Effects of Harvesting on Herbaceous Layer Diversity of a Central Appalachian Hardwood Forest

Clearcutting is a common harvesting practice in many eastern hardwood forests. Among the vegetation strata of these forests, the herbaceous layer is potentially the most sensitive in its response to harvest-mediated disturbances and has the highest species diversity. Thus, it is important to understand the response of herbaceous layer diversity to forest harvesting. Previous work on clearcut and mature stands at the Fernow Experimental Forest (FEF), West Virginia, has shown that, although, harvesting did not alter appreciably herbaceous layer cover, it influenced the relationship of cover to biotic and abiotic factors, such as tree density and soil nutrients, respectively. The purpose of this study was to examine the response of species diversity of the herbaceous layer to harvesting at FEF. Fifteen circular, 0.04 ha sample plots were established in each of four watersheds (60 plots in total) representing two stand age categories: two watersheds with 20 years even-age stands following clearcutting and two watersheds with mature second growth stands. All woody stems ≥2.5 cm diameter at breast height were identified, tallied, and measured for diameter. The herbaceous layer was sampled by identifying all vascular plants ≤1 m in height and estimating cover for each species in each of 10 (1 m2) circular sub-plots per sample plot (600 sub-plots total). Species diversity for each plot was calculated from herbaceous layer data using the ln-based Shannon Index (H′) equation. Ten stand and soil variables also were measured on each plot. Mean herbaceous layer cover for clearcut versus mature stands was 27.2±14.3% versus 20.2±8.1% (P>0.05), respectively and mean H′ was 1.67±0.42 versus 1.55±0.48 (P>0.05), respectively. Herbaceous layer diversity was negatively correlated with cation exchange capacity and extractable Ca and Mg in the mineral soil in clearcut stands. In contrast, herbaceous layer diversity was positively correlated with soil organic matter and clay content. Although, 20 years of recovery after clearcutting did not have significant effects on the species diversity of the herbaceous layer when examining stand age means alone, harvesting did appear to influence the spatial relationships between herbaceous layer diversity and biotic factors (e.g. tree density) and abiotic factors (e.g. soil nutrients).

An introduction to low-level analysis methods of DNA microarray data

This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of nucleic acid abundance in a set of tissues or cell populations for thousands of transcripts or loci simultaneously. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. This includes the design of probes, the experimental design, the image analysis of microarray scanned images, the normalization of fluorescence intensities, the assessment of the quality of microarray data and incorporation of quality information in subsequent analyses, the combination of information across arrays and across sets of experiments, the discovery and recognition of patterns in expression at the single gene and multiple gene levels, and the assessment of significance of these findings, considering the fact that there is a lot of noise and thus random features in the data. For all of these components, access to a flexible and efficient statistical computing environment is an essential aspect.