Host species and geography impact bee-associated RNA virus communities with evidence for isolation by distance in viral populations.

Virus symbionts are important mediators of ecosystem function, yet we know little of their diversity and ecology in natural populations. The alarming decline of pollinating insects in many regions of the globe, especially the European honey bee, Apis mellifera, has been driven in part by worldwide transmission of virus pathogens. Previous work has examined the transmission of known honey bee virus pathogens to wild bee populations, but only a handful of studies have investigated the native viromes associated with wild bees, limiting epidemiological predictors associated with viral pathogenesis. Further, variation among different bee species might have important consequences in the acquisition and maintenance of bee-associated virome diversity. We utilized comparative metatranscriptomics to develop a baseline description of the RNA viromes associated with wild bee pollinators and to document viral diversity, community composition, and structure. Our sampling includes five wild-caught, native bee species that vary in social behavior as well as managed honey bees. We describe 26 putatively new RNA virus species based on RNA-dependent RNA polymerase phylogeny and show that each sampled bee species was associated with a specific virus community composition, even among sympatric populations of distinct host species. From 17 samples of a single host species, we recovered a single virus species despite over 600 km of distance between host populations and found strong evidence for isolation by distance in associated viral populations. Our work adds to the small number of studies examining viral prevalence and community composition in wild bees.

Measuring success: A comparison of ultrasound and landmark guidance for knee arthrocentesis in a cadaver model.

OBJECTIVE: Knee arthrocentesis can be performed by landmark (LM) or ultrasound (US) guidance. The goal of performing knee arthrocentesis is to obtain synovial fluid, however, it is also important to consider the number of attempts required and accidental bone contacts that occur. This study evaluates procedural success without bone contact in knee arthrocentesis and compares both LM and US guided techniques in a cadaver model. METHODS: This was a randomized crossover study comparing US vs LM guidance for arthrocentesis in a single academic center. Volunteers were randomized to perform both LM and US guided knee arthrocentesis on cadavers. The primary outcome was procedural success, defined as first attempt aspiration of synovial fluid without bone contact. Secondary outcomes included number of attempts, number of bone contacts, time to aspiration, and confidence. RESULTS: Sixty-one participants completed the study with a total of 122 procedures performed. Procedural success without bone contact was greater in the US group (84% vs 64% p = 0.02). Time to aspiration was longer for US (38.75 s vs 25.54 s p = 0.004). Participants were more confident with US compared to LM both before the procedure on a Visual Analog Scale from 1 to 100 (29 vs 21 p = 0.03) as well as after the procedure (83 vs 69 p = 0.0001). Participants had a greater median increase in confidence with US following training (44 vs 26 p = 0.01). CONCLUSIONS: Study participants had greater procedural success without bone contact when US guidance was used. The increase in confidence following training was greater for US guidance than the LM method. Use of US guidance may offer a benefit by allowing for better needle control and avoidance of sensitive structures for clinicians performing knee arthrocentesis.

Does the model reflect the system? When two-dimensional biomechanics is not 'good enough'.

Models are mathematical representations of systems, processes or phenomena. In biomechanics, finite-element modelling (FEM) can be a powerful tool, allowing biologists to test form-function relationships in silico, replacing or extending results of in vivo experimentation. Although modelling simplifications and assumptions are necessary, as a minimum modelling requirement the results of the simplified model must reflect the biomechanics of the modelled system. In cases where the three-dimensional mechanics of a structure are important determinants of its performance, simplified two-dimensional modelling approaches are likely to produce inaccurate results. The vertebrate mandible is one among many three-dimensional anatomical structures routinely modelled using two-dimensional FE analysis. We thus compare the stress regimes of our published three-dimensional model of the chimpanzee mandible with a published two-dimensional model of the chimpanzee mandible and identify several fundamental differences. We then present a series of two-dimensional and three-dimensional FE modelling experiments that demonstrate how three key modelling parameters, (i) dimensionality, (ii) symmetric geometry, and (iii) constraints, affect deformation and strain regimes of the models. Our results confirm that, in the case of the primate mandible (at least), two-dimensional FEM fails to meet this minimum modelling requirement and should not be used to draw functional, ecological or evolutionary conclusions.

Comparative biomechanics of the Pan and Macaca mandibles during mastication: finite element modelling of loading, deformation and strain regimes.

