Redundancy among three herbivorous insects across an experimental current velocity gradient

We conducted streamside experiments to determine if the ability of herbivorous insects to remove algal periphyton varies with local current velocity. We used two mayfly species (Baetis bicaudatusand Drunella grandis) and one caddisfly species (Glossosoma verdona), which differ from one another in body morphology and mobility. Periphyton was grown for 30 days on ceramic tiles in constant velocity to create similar initial forage conditions for grazers. Tiles were transferred to three velocity regimes characteristic of the natural streambed: slow (3-5 cm s(-1)), medium (15-20 cm s(-1)) and fast (32-41 cm s(-1)). Four grazer treatments (Baetis, Drunella, and Glossosoma alone, and all species combined) were repeated for each velocity treatment to isolate the effect of local current on grazer ability to crop periphyton. Grazers differed in their abilities to remove periphyton across current treatments. Glossosoma removed significantly (P<0.05) more periphyton at fast versus either slow or medium velocities; Baetis showed a similar (but non-significant) trend; and, Drunella always removed about 75% of periphyton, irrespective of current. At fast current, periphyton removal was equivalent among the species. At medium current, Drunella removed significantly more than both Baetis and Glossosoma, whereas at slow current, Drunella removed more than Baetis, which removed more than Glossosoma. Periphyton removal under the combined three-grazer treatment was similar qualitatively to the combined effects of individual grazers. More periphyton tended to be removed as current increased, with the fast versus slow contrast showing marginal significance (P=0.10). Under all current regimes, the quantity of periphyton removed did not differ from the null model expectation of simple additive effects among individual grazers (i.e., no facilitation or inhibition). These experiments show that for some species, herbivory varies with current, which suggests that the herbivore "function" of cropping periphyton may vary with the environmental context of local current. Under some local velocities, however, different herbivore species "function" similarly and are potentially redundant with respect to periphytic removal. In naturally heterogeneous streams characterized by sharp gradients in local current velocity, we expect current-dependent species interactions to be common and at least partially contribute to intra-guild co-existence of species.     

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications

The development of liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has made it possible to characterize phosphopeptides in an increasingly large-scale and high-throughput fashion. However, extracting confident phosphopeptide identifications from the resulting large data sets in a similar high-throughput fashion remains difficult, as does rigorously estimating the false discovery rate (FDR) of a set of phosphopeptide identifications. This article describes a data analysis pipeline designed to address these issues. The first step is to reanalyze phosphopeptide identifications that contain ambiguous assignments for the incorporated phosphate(s) to determine the most likely arrangement of the phosphate(s). The next step is to employ an expectation maximization algorithm to estimate the joint distribution of the peptide scores. A linear discriminant analysis is then performed to determine how to optimally combine peptide scores (in this case, from SEQUEST) into a discriminant score that possesses the maximum discriminating power. Based on this discriminant score, the p- and q-values for each phosphopeptide identification are calculated, and the phosphopeptide identification FDR is then estimated. This data analysis approach was applied to data from a study of irradiated human skin fibroblasts to provide a robust estimate of FDR for phosphopeptides. The Phosphopeptide FDR Estimator software is freely available for download at http://ncrr.pnl.gov/software/.