Selecting discriminant function models for predicting the expected richness of aquatic macroinvertebrates

1. The predictive modelling approach to bioassessment estimates the macroinvertebrate assemblage expected at a stream site if it were in a minimally disturbed reference condition. The difference between expected and observed assemblages then measures the departure of the site from reference condition. 2. Most predictive models employ site classification, followed by discriminant function (DF) modelling, to predict the expected assemblage from a suite of environmental variables. Stepwise DF analysis is normally used to choose a single subset of DF predictor variables with a high accuracy for classifying sites. An alternative is to screen all possible combinations of predictor variables, in order to identify several ‘best’ subsets that yield good overall performance of the predictive model. 3. We applied best‐subsets DF analysis to assemblage and environmental data from 199 reference sites in Oregon, U.S.A. Two sets of 66 best DF models containing between one and 14 predictor variables (that is, having model orders from one to 14) were developed, for five‐group and 11‐group site classifications. 4. Resubstitution classification accuracy of the DF models increased consistently with model order, but cross‐validated classification accuracy did not improve beyond seventh or eighth‐order models, suggesting that the larger models were overfitted. 5. Overall predictive model performance at model training sites, measured by the root‐mean‐squared error of the observed/expected species richness ratio, also improved steadily with DF model order. But high‐order DF models usually performed poorly at an independent set of validation sites, another sign of model overfitting. 6. Models selected by stepwise DF analysis showed evidence of overfitting and were outperformed by several of the best‐subsets models. 7. The group separation strength of a DF model, as measured by Wilks’Λ, was more strongly correlated with overall predictive model performance at training sites than was DF classification accuracy. 8. Our results suggest improved strategies for developing reliable, parsimonious predictive models. We emphasise the value of independent validation data for obtaining a realistic picture of model performance. We also recommend assessing not just one or two, but several, candidate models based on their overall performance as well as the performance of their DF component. 9. We provide links to our free software for stepwise and best‐subsets DF analysis.     

Plant—herbivore interactions in streams near Mount St Helens

1. In four separate field experiments near Mount St Helens (Washington, U.S.A.) during 1986, the grazing effects of two large benthic herbivores, tadpoles of the tailed frog Ascaphus truei and larvae of the caddisfly Dicosmoecus gilvipes, were investigated using streamside channels and in-stream manipulations. In the experimental channels, abundances of periphyton and small benthic invertebrates declined significantly with increasing density of these larger herbivores. 2. In eleven small, high-gradient streams affected to varying degrees by the May 1980 eruption, in-stream platforms were used to reduce grazing by A, truei tadpoles on tile substrates. Single platforms erected in each tributary and compared to grazed controls revealed only minor grazing effects, and no significant differences among streams varying in disturbance intensity (and, consequently, tadpole density). However, results probably were confounded by high variability among streams in factors other than tadpole abundance. 3. Grazing effects were further examined in two unshaded streams with different tadpole densities, using five platforms per stream. In the stream with five tadpoles m^?2, grazing reduced periphyton biomass by 98% and chlorophyll a by 82%. In the stream lacking tadpoles, no significant grazing effects were revealed. Low algal abundance on both platforms and controls, and high invertebrate density in that stream (c. 30000m^?2) suggests that grazing by small, vagile invertebrates was approximately equivalent to that of tadpoles. 4. The influence of large benthic herbivores on algal and invertebrate communities in streams of Mount St Helens can be important, but reponses vary spatially in relation to stream disturbance history, local environmental factors, and herbivore distributional patterns and abundance.     

Action of Heparin on Platelet Electrophoretic Mobility

THE aggregating agents adenosine diphosphate (ADP) and noradrenaline induce a biphasic change in human platelet electrophoretic mobility¹. Small concentrations (0·005 mg ml.^?1 and 0·05 mg ml.^?1) increase platelet mobility after incubation for 10 min; high concentrations (0·05 mg/ml.) induce a decrease in mobility. The same change also occurs in pig² and rabbit³ platelet mobilities. Hampton and Mitchell⁴ showed that the addition of 1–50 U of heparin to plasma has no effect on the biphasic mobility of human platelets. Nevertheless, measurements of the electrophoretic mobility of pig platelets after intravenous infusion with heparin have led to in vitro studies of both pig and human platelets, which I shall now describe.     

Calyptospora empristica n. sp. (Eimeriorina: Calyptosporidae) from the Liver of the Starhead Topminnow,Fundulus notti1

Oocysts of Calyptospora empristica n. sp., the second described species in its genus, are described from the freshwater starhead topminnow, Fundulus notti, in southern Mississippi. Oocysts are 22 μm in diameter with a wall about 20 nm thick and have no residuum, micropyle, or polar granule. Sporocysts are spheroid, 9 × 5 μm with a two-layered wall approximately 120 nm thick. They have an oblong apical opening at the anterior pole, a single ornamented sporopodium approximately 5.7 μm long at the posterior pole, and a residuum. An intermediate host, most likely the freshwater grass shrimp Palaemonetes kadiakensis, is probably required to complete the life cycle.     

