A comparison of observation-level random effect and Beta-Binomial models for modelling overdispersion in Binomial data in ecology & evolution
Overdispersion is a common feature of models of biological data, but researchers often fail to model the excess variation driving the overdispersion, resulting in biased parameter estimates and standard errors. Quantifying and modeling overdispersion when it is present is therefore critical for robust biological inference. One means to account for overdispersion is to add an observation-level random effect (OLRE) to a model, where each data point receives a unique level of a random effect that can absorb the extra-parametric variation in the data. Although some studies have investigated the utility of OLRE to model overdispersion in Poisson count data, studies doing so for Binomial proportion data are scarce. Here I use a simulation approach to investigate the ability of both OLRE models and Beta-Binomial models to recover unbiased parameter estimates in mixed effects models of Binomial data under various degrees of overdispersion. In addition, as ecologists often fit random intercept terms to models when the random effect sample size is low (<5 levels), I investigate the performance of both model types under a range of random effect sample sizes when overdispersion is present. Simulation results revealed that the efficacy of OLRE depends on the process that generated the overdispersion; OLRE failed to cope with overdispersion generated from a Beta-Binomial mixture model, leading to biased slope and intercept estimates, but performed well for overdispersion generated by adding random noise to the linear predictor. Comparison of parameter estimates from an OLRE model with those from its corresponding Beta-Binomial model readily identified when OLRE were performing poorly due to disagreement between effect sizes, and this strategy should be employed whenever OLRE are used for Binomial data to assess their reliability. Beta-Binomial models performed well across all contexts, but showed a tendency to underestimate effect sizes when modelling non-Beta-Binomial data. Finally, both OLRE and Beta-Binomial models performed poorly when models contained <5 levels of the random intercept term, especially for estimating variance components, and this effect appeared independent of total sample size. These results suggest that OLRE are a useful tool for modelling overdispersion in Binomial data, but that they do not perform well in all circumstances and researchers should take care to verify the robustness of parameter estimates of OLRE models.
Harrison (2015) A comparison of observation-level random effect and Beta-Binomial models for modelling overdispersion in Binomial data in ecology & evolution. PeerJ 3:e1114 https://doi.org/10.7717/peerj.1114
Motor neurons in the escape response circuit of white shrimp (Litopenaeus setiferus)
Many decapod crustaceans perform escape tailflips with a neural circuit involving giant interneurons, a specialized fast flexor motor giant (MoG) neuron, populations of larger, less specialized fast flexor motor neurons, and fast extensor motor neurons. These escape-related neurons are well described in crayfish (Reptantia), but not in more basal decapod groups. To clarify the evolution of the escape circuit, I examined the fast flexor and fast extensor motor neurons of white shrimp (Litopenaeus setiferus; Dendrobranchiata) using backfilling. In crayfish, the MoGs in each abdominal ganglion are a bilateral pair of separate neurons. In L. setiferus, the MoGs have massive, possibly syncytial, cell bodies and fused axons. The non-MoG fast flexor motor neurons and fast extensor motor neurons are generally found in similar locations to where they are found in crayfish, but the number of motor neurons in both the flexor and extensor pools is smaller than in crayfish. The loss of fusion in the MoGs and increased number of fast motor neurons in reptantian decapods may be correlated with an increased reliance on non-giant mediated tailflipping.
