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Many birds vocalize in flight. Since wingbeat and respiratory cycles are often linked in flying vertebrates, birds in these cases must satisfy the respiratory demands of vocal production within the physiological limits imposed by flight. Using acoustic triangulation and high-speed video, we found that avian vocal production in flight exhibits a largely phasic and kinematic relationship with the power stroke. However, the sample of species showed considerable flexibility, especially those from lineages known for vocal plasticity (songbirds, parrots and hummingbirds), prompting a broader phylogenetic analysis. We thus collected data from 150 species across 12 avian orders and examined the links between wingbeat period, flight call duration and body mass. Overall, shorter wingbeat periods, controlling for ancestry and body mass, were correlated with shorter flight call durations. However, species from vocal learner lineages produced flight signals that, on average, exceeded multiple phases of their wingbeat cycle, while vocal non-learners had signal periods that were, on average, closer to the duration of their power stroke. These results raise an additional question: is partial emancipation from respiratory constraints a necessary step in the evolution of vocal learning or an epiphenomenon? Our current study cannot provide the answer, but it does suggest several avenues for future research.
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Aims: Phylogenies are increasingly used in community ecology, biogeography and macroecology. However, sourcing a phylogeny comprising the entire species pool for a focal region can be difficult. Typically, a bespoke phylogeny must be created requiring considerable data manipulation and the use of many standalone software. Here we present a suite of methodological tools within the popular R environment that help to build molecular phylogenies appropriate for ecological studies with a regional focus. Innovation: Our R package regPhylo provides a pipeline to construct a Bayesian posterior distribution of time-calibrated trees suitable to address ecological questions. The novel contributions of regPhylo include options to: use prior phylogenetic knowledge through flexible topological constraints; include spatial metadata in sourcing DNA sequences; and include taxa without DNA sequences and then infer consequent phylogenetic uncertainty. Specifically, regPhylo helps researchers: retrieve DNA sequences; enhance available metadata; select DNA sequences based on their length or spatial proximity to the region of study; align sequences; and perform quality control. Output from the pipeline is a file ready to run in the Bayesian tree reconstruction software BEAST2, appropriate for estimating time-calibrated trees and including phylogenetic uncertainty for downstream analyses. Main conclusions: Overall, regPhylo improves the integration of popular standalone phylogenetic software into the flexible R environment. It provides a novel approach to include topological constraints based on prior knowledge, include taxa without DNA sequences, and select spatially appropriate DNA sequences. When coupled with a Bayesian tree-building process, our approach provides estimates of uncertainty in both topology and branch-lengths. We demonstrate the utility of the package by constructing a posterior distribution of time-calibrated phylogenies for the New Zealand marine ray-finned fishes (Actinopterygii) providing the unprecedented opportunity to include phylogenetic information in downstream ecological analyses for marine fishes in this region.
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How can we explain morphological variations in a holobiont? The genetic determinism of phenotypes is not always obvious and could be circumstantial in complex organisms. In symbiotic cnidarians, it is known that morphology or colour can misrepresent a complex genetic and symbiotic diversity. Anemonia viridis is a symbiotic sea anemone from temperate seas. This species displays different colour morphs based on pigment content and lives in a wide geographical range. Here, we investigated whether colour morph differentiation correlated with host genetic diversity or associated symbiotic genetic diversity by using RAD-sequencing and symbiotic dinoflagellate typing of 140 sea anemones from the English Channel and the Mediterranean Sea. We did not observe genetic differentiation among colour morphs of A. viridis at the animal host or symbiont level, rejecting the hypothesis that A. viridis colour morphs correspond to species level differences. Interestingly, we however identified at least four independent animal host genetic lineages in A. viridis that differed in their associated symbiont populations. In conclusion, although the functional role of the different morphotypes of A. viridis remains to be determined, our approach provides new insights on the existence of cryptic species within A. viridis.
