Revisiting advice on the analysis of count data

Funding: MBM is supported by a University Research Fellowship from the Royal Society (London).1. O’Hara and Kotze (2010; Methods in Ecology and Evolution 1: 118‐122) present simulation results that appear to show very poor behaviour (as judged by bias and overall accuracy) of linear models (LMs) applied to count data, especially in relation to generalised linear model (GLM) analysis. 2. We considered O’Hara and Kotze’s (2010) comparisons, and determined that the finding occurred primarily because the quantity that they estimated in their simulations of the LM analysis (the mean of a transformation of the count data) was not the same quantity that was simulated and to which the results were compared (the logarithm of the mean of the count data). We correct this discrepancy, re‐run O’Hara and Kotze’s simulations, and add additional simple analyses. 3. We found that the apparent superiority of the GLMs over LMs in O’Hara and Kotze’s (2010) simulations was primarily an artefact of divergence in the meanings of results from the two analyses. After converting results from LM analyses of transformed data to estimators of the same quantity as provided by the GLM, results from both analyses rarely differed substantially. Furthermore, under the circumstances considered by O’Hara and Kotze, we find that an even simpler implementation of LM analysis, inference of the mean of the raw data, performs even better, and gives identical results to the GLM. 4. While the analysis of count data with generalised linear models can certainly provide many benefits, we strongly caution against interpreting O’Hara and Kotze’s (2010) results as evidence that simpler approaches are severely flawed.PostprintPeer reviewe

Lived experience and attitudes of people with plantar heel pain:a qualitative exploration

BACKGROUND: Plantar heel pain is a common source of pain and disability. Evidence-based treatment decisions for people with plantar heel pain should be guided by the best available evidence, expert clinical reasoning, and consider the needs of the patient. Education is a key component of care for any patient and needs to be tailored to the patient and their condition. However, no previous work has identified, far less evaluated, the approaches and content required for optimal education for people with plantar heel pain. The aim of this study was to gather the patients' perspective regarding their lived experience, attitudes and educational needs in order to inform the content and provision of meaningful education delivery approaches. METHODS: Using a qualitative descriptive design, semi-structured interviews were conducted with participants with a clinical diagnosis of plantar heel pain. A topic guide was utilised that focused on the experience of living with plantar heel pain and attitudes regarding treatment and educational needs. Interviews were audio recorded, transcribed verbatim and analysed using the Framework approach. Each transcription, and the initial findings, were reported back to participants to invite respondent validation. RESULTS: Eighteen people with plantar heel pain were interviewed. Descriptive analysis revealed eight themes including perceptions of plantar heel pain, impact on self, dealing with plantar heel pain, source of information, patient needs, patient unmet needs, advice to others and interest in online education. Participants revealed doubt about the cause, treatment and prognosis of plantar heel pain. They also expressed a desire to have their pain eliminated and education individually tailored to their condition and needs. Respondent validation revealed that the transcripts were accurate, and participants were able to recognise their own experiences in the synthesised themes. CONCLUSION: Plantar heel pain has a negative impact on health-related quality of life. Participants wanted their pain eliminated and reported that their expectations and needs were frequently unmet. Health professionals have an important role to be responsive to the needs of the patient to improve their knowledge and influence pain and behaviour. Our study informs the content needed to help educate people with plantar heel pain

Multivariate analysis of morphology, behaviour, growth and developmental timing in hybrids brings new insights into the divergence of sympatric Arctic charr morphs