First multi-locus sequence typing scheme for Arcobacter spp.

Background  

Arcobacter spp. are a common contaminant of food and water, and some species, primarily A. butzleri and A. cryaerophilus, have been isolated increasingly from human diarrheal stool samples. Here, we describe the first Arcobacter multilocus sequence typing (MLST) method for A. butzleri, A. cryaerophilus, A. skirrowii, A. cibarius and A. thereius.     

Method of predicting reference condition biota affects the performance and interpretation of ecological indices

1. The statistical rigour and interpretability of ecological assessments is strongly affected by how well we predict the biological assemblages expected to occur in the absence of human‐caused stress, i.e. the reference condition. In this study, we examined how the specific method used to predict the reference condition affected the performance of two commonly used types of ecological index: RIVPACS‐based O/E indices and multimetric indices (MMIs). 2. These two types of index have generally relied on different approaches to predicting the reference condition. For MMIs, some type of regionalisation is typically used to describe the range of metric values among reference sites and hence the expected range at assessed sites. For O/E indices, continuous modelling is used to predict how the biota varies among sites both among and within regions. Because the prediction method differs for these two types of index, it has been impossible to judge if differences in index performance (accuracy, precision, responsiveness and sensitivity) are caused by differences in the way reference condition biota are predicted or by differences in what the indices measure. 3. We used a common data set of 94 reference sites and 255 managed sites and the same potential set of predictor variables to compare the performance of five different MMIs and three O/E indices that were derived from different prediction methods: null models, multiple linear regression (MLR), classification and regression trees, Random Forests (RF) and linear discriminant functions models (LDM). We then calculated values of these indices for samples collected from the managed catchments as well as samples collected from 13 reference sites that were progressively altered in known ways by a simulation programme. 4. Both the type of predictor used and the type of index affected overall index performance. Modelled indices generally had the greatest sensitivity in assessing managed sites as biologically different from reference. Index sensitivity was determined by both an aspect of index precision (10th percentile of reference condition values) and responsiveness. The O/E indices showed the best scope of response to known biological alteration. All three O/E indices decreased linearly in response to simulated alteration in both overall assemblage structure (Bray‐Curtis dissimilarity) and taxa loss. The MMIs declined linearly from low to intermediate levels of assemblage alteration but were less responsive between intermediate and high levels of biological alteration. 5. Insights gained from simulations can aid in testing assumptions regarding index response to stress and help ensure that we select indices that are ecologically interpretable and most useful to resource managers.     

Deep phylogeny,net primary productivity,and global body size gradient in birds

Body size is evolutionarily constrained, but the influence of phylogenetic relationships on global body size (i.e. body mass) gradients is unexplored. We quantify and map the family‐level phylogenetic and non‐phylogenetic structure of the global gradient of birds, evaluating the extent to which it is influenced by phylogenetic inertia in contrast to heat conservation, resource availability, starvation resistance, niche conservatism, or interspecific competition. Phylogenetic eigenvector regression (PVR) partitioned the global bird body size gradient into phylogenetically autocorrelated (PA) and phylogenetically independent (PI) components. Simple, piecewise, and partial regressions were used to investigate associations between the PA and PI components of body size and environmental correlates, and to quantify independent and overlapping contributions of environment, phylogenetic autocorrelation, and species richness to the body size gradient. Two‐thirds of the geographic variation in bird body size can be explained by phylogenetic relationships at the family level. The global variation in body size, independent of phylogenetic relationships, is most strongly associated with net primary productivity, which is consistent with ‘starvation resistance’. However, the New and Old worlds have very different patterns. We found no independent association of species richness with body size. Despite major unresolved regional differences, deep phylogenetic relationships, heat conservation, and starvation resistance probably operate in concert in shaping the global bird body size gradient in different parts of the world. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Phylogenetic systematics of Sternbergia (Amaryllidaceae) based on plastid and ITS sequence data

The phylogenetics of Sternbergia (Amaryllidaceae) were studied using DNA sequences of the plastid ndhF and matK genes and nuclear internal transcribed spacer (ITS) ribosomal region for 38, 37 and 32 ingroup and outgroup accessions, respectively. All members of Sternbergia were represented by at least one accession, except S. minoica and S. schubertii, with additional taxa from Narcissus and Pancratium serving as principal outgroups. Sternbergia was resolved and supported as sister to Narcissus and composed of two primary subclades: S. colchiciflora sister to S. vernalis, S. candida and S. clusiana, with this clade in turn sister to S. lutea and its allies in both Bayesian and bootstrap analyses. A clear relationship between the two vernal flowering members of the genus was recovered, supporting the hypothesis of a single origin of vernal flowering in Sternbergia. However, in the S. lutea complex, the DNA markers examined did not offer sufficient resolving power to separate taxa, providing some support for the idea that S. sicula and S. greuteriana are conspecific with S. lutea. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 166 , 149–162.