.

Darby, BJ, Herman, MA. 2014. Effect of prey richness on a consumer’s growth rateOecologia 175: 243-250.

Caudle, K.L., Johnson, L. C., Baer, S.G., Maricle, B.R. 2014. A comparison of seasonal foliar chlorophyll change among ecotypes and cultivars of Andropogon gerardii (Poaceae) by using non-destructive and destructive methods. Photosynthetica 1-8.

Zhang, K., Johnson, L., Nelson, R., Yuan, W., Pei, Z.J., Wang, D. 2014. Thermal properties of big bluestem as affected by ecotype and planting location along the precipitation gradient of the Great PlainsEnergy 64 (2014) 164-171, 2014.

Hope AG, Ho SYW, Malaney JL, Cook JA, Talbot SL. 2014. Accounting for rate variation among lineages in comparative demographic analyses. Evolution, 68, 2689-2700.

Hope AG, Panter N, Cook JA, Talbot SL, Nagorsen DW. 2014. Multi-locus phylogeography and systematic revision of North American water shrews (genus: Sorex).  Journal of Mammalogy, 95, 722-738.

Dawson NG, Hope AG, Talbot SL, Cook JA. 2014. A multilocus evaluation of ermine (Mustela erminea) across the Holarctic, testing hypotheses of Pleistocene diversification in response to climate change.  Journal of Biogeography 41, 464-475.

Brown, S.P., Huss-Rigdon, A. and Jumpponen, A. 2014. Analyses of ITS and LSU gene regions provide congruent results on fungal community responses. Fungal Ecology 9: 65-68. DOI: 10.1016/j.funeco.2014.02.002

Brown, S.P. and Jumpponen, A. 2014. Contrasting primary successional trajectories of fungi and bacteria in retreating glacier soils. Molecular Ecology 23: 481-497. DOI: 10.1111/mec.12487

Jumpponen, A. and Brown, S.P. 2014. The rich and the sensitive: diverse fungal communities change functionally with the warming Arctic. Molecular Ecology 23: 3127-3129. DOI: 10.1111/mec.12805

Jumpponen, A. and Jones, K.L. 2014. Tallgrass prairie soil fungal communities are resilient to climate change.Fungal Ecology 10: 44-57. DOI: 10.1016/j.funeco.2013.11.003

Lothamer, K, Brown, S.P., Mattox, J.D., and Jumpponen, A. 2014. Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape. Mycorrhiza 24: 267-280. DOI: 10.1007/s00572-013-0539-2

Prestat, E.; David, M., Hultman, J., Taş, N., Lamendella, R., Dvornik, J., Mackelprang, R., Myrold, D., Jumpponen, A., Tringe, S., Holman, E., Mavromatis, K., Jansson, J.K. 2014. FOAM: Functional Ontology Assignments for Metagenomes: a Hidden Markov  Model (HMM) database with environmental focus. Nucleic Acids Research 19: e145. DOI: 10.1093/nar/gku702.

Nilsson, R.H., Hyde, K.D, Pawlowska, J., Ryberg, M., Tedersoo, L., Aas, A.B., Alias, S,A., Alves, A., Anderson, C.L., Antonelli, A., Arnold, A.E., Bahnmann, B., Bahram, M., Bengtsson-Palme, J., Berlin, A., Branco, S., Chomnunti, P., Dissanayake, A., Drenkhan, R, Friberg, H., Frøslev, T.G., Halwachs, B., Hartmann, M., Henricot, B., Jayawardena, R., Jumpponen, A., Kauserud, H., Koskela, S., Kulik, T., Liimatainen, K., Lindahl, B., Lindner, D., Liu, J.-K., Maharachchikumbura, S., Manamgoda, D., Martinsson, S., Neves, M.A., Niskanen, T., Nylinder, S., Pereira, OL., Pinho, D.B., Porter, T.M., Queloz, V., Riit, T., Sanchez-García, M., de Sousa, F., Stefaczyk, E., Tadych, M., Takamatsu, S., Tian, Q., Udayanga, D., Unterseher, M., Wang, Z., Wikee, S., Yan, J., Larsson, E., Larsson K.-H., Kõljalg, U., Abarenkov, K. 2014. Improving ITS sequence data for identification of plant pathogenic fungi.Fungal Diversity 67: 11-19. DOI: 10.1007/s13225-014-0291-8.