This work was fully funded by the Icelandic Centre of Research, RANNÍS (Icelandic Research Fund grant no.173802-051).Background: Studying the development of fitness related traits in hybrids from populations diverging in sympatry is a fundamental approach to understand the processes of speciation. However, such traits are often affected by covariance structures that complicate the comprehension of these processes, especially because the interactive relationships between traits of different nature (e.g. morphology, behaviour, life-history) remain largely unknown in this context. In a common garden setup, we conducted an extensive examination of a large suit of traits putatively involved in the divergence of two morphs of Arctic charr (Salvelinus alpinus), and investigated the consequences of potential patterns of trait covariance on the phenotype of their hybrids. These traits were measured along ontogeny and involved growth, yolk sac resorption, developmental timing (hatching and the onset of exogeneous feeding), head morphology and feeding behaviour. Results: Growth trajectories provided the strongest signal of phenotypic divergence between the two charr. Strikingly, the first-generation hybrids did not show intermediate nor delayed growth but were similar to the smallest morph, suggesting parental biases in the inheritance of growth patterns. However, we did not observe extensive multivariate trait differences  between the two morphs and their hybrids. Growth was linked to head morphology (suggesting that morphological variations in early juveniles relate to simple allometric effects) but this was the only strong signal of covariance observed between all the measured traits. Furthermore, we did not report evidence for differences in overall phenotypic variance between morphs, nor for enhanced phenotypic variability in their hybrids. Conclusion: Our study shed light on the multivariate aspect of development in a context of adaptive divergence. The lack of evidence for the integration of most traits into a single covariance structure suggested that phenotypic constraints may not always favour nor impede divergence toward ecological niches differing in numerous physical and ecological variables, as observed in the respective habitats of the two charr. Likewise, the role of hybridization as a disruptive agent of trait covariance may not necessarily be significant in the evolution of populations undergoing resource polymorphism.Publisher PDFPeer reviewe

Re-identification of individuals from images using spot constellations : a case study in Arctic charr (Salvelinus alpinus)

The long-term monitoring of Arctic charr in lava caves is funded by the Icelandic Research Fund, RANNÍS (research grant nos. 120227 and 162893). E.A.M. was supported by the Icelandic Research Fund, RANNÍS (grant no. 162893) and NERC research grant awarded to M.B.M. (grant no. NE/R011109/1). M.B.M. was supported by a University Research Fellowship from the Royal Society (London). C.A.L. and B.K.K. were supported by Hólar University, Iceland. The Titan Xp GPU used for this research was donated to K.T. by the NVIDIA Corporation.The ability to re-identify individuals is fundamental to the individual-based studies that are required to estimate many important ecological and evolutionary parameters in wild populations. Traditional methods of marking individuals and tracking them through time can be invasive and imperfect, which can affect these estimates and create uncertainties for population management. Here we present a photographic re-identification method that uses spot constellations in images to match specimens through time. Photographs of Arctic charr (Salvelinus alpinus) were used as a case study. Classical computer vision techniques were compared with new deep-learning techniques for masks and spot extraction. We found that a U-Net approach trained on a small set of human-annotated photographs performed substantially better than a baseline feature engineering approach. For matching the spot constellations, two algorithms were adapted, and, depending on whether a fully or semi-automated set-up is preferred, we show how either one or a combination of these algorithms can be implemented. Within our case study, our pipeline both successfully identified unmarked individuals from photographs alone and re-identified individuals that had lost tags, resulting in an approximately 4 our multi-step pipeline involves little human supervision and could be applied to many organisms.Publisher PDFPeer reviewe

A multivariate analysis of genetic constraints to life history evolution in a wild population of red deer.

Evolutionary theory predicts that genetic constraints should be widespread, but empirical support for their existence is surprisingly rare. Commonly applied univariate and bivariate approaches to detecting genetic constraints can underestimate their prevalence, with important aspects potentially tractable only within a multivariate framework. However, multivariate genetic analyses of data from natural populations are challenging because of modest sample sizes, incomplete pedigrees, and missing data. Here we present results from a study of a comprehensive set of life history traits (juvenile survival, age at first breeding, annual fecundity, and longevity) for both males and females in a wild, pedigreed, population of red deer (Cervus elaphus). We use factor analytic modeling of the genetic variance-covariance matrix ( G: ) to reduce the dimensionality of the problem and take a multivariate approach to estimating genetic constraints. We consider a range of metrics designed to assess the effect of G: on the deflection of a predicted response to selection away from the direction of fastest adaptation and on the evolvability of the traits. We found limited support for genetic constraint through genetic covariances between traits, both within sex and between sexes. We discuss these results with respect to other recent findings and to the problems of estimating these parameters for natural populations

The role of selection and evolution in changing parturition date in a red deer population.

