02191nas a2200241 4500008004100000245006300041210006100104300001300165490000800178520150400186653003001690653000901720653001801729653001601747653001101763653001501774100002001789700001601809700002001825700001801845700002001863856006601883 2014 eng d00aPlant-virus interactions and the agro-ecological interface0 aPlantvirus interactions and the agroecological interface a529 -5370 v1383 a

As a result of human activities, an ever-increasing portion of Earth’s natural landscapes now lie adjacent to agricultural lands. This border between wild and agricultural communities represents an agro-ecological interface, which may be populated with crop plants, weeds of crop systems, and non-crop plants that vary from exotic to native in origin. Plant viruses are important components of the agro-ecological interface because of their ubiquity, dispersal by arthropod vectors, and ability to colonize both crop and wild species. Here we provide an overview of research on plant-virus dynamics across this interface and suggest three research priorities: (1) an increased effort to identify and describe plant virus diversity and distribution in its entirety across agricultural and ecological boundaries; (2) multi-scale studies of virus transmission to develop predictive power in estimating virus propagation across landscapes; and (3) quantitative evaluation of the influence of viruses on plant fitness and populations in environmental contexts beyond crop fields. We close by emphasizing that agro-ecological interfaces are dynamic, influenced by the human-mediated redistribution of plants, vectors, and viruses around the world, climate change, and the development of new crops. Consideration of virus interactions within these environmentally complex systems promises new insight into virus, plant, and vector dynamics from molecular mechanisms to ecological consequences.

10aAgro-ecological interface10aCrop10aPlant fitness10aPlant virus10aVector10aWild plant1 aAlexander, H.M.1 aMauck, K.E.1 aWhitfield, A.E.1 aGarrett, K.A.1 aMalmstrom, C.M. uhttps://link.springer.com/article/10.1007%2Fs10658-013-0317-102398nas a2200241 4500008004100000245010400041210006900145300001500214490000700229520165400236653003801890653001801928653001701946653001301963653002401976653001602000100001402016700001702030700001502047700001302062700001802075856006302093 2013 eng d00aSpatial connectedness of plant species: potential links for apparent competition via plant diseases0 aSpatial connectedness of plant species potential links for appar a1195 -14280 v623 a

This study evaluated the reactions of seven common C4 grasses of the tallgrass prairie of the USA Great Plains to the economically important wheat pathogens Pyrenophora tritici-repentis and Gaeumannomyces graminis var. tritici (Ggt) isolated from wheat. The P. tritici-repentis isolates (race 1) were pathogenic on all grasses tested, but symptom severity was markedly low. Three of the grass species inoculated with Ggt were highly susceptible, while four species exhibited no symptoms. Because measures of connectedness can provide a proxy for population processes, connectedness was evaluated within and among the seven grass species in representative tallgrass prairie environments for all potential pathogen-sharing patterns. Andropogon gerardii was ubiquitous, so all plant species were well connected to it. Andropogon scoparius (= Schizachyrium scoparium), Sorghastrum nutans and Panicum virgatum were fairly common but specialized to particular environments. Bouteloua curtipendula was uncommon but occurred in all environments, while Buchloë dactyloides and Bouteloua gracilis were uncommon and only occurred in upland sites. Co-occurrence of plant species was generally not reciprocal in that, for many species pairs, species A rarely occurred without potential exposure to inoculum from species B, while species B commonly occurred without species A. The three grass species susceptible to Ggt may act as sources of inoculum for each other within tallgrass prairie, with the potential to influence fitness, and tallgrass prairie and commercial wheat ecosystems in the Great Plains also have the potential to share both pathogens.

10aagriculture–wildlands interface10abiofuel crops10agraph theory10anetworks10apathogen spill-over10aswitchgrass1 aCox, C.M.1 aBockus, W.W.1 aHolt, R.D.1 aFang, L.1 aGarrett, K.A. uhttps://onlinelibrary.wiley.com/doi/full/10.1111/ppa.1204502739nas a2200349 4500008004100000245010400041210006900145300001100214490000700225520170500232653002301937653001701960653002301977653002502000653002702025653002302052100001802075700001702093700001502110700001602125700001702141700001702158700002402175700001902199700001502218700001802233700001802251700001402269700001502283700001302298856007802311 2011 eng d00aComplexity in climate change impacts: An analytical framework for effects mediated by plant disease0 aComplexity in climate change impacts An analytical framework for a15 -300 v603 a