The mechanical behaviour of the mandibles of Pan and Macaca during mastication was compared using finite element modelling. Muscle forces were calculated using species-specific measures of physiological cross-sectional area and scaled using electromyographic estimates of muscle recruitment in Macaca. Loading regimes were compared using moments acting on the mandible and strain regimes were qualitatively compared using maps of principal, shear and axial strains. The enlarged and more vertically oriented temporalis and superficial masseter muscles of Pan result in larger sagittal and transverse bending moments on both working and balancing sides, and larger anteroposterior twisting moments on the working side. The mandible of Pan experiences higher principal strain magnitudes in the ramus and mandibular prominence, higher transverse shear strains in the top of the symphyseal region and working-side corpus, and a predominance of sagittal bending-related strains in the balancing-side mandible. This study lays the foundation for a broader comparative study of Hominidae mandibular mechanics in extant and fossil hominids using finite element modelling. Pan's larger and more vertical masseter and temporalis may make it a more suitable model for hominid mandibular biomechanics than Macaca.

Variation in accessory mental foramen frequency and number in extant hominoids.

Nerves providing sensation to the lower face and jaw exit the mandibular canal via the mental foramen. In humans, there are many documented occurrences of additional foramina (accessory mental foramina, AMFs) on the lateral mandibular surface that may also contain nervous structures. There are large discrepancies in the literature regarding how often AMFs occur in humans, and investigations of non-human hominoid AMFs are rare. Consequently, the causes of interspecific diversity in this variable have not been explored. This project seeks to compare the frequency and number of AMFs between males and females, and among human regional groups and hominoid subspecies and species, and to investigate possible causal factors for any differences identified. No significant differences were found between males and females in any group. Gorillas and orangutans had the highest percentages of individuals with AMFs and the highest mean number of foramina, while modern humans and siamangs had the lowest figures for these variables. Significant differences (p < .05) were found for the mean number of foramina between most pairs of species. The results also showed that species with mandibles that are larger overall, have a larger area anterior to mental foramen, and a longer mandibular canal typically present more AMFs. The strongest correlation was found between the mean number of mental foramina and mandibular canal length. We suggest that these results provide preliminary support for the hypothesis that increasing mandibular canal length increases the likelihood that that nerves will ramify, leading to greater frequencies of accessory mental foramina.

Oblique human symphyseal angle is associated with an evolutionary rate-shift early in the hominin clade.

The rate of change in primate mandibular symphyseal angles was modeled with particular aim of locating a rate-shift within the hominin clade. Prior work noted that the human symphyseal angle must have experienced a rapid rate of change in order to assume the modern human form, suggestive of the non-random work of natural selection. This study indicates that the rate of symphyseal evolution rose dramatically between Australopithecus anamensis and Australopithecus afarensis and continued throughout the diversification of the hominin clade. Noting the timing of this event, we speculate as to what ecological factors could have been at play in driving this rearrangement of the anterior mandible, contributing to the eventual appearance of the human chin.

Mandibular ramus shape variation and ontogeny in Homo sapiens and Homo neanderthalensis.

As the interface between the mandible and cranium, the mandibular ramus is functionally significant and its morphology has been suggested to be informative for taxonomic and phylogenetic analyses. In primates, and particularly in great apes and humans, ramus morphology is highly variable, especially in the shape of the coronoid process and the relationship of the ramus to the alveolar margin. Here we compare ramus shape variation through ontogeny in Homo neanderthalensis to that of modern and fossil Homo sapiens using geometric morphometric analyses of two-dimensional semilandmarks and univariate measurements of ramus angulation and relative coronoid and condyle height. Results suggest that ramus, especially coronoid, morphology varies within and among subadult and adult modern human populations, with the Alaskan Inuit being particularly distinct. We also identify significant differences in overall anterosuperior ramus and coronoid shapes between H. sapiens and H. neanderthalensis, both in adults and throughout ontogeny. These shape differences are subtle, however, and we therefore suggest caution when using ramus morphology to diagnose group membership for individual specimens of these taxa. Furthermore, we argue that these morphologies are unlikely to be representative of differences in masticatory biomechanics and/or paramasticatory behaviors between Neanderthals and modern humans, as has been suggested by previous authors. Assessments of ontogenetic patterns of shape change reveal that the typical Neanderthal ramus morphology is established early in ontogeny, and there is little evidence for divergent postnatal ontogenetic allometric trajectories between Neanderthals and modern humans as a whole. This analysis informs our understanding of intraspecific patterns of mandibular shape variation and ontogeny in H. sapiens and can shed further light on overall developmental and life history differences between H. sapiens and H. neanderthalensis.

