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Summary1. There has been a lack of software available to ecologists for the management, visualisation and analysis of ecological community and food web data. Researchers have been forced to implement their own data formats and software, often from scratch, resulting in duplicated effort and bespoke solutions that are difficult to apply to future analyses and comparative studies. 2. We introduce Cheddar -an R package that provides standard, transparent implementations of a wide range of food web and community-level analyses and plots, focussing on ecological network data that are augmented with estimates of body mass and/or numerical abundance. 3. The package allows analysis of individual communities, as well as collections of communities, allowing examination of changes in structure through time, across environmental gradients, or due to experimental manipulations. Several commonly analysed food web data sets are included and used in worked examples. 4. This is the first time these important features have been combined in a single package that helps improve research efficiency and serves as a unified framework for future development.

Evidence of chemical recovery from acidification in European freshwaters has emerged in recent years, with many previously damaged systems responding to decades of reduced acidifying emissions. Biological recovery, however, has often lagged behind, and this has been ascribed to several possible mechanisms, including inertia in the food web. We examined two decades of change in hindcasted food webs for Lochnagar, a Scottish mountain lake, to make inferences about the potential dynamical stability of the system and to assess the prospects for future biological recovery. Although community composition tracked temporal changes in acidity, this was neither sustained nor directional, and mainly manifested as shifts in relative abundances rather than the establishment of more acidsensitive species. The food web was highly interconnected and reticulate, especially in years when species richness was low, and subsidized by external inputs of detritus. Among the primary consumers, generalist herbivoredetritivores maintained feeding links with the scant algal resources, which appeared insufficient to support viable populations of specialist grazers. Together, these characteristics, which are shared with many other acidified freshwaters, are likely to make the community dynamically stable and resistant to invasions of potential new colonists, thereby slowing the pace of future biological recovery.

Acidity is a major driving variable in the ecology of fresh waters, and we sought to quantify macroecological patterns in stream food webs across a wide pH gradient. We postulated that a few generalist herbivore-detritivores would dominate the invertebrate assemblage at low pH, with more specialists grazers at high pH. We also expected a switch towards algae in the diet of all primary consumers as the pH increased. For 20 stream food webs across the British Isles, spanning pH 5.0–8.4 (the acid sites being at least partially culturally acidified), we characterised basal resources and primary consumers, using both gut contents analysis and stable isotopes to study resource use by the latter. We found considerable species turnover across the pH gradient, with generalist herbivore-detritivores dominating the primary consumer assemblage at low pH and maintaining grazing. These were joined or replaced at higher pH by a suite of specialist grazers, while many taxa that persisted across the pH gradient broadened the range of algae consumed as acidity declined and increased their ingestion of biofilm, whose nutritional quality was higher than that of coarse detritus. There was thus an increased overall reliance on algae at higher pH, both by generalist herbivore-detritivores and due to the presence of specialist grazers, although detritus was important even in non-acidic streams. Both the ability of acid-tolerant, herbivore-detritivores to exploit both autochthonous and allochthonous food and the low nutritional value of basal resources might render chemically recovering systems resistant to invasion by the specialist grazers and help explain the sluggish ecological recovery of fresh waters whose water chemistry has ameliorated.Electronic supplementary materialThe online version of this article (doi:10.1007/s00442-012-2421-x) contains supplementary material, which is available to authorized users.

A mouse strain was identified with a recessive genetic lesion, which spontaneously developed a lymphoproliferative autoimmune syndrome exhibiting features of systemic lupus erythematosus. Positional mapping of the disease-associated locus revealed a lesion in Rasgrp1 that prevented the translation of the RasGRP1 protein. T cells from these mice failed to activate Ras or proliferate vigorously following antigen encounter and showed defects in positive selection. Peripheral RasGRP1lag T cells spontaneously adopted a memory phenotype and were able to transfer disease to lymphopenic recipient mice. CD4+ T cells accumulated in the lymphoid tissues of older RasGRP1lag mice and were resistant to activation-induced cell death. RasGRP1lag B cells were functionally normal, but activated B cells were detected in older mice, as were autoantibodies directed against self-antigens. Our findings indicate that Ras signaling pathways are required to maintain T cell tolerance and to prevent autoimmune disease.