Effects of sample size and intraspecific variation in phylogenetic comparative studies: a meta‐analytic review

Comparative analyses aim to explain interspecific variation in phenotype among taxa. In this context, phylogenetic approaches are generally applied to control for similarity due to common descent, because such phylogenetic relationships can produce spurious similarity in phenotypes (known as phylogenetic inertia or bias). On the other hand, these analyses largely ignore potential biases due to within‐species variation. Phylogenetic comparative studies inherently assume that species‐specific means from intraspecific samples of modest sample size are biologically meaningful. However, within‐species variation is often significant, because measurement errors, within‐ and between‐individual variation, seasonal fluctuations, and differences among populations can all reduce the repeatability of a trait. Although simulations revealed that low repeatability can increase the type I error in a phylogenetic study, researchers only exercise great care in accounting for similarity in phenotype due to common phylogenetic descent, while problems posed by intraspecific variation are usually neglected. A meta‐analysis of 194 comparative analyses all adjusting for similarity due to common phylogenetic descent revealed that only a few studies reported intraspecific repeatabilities, and hardly any considered or partially dealt with errors arising from intraspecific variation. This is intriguing, because the meta‐analytic data suggest that the effect of heterogeneous sampling can be as important as phylogenetic bias, and thus they should be equally controlled in comparative studies. We provide recommendations about how to handle such effects of heterogeneous sampling.     

Pedodiversity deserves attention in plant biodiversity research

We suggest that pedodiversity, an expression of environmental heterogeneity, should deserve the attention of plant ecologists interested to study the spatial pattern of plant biodiversity at different scales. Using the FAO pedological and the IUCN-WCMC biological data bases of the world countries, we show that the prediction on plant biodiversity (number of vascular plants) improves significantly when the extent of the area is combined with pedodiversity in a multiple polynomial regression. Partial correlation analysis proves that, by removing the effect of pedodiversity, the correlation “number of species–area” remains statistically significant for the tropical countries while it loses significance for the countries outside the tropics.     

Developmental temperatures and phenotypic plasticity in reptiles: a systematic review and meta‐analysis

Early environments can profoundly influence an organism in ways that persist over its life. In reptiles, early thermal environments (nest temperatures) can impact offspring phenotype and survival in important ways, yet we still lack an understanding of whether general trends exist and the magnitude of impact. Understanding these patterns is important in predicting how climate change will affect reptile populations and the role of phenotypic plasticity in buffering populations. We compiled data from 175 reptile studies to examine, and quantify, the effect of incubation temperature on phenotype and survival. Using meta‐analytic approaches (standardized mean difference between incubation treatments, Hedges' g), we show that across all trait types examined there is, on average, a moderate to large magnitude of effect of incubation temperatures (absolute effect: |g| = 0.75). Unsurprisingly, this influence was extremely large for incubation duration, as predicted, with warmer temperatures decreasing incubation time overall (g = −8.42). Other trait types, including behaviour, physiology, morphology, performance, and survival experienced reduced, but still mostly moderate to large effects, with particularly strong effects on survival. Moreover, the impact of incubation temperature persisted at least one‐year post‐hatching, suggesting that these effects have the potential to impact fitness in the long term. The magnitude of effect increased as the change in temperature increased (e.g. 6°C versus 2°C) in almost all cases, and tended to decrease when temperatures of the treatments fluctuated around a mean temperature compared to when they were constant. The effect also depended on the mid‐temperature of the comparison, but not in consistent ways, with some traits experiencing the greatest effects at extreme temperatures, while others did not. The highly heterogeneous nature of the effects we observe, along with a large amount of unexplained variability, indicates that the shape of reaction norms between phenotype and temperature, along with ecological and/or experimental factors, are important when considering general patterns. Our analyses provide new insights into the effects of incubation environments on reptile phenotype and survival and allow general, albeit coarse, predictions for taxa experiencing warming nest temperatures under climatic change.     