Error in geometric morphometric data collection: Combining data from multiple sources.

OBJECTIVES: This study compares two- and three-dimensional morphometric data to determine the extent to which intra- and interobserver and intermethod error influence the outcomes of statistical analyses. MATERIALS AND METHODS: Data were collected five times for each method and observer on 14 anthropoid crania using calipers, a MicroScribe, and 3D models created from NextEngine and microCT scans. ANOVA models were used to examine variance in the linear data at the level of genus, species, specimen, observer, method, and trial. Three-dimensional data were analyzed using geometric morphometric methods; principal components analysis was employed to examine how trials of all specimens were distributed in morphospace and Procrustes distances among trials were calculated and used to generate UPGMA trees to explore whether all trials of the same individual grouped together regardless of observer or method. RESULTS: Most variance in the linear data was at the genus level, with greater variance at the observer than method levels. In the 3D data, interobserver and intermethod error were similar to intraspecific distances among Callicebus cupreus individuals, with interobserver error being higher than intermethod error. Generally, taxa separate well in morphospace, with different trials of the same specimen typically grouping together. However, trials of individuals in the same species overlapped substantially with one another. CONCLUSION: Researchers should be cautious when compiling data from multiple methods and/or observers, especially if analyses are focused on intraspecific variation or closely related species, as in these cases, patterns among individuals may be obscured by interobserver and intermethod error. Conducting interobserver and intermethod reliability assessments prior to the collection of data is recommended.

Mandibular ramus shape of Australopithecus sediba suggests a single variable species.

The fossils from Malapa cave, South Africa, attributed to Australopithecus sediba, include two partial skeletons-MH1, a subadult, and MH2, an adult. Previous research noted differences in the mandibular rami of these individuals. This study tests three hypotheses that could explain these differences. The first two state that the differences are due to ontogenetic variation and sexual dimorphism, respectively. The third hypothesis, which is relevant to arguments suggesting that MH1 belongs in the genus Australopithecus and MH2 in Homo, is that the differences are due to the two individuals representing more than one taxon. To test these hypotheses, we digitized two-dimensional sliding semilandmarks in samples of Gorilla, Pan, Pongo, and Homo, as well as MH1 and MH2. We document large amounts of shape variation within all extant species, which is related neither to ontogeny nor sexual dimorphism. Extant species nevertheless form clusters in shape space, albeit with some overlap. The shape differences in extant taxa between individuals in the relevant age categories are minimal, indicating that it is unlikely that ontogeny explains the differences between MH1 and MH2. Similarly, the pattern of differences between MH1 and MH2 is inconsistent with those found between males and females in the extant sample, suggesting that it is unlikely that sexual dimorphism explains these differences. While the difference between MH1 and MH2 is large relative to within-species comparisons, it does not generally fall outside of the confidence intervals for extant intraspecific variation. However, the MH1-MH2 distance also does not plot outside and below the between-species confidence intervals. Based on these results, as well as the contextual and depositional evidence, we conclude that MH1 and MH2 represent a single species and that the relatively large degree of variation in this species is due to neither ontogeny nor sexual dimorphism.

Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles.

BACKGROUND: Technological advances have enabled the analysis of very small amounts of DNA in forensic cases. However, the DNA profiles from such evidence are frequently incomplete and can contain contributions from multiple individuals. The complexity of such samples confounds the assessment of the statistical weight of such evidence. One approach to account for this uncertainty is to use a likelihood ratio framework to compare the probability of the evidence profile under different scenarios. While researchers favor the likelihood ratio framework, few open-source software solutions with a graphical user interface implementing these calculations are available for practicing forensic scientists. RESULTS: To address this need, we developed Lab Retriever, an open-source, freely available program that forensic scientists can use to calculate likelihood ratios for complex DNA profiles. Lab Retriever adds a graphical user interface, written primarily in JavaScript, on top of a C++ implementation of the previously published R code of Balding. We redesigned parts of the original Balding algorithm to improve computational speed. In addition to incorporating a probability of allelic drop-out and other critical parameters, Lab Retriever computes likelihood ratios for hypotheses that can include up to four unknown contributors to a mixed sample. These computations are completed nearly instantaneously on a modern PC or Mac computer. CONCLUSIONS: Lab Retriever provides a practical software solution to forensic scientists who wish to assess the statistical weight of evidence for complex DNA profiles. Executable versions of the program are freely available for Mac OSX and Windows operating systems.