The impacts of climate change on ecosystem services are complex in the sense that effective prediction requires consideration of a wide range of factors. Useful analysis of climate-change impacts on crops and native plant systems will often require consideration of the wide array of other biota that interact with plants, including plant diseases, animal herbivores, and weeds. We present a framework for analysis of complexity in climate-change effects mediated by plant disease. This framework can support evaluation of the level of model complexity likely to be required for analysing climate-change impacts mediated by disease. Our analysis incorporates consideration of the following set of questions for a particular host, pathogen, host–pathogen combination, or geographic region. 1. Are multiple biological interactions important? 2. Are there environmental thresholds for population responses? 3. Are there indirect effects of global change factors on disease development? 4. Are spatial components of epidemic processes affected by climate? 5. Are there feedback loops for management? 6. Are networks for intervention technologies slower than epidemic networks? 7. Are there effects of plant disease on multiple ecosystem services? 8. Are there feedback loops from plant disease to climate change? Evaluation of these questions will help in gauging system complexity, as illustrated for fusarium head blight and potato late blight. In practice, it may be necessary to expand models to include more components, identify those components that are the most important, and synthesize such models to include the optimal level of complexity for planning and research prioritization.

10acereal head blight10adisease risk10aecosystem services10afusarium graminearum10aphytophthora infestans10apotato late blight1 aGarrett, K.A.1 aForbes, G.A.1 aSavary, S.1 aSkelsey, P.1 aSparks, A.H.1 aValdivia, C.1 avan Bruggen, A.H.C.1 aWillocquet, L.1 aDjurle, A.1 aDuveiller, E.1 aEckersten, H.1 aPande, S.1 aCruz, Vera1 aYuen, J. uhttps://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-3059.2010.02409.x02634nas a2200277 4500008004100000245014400041210006900185490001300254520174100267653004302008653001202051653001502063653001002078653001902088653002002107653001102127653002402138100001602162700001602178700001302194700001702207700001802224700001802242700001802260856007802278 2011 eng d00aGenomic and resistance gene homolog diversity of the dominant tallgrass prairie species across the U.S. Great Plains precipitation gradient0 aGenomic and resistance gene homolog diversity of the dominant ta0 v6:e176413 a

Background Environmental variables such as moisture availability are often important in determining species prevalence and intraspecific diversity. The population genetic structure of dominant plant species in response to a cline of these variables has rarely been addressed. We evaluated the spatial genetic structure and diversity of Andropogon gerardii populations across the U.S. Great Plains precipitation gradient, ranging from approximately 48 cm/year to 105 cm/year. Methodology/Principal Findings Genomic diversity was evaluated with AFLP markers and diversity of a disease resistance gene homolog was evaluated by PCR-amplification and digestion with restriction enzymes. We determined the degree of spatial genetic structure using Mantel tests. Genomic and resistance gene homolog diversity were evaluated across prairies using Shannon's index and by averaging haplotype dissimilarity. Trends in diversity across prairies were determined using linear regression of diversity on average precipitation for each prairie. We identified significant spatial genetic structure, with genomic similarity decreasing as a function of distance between samples. However, our data indicated that genome-wide diversity did not vary consistently across the precipitation gradient. In contrast, we found that disease resistance gene homolog diversity was positively correlated with precipitation. Significance Prairie remnants differ in the genetic resources they maintain. Selection and evolution in this disease resistance homolog is environmentally dependent. Overall, we found that, though this environmental gradient may not predict genomic diversity, individual traits such as disease resistance genes may vary significantly.