Faulkes (2015) Motor neurons in the escape response circuit of white shrimp (Litopenaeus setiferus). PeerJ 3:e1112 https://doi.org/10.7717/peerj.1112
Not all jellyfish are equal: isotopic evidence for inter- and intraspecific variation in jellyfish trophic ecology
Jellyfish are highly topical within studies of pelagic food-webs and there is a growing realisation that their role is more complex than once thought. Efforts being made to include jellyfish within fisheries and ecosystem models are an important step forward, but our present understanding of their underlying trophic ecology can lead to their oversimplification in these models. Gelatinous zooplankton represent a polyphyletic assemblage spanning >2,000 species that inhabit coastal seas to the deep-ocean and employ a wide variety of foraging strategies. Despite this diversity, many contemporary modelling approaches include jellyfish as a single functional group feeding at one or two trophic levels at most. Recent reviews have drawn attention to this issue and highlighted the need for improved communication between biologists and theoreticians if this problem is to be overcome. We used stable isotopes to investigate the trophic ecology of three co-occurring scyphozoan jellyfish species (Aurelia aurita, Cyanea lamarckii and C. capillata) within a temperate, coastal food-web in the NE Atlantic. Using information on individual size, time of year and δ13C and δ15N stable isotope values, we examined: (1) whether all jellyfish could be considered as a single functional group, or showed distinct inter-specific differences in trophic ecology; (2) Were size-based shifts in trophic position, found previously in A. aurita, a common trait across species?; (3) When considered collectively, did the trophic position of three sympatric species remain constant over time? Differences in δ15N (trophic position) were evident between all three species, with size-based and temporal shifts in δ15N apparent in A. aurita and C. capillata. The isotopic niche width for all species combined increased throughout the season, reflecting temporal shifts in trophic position and seasonal succession in these gelatinous species. Taken together, these findings support previous assertions that jellyfish require more robust inclusion in marine fisheries or ecosystem models.
Fleming et al. (2015) Not all jellyfish are equal: isotopic evidence for inter- and intraspecific variation in jellyfish trophic ecology. PeerJ 3:e1110 https://doi.org/10.7717/peerj.1110
Linear and nonlinear characteristics of the runoff response to regional climate factors in the Qira River basin, Xinjiang, Northwest China
The inland river watersheds of arid Northwest China represent an example of how, in recent times, climatic warming has increased the complexity of Earth’s hydrological processes. In the present study, the linear and nonlinear characteristics of the runoff response to temperature and precipitation were investigated in the Qira River basin, located on the northern slope of the Kunlun Mountains. The results showed that average temperature on annual and seasonal scales has displayed a significantly increasing trend, but this has not been reflected in accumulated precipitation and runoff. Using path analysis, a positive link between precipitation and runoff was found both annually and in the summer season. Conversely, it was found that the impact of temperature on runoff has been negative since the 1960s, attributable to higher evaporation and infiltration in the Qira River basin. Over the past 50 years, abrupt changes in annual temperature, precipitation and runoff occurred in 1997, 1987 and 1995, respectively. Combined with analysis using the correlation dimension method, it was found that the temperature, precipitation and runoff, both annually and seasonally, possessed chaotic dynamic characteristics, implying that complex hydro-climatic processes must be introduced into other variables within models to describe the dynamics. In addition, as determined via rescaled range analysis, a consistent annual and seasonal decreasing trend in runoff under increasing temperature and precipitation conditions in the future should be taken into account. This work may provide a theoretical perspective that can be applied to the proper use and management of oasis water resources in the lower reaches of river basins like that of the Qira River.
Xue et al. (2015) Linear and nonlinear characteristics of the runoff response to regional climate factors in the Qira River basin, Xinjiang, Northwest China. PeerJ 3:e1104 https://doi.org/10.7717/peerj.1104
Indicators of distress in newly diagnosed breast cancer patients
Background. The diagnosis, treatment, and long-term management of cancer can present individuals with a multitude of stressors at various points in that trajectory. Psychosocial distress may appear early in the diagnostic process and have negative effects on compliance with treatment and subsequent quality of life. Purpose. The aim of the study was to determine early-phase predictors of distress before any medical treatment. Method. Consistent with the goals of the study, 123 newly diagnosed breast cancer patients (20 to 74 years old) completed multiple indicators of knowledge about breast cancer management and treatment, attitudes toward cancer, social support, coping efficacy, and distress. Results. SEM analysis confirmed the hypothesized model. Age was negatively associated with the patient’s knowledge (β = − 0.22), which, in turn, was positively associated with both attitudes toward breast cancer (β = 0.39) and coping self-efficacy (β = 0.36). Self-efficacy was then directly related to psychological distress (β = − 0.68). Conclusions. These findings establish indicators of distress in patients early in the cancer trajectory. From a practical perspective, our results have implications for screening for distress and for the development of early interventions that may be followed by healthcare professionals to reduce psychological distress.