Accumulation of amyloid-ß in the cerebellar cortex of essential tremor patients.

The accumulation of insoluble amyloid-beta (Aß) peptides is associated with neurodegenerative disorders, such as Alzheimer's disease (AD). As essential tremor (ET) could involve neurodegenerative processes in the cerebellum, we quantified soluble and insoluble Aß in cerebellar cortices from patients diagnosed with ET (n=9), compared to Controls (n=16) or individuals with Parkinson's disease (n=10). Although ante-mortem cognitive performance was not documented, all individuals included had the diagnosis of AD ruled out by a neuropathologist. ELISA-determined concentrations of insoluble Aß42 in ET patients displayed a bimodal distribution, with a median 246-fold higher than in Controls (P<0.01, Kruskal-Wallis). Higher Aß42 concentrations were measured in the parietal cortex of the same ET patients, compared to Controls (107-fold median increase, P<0.01, Kruskal-Wallis), but similar phosphorylated tau levels were detected. The rise in cerebellar insoluble Aß42 concentrations is not associated to APP expression and processing or the ApoE4 status. However, Aß42 levels in ET individuals were correlated with cerebellar insoluble phosphorylated tau (r(2)=0.71, P=0.005), unphosphorylated neurofilament heavy chain (NF-H; r(2)=0.50, P=0.030) and Lingo-1 (r(2)=0.73, P=0.007), indicative of a generalized neurodegenerative process involving the cerebellum. Our results suggest prevalent accumulations of insoluble Aß42 in the cerebellum of ET, but not in age-matched PD. Whether this anomaly plays a role in ET symptoms warrants further investigations.

Clinical, positron emission tomography, and pathological studies of DNAJC13 p.N855S Parkinsonism.

BACKGROUND: Families of Dutch-German-Russian Mennonite descent with multi-incident parkinsonism have been identified as harboring a pathogenic DNAJC13 p.N855S mutation and are awaiting clinical and pathophysiological characterization. METHODS: Family members were examined clinically longitudinally, and 5 underwent dopaminergic PET imaging. Four family members came to autopsy. RESULTS: Of the 16 symptomatic DNAJC13 mutation carriers, 12 had clinically definite, 3 probable, and 1 possible Parkinson's disease (PD). Symptoms included bradykinesia, tremor, rigidity, and postural instability, with a mean onset of 63 years (range, 40-85) and slow progression. Eight of ten subjects who required treatment had a good levodopa response; motor complications and nonmotor symptoms were observed. Dopaminergic PET imaging revealed rostrocaudal striatal deficits typical for idiopathic PD in established disease and subtle abnormalities in incipient disease. Pathological examinations revealed Lewy body pathology. CONCLUSION: PD associated with a DNAJC13 p.N855S mutation presents as late-onset, often slowly progressive, usually dopamine-responsive typical PD.

Ontogenetic variation in the mandibular ramus of great apes and humans.

Considerable variation exists in mandibular ramus form among primates, particularly great apes and humans. Recent analyses of adult ramal morphology have suggested that features on the ramus, especially the coronoid process and sigmoid notch, can be treated as phylogenetic characters that can be used to reconstruct relationships among great ape and fossil hominin taxa. Others have contended that ramal morphology is more influenced by function than phylogeny. In addition, it remains unclear how ontogeny of the ramus contributes to adult variation in great apes and humans. Specifically, it is unclear whether differences among adults appear early and are maintained throughout ontogeny, or if these differences appear, or are enhanced, during later development. To address these questions, the present study examined a broad ontogenetic sample of great apes and humans using two-dimensional geometric morphometric analysis. Variation within and among species was summarized using principal component and thin plate spline analyses, and Procrustes distances and discriminant function analyses were used to statistically compare species and age classes. Results suggest that morphological differences among species in ramal morphology appear early in ontogeny and persist into adulthood. Morphological differences among adults are particularly pronounced in the height and angulation of the coronoid process, the depth and anteroposterior length of the sigmoid notch, and the inclination of the ramus. In all taxa, the ascending ramus of the youngest specimens is more posteriorly inclined in relation to the occlusal plane, shifting to become more upright in adults. These results suggest that, although there are likely functional influences over the form of the coronoid process and ramus, the morphology of this region can be profitably used to differentiate among great apes, modern humans, and fossil hominid taxa.