Mandyam, K., Jumpponen, A. 2014. Unraveling the dark septate endophyte functions: Insights from the Arabidopsis model. In: Advances in Endophytic Research. Ed. Verma, V.C., Gange, A.C. Springer-Verlag, Berlin, pp. 115-141. DOI 10.1007/978-81-322-1575-2_6

Hieu Sy Vu, Sunitha Shiva, Mary R. Roth, Pamela Tamura, Lianqing Zheng, Maoyin Li, Sujon Sarowar, Samuel Honey, Dedan McEllhiney, Paul Hinkes, Lawrence Seib, Todd D. Williams, Gary Gadbury, Xuemin Wang, Jyoti Shah and Ruth Welti (2014). Lipid changes after leaf wounding in Arabidopsis thaliana: expanded lipidomic data form the basis for lipid co-occurrence analysisThe Plant Journal. 80, 728 – 743. 

Gray, M., P. St. Amand,  N. M. Bello, M. B. Galliart, M. Knapp, K. Garrett, T. J. Morgan, S. G. Baer, B. R. Maricle, E. Akhunov and L. Johnson. 2014. Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands environmental gradient. Molecular Ecology 23(24): 6011-28. DOI: 10.1111/mec.12993.

Larrabee, B., H. M. Scott and N. M. Bello. 2014. Ordinary least squares regression of ordered categorical data: Inferential implications.Journal of Agricultural, Biological and Environmental Statistics 19(3): 373-386. DOI: 10.1007/s13253-014-0176-z.

Greenway, R., L. Arias-Rodriguez, P. Diaz & M. Tobler. 2014. Patterns of macroinvertebrate and fish diversity in freshwater sulphide springs.Diversity 6 (3): 597‑632.

Culumber, Z. W., C. E. Bautista-Hernandez, S. Monk, L. Arias-Rodriguez & M. Tobler. 2014. Variation in melanism and female preference in proximate but ecologically distinct environmentsEthology 120 (11): 1090-1100.

Alberici da Barbiano, L., R. J. Robinson, M. Tobler, A. S. Aspbury & C. R. Gabor. 2014. Differences in resource assimilation between the unisexual Amazon molly, Poecilia formosa (Poeciliidae) and its sexual host (Poecilia latipinna).Environmental Biology of Fishes 97 (8): 875-880.

Tobler, M., C. Henpita, B. Bassett, J. L. Kelley & J. H. Shaw. 2014. H2S exposure elicits differential expression of candidate genes in fish adapted to sulfidic and non‑sulfidic environments.Comparative Biochemistry and Physiology A: Molecular & Integrative Physiology 175: 7-14.

Pfenninger, M., H. Lerp, M. Tobler, C. Passow, J. L. Kelley, E. Funke, B. Greshake, U. K. Erkoc, T. Berberich & M. Plath. 2014. Parallel evolution of cox-genes in H2S-tolerant fish as key adaptation to a toxic environment. Nature Communications 5: 3873.

Tobler, M., M. Plath, R. Riesch, I. Schlupp, A. Grasse, G. Munimanda, C. Setzer, D. J. Penn & Y. Moodley. 2014. Selection from parasites favors immunogenetic diversity but not divergence among locally adapted host populations.Journal of Evolutionary Biology 27 (5): 960‑974.

Husemann, M., M. Tobler, C. McCauley, B. Ding & P. D. Danley. 2014. Evolution of body shape in differently colored sympatric congeners and allopatric populations of Lake Malawi'ʹs rock-dwelling cichlids.Journal of Evolutionary Biology 27 (5): 826‑839.

Jeyasingh, P. D., R. D. Cothran & M. Tobler. 2014. Testing the ecological consequences of evolutionary change using elements.Ecology and Evolution 4 (4): 528-538.

Tobler, M.& N. Bertrand. 2014. Morphological variation in vanishing Mexican desert fishes of the genus Characodon (Goodeidae).Journal of Fish Biology 84 (2): 283-296.