Chirico et al. (2015) Indicators of distress in newly diagnosed breast cancer patients. PeerJ 3:e1107 https://doi.org/10.7717/peerj.1107
The majority are not performing home-exercises correctly two weeks after their initial instruction—an assessor-blinded study
Introduction. Time-under-tension (TUT) reflects time under load during strength training and is a proxy of the total exercise dose during strength training. The purpose of this study was to investigate if young participants are able to reproduce TUT and exercise form after two weeks of unsupervised exercises. Material and Methods. The study was an assessor-blinded intervention study with 29 participants. After an initial instruction, all participants were instructed to perform two weeks of home-based unsupervised shoulder abduction exercises three times per week with an elastic exercise band. The participants were instructed in performing an exercise with a predefined TUT (3 s concentric; 2 s isometric; 3 s eccentric; 2 s break) corresponding to a total of 240 s of TUT during three sets of 10 repetitions. After completing two weeks of unsupervised home exercises, they returned for a follow-up assessment of TUT and exercise form while performing the shoulder abduction exercise. A stretch sensor attached to the elastic band was used to measure TUT at baseline and follow-up. A physiotherapist used a pre-defined clinical observation protocol to determine if participants used the correct exercise form. Results. Fourteen of the 29 participants trained with the instructed TUT at follow-up (predefined target: 240 s ±8%). Thirteen of the 29 participants performed the shoulder abduction exercise with a correct exercise form. Seven of the 29 participants trained with the instructed TUT and exercise form at follow-up. Conclusion. The majority of participants did not use the instructed TUT and exercise form at follow-up after two weeks of unsupervised exercises. These findings emphasize the importance of clear and specific home exercise instructions if participants are to follow the given exercise prescription regarding TUT and exercise form as too many or too few exercise stimuli in relation to the initially prescribed amount of exercise most likely will provide a misinterpretation of the actual effect of any given specific home exercise intervention.
Faber et al. (2015) The majority are not performing home-exercises correctly two weeks after their initial instruction—an assessor-blinded study. PeerJ 3:e1102 https://doi.org/10.7717/peerj.1102
Age, growth, and natural mortality of yellowfin grouper (Mycteroperca venenosa) from the southeastern United States
Ages of yellowfin grouper (n = 306) from the southeastern United States coast from 1979–2014 were determined using sectioned sagittal otoliths. Opaque zones were annular, forming January–June (peaking in February–March). Yellowfin grouper ranged in age from 3 to 31 years; the largest fish measured 1,000 mm fork length (FL). Body size relationships for yellowfin grouper were: W = 1.22 × 10−5 FL3.03 (n = 229, r2 = 0.92); TL = 1.06 FL − 14.53 (n = 60, r2 = 0.99); and FL = 0.93 TL + 18.63 (n = 60, r2 = 0.99), where W = whole weight in grams, FL in mm, and TL = total length in mm. The von Bertalanffy growth equation was: Lt = 958 (1 − e−0.11(t+2.94)) (n = 306). The point estimate of natural mortality for yellowfin grouper was M = 0.14, while age-specific estimates of M ranged from 1.59 to 0.17 for ages 1–31.
Burton et al. (2015) Age, growth, and natural mortality of yellowfin grouper (Mycteroperca venenosa) from the southeastern United States. PeerJ 3:e1099 https://doi.org/10.7717/peerj.1099
Coping with shorter days: do phenology shifts constrain aphid fitness?
Climate change can alter the phenology of organisms. It may thus lead seasonal organisms to face different day lengths than in the past, and the fitness consequences of these changes are as yet unclear. To study such effects, we used the pea aphid Acyrthosiphon pisum as a model organism, as it has obligately asexual clones which can be used to study day length effects without eliciting a seasonal response. We recorded life-history traits under short and long days, both with two realistic temperature cycles with means differing by 2 °C. In addition, we measured the population growth of aphids on their host plant Pisum sativum. We show that short days reduce fecundity and the length of the reproductive period of aphids. Nevertheless, this does not translate into differences at the population level because the observed fitness costs only become apparent late in the individual’s life. As expected, warm temperature shortens the development time by 0.7 days/°C, leading to faster generation times. We found no interaction of temperature and day length. We conclude that day length changes cause only relatively mild costs, which may not decelerate the increase in pest status due to climate change.
