Toby Hunt

Recalibrated Tree of Leaf Beetles (Chrysomelidae) Indicates Independent Diversification of Angiosperms and Their Insect Herbivores

Background The great diversity of the “Phytophaga” (weevils, longhorn beetles and leaf beetles) has been attributed to their co-radiation with the angiosperms based on matching age estimates for both groups, but phylogenetic information and molecular clock calibrations remain insufficient for this conclusion. Methodology A phylogenetic analysis of the leaf beetles (Chrysomelidae) was conducted based on three partial ribosomal gene markers (mitochondrial rrnL, nuclear small and large subunit rRNA) including over 3000 bp for 167 taxa representing most major chrysomelid lineages and outgroups. Molecular clock calibrations and confidence intervals were based on paleontological data from the oldest (K-T boundary) leaf beetle fossil, ancient feeding traces ascribed to hispoid Cassidinae, and the vicariant split of Nearctic and Palearctic members of the Timarchini. Principal Findings The origin of the Chrysomelidae was dated to 73–79 Mya (confidence interval 63–86 Mya), and most subfamilies were post-Cretaceous, consistent with the ages of all confirmed body fossils. Two major monocot feeding chrysomelid lineages formed widely separated clades, demonstrating independent colonization of this ancient (early Cretaceous) angiosperm lineage. Conclusions Previous calibrations proposing a much older origin of Chrysomelidae were not supported. Therefore, chrysomelid beetles likely radiated long after the origin of their host lineages and their diversification was driven by repeated radiaton on a pre-existing diverse resource, rather than ancient host associations.

Molecular phylogenetics of Elateriformia (Coleoptera): evolution of bioluminescence and neoteny

Phylogenetic relationships in the coleopteran Series Elateriformia (click beetles, jewel beetles, fireflies and allies) were investigated using > 3800 nucleotides of partial nuclear (small and large subunit rRNA genes) and mitochondrial (large subunit rRNA and cytochrome oxidase subunit I) gene sequences. The Elateriformia includes several soft‐bodied lineages, some of which retain larviform features in the adult stage (neoteny), and several major bioluminescent groups, including the families Lampyridae (fireflies), Phengodidae and Rhagophthalmidae whose relationships have been contentious. All recognized superfamilies (Elateroidea, Cantharoidea, Byrrhoidea, Buprestoidea, Dascilloidea, Scirtoidea) and 28 of the 37 families, represented in 112 individuals, were included in the analysis. Sequence alignment was based on static and dynamic homology assignments and partial removal of sequences of uncertain homology. Alignment variable regions caused a great deal of uncertainty but also contributed much of the phylogenetic signal that was insufficient to resolve deep relationships when these were removed. The main features of most analyses were the monophyly of Elateroidea + Cantharoidea (= Elateroidea sensu lato), with Omethidae + Telegeusidae frequently occupying the basal node in this group; the affinities of Dascilloidea, Buprestoidea and a (broadly paraphyletic) Byrrhoidea, with unclear relationships among them; and the monophyly of Scirtoidea (including Decliniidae) as a rather distant outgroup to all others. When mapped on the resulting trees, soft‐bodied lineages were polyphyletic, contradicting the former Cantharoidea that had been united by this trait. Transitions to neoteny were either simultaneous with, or subsequent to, the origin of soft‐bodiedness in a minimum of seven lineages. The bioluminescent groups Lampyridae (including the enigmatic genus Drilaster) and the tightly allied Phengodidae + Rhagophthalmidae were never monophyletic. The former showed close relationship to the species‐rich, soft‐bodied families Lycidae and Cantharidae, while the latter grouped with poorly resolved lineages at the base of Elateridae (click beetles). Hence, although key features as soft‐bodiedness, neoteny and bioluminescence in Coleoptera are largely confined to the Elateriformia, they appear to result from multiple origins, showing the propensity of closely related lineages to acquire similar features independently.

A protocol for large-scale rRNA sequence analysis: Towards a detailed phylogeny of Coleoptera