Riesch, R. W., M. Plath, I. Schlupp, M. Tobler & B. Langerhans. 2014. Colonization of toxic environments drives predictable life-history evolution in livebearing fishes (Poeciliidae). Ecology Letters 17 (1): 65-71. Featured in the Research Highlights of Nature and Evolutionary Applications.

Renaut S, Rowe HC, Ungerer MC, Rieseberg LH. 2014. Genomics of homoploid hybrid speciation: diversity and transcriptional activity of LTR retrotransposons in hybrid sunflowers.Phil. Trans. R. Soc. B 369: 20130345

Kawakami T, Darby BJ, Ungerer MC. 2014. Transcriptome resources for the perennial sunflower Helianthus maximiliani obtained from ecologically divergent populations. Molecular Ecology Resources 14: 812-819

Rhodes DH, Hoffmann L, Rooney WL, Ramu P, Morris GP, Kresovich S. 2014. Genome-wide association study of grain polyphenol concentrations in global sorghum [Sorghum bicolor (L.) Moench] germplasm. Journal of Agricultural and Food Chemistry, 62(45):10916–27

Grabowski PP, Morris GP, Casler MD, Borevitz JO. 2014. Population genomic variation reveals roles of history, adaptation, and ploidy in switchgrass.Molecular Ecology. 23(16):4059–73.

Shakoor N, Nair R, Crasta O, Morris GP, Feltus FA, Kresovich S. 2014. A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetativetissues of grain, sweet and bioenergy sorghums.BMC Plant Biology, 14:35.

Lowry DB, Behrman KD, Grabowski P, Morris GP, Kiniry JR, Juenger TE. 2014. Local and Climatic Adaptations Across the Panicum virgatum Species Complex.AmericanNaturalist. 183(5):682–92.

D. D. Myrold, L. H. Zeglin and J. K. Jansson. 2014. The potential of metagenomic approaches for understanding soil microbial processesSoil Science Society of America Journal, 78: 3-10.

Beck, J. B., C. J. Ferguson, M. H. Mayfield and J. Shaw. 2014. Reduced population genetic variation in black cherry (Prunus serotina subsp. serotina, Rosaceae) at its western range limit in Kansas.Northeastern Naturalist 21: 472-478.

Fehlberg, S. D., M. C. Ty and C. J. Ferguson. 2014. Rexamination of a putative diploid hybrid taxon using genetic evidence: the distinctiveness of Phlox pilosa subsp. Deamii (Polemoniaceae).International Journal of Plant Sciences 175: 781-793.

Peirson, J. A., R. Riina, M. H. Mayfield, C. J. Ferguson, L. E. Urbatsch and P. E. Berry. 2014. Phylogeny and taxonomy of the New World leafy spurges, Euphorbia section Tithymalus (Euphorbiaceae).Botanical Journal of the Linnean Society 175: 191-228.

Williams C.M., M. Watanabe, M.R. Guarracino, M.B. Ferrero, A.S. Edison, T.J. Morgan, A. Boroujerdi, and D.A. Hahn. 2014. Cold adaptation shapes the robustness of metabolic networks in Drosophila melanogaster. Evolution. 68: 3505-23

Fallis, L.C., J.J. Fanara, and T.J. Morgan. 2014. Developmental thermal plasticity among Drosophila melanogaster populations. Journal of Evolutionary Biology 27: 557–64.

H Kawai-Toyooka, T Mori, T Hamaji, M Suzuki, BJSC Olson, T Uemura, T Ueda, A Nakano, A Toyoda, A Fujiyama, and H Nozakiø. 2014. Sex-specific posttranslational regulation of the gamete fusogen GCS1 in the isogamous volvocine alga Gonium pectorale.Eukaryotic Cell, 13(5), 648–56. DOI:10.1128/EC.00330-13.

Stafford-Banks, C.A., Rotenberg, D.; Johnson, B.R., Whitfield, A.E., and Ullman, D.E. 2014. Analysis of the salivary gland transcriptome of Frankliniella occidentalis.PLoS ONE 9:e94447.

Montero-Astúa, M., Rotenberg, D., Leach, A., Schneweis, B., Park, K., Park, S.H., German, T.L., and Whitfield, A.E. 2014. Disruption of vector transmission by a plant-expressed viral glycoprotein.Molecular Plant-Microbe Interactions. 27:296-304.