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1. Co-infections with multiple parasite taxa are ubiquitous in nature and have the potential to impact the co-evolutionary dynamics between host and parasite, though patterns of phylogenetic community structure of co-infecting parasites and the processes that generate these patterns have rarely been studied across diverse host-parasite communities. 2. Here, we tested for the roles of host and parasite evolutionary history as well as environmental variables as drivers of phylogenetic community structure among co-infecting haemosporidian (malaria) parasites and their avian hosts in the North American boreal forest, a region characterized by an extraordinarily high blood parasite co-infection rate. 3. We used multiple methods to identify non-random patterns of co-infection among parasite species and determined whether these patterns were influenced more by co-evolutionary host associations or environmental variables. We used model-based approaches to test whether parasites that occurred together in a single host individual exhibited phylogenetic clustering or overdispersion. Lastly, we tested whether the observed phylogenetic community structure could be explained by parasites having convergently evolved similar patterns of host associations. 4. We found that haemosporidian parasite co-infections occurred at a high frequency in the boreal forest system, and that parasite taxa co-occurred in significantly non-random patterns within host individuals and among host species. Parasite taxa that occurred in co-infections tended to be phylogenetically overdispersed. We show that this pattern of phylogenetic overdispersion can be attributed largely to the effect of evolutionarily labile, convergent host associations that have resulted in the pool of parasites that have the potential to infect a given host consisting nearly exclusively of distantly related lineages. 5. Our findings illustrate that environmental filtering of convergent traits can produce phylogenetically overdispersed communities, even at the level of co-infecting parasites within an individual host organism. Broadly, this analysis illustrates how co-evolutionary history can have a strong influence on the modern phylogenetic community assembly of diverse host-symbiont communities.
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Complex ethological behaviors could be constructed from finite modules that are reproducible functional units of behavior. Here, we test this idea for foraging and develop methods to dissect rich behavior patterns in mice. We uncover discrete modules of foraging behavior reproducible across different strains and ages, as well as nonmodular behavioral sequences. Modules differ in terms of form, expression frequency, and expression timing and are expressed in a probabilistically determined order. Modules shape economic patterns of feeding, exposure, activity, and perseveration responses. The modular architecture of foraging changes developmentally, and different developmental, genetic, and parental effects are found to shape the expression of specific modules. Dissecting modules from complex patterns is powerful for phenotype analysis. We discover that both parental alleles of the imprinted Prader-Willi syndrome gene Magel2 are functional in mice but regulate different modules. Our study found that complex economic patterns are built from finite, genetically controlled modules.
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Microbes can play an important role in the physiology of animals by providing essential nutrients, inducing immune pathways, and influencing the specific species that compose the microbiome through competitive or facilitatory interactions. The community of microbes associated with animals can be dynamic depending on the local environment, and factors that influence the composition of the microbiome are essential to our understanding of how microbes may influence the biology of their animal hosts. Regularly repeated changes in the environment, such as diel lighting, can result in two different organismal responses: a direct response to the presence and absence of exogenous light and endogenous rhythms resulting from a molecular circadian clock, both of which can influence the associated microbiota. Here, we report how diel lighting and a potential circadian clock impacts the diversity and relative abundance of bacteria in the model cnidarian Nematostella vectensis using an amplicon-based sequencing approach. Comparisons of bacterial communities associated with anemones cultured in constant darkness and in light:dark conditions revealed that individuals entrained in the dark had a more diverse microbiota. Overall community composition showed little variation over a 24-hour period in either treatment; however, abundances of individual bacterial OTUs showed significant cycling in each treatment. A comparative analysis of genes involved in the innate immune system of cnidarians showed differential expression between lighting conditions in N. vectensis, with significant up-regulation during long-term darkness for a subset of genes. Together, our studies support a hypothesis that the bacterial community associated with this species is relatively stable under diel light conditions when compared with static conditions and that particular bacterial members may have time-dependent abundance that coincides with the diel photoperiod in an otherwise stable community.
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C. difficile is an endospore-forming pathogen, which is becoming a common cause of microbial health-care associated gastrointestinal disease in the United States. Both healthy and symptomatic patients can shed C. difficile spores into the environment, which can survive for long periods, being resistant to desiccation, heat, and disinfectants. In healthcare facilities, environmental contamination with C. difficile is a major concern as a potential source of exposure to this pathogen and risk of disease in susceptible patients. Although hospital-acquired infection is recognized, community-acquired infection is an increasingly recognized health problem. Primary care clinics may be a significant source of exposure to this pathogen; however, there are limited data about presence of environmental C. difficile within clinics. To address the potential for primary care clinics as a source of environmental exposure to virulent C. difficile, we measured the frequency of environmental contamination with spores in clinic examination rooms and hospital rooms in Dallas-Fort Worth (DFW) area of Texas. The ribotypes and presence of toxin genes from some environmental isolates were compared. Our results indicate primary care clinics have higher frequencies of contamination than hospitals. After notification of the presence of C. difficile spores in the clinics and an educational discussion to emphasize the importance of this infection and methods of infection prevention, environmental contamination in clinics was reduced on subsequent sampling to that found in hospitals. Thus, primary care clinics can be a source of exposure to virulent C. difficile, and recognition of this possibility can result in improved infection prevention, potentially reducing community-acquired C. difficile infections and subsequent disease.