10aAmplified fragment length polymorphism10aCloning10aHexaploidy10aMaize10aPlant genomics10aPlant pathology10aPloidy10aPopulation genetics1 aRouse, M.N.1 aSaleh, A.A.1 aSeck, A.1 aKeeler, K.H.1 aTravers, S.E.1 aHulbert, S.H.1 aGarrett, K.A. uhttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.001764102523nas a2200193 4500008004100000245010500041210006900146300001100215490000700226520190200233100001602135700001602151700001502167700001802182700001702200700001702217700001802234856007702252 2010 eng d00aRelatedness of Macrophomina phaseolina isolates from tallgrass prairie, maize, soybean, and sorghum0 aRelatedness of Macrophomina phaseolina isolates from tallgrass p a79 -910 v193 a

Agricultural and wild ecosystems may interact through shared pathogens such as Macrophomina phaseolina, a generalist clonal fungus with more than 284 plant hosts that is likely to become more important under climate change scenarios of increased heat and drought stress. To evaluate the degree of subdivision in populations of M. phaseolina in Kansas agriculture and wildlands, we compared 143 isolates from maize fields adjacent to tallgrass prairie, nearby sorghum fields, widely dispersed soybean fields and isolates from eight plant species in tallgrass prairie. Isolate growth phenotypes were evaluated on a medium containing chlorate. Genetic characteristics were analysed based on amplified fragment length polymorphisms and the sequence of the rDNA-internal transcribed spacer (ITS) region. The average genetic similarity was 58% among isolates in the tallgrass prairie, 71% in the maize fields, 75% in the sorghum fields and 80% in the dispersed soybean fields. The isolates were divided into four clusters: one containing most of the isolates from maize and soybean, two others containing isolates from wild plants and sorghum, and a fourth containing a single isolate recovered from Solidago canadensis in the tallgrass prairie. Most of the sorghum isolates had the dense phenotype on media containing chlorate, while those from other hosts had either feathery or restricted phenotypes. These results suggest that the tallgrass prairie supports a more diverse population of M. phaseolina per area than do any of the crop species. Subpopulations show incomplete specialization by host. These results also suggest that inoculum produced in agriculture may influence tallgrass prairie communities, and conversely that different pathogen subpopulations in tallgrass prairie can interact there to generate ‘hybrids’ with novel genetic profiles and pathogenic capabilities.

1 aSaleh, A.A.1 aAhmed, H.U.1 aTodd, T.C.1 aTravers, S.E.1 aZeller, K.A.1 aLeslie, J.F.1 aGarrett, K.A. uhttps://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2009.04433.x02253nas a2200265 4500008004100000245013500041210006900176300001300245490000700258520141500265100001801680700001301698700001601711700001801727700001801745700001601763700001201779700001401791700002001805700001401825700002301839700001901862700001601881856009001897 2010 eng d00aVariation in gene expression of Andropogon gerardii in response to altered environmental conditions associated with climate change0 aVariation in gene expression of Andropogon gerardii in response  a374 -3830 v983 a

1. If we are to understand the mechanisms underlying species responses to climate change in natural systems, studies are needed that focus on responses of non-model species under field conditions. We measured transcriptional profiles of individuals of Andropogon gerardii, a C4 grass native to North American grasslands, in a field experiment in which both temperature and precipitation were manipulated to simulate key aspects of forecasted climate change. 2. By using microarrays developed for a closely related model species, Zea mays, we were able to compare the relative influence of warming versus altered soil moisture availability on expression levels of over 7000 genes, identify responsive functional groups of genes and correlate changes in gene transcription with physiological responses. 3. We observed more statistically significant shifts in transcription levels of genes in response to thermal stress than in response to water stress. We also identified candidate genes that demonstrated transcription levels closely associated with physiological variables, in particular chlorophyll fluorescence. 4.Synthesis. These results suggest that an ecologically important species responds differently to different environmental aspects of forecast climate change. These translational changes have the potential to influence phenotypic characters and ultimately adaptive responses.

1 aTravers, S.E.1 aTang, Z.1 aCaragea, D.1 aGarrett, K.A.1 aHulbert, S.H.1 aLeach, J.E.1 aBai, J.1 aSaleh, A.1 aKnapp, Alan, K.1 aFay, P.A.1 aNippert, Jesse, B.1 aSchnable, P.S.1 aSmith, M.D. uhttps://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2745.2009.01618.x02090nas a2200241 4500008004100000245006900041210006800110300001500178490000700193520139300200653002301593100001901616700001601635700001601651700001601667700001501683700001701698700001701715700001701732700001701749700001801766856006401784 2009 eng d00aBeyond yield: plant disease in the context of ecosystem services0 aBeyond yield plant disease in the context of ecosystem services a1228 -12360 v993 a

