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FIGURE 6 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 6. External morphology of the eggs from clade 2 and their respective operculum. a1-c1, dorsal view; a2-c2 operculum. The order of the eggs and operculum from right to left is A. grylloidea, A. elegans, A. mesoauriculae (escale = 1mm).

FIGURE 7 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 7. Ultrastructure surface of the micropylar plate of the eggs from clade 1 and their respective operculum. A1-E1, micropylar plate ultrastructure; A2-E2 ultrastructure surface of the operculum. The order of the micropylar plates and operculum from top to bottom is A. luteola, A. maculafulgens, A. crassa. A. millepunctata, A. claraziana.

FIGURE 8 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 8. Ultrastructure surface of the micropylar plate of the eggs from clade 2 and their respective operculum. A1-C1, micropylar plate ultrastructure; A2-C2 ultrastructure surface of the operculum. The order of the micropylar plates and operculum from top to botom is A. grylloidea, A. elegans, A. mesoauriculae.

FIGURE 9 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 9. Character states reconstruction by maximum parsimony over the molecular phylogeny (sensu Vera et al. 2012). The character states for both the ancestral nodes A-G and actual species (H-O) are represented by color-coded boxes, where numbers indicate the character and colors the state. Besides, examples of the micropylar plate open (A. maculafulgens) and closed (A. elegans) are shown. Note: character numbers are consistent with those throughout the text.

FIGURE 5 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 5. External morphology of the eggs from clade 1 and their respective operculum. a1-e1, dorsal view; a2-e2 operculum. The order of the eggs and operculum from right to left is A. luteola, A. maculafulgens, A. crassa. A. millepunctata, A. claraziana (escale = 1mm).

FIGURE 3 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 3. Principal component analysis for the Agathemera eggs. The percentage of the variance explained by each principal component plotted is in parentheses. Every line connects a data point with its corresponding centroid. a. PCA for the eight Agathemera species; b. PCA for the species from clade 1; c. PCA for species from clade 2.

FIGURE 2 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 2. Distribution of the nine morphometric variables measured. the species are ordered following the phylogenetic relationships. Boxes represent the values between the 25 and 75 percentiles respectively, the horizontal line is the median and the point within each box is the mean and the whiskers indicate the sample range. Light grey boxplots correspond to species from clade 1 and dark grey boxplots correspond to species from clade 2. a. Capsule width; b. Capsule length; c. Capsule height; d. Micropylar plate length; e. Micropylar plate width; f. Operculum length; g. Operculum width; h. Operculum height; i. Opercular angle.

FIGURE 1 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 1. schematic drawing of an Agathemera egg showing the different variables measured. a. dorsal view. b. lateral view. c. upper view. Abbreviations: w = width; mpl = micropylar plate width; mpl = micropylar plate length; h = capsule height; l = capsule length; opl = operculum length; opa = opercular angle; opw = operculum width; operculum height.

opencc-zeroJan 2021View details →

Detection dogs in nature conservation: a database on their worldwide deployment with a review on breeds used and their performance compared to other methods

Over the last century, dogs have been increasingly used to detect rare and elusive species or traces of them. The use of wildlife detection dogs (WDD) is particularly well established in North America, Europe and Oceania, and projects deploying them have increased worldwide. However, if they are to make a significant contribution to conservation and management, their strengths, abilities, and limitations should be fully identified. We reviewed the use of WDD with particular focus on the breeds used in different countries and for various targets, as well as their overall performance compared to other methods, by developing and analysing a database of 1220 publications, including 916 scientific ones, covering 2464 individual cases - most of them (1840) scientific. With the worldwide increase in the use of WDD, associated tasks have changed and become much more diverse. Since 1930, reports exist for 62 countries and 407 animal, 42 plant, 26 fungi and 6 bacteria species. Altogether, 108 FCI-classified and 20 non-FCI-classified breeds have worked as WDD. While certain breeds have been preferred on different continents and for specific tasks and targets, they were not generally better suited for detection tasks than others. Overall, WDD usually worked more effectively than other monitoring methods. For each species group, regardless of breed, detection dogs were better than other methods in 88.71% of all cases and only worse in 0.98%. It was only for arthropods that Pinshers and Schnauzers performed worse than other breeds. For mono- and dicotyledons, detection dogs did less often outperform other methods. Although every breed can be trained as a WDD, choosing the most suitable dog for the task and target may speed up training and increase the chance of success. Albeit selection of the most appropriate WDD is important, excellent training, knowledge about the target density and suitability, and a proper study design all appeared to have the highest impact on performance. Moreover, an appropriate area, habitat and weather are crucial for detection dog work. When these factors are taken into consideration, WDD can be an outstanding monitoring method.

