A brief introduction to mixed effects modelling and multi-model inference in ecology

Harrison, Xavier A.; Donaldson, Lynda; Correa-Cano, M.; Evans, Julian C.; Fisher, David N.; Goodwin, Cecily E. D.; Robinson, Beth; Hodgson, David J.; Inger, Richard

doi:10.7287/peerj.preprints.3113

Cited by 403 publications

(566 citation statements)

References 5 publications

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“…Full models are reported along with the simplified version of the models (i.e., reduced models; Crawley 2012). To compare models, we also used likelihood-ratio tests and report on changes in the likelihood ratio (LRT in mixed models) or F statistics (in generalized linear models) between two models of interest, and associated change in degrees of freedom ( df) and P values (Crawley 2012;Harrison et al 2018). Post hoc tests were performed using the multcomp package and glht function (Hothorn et al 2008).…”

Section: Resultsmentioning

confidence: 99%

Sperm divergence in a passerine contact zone: Indication of reinforcement at the gametic level

et al. 2019

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Postcopulatory sexual selection may promote evolutionary diversification in sperm form, but the contribution of between‐species divergence in sperm morphology to the origin of reproductive isolation and speciation remains little understood. To assess the possible role of sperm diversification in reproductive isolation, we studied sperm morphology in two closely related bird species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia), that hybridize in a secondary contact zone spanning Central and Eastern Europe. We found: (1) striking divergence between the species in total sperm length, accompanied by a difference in the length of the mitochondrial sperm component; (2) greater divergence between species in sperm morphology in sympatry than in allopatry, with evidence for character displacement in sperm head length detected in L. megarhynchos; (3) interspecific hybrids showing sperm with a length intermediate between the parental species, but no evidence for decreased sperm quality (the proportion of abnormal spermatozoa in ejaculates). Our results demonstrate that divergence in sperm morphology between the two nightingale species does not result in intrinsic postzygotic isolation, but may contribute to postcopulatory prezygotic isolation. This isolation could be strengthened in sympatry by reinforcement.

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Section: Resultsmentioning

confidence: 99%

Sperm divergence in a passerine contact zone: Indication of reinforcement at the gametic level

et al. 2019

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“…Post hoc analysis was performed with "multcomp" package and corrected for multiple testing. 28,29 We used the packages "ape" and "vegan" for MDS and PERMANOVA, respectively. 30 In this model, we accounted for repeated measurements using the "strata" argument.…”

Section: Resultsmentioning

confidence: 99%

The influence of treatment in alpine and moderate maritime climate on the composition of the skin microbiome in patients with difficult to treat atopic dermatitis

Mierlo

Totté

Fieten

et al. 2019

Clin Experimental Allergy

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Background The skin microbiome, characterized by an overgrowth of Staphylococcus aureus, plays an important role in the pathogenesis of atopic dermatitis (AD). Multidisciplinary treatment in alpine climate is known for its positive effect on disease severity in children with AD and can result in a different immune response compared with moderate maritime climate. However, the effect on the composition of the skin microbiome in AD is unknown. Objective To determine the effect of treatment in alpine climate and moderate maritime climate on the microbiome for lesional and non‐lesional skin in children with difficult to treat AD. Results Alpine climate treatment led to a significant change in the microbiota on lesional skin, whereas no significant change was found after moderate maritime climate. On both lesional and non‐lesional skin, we observed a significant increase in Shannon diversity and a significant decrease in both Staphylococcus abundance and S aureus load after alpine climate treatment. The decrease in S aureus was significantly larger on lesional skin following alpine climate treatment compared with moderate maritime climate treatment. Staphylococcus epidermidis load was stable over time. Conclusions and clinical relevance Alpine climate treatment leads to significant changes in the composition of the skin microbiome in children with AD, mainly caused by a reduction in the Staphylococcus genus. This study shows new perspectives in the potential mode of action for therapies in AD.

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“…We used AIC and Akaike model weights to reduce the whole set of models employing a dredging approach that retains a confidence subset of models that lay within six AIC units of the most informative model. This method removes models that have spurious parameter estimates due to poor model fit above the chosen AIC threshold (Richards 2005, Harrison et al 2018. The importance of each explanatory variable was judged according to AIC-weighted mean effect sizes averaged across the subset of regression models, and are presented as AIC-weighted slope estimates ±95% confidence intervals to estimate the significance of the effect of each predictor on body size (Table 1).…”

Section: Quantitative Analyses and Phylogenetic Controlmentioning

confidence: 99%

Global patterns of body size evolution are driven by precipitation in legless amphibians

et al. 2019

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Body size shapes ecological interactions across and within species, ultimately influencing the evolution of large‐scale biodiversity patterns. Therefore, macroecological studies of body size provide a link between spatial variation in selection regimes and the evolution of animal assemblages through space. Multiple hypotheses have been formulated to explain the evolution of spatial gradients of animal body size, predominantly driven by thermal (Bergmann's rule), humidity (‘water conservation hypothesis’) and resource constraints (‘resource rule’, ‘seasonality rule’) on physiological homeostasis. However, while integrative tests of all four hypotheses combined are needed, the focus of such empirical efforts needs to move beyond the traditional endotherm–ectotherm dichotomy, to instead interrogate the role that variation in lifestyles within major lineages (e.g. classes) play in creating neglected scenarios of selection via analyses of largely overlooked environment–body size interactions. Here, we test all four rules above using a global database spanning 99% of modern species of an entire Order of legless, predominantly underground‐dwelling amphibians (Gymnophiona, or caecilians). We found a consistent effect of increasing precipitation (and resource abundance) on body size reductions (supporting the water conservation hypothesis), while Bergmann's, the seasonality and resource rules are rejected. We argue that subterranean lifestyles minimize the effects of aboveground selection agents, making humidity a dominant selection pressure – aridity promotes larger body sizes that reduce risk of evaporative dehydration, while smaller sizes occur in wetter environments where dehydration constraints are relaxed. We discuss the links between these principles with the physiological constraints that may have influenced the tropically‐restricted global radiation of caecilians.

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A brief introduction to mixed effects modelling and multi-model inference in ecology

Cited by 403 publications

References 5 publications

Sperm divergence in a passerine contact zone: Indication of reinforcement at the gametic level

Sperm divergence in a passerine contact zone: Indication of reinforcement at the gametic level

The influence of treatment in alpine and moderate maritime climate on the composition of the skin microbiome in patients with difficult to treat atopic dermatitis

Global patterns of body size evolution are driven by precipitation in legless amphibians

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