%0 Journal Article %J American Journal of Botany %D 2013 %T Temperature dependant shifts in phenology contribute to the success of exotic species with climate change %A Wolkovich, E.M. %A Davies, T.J. %A Schaefer, H. %A Cleland, E.E. %A Cook, B.I. %A Travers, S.E. %A Willis, C.G. %A Davis, C.C. %K flowering time %K introduced species %K invasion biology %K non-native species %K North American prairies %K plant phenology %K temperate grasslands %X

• Premise of the study: The study of how phenology may contribute to the assembly of plant communities has a long history in ecology. Climate change has brought renewed interest in this area, with many studies examining how phenology may contribute to the success of exotic species. In particular, there is increasing evidence that exotic species occupy unique phenological niches and track climate change more closely than native species. • Methods: Here, we use long-term records of species’ first flowering dates from five northern hemisphere temperate sites (Chinnor, UK and in the United States, Concord, Massachusetts; Fargo, North Dakota; Konza Prairie, Kansas; and Washington, D.C.) to examine whether invaders have distinct phenologies. Using a broad phylogenetic framework, we tested for differences between exotic and native species in mean annual flowering time, phenological changes in response to temperature and precipitation, and longer-term shifts in first flowering dates during recent pronounced climate change (“flowering time shifts”). • Key results: Across North American sites, exotic species have shifted flowering with climate change while native species, on average, have not. In the three mesic systems, exotic species exhibited higher tracking of interannual variation in temperature, such that flowering advances more with warming, than native species. Across the two grassland systems, however, exotic species differed from native species primarily in responses to precipitation and soil moisture, not temperature. • Conclusions: Our findings provide cross-site support for the role of phenology and climate change in explaining species’ invasions. Further, they support recent evidence that exotic species may be important drivers of extended growing seasons observed with climate change in North America.

%B American Journal of Botany %V 100 %P 1407 -1421 %G eng %U https://bsapubs.onlinelibrary.wiley.com/doi/full/10.3732/ajb.1200478 %M KNZ001616 %R 10.3732/ajb.1200478 %0 Journal Article %J PLoS ONE %D 2011 %T Genomic and resistance gene homolog diversity of the dominant tallgrass prairie species across the U.S. Great Plains precipitation gradient %A Rouse, M.N. %A Saleh, A.A. %A Seck, A. %A Keeler, K.H. %A Travers, S.E. %A Hulbert, S.H. %A Garrett, K.A. %K Amplified fragment length polymorphism %K Cloning %K Hexaploidy %K Maize %K Plant genomics %K Plant pathology %K Ploidy %K Population genetics %X

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.

%B PLoS ONE %V 6:e17641 %G eng %U https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017641 %M KNZ001395 %R 10.1371/journal.pone.0017641 %0 Journal Article %J Molecular Ecology %D 2010 %T Relatedness of Macrophomina phaseolina isolates from tallgrass prairie, maize, soybean, and sorghum %A Saleh, A.A. %A Ahmed, H.U. %A Todd, T.C. %A Travers, S.E. %A Zeller, K.A. %A Leslie, J.F. %A Garrett, K.A. %X

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.

%B Molecular Ecology %V 19 %P 79 -91 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2009.04433.x %M KNZ001266 %R 10.1111/j.1365-294X.2009.04433.x %0 Journal Article %J Journal of Ecology %D 2010 %T Variation in gene expression of Andropogon gerardii in response to altered environmental conditions associated with climate change %A Travers, S.E. %A Tang, Z. %A Caragea, D. %A Garrett, K.A. %A Hulbert, S.H. %A Leach, J.E. %A Bai, J. %A Saleh, A. %A Alan K. Knapp %A Fay, P.A. %A Jesse B. Nippert %A Schnable, P.S. %A M.D. Smith %X

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.

%B Journal of Ecology %V 98 %P 374 -383 %G eng %U https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2745.2009.01618.x %M KNZ001293 %R 10.1111/j.1365-2745.2009.01618.x %0 Journal Article %J Frontiers in Ecology and the Environment %D 2007 %T Ecological genomics: making the leap from model systems in the lab to native populations in the field. Frontiers in Ecology and the Environment %A Travers, S.E. %A M.D. Smith %A Bai, J. %A Hulbert, S.H. %A Leach, J.E. %A Schnable, P.S. %A Alan K. Knapp %A Milliken, G.A. %A Fay, P.A. %A Saleh, A. %A Garrett, K.A. %X Recent 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. %B Frontiers in Ecology and the Environment %V 5 %P 19 -24 %G eng %M KNZ001083 %R 10.1890/1540-9295(2007)5[19:EGMTLF]2.0.CO;2 %0 Journal Article %J Statistical Applications in Genetics and Molecular Biology %D 2007 %T Experimentaldesign for two-color microarrays applied in a pre-existing split-plotexperiment %A Milliken, G.A. %A Garrett, K.A. %A Travers, S.E. %K Ecological genomics %K experimental design %K gene expression %K microarray analysis %K split-plot design %X Microarray 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. %B Statistical Applications in Genetics and Molecular Biology %V 6 %G eng %U http://www.bepress.com/sagmb/vol6/iss1/art20 %M KNZ001199 %R 10.2202/1544-6115.1245 %0 Journal Article %J Annual Review of Phytopathology %D 2006 %T Climate change effects on plant disease: from genes to ecosystems %A Garrett, K.A. %A Dendy, S.P. %A Frank, E.E. %A Rouse, M.N. %A Travers, S.E. %X 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 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. %B Annual Review of Phytopathology %V 44 %P 489 -509 %G eng %M KNZ001063 %R 10.1146/annurev.phyto.44.070505.143420 %0 Journal Article %J European Journal of PlantPathology %D 2006 %T Ecological genomics and epidemiology %A Garrett, K.A. %A Hulbert, S.H. %A Leach, J.E. %A Travers, S.E. %X The 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. %B European Journal of PlantPathology %V 115 %P 35 -51 %G eng %M KNZ001028 %R 10.1007/s10658-005-4050-2 %0 Journal Article %J Journal of Mammalogy %D 1988 %T Differential use of experimental habitat patches by foraging Peromyscus maniculatus on dark and bright nights %A Travers, S.E. %A D.W. Kaufman %A Kaufman, G.A. %X

To assess the influence of illumination on choice of microhabitat by foraging rodents, we tested the use of exposed and protected patches by deer mice (Peromyscus maniculatus) when seeds were equally available in two or more patch types in large laboratory arenas. Based on field observations, we expected that, under higher levels of illumination, the ratio of foraging activity in exposed microhabitats to that in protected ones would be lower. We present data from three experiments that uphold this expectation

%B Journal of Mammalogy %V 69 %P 869 -872 %G eng %M KNZ00211 %R 10.2307/1381652