Data from: Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: a case study with ant cuticular bacteria

High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behavior of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties to working with low bacterial DNA quantities as in individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex penetrator (~5 mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial communities' characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in term of bacterial diversity and composition for A. cephalotes (~15 mm). In contrast, greater amounts of artifactual sequences and contaminations, as well as noticeable differences in bacterial communities' characteristics were observed between the extraction methods for P. penetrator (~5 mm). We also found that large (~15 mm) and small (~5 mm) A. cephalotes individuals harbor different bacterial communities. Our benchmark hence suggests that cuticular microbiota of single insect individuals can be reliably retrieved provided that blank controls, appropriate data cleaning, and standardization of individual body size are considered in the experiment.

Data from: Comparing safety climate for nurses working in operating theatres, critical care and ward areas in the UK: a mixed methods study

Objectives: The main aim of the study was to explore the potential sources of variation and understand the meaning of safety climate for nursing practice in acute hospital settings in the UK. Design: A sequential mixed methods design included a cross-sectional survey using the Safety Climate Questionnaire (SCQ) and thematic analysis of focus group discussions. Confirmatory Factor Analysis (CFA) was used to validate the factor structure of the SCQ. Factor scores were compared between nurses working in operating theatres, critical care and ward areas. Results from the survey and the thematic analysis were then compared and synthesised. Setting: A London University. Participants: 319 registered nurses working in acute hospital settings completed the SCQ and a further 23 nurses participated in focus groups. Results: CFA indicated that there was a good model fit on some criteria (χ2 = 1683.699, df 824, p < 0.001; χ2/ df = 2.04; RMSEA = 0.058) but a less acceptable fit on Comparative Fit Index (CFI) = 0.804. There was a statistically significant difference between clinical specialisms in Management Commitment (F [4,266] = 4.66, p = 0.001). Nurses working in operating theatres had lower scores compared with ward areas and they also reported negative perceptions about management in their focus group. There was significant variation in scores for Communication across clinical specialism (F [4,266] = 2.62, p = 0.035) but none of the pair-wise comparisons achieved statistical significance. Thematic analysis identified themes of Human Factors, Clinical Management and Protecting Patients. The System and the Human Side of Caring was identified as a meta-theme. Conclusions: The results suggest that the SCQ has some utility but requires further exploration. The findings indicate that safety in nursing practice is a complex interaction between safety systems and the social and interpersonal aspects of clinical practice.

opencc-zeroFeb 2020View details →

Comparative study on photocatalytic activity of transition metals (Ag and Ni doped ZnO) nanomaterials synthesised via sol-gel method