Whitfield, A.E., Rotenberg, D., and German, T. L. 2014. Plant pest destruction goes viral.Nature Biotechnology 32:65-66.

Herndon, N. and Caragea, D. 2014. Predicting Protein Localization Using a Domain Adaptation Approach. In Lecture Notes in Communications in Computer and Information Science (CCIS) 452, Springer-Verlag Berlin Heidelberg, pp. 191-206.

Zhang K.; Johnson L.; Yuan W.; Pei Z.; and Wang D. 2014. Glucan yield from enzymatic hydrolysis of big bluestem as affected by ecotype and planting location along the precipitation gradient of the Great PlainsBioEnergy Research 1-12.

Zhang X., Wang J., Zhang M., Qin G., Li D., Zhu K. Y., Ma E. & Zhang J. 2014. Molecular cloning, characterization and positively selected sites of the glutathione S-transferase family from Locusta migratoria.PLOS ONE 9(12): e114776.

Chen H., Zhang H., Throne J. & Zhu K. Y. 2014. Transcript analysis and expression profiling of three heat shock protein 70 genes in the ectoparasitoid Habrobracon hebetor (Hymenoptera: Braconidae).Insect Science. 21: 415-428.

Yao J., Buschman L. L., Lu N., Khajuria C. & Zhu K. Y. 2014. Changes in gene expression in the larval gut of Ostrinia nubilalis in response to Bacillus thuringiensis Cry1Ab protoxin ingestion.Toxins 6: 1274-1294.

Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R. 2014. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding.Plant Biotechnology. Nov 26. doi: 10.1111/pbi.12288.

Crespo-Herrera LA, Akhunov E, Garkava-Gustavsson L, Jordan KW, Smith CM, Singh RP, Ahman I. 2014. Mapping resistance to the bird cherry-oat aphid and the greenbug in wheat using sequence-based genotyping.Theorical Applied Genetics. 2014 127:1963-73.

International Wheat Genome Sequencing Consortium (IWGSC). A chromosome-baseddraft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. 2014 Jul 18;345(6194):1251788. doi: 10.1126/science.1251788. PubMed PMID:25035500

Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M; International Wheat Genome Sequencing Consortium, Jakobsen KS, Wulff BB, Steuernagel B, Mayer KF, Olsen OA. Ancient hybridizations among the ancestral genomes of bread wheat. Science. 2014 Jul 18;345(6194):1250092. doi: 10.1126/science.1250092. PubMed PMID: 25035499.

Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR; International Wheat Genome Sequencing Consortium, Mayer KF, Olsen OA. Genome interplay in the grain transcriptome of hexaploid bread wheat. Science. 2014 Jul 18;345(6194):1250091. doi: 10.1126/science.1250091. PubMed PMID: 25035498.

Bruce M, Neugebauer KA, Joly DL, Migeon P, Cuomo C, Wang S, Akhunov E, Bakkeren G, Kolmer JA, Fellers JP. Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat, Frontiers in Plant-Microbe Interaction, Frontier Plant Science. 2014 Jan 13;4:520.

Middleton C, Kilian B, Akhunov E, Keller B, Wicker T. Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One. 2014 Mar 10;9(3):e85761.

Wang S, Wong D, Forrest K, Allen A, Chao S, Huang B, Maccaferri M, Salvi S, Milner S, Cattivelli L , Mastrangelo A, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, (IWGSC) Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova A, Feuillet C, SALSE J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M , Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards K, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high-density 90,000 SNP array.Plant Biotechnology Journal 2014 Mar 20. doi: 10.1111/pbi.12183.

Tiwari VK, Wang S, Sehgal S, Vrána J, Friebe B, Kubaláková M, Chhuneja P, Dole El J, Akhunov E, Kalia B, Sabir J, Gill BS. SNP Discovery for mapping alien introgressions in wheat.BMC Genomics. 2014 Apr 10;15(1):273.

Henry IM, Nagalakshmi U, Lieberman M. C., Ngo K. J, Krasileva KV, Vasquez-Gross H, Akhunova A, Akhunov E, Dubcovsky J, Tai H, Comai L Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing. Plant Cell, 2014, doi:10.1105/tpc.113.121590.