The ecosystem services concept provides a means to define successful disease management more broadly, beyond short-term crop yield evaluations. Plant disease can affect ecosystem services directly, such as through removal of plants providing services, or indirectly through the effects of disease management activities, including pesticide applications, tillage, and other methods of plant removal. Increased plant biodiversity may reduce disease risk if susceptible host tissue becomes less common, or may increase risk if additional plant species are important in completing pathogen life cycles. Arthropod and microbial biodiversity may play similar roles. Distant ecosystems may provide a disservice as the setting for the evolution of pathogens that later invade a focal ecosystem, where plants have not evolved defenses. Conversely, distant ecosystems may provide a service as sources of genetic resources of great value to agriculture, including disease resistance genes. Good policies are needed to support conservation and optimal use of genetic resources, protect ecosystems from exotic pathogens, and limit the homogeneity of agricultural systems. Research is needed to provide policy makers, farmers, and consumers with the information required for evaluating trade-offs in the pursuit of the full range of ecosystem services desired from managed and native ecosystems.

10abiological control1 aCheatham, M.R.1 aRouse, M.N.1 aEsker, P.D.1 aIgnacio, S.1 aPradel, W.1 aRaymundo, R.1 aSparks, A.H.1 aForbes, G.A.1 aGordon, T.R.1 aGarrett, K.A. uhttps://apsjournals.apsnet.org/doi/10.1094/PHYTO-99-11-122802078nas a2200229 4500008004100000245010100041210006900142260003700211300001300248520134900261653000801610653001301618653002101631653001501652653002101667653001501688100001801703700001801721700001801739700002201757856006901779 2009 eng d00aChallenges and approaches to statistical design and inference in high dimensional investigations0 aChallenges and approaches to statistical design and inference in aTotowa, NJbThe Humana Press Inc a181 -2063 a

Advances in modern technologies have facilitated high-dimensional experiments (HDEs) that generate tremendous amounts of genomic, proteomic, and other “omic” data. HDEs involving whole-genome sequences and polymorphisms, expression levels of genes, protein abundance measurements, and combinations thereof have become a vanguard for new analytic approaches to the analysis of HDE data. Such situations demand creative approaches to the processes of statistical inference, estimation, prediction, classification, and study design. The novel and challenging biological questions asked from HDE data have resulted in many specialized analytic techniques being developed. This chapter discusses some of the unique statistical challenges facing investigators studying high-dimensional biology and describes some approaches being developed by statistical scientists. We have included some focus on the increasing interest in questions involving testing multiple propositions simultaneously, appropriate inferential indicators for the types of questions biologists are interested in, and the need for replication of results across independent studies, investigators, and settings. A key consideration inherent throughout is the challenge in providing methods that a statistician judges to be sound and a biologist finds informative.

10aFDR10agenomics10ahigh-dimensional10amicroarray10amultiple testing10astatistics1 aGadbury, G.L.1 aGarrett, K.A.1 aAllison, D.B.1 aBelostotsky, D.A. uhttps://link.springer.com/protocol/10.1007%2F978-1-60327-563-7_901888nas a2200217 4500008004100000245011700041210006900158300001300227490000700240520117000247653003501417653001701452653002101469653002701490653001301517100002001530700001801550700002301568700001501591856006401606 2009 eng d00aConnectivity of the American agricultural landscape: Assessing the national risk of crop pest and disease spread0 aConnectivity of the American agricultural landscape Assessing th a141 -1510 v593 a

More than two-thirds of cropland in the United States is devoted to the production of just four crop species—maize, wheat, soybeans, and cotton—raising concerns that homogenization of the American agricultural landscape could facilitate widespread disease and pest outbreaks, compromising the national food supply. As a new component in national agricultural risk assessment, we employed a graph-theoretic approach to examine the connectivity of these crops across the United States. We used county crop acreage to evaluate the landscape resistance to transmission—the degree to which host availability limits spread in any given region—for pests or pathogens dependent on each crop. For organisms that can disperse under conditions of lower host availability, maize and soybean are highly connected at a national scale, compared with the more discrete regions of wheat and cotton production. Determining the scales at which connectivity becomes disrupted for organisms with different dispersal abilities may help target rapid-response regions and the development of strategic policies to enhance agricultural landscape heterogeneity.