Changing environmental conditions cause changes in the distributions of phenotypic traits in natural populations. However, determining the mechanisms responsible for these changes-and, in particular, the relative contributions of phenotypic plasticity versus evolutionary responses-is difficult. To our knowledge, no study has yet reported evidence that evolutionary change underlies the most widely reported phenotypic response to climate change: the advancement of breeding times. In a wild population of red deer, average parturition date has advanced by nearly 2 weeks in 4 decades. Here, we quantify the contribution of plastic, demographic, and genetic components to this change. In particular, we quantify the role of direct phenotypic plasticity in response to increasing temperatures and the role of changes in the population structure. Importantly, we show that adaptive evolution likely played a role in the shift towards earlier parturition dates. The observed rate of evolution was consistent with a response to selection and was less likely to be due to genetic drift. Our study provides a rare example of observed rates of genetic change being consistent with theoretical predictions, although the consistency would not have been detected with a solely phenotypic analysis. It also provides, to our knowledge, the first evidence of both evolution and phenotypic plasticity contributing to advances in phenology in a changing climate

Herbivore-mediated negative frequency-dependent selection underlies a trichome dimorphism in nature

Authors are grateful for funding provided by an NSF GRFP to J.K.G. (2015195769) and DEB‐1353970 to L.F.D.Negative frequency‐dependent selection (NFDS) has been shown to maintain polymorphism in a diverse array of traits. The action of NFDS has been confirmed through modeling, experimental approaches, and genetic analyses. In this study, we investigated NFDS in the wild using morph‐frequency changes spanning a 20‐year period from over 30 dimorphic populations of Datura wrightii. In these populations, plants either possess glandular (sticky) or non‐glandular (velvety) trichomes, and the ratio of these morphs varies substantially among populations. Our method provided evidence that NFDS, rather than drift or migration, is the primary force maintaining this dimorphism. Most populations that were initially dimorphic remained dimorphic, and the overall mean and variance in morph frequency did not change over time. Furthermore, morph‐frequency differences were not related to geographic distances. Together, these results indicate that neither directional selection, drift, or migration played a substantial role in determining morph frequencies. However, as predicted by negative frequency‐dependent selection, we found that the rare morph tended to increase in frequency, leading to a negative relationship between the change in the frequency of the sticky morph and its initial frequency. In addition, we found that morph‐frequency change over time was significantly correlated with the damage inflicted by two herbivores: Lema daturaphila and Tupiochoris notatus. The latter is a specialist on the sticky morph and damage by this herbivore was greatest when the sticky morph was common. The reverse was true for L. daturaphila, such that damage increased with the frequency of the velvety morph. These findings suggest that these herbivores contribute to balancing selection on the observed trichome dimorphism.Publisher PDFPeer reviewe

The Star Formation and Extinction Co-Evolution of UV-Selected Galaxies over 0.05<z<1.2

We use a new stacking technique to obtain mean mid IR and far IR to far UV flux ratios over the rest near-UV/near-IR color-magnitude diagram. We employ COMBO-17 redshifts and COMBO-17 optical, GALEX far and near UV, Spitzer IRAC and MIPS Mid IR photometry. This technique permits us to probe infrared excess (IRX), the ratio of far IR to far UV luminosity, and specific star formation rate (SSFR) and their co-evolution over two orders of magnitude of stellar mass and redshift 0.1<z<1.2. We find that the SSFR and the characteristic mass (M_0) above which the SSFR drops increase with redshift (downsizing). At any given epoch, IRX is an increasing function of mass up to M_0. Above this mass IRX falls, suggesting gas exhaustion. In a given mass bin below M_0 IRX increases with time in a fashion consistent with enrichment. We interpret these trends using a simple model with a Schmidt-Kennicutt law and extinction that tracks gas density and enrichment. We find that the average IRX and SSFR follows a galaxy age parameter which is determined mainly by the galaxy mass and time since formation. We conclude that blue sequence galaxies have properties which show simple, systematic trends with mass and time such as the steady build-up of heavy elements in the interstellar media of evolving galaxies and the exhaustion of gas in galaxies that are evolving off the blue sequence. The IRX represents a tool for selecting galaxies at various stages of evolution.Comment: Accepted for publication in GALEX Special Ap.J.Suppl., December, 200