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Landing maneuvers of flies are complex behaviors which can be conceptually decomposed into sequences of modular actions, including body-deceleration, leg-extension, and body rotations. These behavioral ‘modules’ must be coordinated to ensure well-controlled landing. The composite nature of these behaviors induces kinematic variability, making it difficult to identify the central rules that govern landing. Many previous studies have relied on tethered preparations to study landing behaviors, but tethering induces experimental artefacts by forcing some behaviors to operate in open-feedback control loop while others remain closed-loop. On the other hand, freely-flying insects are harder to precisely control, and hence inherently prone to behavioral variability. One approach towards understanding general mechanisms of landing is to determine the common elements of their kinematics on surfaces of different orientations. We conducted a series of experiments in which the houseflies, Musca domestica, were lured to land on vertical (vertical landings) or inverted (inverted landings) substrates, while their flight was recorded with multiple high-speed cameras. We observed that, in both cases, well-controlled landings occurred when the distance at which flies initiated deceleration was proportional to flight velocity component in the direction of substrate. The ratio of substrate distance and velocity at onset of deceleration (tau) was conserved, despite substantial differences in mechanics of vertical vs. inverted landings. When these conditions were not satisfied, their landing performance was compromised, causing their heads to collide into the substrate. Unlike body-deceleration, leg-extension in flies was independent of substrate distance or approach velocity. Thus, the robust reflexive visual initiation of deceleration is independent of substrate orientation, and combines with a more variable initiation of leg-extension which depends on surface orientation. Together, these combinations of behaviors enable flies to land in a versatile manner on substrates of various orientations.
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Background: The low bacterial load in samples acquired from the lungs, have made studies on the airway microbiome vulnerable to contamination from bacterial DNA introduced during sampling and laboratory processing. We have examined the impact of laboratory contamination on samples collected from the lower airways by protected (through a sterile catheter) bronchoscopy and explored various in silico approaches to dealing with the contamination post-sequencing. Our analyses included quantitative PCR and targeted amplicon sequencing of the bacterial 16S rRNA gene. Results: The mean bacterial load varied by sample type for the 23 study subjects (oral wash>1st fraction of protected bronchoalveolar lavage>protected specimen brush>2nd fraction of protected bronchoalveolar lavage; p < 0.001). By comparison to a dilution series of know bacterial composition and load, an estimated 10-50% of the bacterial community profiles for lower airway samples could be traced back to contaminating bacterial DNA introduced from the laboratory. We determined the main source of laboratory contaminants to be the DNA extraction kit (FastDNA Spin Kit). The removal of contaminants identified using tools within the Decontam R package appeared to provide a balance between keeping and removing taxa found in both negative controls and study samples. Conclusions: The influence of laboratory contamination will vary across airway microbiome studies. By reporting estimates of contaminant levels and taking use of contaminant identification tools (e.g. the Decontam R package) based on statistical models that limit the subjectivity of the researcher, the accuracy of inter-study comparisons can be improved.
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Arbuscular mycorrhizal fungi (AMF) are important plant symbionts, but we know little about the effects of plant taxonomic identity or functional group on the AMF community composition. To examine effects of the surrounding plant community, of host, and of the AMF pool on the AMF community in plant roots, we manipulated plant community composition in a long-term field experiment. Within four types of manipulated grassland plots, seedlings of eight grassland plant species were planted for 12 weeks, and AMF in their roots were quantified. Additionally, we characterised the AMF community of individual plots (as their AMF pool) and quantified plot abiotic conditions. The largest determinant of AMF community composition was the pool of available AMF, varying at metre scale due to changing soil conditions. The second strongest predictor was the host functional group. The differences between grasses and dicotyledonous forbs in AMF community variation and diversity were much larger than the differences among species within those groups. High cover of forbs in the surrounding plant community had a strong positive effect on AMF colonisation intensity in grass hosts. Using a manipulative field experiment enabled us to demonstrate direct causal effects of plant host and surrounding vegetation.
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