Ag and Ni/ZnO photocatalyst nanostructures were successfully synthesized by a sol-gel method. In this work, the photocatalyst sample was systematically studied based on several factors affecting the performance of photocatalyst which are size, morphology, band gap, textural properties and the number of active sites presence on the surface of the nanocatalyst. X-ray Diffraction (XRD) revealed that Ag/ZnO nanomaterials experienced multiple phases, meanwhile for Ni/ZnO the phase of nanomaterials were pure and single phase for stochiometry less than 5%. Field emission scanning electron microscope (FESEM) showed almost all of the synthesised nanomaterials possessed a mixture of nanorods and spherical-like shape morphology. The Ag/ZnO showed high photocatalytic activity, producing at least 14th trials of nanocatalyst reusability on the degradation of Methyl Orange under UV irradiation. Interestingly this phenomenon was not observed in larger surface area of Ni/ZnO nanomaterials which supposedly favour photocatalytic activity, but instead producing poor photocatalytic performance. The main reason were studied and exposed by temperature-programmed desorption of carbon dioxide (TPD–CO2) which showed that incorporation of Ag into ZnO lattice has enhanced the number of active sites on the surface of the nanocatalyst. Whereas incorporation of Ni in ZnO has lowered the number of active sites with respect to undoped ZnO. Active sites measurement is effective and significant, providing opportunities in developing an intensive study as an additional factor.

opencc-zeroDec 2014View details →

Data from: Body mass estimates of an exceptionally complete Stegosaurus (Ornithischia: Thyreophora): comparing volumetric and linear bivariate mass estimation methods

Body mass is a key biological variable, but difficult to assess from fossils. Various techniques exist for estimating body mass from skeletal parameters, but few studies have compared outputs from different methods. Here, we apply several mass estimation methods to an exceptionally complete skeleton of the dinosaur Stegosaurus. Applying a volumetric convex-hulling technique to a digital model of Stegosaurus, we estimate a mass of 1560 kg (95% prediction interval 1082–2256 kg) for this individual. By contrast, bivariate equations based on limb dimensions predict values between 2355 and 3751 kg and require implausible amounts of soft tissue and/or high body densities. When corrected for ontogenetic scaling, however, volumetric and linear equations are brought into close agreement. Our results raise concerns regarding the application of predictive equations to extinct taxa with no living analogues in terms of overall morphology and highlight the sensitivity of bivariate predictive equations to the ontogenetic status of the specimen. We emphasize the significance of rare, complete fossil skeletons in validating widely applied mass estimation equations based on incomplete skeletal material and stress the importance of accurately determining specimen age prior to further analyses.

opencc-zeroDec 2015View details →

Data from: Stable isotope-based location in a shelf sea setting: accuracy and precision are comparable to light-based location methods

Retrospective determination of location for marine animals would facilitate investigations of migration, connectivity and food provenance. Predictable spatial variations in carbon and nitrogen isotopes in primary production across shelf seas provide a basis for stable isotope-based location. Here, we assess the accuracy and precision that can be obtained through dietary-isotope-based location methods. We build isoscapes from jellyfish tissues and use these to assign scallops of fixed and known individual location, and herring with well-understood population-level distributions in the North Sea. Accuracy and precision for retrospective isotope-based location in the North Sea were of a similar order to light-based location devices, with 75% of individual scallops assigned correctly to areas representing c. 30% of the North Sea, with a mean linear error on the order of 102 km. Applying assignment methods to an alternative migratory species (herring) resulted in ecologically realistic assignments consistent with fisheries survey data. Location methods based on dietary isotopes such as carbon and nitrogen recover the spatial origin of nutrients assimilated into tissues, and this may not correspond directly to the physical location if either the test animal or its prey is highly migratory. Stable isotope-based location can be applied to any marine-feeding organism or derived food product, but the ecological meaning of any assigned area will be more difficult to interpret for large, high trophic level, migratory animals with relatively slow isotopic assimilation rates.

opencc-zeroDec 2017View details →

Data from: Rethinking phylogenetic comparative methods

As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have been framed as a solution to this problem. In this paper, we argue that this way of thinking about PCMs is deeply misleading. Not only has this sowed widespread confusion in the literature about what PCMs are doing but has led us to develop methods that are susceptible to the very thing we sought to build defenses against --- unreplicated evolutionary events. Through three Case Studies, we demonstrate that the susceptibility to singular events is indeed a recurring problem in comparative biology that links several seemingly unrelated controversies. In each Case Study we propose a potential solution to the problem. While the details of our proposed solutions differ, they share a common theme: unifying hypothesis testing with data-driven approaches (which we term ``phylogenetic natural history'') to disentangle the impact of singular evolutionary events from that of the factors we are investigating. More broadly, we argue that our field has, at times, been sloppy when weighing evidence in support of causal hypotheses. We suggest that one way to refine our inferences is to re-imagine phylogenies as probabilistic graphical models; adopting this way of thinking will help clarify precisely what we are testing and what evidence supports our claims.