Joschinski et al. (2015) Coping with shorter days: do phenology shifts constrain aphid fitness?. PeerJ 3:e1103 https://doi.org/10.7717/peerj.1103
Marked increase in rat red blood cell membrane protein glycosylation by one-month treatment with a cafeteria diet
Background and Objectives. Glucose, an aldose, spontaneously reacts with protein amino acids yielding glycosylated proteins. The compounds may reorganize to produce advanced glycosylation products, which regulatory importance is increasingly being recognized. Protein glycosylation is produced without the direct intervention of enzymes and results in the loss of function. Glycosylated plasma albumin, and glycosylated haemoglobin are currently used as index of mean plasma glucose levels, since higher glucose availability results in higher glycosylation rates. In this study we intended to detect the early changes in blood protein glycosylation elicited by an obesogenic diet. Experimental Design. Since albumin is in constant direct contact with plasma glucose, as are the red blood cell (RBC) membranes, we analyzed their degree or glycosylation in female and male rats, either fed a standard diet or subjected to a hyper-energetic self-selected cafeteria diet for 30 days. This model produces a small increase in basal glycaemia and a significant increase in body fat, leaving the animals in the initial stages of development of metabolic syndrome. We also measured the degree of glycosylation of hemoglobin, and the concentration of glucose in contact with this protein, that within the RBC. Glycosylation was measured by colorimetric estimation of the hydroxymethylfurfural liberated from glycosyl residues by incubation with oxalate. Results. Plasma glucose was higher in cafeteria diet and in male rats, both independent effects. However, there were no significant differences induced by sex or diet in either hemoglobin or plasma proteins. Purified RBC membranes showed a marked effect of diet: higher glycosylation in cafeteria rats, which was more marked in females (not in controls). In any case, the number of glycosyl residues per molecule were higher in hemoglobin than in plasma proteins (after correction for molecular weight). The detected levels of glucose in RBC were lower than those of plasma, even when expressed in molal units, and were practically nil in cafeteria-diet fed rats compared with controls; there was no effect of sex. Conclusions. RBC membrane glycosylation is a sensitive indicator of developing metabolic syndrome-related hyperglycemia, more sensitive than the general measurement of plasma or RBC protein glycosylation. The extensive glycosylation of blood proteins does not seem to be markedly affected by sex; and could be hardly justified from an assumedly sustained plasma hyperglycemia. The low levels of glucose found within RBC, especially in rats under the cafeteria diet, could hardly justify the extensive glycosylation of hemoglobin and the lack of differences with controls, which contained sizeable levels of intracellular glucose. Additional studies are needed to study the dynamics of glucose in vivo in the RBC to understand how such extensive protein glycosylation could take place.
Oliva et al. (2015) Marked increase in rat red blood cell membrane protein glycosylation by one-month treatment with a cafeteria diet. PeerJ 3:e1101 https://doi.org/10.7717/peerj.1101
Do the effects of crops on skylark (Alauda arvensis) differ between the field and landscape scales?
The promotion of biodiversity in agricultural areas involves actions at the landscape scale, and the management of cropping patterns is considered an important means of achieving this goal. However, most of the available knowledge about the impact of crops on biodiversity has been obtained at the field scale, and is generally grouped together under the umbrella term “crop suitability.” Can field-scale knowledge be used to predict the impact on populations across landscapes? We studied the impact of maize and rapeseed on the abundance of skylark (Alauda arvensis). Field-scale studies in Western Europe have reported diverse impacts on habitat selection and demography. We assessed the consistency between field-scale knowledge and landscape-scale observations, using high-resolution databases describing crops and other habitats for the 4 km2 grid scales analyzed in the French Breeding Bird Survey. We used generalized linear models to estimate the impact of each studied crop at the landscape scale. We stratified the squares according to the local and geographical contexts, to ensure that the conclusions drawn were valid in a wide range of contexts. Our results were not consistent with field knowledge for rapeseed, and were consistent for maize only in grassland contexts. However, the effect sizes were much smaller than those of structural landscape features. These results suggest that upscaling from the field scale to the landscape scale leads to an integration of new agronomic and ecological processes, making the objects studied more complex than simple “crop ∗ species” pairs. We conclude that the carrying capacity of agricultural landscapes cannot be deduced from the suitability of their components.
Spatial and Geographic Information Science
Sausse et al. (2015) Do the effects of crops on skylark (Alauda arvensis) differ between the field and landscape scales?. PeerJ 3:e1097 https://doi.org/10.7717/peerj.1097