Spatial heterogeneity of soil nutrients and plant species in herb-dominated communities of contrasting land use

Recent interest in spatial pattern in terrestrial ecosystems has come from an awareness of theintimate relationship between spatial heterogeneity of soil resources and maintenance of plant species diversity. Soil and vegetation can vary spatially inresponse to several state factors of the system. In this study, we examined fine-scale spatial variability of soil nutrients and vascular plant species in contrasting herb-dominated communities (a pasture and an oldfield) to determine degree of spatial dependenceamong soil variables and plant community characteristics within these communities by sampling at 1-m intervals. Each site was divided into 25 1-m 2 plots. Mineral soil was sampled (2-cm diameter, 5-cm depth) from each of four 0.25-m2 quarters and combined into a single composite sample per plot. Soil organic matter was measured as loss-on-ignition. Extractable NH4 and NO3 were determined before and after laboratory incubation to determine potential net N mineralization and nitrification. Cations were analyzed using inductively coupled plasma emission spectrometry. Vegetation was assessed using estimated percent cover. Most soiland plant variables exhibited sharp contrasts betweenpasture and old-field sites, with the old field having significantly higher net N mineralization/nitrification, pH, Ca, Mg, Al, plant cover, and species diversity, richness, and evenness. Multiple regressions revealedthat all plant variables (species diversity, richness,evenness, and cover) were significantly related to soil characteristics (available nitrogen, organic matter,moisture, pH, Ca, and Mg) in the pasture; in the old field only cover was significantly related to soil characteristics (organic matter and moisture). Both sites contrasted sharply with respect to spatial pattern of soil variables, with the old field exhibiting a higher degree of spatial dependence. These results demonstrate that land-use practices can exert profound influence on spatial heterogeneity of both soil properties and vegetation in herb-dominated communities.

Multiple Lab Comparison of Microarray Platforms

Microarray technology is a powerful tool able to measure RNA expression for thousands of genes at once. Various studies have been published comparing competing platforms with mixed results: some find agreement, others do not. As the number of researchers starting to use microarrays and the number of crossplatform meta-analysis studies rapidly increase, appropriate platform assessments become more important. Here we present results from a comparison study that offers important improvements over those previously described in the literature. In particular, we notice that none of the previously published papers consider differences between labs. For this paper, a consortium of ten labs from the Washington DC/Baltimore (USA) area was formed to compare three heavily used platforms using identical RNA samples: Appropriate statistical analysis demonstrates that relatively large differences exist between labs using the same platform, but that the results from the best performing labs agree rather well. Supplemental material is available from http://www.biostat.jhsph.edu/~ririzarr/techcomp/

Multiple Testing With an Empirical Alternative Hypothesis

An optimal multiple testing procedure is identified for linear hypotheses under the general linear model, maximizing the expected number of false null hypotheses rejected at any significance level. The optimal procedure depends on the unknown data-generating distribution, but can be consistently estimated. Drawing information together across many hypotheses, the estimated optimal procedure provides an empirical alternative hypothesis by adapting to underlying patterns of departure from the null. Proposed multiple testing procedures based on the empirical alternative are evaluated through simulations and an application to gene expression microarray data. Compared to a standard multiple testing procedure, it is not unusual for use of an empirical alternative hypothesis to increase by 50% or more the number of true positives identified at a given significance level.