10ageographic information systems10agraph theory10aInvasive species10alandscape connectivity10anetworks1 aMargosian, M.L.1 aGarrett, K.A.1 aHutchinson, J.M.S.1 aWith, K.A. uhttps://academic.oup.com/bioscience/article/59/2/141/22829701771nas a2200241 4500008004100000245011100041210006900152300001300221490000800234520102800242653001901270653001801289653001301307653001401320653001501334653002801349100001701377700001601394700001301410700001401423700001801437856007401455 2009 eng d00aLimiting temperatures for urediniospore germination are low in a systemic rust fungus of tallgrass prairie0 aLimiting temperatures for urediniospore germination are low in a a390 -3940 v1013 a

Potential responses of plant disease phenology to climate change have been addressed primarily in agricultural systems. As a first step toward understanding the phenology of Uropyxis petalostemonis, a rust fungus commonly infecting the legume Dalea candida in USA tallgrass prairie, we evaluated the effects of temperature on urediniospore germination. While urediniospore germination for many rust fungi has been reported to decline only when temperatures are well above 25 C, in vitro germination of U petalostemonis dropped sharply at this temperature. Responses observed on water agar, potato dextrose agar and lima bean agar were similar, although lima bean agar supported a higher percentage germination overall. The low limiting temperatures suggest that most epidemically important new infections by U petalostemonis occur in spring. High summer temperatures in tallgrass prairie might push infection by this rust fungus species to earlier in the year and select for stronger systemic growth characteristics.

10aBasidiomycetes10aDalea candida10aFabaceae10aphenology10aUredinales10aUropyxis petalostemonis1 aWorapong, J.1 aDendy, S.P.1 aTang, Z.1 aAwl, D.J.1 aGarrett, K.A. uhttps://www.tandfonline.com/doi/abs/10.3852/08-102?journalCode=umyc2000484nas a2200169 4500008004100000245005200041210005200093260001300145300001300158100001800171700001300189700001800202700001400220700001700234700001600251856004700267 2009 eng d00aPlant pathogens as indicators of climate change0 aPlant pathogens as indicators of climate change bElsevier a425 -4371 aGarrett, K.A.1 aNita, M.1 aDe Wolf, E.D.1 aGomez, L.1 aSparks, A.H.1 aLetcher, T. uhttp://pdf.usaid.gov/pdf_docs/PNADU515.pdf00615nas a2200157 4500008004100000245010300041210006900144260003100213300001300244100001800257700001400275700001600289700001600305700001500321856012100336 2008 eng d00aApplied biodiversity science: Managing emerging diseases in agriculture and linked natural systems0 aApplied biodiversity science Managing emerging diseases in agric bPrinceton University Press a368 -3861 aGarrett, K.A.1 aCox, C.M.1 aOstfeld, R.1 aKeesing, F.1 aEviner, V. uhttp://129.130.186.12/content/applied-biodiversity-science-managing-emerging-diseases-agriculture-and-linked-natural01433nas a2200121 4500008004100000245004200041210004200083260002900125300001300154520107300167100001801240856005301258 2008 eng d00aClimate change and plant disease risk0 aClimate change and plant disease risk bNational Academies Press a143 -1553 a

Research in the effects of climate change on plant disease continues to be limited, but some striking progress has been made. At the genomic level, advances in technologies for the high-throughput analysis of gene expression have made it possible to begin discriminating responses to different biotic and abiotic stressors and potential trade-offs in responses. At the scale of the individual plant, enough experiments have been performed to begin synthesizing the effects of climate variables on infection rates, though pathosystemspecific characteristics make synthesis challenging. Models of plant disease have now been developed to incorporate more sophisticated climate predictions. At the population level, the adaptive potential of plant and pathogen populations may prove to be one of the most important predictors of the magnitude of climate change effects. Ecosystem ecologists are now addressing the role of plant disease in ecosystem processes and the challenge of scaling up from individual infection probabilities to epidemics and broader impacts.