Robust Summarization and Inference in Proteome-wide Label-free Quantification

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Highlights

• •In depth performance assessment of leading tools for differential protein abundance.
• •Novel fast modular framework MSqRobSum for robust protein summarization and inference.
• •MsqRobSum outperforms leading protein summarization-based tools.
• •MSqRobSum is on par with top-performing peptide based tool MSqRob.

     

A comparison of different ways of including baseline counts in negative binomial models for data from falls prevention trials

A common design for a falls prevention trial is to assess falling at baseline, randomize participants into an intervention or control group, and ask them to record the number of falls they experience during a follow‐up period of time. This paper addresses how best to include the baseline count in the analysis of the follow‐up count of falls in negative binomial (NB) regression. We examine the performance of various approaches in simulated datasets where both counts are generated from a mixed Poisson distribution with shared random subject effect. Including the baseline count after log‐transformation as a regressor in NB regression (NB‐logged) or as an offset (NB‐offset) resulted in greater power than including the untransformed baseline count (NB‐unlogged). Cook and Wei's conditional negative binomial (CNB) model replicates the underlying process generating the data. In our motivating dataset, a statistically significant intervention effect resulted from the NB‐logged, NB‐offset, and CNB models, but not from NB‐unlogged, and large, outlying baseline counts were overly influential in NB‐unlogged but not in NB‐logged. We conclude that there is little to lose by including the log‐transformed baseline count in standard NB regression compared to CNB for moderate to larger sized datasets.     

Statistical analysis of a dynamic model for dietary contaminant exposure

This paper is devoted to the statistical analysis of a stochastic model introduced in [P. Bertail, S. Clémençon, and J. Tressou, A storage model with random release rate for modelling exposure to food contaminants, Math. Biosci. Eng. 35 (1) (2008), pp. 35–60] for describing the phenomenon of exposure to a certain food contaminant. In this modelling, the temporal evolution of the contamination exposure is entirely determined by the accumulation phenomenon due to successive dietary intakes and the pharmacokinetics governing the elimination process inbetween intakes, in such a way that the exposure dynamic through time is described as a piecewise deterministic Markov process. Paths of the contamination exposure process are scarcely observable in practice, therefore intensive computer simulation methods are crucial for estimating the time-dependent or steady-state features of the process. Here we consider simulation estimators based on consumption and contamination data and investigate how to construct accurate bootstrap confidence intervals (CI) for certain quantities of considerable importance from the epidemiology viewpoint. Special attention is also paid to the problem of computing the probability of certain rare events related to the exposure process path arising in dietary risk analysis using multilevel splitting or importance sampling (IS) techniques. Applications of these statistical methods to a collection of data sets related to dietary methyl mercury contamination are discussed thoroughly.     

Offspring performance in dynamic habitats: key factors for a riparian carabid beetle

Abstract.  1. Knowledge of the ecology of carabid species is largely restricted to adults, although larval mortality is assumed to be the key factor in overall mortality. As low-mobility larvae are unable to avoid unfavourable conditions, habitat selection of reproducing adults should be clearly affected by the habitat factors which determine offspring performance.
2. The present study examines the key habitat factors governing the distribution patterns of Bembidion velox larvae and adults on the river banks of the River Elbe by means of habitat suitability models. The validity of the determined habitat factors for offspring performance and survival was tested in laboratory experiments.
3. In the field, B. velox adults as well as larvae show a strong association with semi-terrestrial, sandy, open soil habitats.
4. In the laboratory, overall mortality of larvae reared in different substrates was lowest in sand of medium grain size mixed with fine and coarse sand. The first larval instars in particular reacted sensitively to variations in grain size. Furthermore, flood resistance of eggs was demonstrated, as 90% of larvae hatched under permanently flooded conditions.
5. Short development times were recorded, with 4–7 days for hatching of young larvae from eggs after oviposition and approximately 28 days for the development of adults from newly hatched larvae. This probably increases the survival probability for the pre-imaginal stages in dynamic habitats.
6. In conclusion, it can be said that reproductive success is strongly dependent on oviposition site selection by adults as this reflects the ecological demands of the immature stages.