In this paper, we review recent advances in stable isotope mixing models (SIMMs) and place them into an overarching Bayesian statistical framework, which allows for several useful extensions. SIMMs are used to quantify the proportional contributions of various sources to a mixture. The most widely used application is quantifying the diet of organisms based on the food sources they have been observed to consume. At the centre of the multivariate statistical model we propose is a compositional mixture of the food sources corrected for various metabolic factors. The compositional component of our model is based on the isometric log‐ratio transform. Through this transform, we can apply a range of time series and non‐parametric smoothing relationships. We illustrate our models with three case studies based on real animal dietary behaviour. Copyright © 2013 John Wiley & Sons, Ltd.

Maximum lifespan in birds and mammals varies strongly with body mass such that large species tend to live longer than smaller species. However, many species live far longer than expected given their body mass. This may reflect interspecific variation in extrinsic mortality, as life-history theory predicts investment in long-term survival is under positive selection when extrinsic mortality is reduced. Here, we investigate how multiple ecological and mode-of-life traits that should reduce extrinsic mortality (including volancy (flight capability), activity period, foraging environment and fossoriality), simultaneously influence lifespan across endotherms. Using novel phylogenetic comparative analyses and to our knowledge, the most species analysed to date (n ¼ 1368), we show that, over and above the effect of body mass, the most important factor enabling longer lifespan is the ability to fly. Within volant species, lifespan depended upon when (day, night, dusk or dawn), but not where (in the air, in trees or on the ground), species are active. However, the opposite was true for non-volant species, where lifespan correlated positively with both arboreality and fossoriality. Our results highlight that when studying the molecular basis behind cellular processes such as those underlying lifespan, it is important to consider the ecological selection pressures that shaped them over evolutionary time.

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.

Potential climate-related impacts on future crop yield are a major societal concern. Previous projections of the Agricultural Model Intercomparison and Improvement Project's Global Gridded Crop Model Intercomparison based on CMIP5 identified substantial climate impacts on all major crops, but associated uncertainties were substantial. Here we report new 21st-century projections using ensembles of latest-generation crop and climate models. Results suggest markedly more pessimistic yield responses for maize, soybean and rice compared to the original ensemble. Mean end-of-century maize productivity is shifted from +5% to −6% (SSP126) and from +1% to −24% (SSP585)-explained by warmer climate projections and improved crop model sensitivities. In contrast, wheat shows stronger gains (+9% shifted to +18%, SSP585), linked to higher CO 2 concentrations and expanded high-latitude gains. The 'emergence' of climate impacts consistently occurs earlier in the new projectionsbefore 2040 for several main producing regions. While future yield estimates remain uncertain, these results suggest that major breadbasket regions will face distinct anthropogenic climatic risks sooner than previously anticipated.

Reports of unexpectedly 13C-depleted chironomid larvae in lakes have led to an hypothesis that significant transfer of detrital organic matter to chironomid larvae may occur via methane-cycle bacteria. However, to date little is known of how such transfer might vary across species and lakes. We gathered data from 87 lakes to determine how widespread this phenomenon might be and to define boundaries for its likely magnitude. Carbon stable isotope values of chironomid larvae varied greatly between taxa. Very marked 13C-depletion was evident only in certain taxa, especially Chironomus plumosus, C. anthracinus, and C. tenuistylus, all characteristic of eutrophic or dystrophic lakes and known to be tolerant of low oxygen conditions. Furthermore, marked 13C-depletion was only found in larvae from lakes in which late-summer hypolimnetic oxygen depletion near the sediment surface was below an apparent threshold concentration of 2-4 mg O2/L. Similarly, application of a two-source mixing model suggested that methanotrophic bacteria made the greatest contribution to profundal chironomid growth (0-70% of larval carbon) when the late-summer oxygen concentration dropped below approximately 2 mg O2/L. Our study demonstrates that methane-derived carbon is an important, but often neglected, contribution to the flux of carbon through the food webs of many productive or dystrophic lakes.

1. Refugia are critical to the persistence of individuals, populations and communities in disturbed environments, yet few studies have considered how the position of refugia within the landscape interacts with the behavioural responses of component species to determine the influence of disturbance events on mobile animals.2. An 18-month quantitative electrofishing survey was undertaken on the Selwyn River, a stream that is intermittent in its middle reaches, to determine how the direction and distance to refugia affect the response of fish populations to drying, and how landscape context interacts with flow permanence to produce spatial patterns in communities. 3. Overall, the propensity of fish to take refuge in perennial reaches during drying episodes, and the rate and extent of recolonization from these refugia upon rewetting, depended upon the direction and distance to refugia and the behaviour of component species. 4. In the upper river, Canterbury galaxias (Galaxias vulgaris), upland bullies (Gobiomorphus breviceps) and brown trout (Salmo trutta) migrated upstream to permanent water as the stream dried from the bottom up, but frequent drying and slow recolonization by most species combined to produce a fish community in intermittent reaches that was quantitatively and qualitatively different to that in neighbouring perennial reaches. 5. In the lower river, fish did not appear to migrate downstream to permanent water as the stream dried from the top down, but a lower frequency of drying episodes and faster recolonization by upland bullies and eels (Anguilla spp.) from downstream refugia allowed the fish community in intermittent reaches to converge with that in neighbouring perennial reaches during prolonged wetted periods. 6. Longitudinal patterns of increasing fish density and species richness with flow permanence are interpreted as the product of species-specific responses to drying events and the spatial position of refugia within the riverscape.

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1. Modification of natural landscapes and land-use intensification are global phenomena that can result in a range of differing pressures on lotic ecosystems. We analysed national-scale databases to quantify the relationship between three land uses (indigenous vegetation, urbanisation and agriculture) and indicators of stream ecological integrity. Boosted regression tree modelling was used to test the response of 14 indicators belonging to four groups -water quality (at 578 sites), benthic invertebrates (at 2666 sites), fish (at 6858 sites) and ecosystem processes (at 156 sites). Our aims were to characterise the ecological response curves of selected functional and structural metrics in relation to three land uses, examine the environmental moderators of these relationships and quantify the relative utility of metrics as indicators of stream ecological integrity. 2. The strongest indicators of land-use effects were nitrate + nitrite, delta-15 nitrogen value (d 15 N) of primary consumers and the Macroinvertebrate Community Index (a biotic index of organic pollution), while the weakest overall indicators were gross primary productivity, benthic invertebrate richness and fish richness. All indicators declined in response to removal of indigenous vegetation and urbanisation, while variable responses to agricultural intensity were observed for some indicators. 3. The response curves for several indicators suggested distinct thresholds in response to urbanisation and agriculture, specifically at 10% impervious cover and at 0.1 g m )3 nitrogen concentration, respectively. 4. Water quality and ecosystem process indicators were influenced by a combination of temperature, slope and flow variables, whereas for macroinvertebrate indicators, catchment rainfall, segment slope and temperature were significant environmental predictor variables. Downstream variables (e.g. distance to the coast) were significant in explaining residual variation in fish indicators, not surprisingly given the preponderance of diadromous fish species in New Zealand waterways. The inclusion of continuous environmental variables used to develop a stream typology improved model performance more than the inclusion of stream type alone. 5. Our results reaffirm the importance of accounting for underlying spatial variation in the environment when quantifying relationships between land use and the ecological integrity of streams. Of distinctive interest, however, were the contrasting and complementary responses of different indicators of stream integrity to land use, suggesting that multiple indicators are required