1 aGarrett, K.A. uhttps://vtechworks.lib.vt.edu/handle/10919/6809102018nas a2200229 4500008004100000245009000041210006900131300001300200490000800213520133600221653002901557653001401586653001701600653001601617653001501633100001201648700001501660700001801675700001301693700001601706856006601722 2008 eng d00aComparison of damage to native and exotic tallgrass prairie plants by natural enemies0 aComparison of damage to native and exotic tallgrass prairie plan a197 -2100 v1983 a

We surveyed the prevalence and amount of leaf damage related to herbivory and pathogens on 12 pairs of exotic (invasive and noninvasive) and ecologically similar native plant species in tallgrass prairie to examine whether patterns of damage match predictions from the enemy release hypothesis. We also assessed whether natural enemy impacts differed in response to key environmental factors in tallgrass prairie by surveying the prevalence of rust on the dominant C4 grass, Andropogon gerardii, and its congeneric invasive exotic C4 grass, A. bladhii, in response to fire and nitrogen fertilization treatments. Overall, we found that the native species sustain 56.4% more overall leaf damage and 83.6% more herbivore-related leaf damage when compared to the exotic species. Moreover, we found that the invasive exotic species sustained less damage from enemies relative to their corresponding native species than the noninvasive exotic species. Finally, we found that burning and nitrogen fertilization both significantly increased the prevalence of rust fungi in the native grass, while rust fungi rarely occurred on the exotic grass. These results indicate that reduced damage from enemies may in part explain the successful naturalization of exotic species and the spread of invasive exotic species in tallgrass prairie.

