@article {KNZ001083,
	title = {Ecological genomics: making the leap from model systems in the lab to native populations in the field. Frontiers in Ecology and the Environment},
	journal = {Frontiers in Ecology and the Environment},
	volume = {5},
	year = {2007},
	pages = {19 -24},
	abstract = {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{\textquoteright}s genome (the transcription profile), thereby revealing the genetic mechanisms that underlie species{\textquoteright} 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.},
	keywords = {LTER-KNZ},
	doi = {10.1890/1540-9295(2007)5[19:EGMTLF]2.0.CO;2},
	author = {Travers, S.E. and M.D. Smith and Bai, J. and Hulbert, S.H. and Leach, J.E. and Schnable, P.S. and Alan K. Knapp and Milliken, G.A. and Fay, P.A. and Saleh, A. and Garrett, K.A.}
}
@article {KNZ001199,
	title = {Experimentaldesign for two-color microarrays applied in a pre-existing split-plotexperiment},
	journal = {Statistical Applications in Genetics and Molecular Biology},
	volume = {6},
	year = {2007},
	abstract = {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.},
	keywords = {LTER-KNZ, Ecological genomics, experimental design, gene expression, microarray analysis, split-plot design},
	doi = {10.2202/1544-6115.1245},
	url = {http://www.bepress.com/sagmb/vol6/iss1/art20},
	author = {Milliken, G.A. and Garrett, K.A. and Travers, S.E.}
}
@article {KNZ00715,
	title = {Effects of altered soil water availability on a tallgrass prairie nematode community},
	journal = {Applied Soil Ecology},
	volume = {13},
	year = {1999},
	pages = {45 -55},
	abstract = {Climate change predictions for the Great Plains region of North America include reduced growing season precipitation. The consequence of this prediction for soil fauna and belowground processes was investigated at two spatial scales by integrating experimental manipulation of soil moisture levels with natural variation in soil-water availability. Experiments consisted of (1) reciprocal core transplants across a regional precipitation gradient and (2) supplemental irrigation applied across a local topographic gradient. This report examines functional-level responses by the tallgrass prairie nematode community to differences in soil moisture levels over a four-year period. Effects on nematode community structure were complex and dependent upon nematode trophic habit and depth in the soil profile. The strongest and most consistent responses to changes in soil-water availability were displayed by herbivorous taxa, with 71\% higher densities observed under wetter soil conditions across experiments and years. Responses of microbial-feeding nematodes were more variable, with lower densities observed, in some cases, in the presence of experimentally-increased soil moisture levels. Effects of regional differences in soil-water availability on the nematode community were uniformly restricted to depths >20 cm. Community responses to short-term changes in soil moisture were not consistent with patterns in community structure developed under different natural moisture regimes, suggesting divergent short-term and long-term responses of belowground biota and processes to changes in soil-water availability.},
	keywords = {LTER-KNZ, Climate change, community structure, Nematode, soil moisture, tallgrass prairie},
	doi = {10.1016/S0929-1393(99)00022-0},
	author = {Todd, T.C. and John M. Blair and Milliken, G.A.}
}