Large-scale phylogenetic analyses involving thousands of rRNA sequences are complicated due to length variability which compounds the already complex problem of large tree searches. Here, we generated a large data matrix and test phylogenetic procedures for large-scale analysis in the Coleoptera (beetles), as a resource for evolutionary biology and identification of this hugely diverse group. The analysis included nearly 1200 species, including representatives of 126 (75%) families, all 18 superfamilies of Polyphaga, and the four suborders. Alignments were obtained by a fragment-extension method derived from the BLAST algorithm using the BlastAlign script [Belshaw, R., Katzourakis, A., 2005. BlastAlign: a program that uses blast to align problematic nucleotide sequences. Bioinformatics 21, 122-123], followed by fast parsimony and maximum likelihood searches. Trees were assessed against the existing classification, using a formal procedure for coding the hierarchical position of taxa and establishing taxonomic congruence. We found that the BlastAlign procedure greatly exceeded the performance of standard progressive alignment methods such as Clustal. The resulting trees, when used as guide tree, also greatly improved the Clustal-based alignments. Long-branch attraction potentially affecting the quality of the tree was reduced by the systematic removal of all branches longer than a 95% interval of the distribution of branch lengths. We applied this protocol to the test for monophyly of major proposed lineages of Coleoptera, including Crowsons 18 superfamilies in the hyperdiverse suborder Polyphaga. While searches for very large trees remained challenging and details of the tree topology were not always satisfactory, the strategy for alignment and tree searches used here makes large-scale phylogenetics of super-diverse groups such as Coleoptera amenable to desktop computing.

Heliox, dyspnoea and exercise in COPD.

One of the most important determinants of physical and mental well-being of people with chronic obstructive pulmonary disease (COPD) is participation in physical activity. The ability to alter the sensation of dyspnoea during exercise may improve both exercise duration and intensity. Despite the low density, inert nature, strong safety profile and multiple applications of helium gas, the potential benefit of helium–oxygen gas mixtures as an adjunct therapy to modify disease symptoms and exercise capabilities in obstructive lung diseases has only recently been explored. This is a systematic review of the available peer-reviewed evidence exploring whether symptom modification (perceived levels of dyspnoea) and exercise performance in COPD (either intensity or duration of work) are modified by inhalation of Heliox. Eight experimental studies met inclusion for this review. A variety of methodologies and outcome variables were used negating meta-analysis and hampering direct comparison between interventions. Overall, there was high level of evidence with a low risk of bias supporting Helioxs effectiveness in improving the intensity and endurance of exercise when compared to room air for people with COPD. Little conclusive evidence was found to determine whether Heliox altered the sensation of dyspnoea during exercise.

Use of time in people with chronic obstructive pulmonary disease--a systematic review.

“Physical inactivity” and “sedentary lifestyles” are phrases often used when describing lifestyles of people with chronic obstructive pulmonary disease (COPD). Evidence suggests activity types, independent of energy expenditure, influence health outcomes, so understanding patterns of time use is important, particularly in chronic disease. We aimed to identify reports of time use in people with COPD. Predefined search strategies were used with six electronic databases to identify individual activity reports (including frequencies and/or durations) in which community-dwelling people with COPD engaged. Eligible studies were assessed independently against predefined criteria and data were extracted by two reviewers. Data synthesis was achieved by aggregating activity reports into activity domains (sports/exercise, screen time, transport, quiet time, self-care, sociocultural, work/study, chores, and sleep). Twenty-six publications reported 37 specific daily activities. People with COPD were found to spend extended periods in sedentary behaviors (eg, standing [194 min/day]; sitting [359 min/day]; lying [88 min/day]), have limited engagement in physical activity (eg, walking [51 min/day]; exercising [1.2 episodes per week {ep/w}, 13 min/day]), have high health care needs (medical appointments [1.0 ep/w]), and experience difficulties associated with activities of daily living (eg, showering [2.5 ep/w, 60 minutes per episode]; preparing meals [4.7 ep/w]). Little data could be found describing how people with COPD use their time, and data synthesis was problematic because of variations in methodologies, population differences, and research emphases. Identified data largely referred to posture and were skewed according to country, assessment methods, and disease severity. Comparisons with age-matched population data showed people with COPD spent less time engaged in personal-care activities (self-care and sleeping) and chores than people in similar age groups. The incorporation of time-use outcomes in future research designs should be encouraged. Ideally, these tools should use consistent frameworks and comparable outcome measures in order to provide clearer descriptions of time use in chronic disease.

Reliability and Validity of the Multimedia Activity Recall in Children and Adults (MARCA) in People with Chronic Obstructive Pulmonary Disease