10aEnemy release hypothesis10agrassland10aInvasiveness10aLeaf damage10aRust fungi1 aHan, X.1 aDend, S.P.1 aGarrett, K.A.1 aFang, L.1 aSmith, M.D. uhttps://link.springer.com/article/10.1007%2Fs11258-008-9395-002176nas a2200241 4500008004100000245014800041210006900189300001100258490000600269520134800275100001801623700001601641700001201657700001801669700001601687700001901703700002001722700001901742700001401761700001401775700001801789856012701807 2007 eng d00aEcological genomics: making the leap from model systems in the lab to native populations in the field. Frontiers in Ecology and the Environment0 aEcological genomics making the leap from model systems in the la a19 -240 v53 aRecent reviews have emphasized the need to incorporate genomics into ecological field studies to further understand how species respond to changing environmental conditions. Genomic tools, such as cDNA (complementary DNA) microarrays, allow for the simultaneous analysis of gene expression of thousands of genes from all or part of an organism's genome (the transcription profile), thereby revealing the genetic mechanisms that underlie species' responses to environmental change. However, despite their potential, two major limitations have hindered the incorporation of microarrays and other genomic tools into field studies: (1) the limited availability of microarrays for ecologically relevant, non-model species and limited financial resources for developing new microarrays; and (2) concern that high sensitivity of gene expression to even subtle alterations in environmental conditions will hinder detection of relevant changes in field measures of transcription profiles. Here, we show that with cross-species hybridizations of microarrays developed for a closely related model organism, an appropriate experimental design, and sufficient replication, transcriptional profiling can successfully be incorporated into field studies. In this way, relevant changes in gene expression with changing environmental conditions can be detected.1 aTravers, S.E.1 aSmith, M.D.1 aBai, J.1 aHulbert, S.H.1 aLeach, J.E.1 aSchnable, P.S.1 aKnapp, Alan, K.1 aMilliken, G.A.1 aFay, P.A.1 aSaleh, A.1 aGarrett, K.A. uhttp://129.130.186.12/content/ecological-genomics-making-leap-model-systems-lab-native-populations-field-frontiers-ecology02078nas a2200193 4500008004100000245009600041210006900137490000600206520145400212653002401666653002401690653002001714653002401734653002201758100001901780700001801799700001801817856004901835 2007 eng d00aExperimentaldesign for two-color microarrays applied in a pre-existing split-plotexperiment0 aExperimentaldesign for twocolor microarrays applied in a preexis0 v63 aMicroarray applications for the study of gene expression are becoming accessible for researchers in more and more systems. Applications from field or laboratory experiments are often complicated by the need to superimpose sample pairing for two-color arrays on experimental designs that may already be complex. For example, split-plot designs are commonly used in biological systems where experiments involve two types of treatments that are not readily applied at the same scale. We demonstrate how effects that are confounded with arrays can still be estimated when there is sufficient replication. To illustrate, we evaluate three methods of sample pairing superimposed on a split-plot design with two treatments, deriving the variance associated with parameter estimates for each. Design A has levels of the whole plot treatment paired on the same microarray within a level of the subplot treatment. Design B has crossed levels paired on the same microarray. Design C has levels of the treatment applied to subplots paired on the same microarray within a whole plot. Designs A and B have lower variance than design C for comparing the levels of the whole plot treatment. Designs B and C have lower variance for comparing the levels of the subplot treatment and design C has lower variance for comparing the levels of the subplot treatment within each level of the whole plot treatment. We provide SAS code for the analyses of variance discussed.10aEcological genomics10aexperimental design10agene expression10amicroarray analysis10asplit-plot design1 aMilliken, G.A.1 aGarrett, K.A.1 aTravers, S.E. uhttp://www.bepress.com/sagmb/vol6/iss1/art2001609nas a2200169 4500008004100000245007000041210006900111300001300180490000700193520106700200100001801267700001601285700001601301700001601317700001801333856008801351 2006 eng d00aClimate change effects on plant disease: from genes to ecosystems0 aClimate change effects on plant disease from genes to ecosystems a489 -5090 v443 aResearch in the effects of climate change on plant disease continues to be limited, but some striking progress has been made. At the genomic level, advances in technologies for the high-throughput analysis of gene expression have made it possible to begin discriminating responses to different biotic and abiotic stressors and potential trade-offs in responses. At the scale of the individual plant, enough experiments have been performed to begin synthesizing the effects of climate variables on infection rates, though pathosystem-specific characteristics make synthesis challenging. Models of plant disease have now been developed to incorporate more sophisticated climate predictions. At the population level, the adaptive potential of plant and pathogen populations may prove to be one of the most important predictors of the magnitude of climate change effects. Ecosystem ecologists are now addressing the role of plant disease in ecosystem processes and the challenge of scaling up from individual infection probabilities to epidemics and broader impacts.1 aGarrett, K.A.1 aDendy, S.P.1 aFrank, E.E.1 aRouse, M.N.1 aTravers, S.E. uhttp://129.130.186.12/content/climate-change-effects-plant-disease-genes-ecosystems02352nas a2200157 4500008004100000245004100041210004100082300001100123490000800134520191100142100001802053700001802071700001602089700001802105856007102123 2006 eng d00aEcological genomics and epidemiology0 aEcological genomics and epidemiology a35 -510 v1153 aThe huge amount of genomic data now becoming available offers both opportunities and challenges for epidemiologists. In this “preview” of likely developments as the field of ecological genomics evolves and merges with epidemiology, we discuss how epidemiology can use new information about genetic sequences and gene expression to form