Data from: A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species

Evaluating trait correlations across species within a lineage via phylogenetic regression is fundamental to comparative evolutionary biology, but when traits of interest are derived from two sets of lineages that co-evolve with one another, methods for evaluating such patterns in a dual-phylogenetic context remain underdeveloped. Here we extend multivariate permutation-based phylogenetic regression to evaluate trait correlations in two sets of interacting species while accounting for their respective phylogenies. This extension is appropriate for both univariate and multivariate response data, and may utilize one or more independent variables, including environmental covariates. Imperfect correspondence between species in the interacting lineages can also be accommodated, such as when species in one lineage associate with multiple species in the other, or when there are unmatched taxa in one or both lineages. For both univariate and multivariate data, the method displays appropriate type I error, and statistical power increases with the strength of the trait covariation and the number of species in the phylogeny. These properties are retained even when there is not a 1:1 correspondence between lineages. Finally, we demonstrate the approach by evaluating the evolutionary correlation between traits in fig species and traits in their agaonid wasp pollinators. R computer code is provided.

Data from: Multivariate phylogenetic comparative methods: evaluations, comparisons, and recommendations

Recent years have seen increased interest in phylogenetic comparative analyses of multivariate datasets, but to date the varied proposed approaches have not been extensively examined. Here we review the mathematical properties required of any multivariate method, and specifically evaluate existing multivariate phylogenetic comparative methods in this context. Phylogenetic comparative methods based on the full multivariate likelihood are robust to levels of covariation among trait dimensions and are insensitive to the orientation of the dataset, but display increasing model misspecification as the number of trait dimensions increases. This is because the expected evolutionary covariance matrix (V) used in the likelihood calculations becomes more ill-conditioned as trait dimensionality increases, and as evolutionary models become more complex. Thus, these approaches are only appropriate for datasets with few traits and many species. Methods that summarize patterns across trait dimensions treated separately (e.g., SURFACE) incorrectly assume independence among trait dimensions, resulting in nearly a 100% model misspecification rate. Methods using pairwise composite likelihood are highly sensitive to levels of trait covariation, the orientation of the dataset, and the number of trait dimensions. The consequences of these debilitating deficiencies is that a user can arrive at differing statistical conclusions, and therefore biological inferences, simply from a dataspace rotation, like principal component analysis. By contrast, algebraic generalizations of the standard phylogenetic comparative toolkit that use the trace of covariance matrices are insensitive to levels of trait covariation, the number of trait dimensions, and the orientation of the dataset. Further, when appropriate permutation tests are used, these approaches display acceptable Type I error and statistical power. We conclude that methods summarizing information across trait dimensions, as well as pairwise composite likelihood methods should be avoided, while algebraic generalizations of the phylogenetic comparative toolkit provide a useful means of assessing macroevolutionary patterns in multivariate data. Finally, we discuss areas in which multivariate phylogenetic comparative methods are still in need of future development; namely highly multivariate Ornstein-Uhlenbeck models and approaches for multivariate evolutionary model comparisons.

opencc-zeroJun 2015View details →

Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics - Data Supplement

This the is Data Supplement for the article "Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics" submitted to the Journal of Proteomics 2015.

opencc-by-4.0Dec 2023View details →

How to better count elusive birds? Comparing non-invasive monitoring methods to estimate population size of the endangered Pin-tailed sandgrouse (Pterocles alchata)

Data to run analyses for manuscript comparing non-invasive monitoring methods to estimate Pin-tailed sandgrouse abundance