Objective To determine the reliability and validity of the Multimedia Activity Recall for Children and Adults (MARCA) in people with chronic obstructive pulmonary disease (COPD). Design People with COPD and their carers completed the Multimedia Activity Recall for Children and Adults (MARCA) for four, 24-hour periods (including test-retest of 2 days) while wearing a triaxial accelerometer (Actigraph GT3X+®), a multi-sensor armband (Sensewear Pro3®) and a pedometer (New Lifestyles 1000®). Setting Self reported activity recalls (MARCA) and objective activity monitoring (Accelerometry) were recorded under free-living conditions. Participants 24 couples were included in the analysis (COPD; age 74.4±7.9 yrs, FEV1 54±13% Carer; age 69.6±10.9 yrs, FEV1 99±24%). Interventions Not applicable. Main Outcome Measure(s) Test-retest reliability was compared for MARCA activity domains and different energy expenditure zones. Validity was assessed between MARCA-derived physical activity level (in metabolic equivalent of task (MET) per minute), duration of moderate to vigorous physical activity (min) and related data from the objective measurement devices. Analysis included intra-class correlation coefficients (ICC), Bland-Altman analyses, paired t-tests (p) and Spearmans rank correlation coefficients (rs). Results Reliability between occasions of recall for all activity domains was uniformly high, with test-retest correlations consistently >0.9. Validity correlations were moderate to strong (rs = 0.43–0.80) across all comparisons. The MARCA yields comparable PAL estimates and slightly higher moderate to vigorous physical activity (MVPA) estimates. Conclusion In older adults with chronic illness, the MARCA is a valid and reliable tool for capturing not only the time and energy expenditure associated with physical and sedentary activities but also information on the types of activities.

Patterns of Time Use across the Chronic Obstructive Pulmonary Disease Severity Spectrum

Descriptions of time use patterns in people with chronic obstructive pulmonary disease (COPD) are scarce and the relationship between use-of-time and COPD severity remains unclear. This study aimed to describe a typical day for people with COPD and to explore the differences in time-use patterns across the Body Mass-Index, Airflow Obstruction, Dyspnoea and Exercise Capacity (BODE) index using compositional analyses. Using a cross-sectional design, 141 adults with clinically stable COPD had their demographics, objective measures of function (pulmonary, exercise capacity and physical activity), and self-reported COPD-related impairment recorded. Daily time-use compositions were derived from 24-h accelerometry and 24-h use-of-time recall interviews. Compositional multiple linear regression models were used to explore the relationship between the BODE index and 24-h time-use compositions. These models were used to predict daily time (min/d) that is spent in time-use components across the BODE index. The BODE index score was clearly associated with 24-h accelerometry (p < 0.0001) and 24-h use-of-time recall (p < 0.0001) compositions. Relative to the remaining time-use components, higher BODE index scores were associated with greater sedentary behaviour (p < 0.0001), Quiet time (p < 0.0001), Screen time (p = 0.001) and Self-care (p = 0.022), and less daily Chores (p < 0.0001) and Household administration (p = 0.015) time. As the BODE index scores increased, time-use predictions were strongly associated with decreases in Chores (up to 206 min/d), and increases in Screen (up to 156 min/d) and Quiet time (up to 131 min/d). Time–use patterns may provide a basis for planning interventions relative to the severity of COPD.

Sedentary Behavior in People with and without a Chronic Health Condition: How Much, What and When?

Purpose To describe sedentary behaviors (duration, bouts and context) in people with and without a chronic health condition. Methods Design: Secondary analysis of two cross-sectional studies. Participants: People with stable chronic obstructive pulmonary disease (COPD) (n = 24, male:female 18:6) and their spousal carers (n = 24, 6:18); stroke survivors (n = 24, 16:8) and age- and sex-matched healthy adults (n = 19, 11:8). Level of physiological impairment was measured with post-bronchodilator spirometry (FEV1 %predicted) for people with COPD, and walking speed for people with stroke. Outcomes: Participants were monitored over seven days (triaxial accelerometer, Sensewear armband) to obtain objective data on daily sedentary time, and prolonged sedentary bouts (≥ 30 min). During the monitoring period, a 24-hour use of time recall instrument was administered by telephone interview to explore the context of sedentary activities (e.g. television, computer or reading). Sedentary time was quantified using accelerometry and recall data, and group differences were explored. Linear regression examined associations between physiological impairment and sedentary time. Results Participant groups were similar in terms of age (COPD 75 ± 8, carers 70 ± 11, stroke 69 ± 10, healthy 73 ± 7 years) and body mass index (COPD 28 ± 4, carers 27 ± 4, stroke 31 ± 4, healthy 26 ± 4 kg.m−2). The healthy group had the lowest sedentary time (45% of waking hours), followed by the carer (54%), stroke (60%) and COPD (62%) groups (p < 0.0001). Level of physiological impairment was an independent predictor of waking sedentary time (p = 0.001). Conclusions People with a chronic health condition spent more time sedentary than those without a chronic condition, and there were small but clear differences between groups in the types of activities undertaken during sedentary periods. The study findings may aid in the design of targeted interventions to decrease sedentary time in people with chronic health conditions.