predictions about epidemic features and outcomes and for understanding host resistance and pathogen evolution. DNA sequencing is now complete for some hosts and several pathogens. Microarrays make it possible to measure gene expression simultaneously for thousands of genes. These tools will contribute to plant disease epidemiology by providing information about which resistance or pathogenicity genes are present in individuals and populations, what genes other than those directly involved in resistance and virulence are important in epidemics, the role of the phenotypic status of hosts and pathogens, and the role of the status of the environmental metagenome. Conversely, models of group dynamics supplied by population biology and ecology may be used to interpret gene expression within individual organisms and in populations of organisms. Genomic tools have great potential for improving understanding of resistance gene evolution and the durability of resistance. For example, DNA sequence analysis can be used to evaluate whether an arms race model of co-evolution is supported. Finally, new genomic tools will make it possible to consider the landscape ecology of epidemics in terms of host resistance both as determined by genotype and as expressed in host phenotypes in response to the biotic and abiotic environment. Host phenotype mixtures can be modeled and evaluated, with epidemiological predictions based on phenotypic characteristics such as physiological age and status in terms of induced systemic resistance or systemic acquired resistance.1 aGarrett, K.A.1 aHulbert, S.H.1 aLeach, J.E.1 aTravers, S.E. uhttp://129.130.186.12/content/ecological-genomics-and-epidemiology01900nas a2200205 4500008004100000245008100041210006900122300001300191490000800204520121900212653002801431653001701459653002301476653002201499653001501521100001701536700001801553700001701571856010601588 2005 eng d00aCompetition, facilitation, and niche differentiation in two foliar pathogens0 aCompetition facilitation and niche differentiation in two foliar a449 -4570 v1433 aWe studied competition between the obligate biotroph Puccinia triticina (designated here as Puccinia) and the facultative saprophyte Pyrenophora tritici-repentis (designated here as Pyrenophora) in older and younger leaves in a set of three host genotypes selected to be resistant to Puccinia only, Pyrenophora only, or neither. Age-related resistance is important for both of these pathogens. The facultative saprophyte Pyrenophora was generally a stronger competitor than the biotrophic Puccinia, even experiencing facilitation from the presence of Puccinia when Pyrenophora had the advantage of earlier inoculation. Both pathogen species produced the most spores when they were introduced before the competing species and more spores when introduced simultaneously compared to after the competitor. The pre-interactive niche of Puccinia was larger than the post-interactive niche and sporulation by Puccinia was substantially reduced in environments in which Pyrenophora had high sporulation rates. The pre-interactive niche of Pyrenophora was similar to the post-interactive niche and Pyrenophora had proportionally lower reductions in sporulation due to interspecific competition in the pre-interactive niche.10aFacultative saprophytes10aImpact niche10aObligate parasites10aRequirement niche10aRust fungi1 aAl-Naimi, F.1 aGarrett, K.A.1 aBockus, W.W. uhttp://129.130.186.12/content/competition-facilitation-and-niche-differentiation-two-foliar-pathogens03012nas a2200181 4500008004100000245010300041210006900144300001000213490000700223520236700230100001802597700001602615700001602631700002002647700002002667700001902687856012402706 2004 eng d00aBarley yellow dwarf disease in natural populations of dominant tallgrass prairie species in Kansas0 aBarley yellow dwarf disease in natural populations of dominant t a574 -0 v883 aThe grasses Sorghastrum nutans (Indian grass), Schizachyrium scoparium (little bluestem), Panicum virgatum (switchgrass), and Andropogon gerardii (big bluestem) are four of the most common plant species present in a tallgrass prairie (1). Infection with barley yellow dwarf virus (BYDV, family Luteoviridae) is of interest in these species because of the potential effects of the virus on tallgrass prairie plant communities and the potential for tallgrass prairie to function as a reservoir of the virus for infection in wheat or barley fields. In a previous inoculation experiment, an unidentified strain of BYDV transmitted by the aphid species Rhopalosiphum padi was reported to infect S. scoparium but none of the other three grass species (2). We sampled for the presence of five virus strains in at least 50 blooming plants of each grass species in a natural tallgrass prairie stand in August 2000. Samples were collected in watersheds that were designated 1B, 1D, K1A, 20B, and 20C at Konza Prairie Biological Station in the Flint Hills near Manhattan, KS. To detect the virus, we used enzyme-linked immunosorbent assay (ELISA) with antibodies purchased from Agdia (Elkhart, IN). For the PAV, MAV, RMV, and SGV strains, we used double-antibody sandwich ELISA with alkaline phosphatase label. For Cereal yellow dwarf virus (RPV), we used compound direct ELISA with alkaline phosphatase label. The scoring of ELISA results was based on comparison with infected and uninfected control plants of the same species. Symptoms of infection in the field were difficult to interpret visually, since plants in this natural environment often showed multiple symptoms of stress. None of the five strains were detected in 51 individuals of S. nutans. For 50 individuals of S. scoparium, the incidence of infection by the different strains was 4% for MAV, 0% for PAV, 2% for RMV, 0% for RPV, and 58% for SGV. For 51 individuals of P. virgatum, the incidence of infection was 31% for MAV, 0% for PAV, 0% for RMV, 0% for RPV, and 4% for SGV. For 64 individuals of A. gerardii, the incidence of infection was 59% for MAV, 0% for PAV, 0% for RMV, 0% for RPV, and 3% for SGV. The impact of BYDV on these tallgrass prairie species remains to be determined. The PAV strain is the most commonly reported strain in wheat in Kansas but was not recovered from these grass species.1 aGarrett, K.A.1 aDendy, S.P.1 aPower, A.G.1 aBlaisdell, G.K.1 aAlexander, H.M.1 aMcCarron, J.K. uhttp://129.130.186.12/content/barley-yellow-dwarf-disease-natural-populations-dominant-tallgrass-prairie-species-kansas