Geometric morphometric analysis of mandibular shape diversity in Pan.

The aim of this research is to determine whether geometric morphometric (GM) techniques can provide insights into how the shape of the mandibular corpus differs between bonobos and chimpanzees and to explore the potential implications of those results for our understanding of hominin evolution. We focused on this region of the mandible because of the relative frequency with which it has been recovered in the hominin fossil record. In addition, no previous study had explored in-depth three-dimensional (3D) mandibular corpus shape differences between adults of the two Pan species using geometric morphometrics. GM methods enable researchers to quantitatively analyze and visualize 3D shape changes in skeletal elements and provide an important compliment to traditional two-dimensional analyses. Eighteen mandibular landmarks were collected using a Microscribe 3DX portable digitizer. Specimen configurations were superimposed using Generalized Procrustes analysis and the projections of the fitted coordinates to tangent space were analyzed using multivariate statistics. The size-adjusted corpus shapes of Pan paniscus and Pan troglodytes could be assigned to species with approximately 93% accuracy and the Procrustes distance between the two species was significant. Analyses of the residuals from a multivariate linear regression of the data on centroid size suggested that much of the shape difference between the species is size-related. Chimpanzee subspecies and a small sample of Australopithecus specimens could be correctly identified to taxon, at best, only 75% of the time, although the Procrustes distances between these taxa were significant. The shape of the mandibular symphysis was identified as especially useful in differentiating Pan species from one another. This suggests that this region of the mandible has the potential to be informative for taxonomic analyses of fossil hominoids, including hominins. The results also have implications for phylogenetic hypotheses of hominoid evolution.

A 12-week Interdisciplinary Intervention Program for Children who are Obese.

UNLABELLED: Childhood obesity is a growing problem, for which multi-disciplinary interventions are needed. PURPOSE: This interdisciplinary intervention program was designed to improve the health of children who were obese. METHODS: Twenty-five children, mean age 8.1 (1.5) years; body mass index (BMI)> 98(th) percentile, and their parents completed the 12-week (3 days/wk) intervention consisting of aerobic and resistance exercise appropriate to age and developmental levels. Baseline and posttest measures of blood values, fitness, and cardiovascular risk factors were performed. Data were analyzed using paired t-tests with significance accepted at P ≤ .05. RESULTS: Significant differences between means (SD) for pre- and post-measurements were, respectively: BMI 30.31 (4.56), 27.80 (4.54), body-fat percent 43.7 (11.5), 40.7 (10.9), waist circumference 82.1 (7.1), 80.4(6.1) cm, calf circumference 34.2 (3.1), 35.2 (3.1) cm; step-test heart rate 137 (20), 126 (12) bpm, push-ups 1.0 (1.8), 5.6 (3.8), sit-ups 23.6 (12.7), 33.2 (13.8), sit-and-reach 35.1 (7.4), 41.2 (5.8) cm; systolic BP 102 (10), 108 (9) mmHg, glucose 4.9(0.3), 4.8 (0.4) mmol/L, total cholesterol 4.6 (1.0), 4.2 (0.8) mmol/L, ALT 41 (9), 35 (8) U/L, bilirubin 6.3 (2.4), 5.6 (2.1) µmol/L, and BUN 4.9 (1.1), 4.3 (0.9) mmol/L. CONCLUSIONS: This interdisciplinary intervention program positively affected the fitness and health status of children who were obese by involving the children and parents.

Allometric and metameric shape variation in Pan mandibular molars: a digital morphometric analysis.

The predominance of molar teeth in fossil hominin assemblages makes the patterning of molar shape variation a topic of bioanthropological interest. Extant models are the principal basis for understanding dental variation in the fossil record. As the sister taxon to the hominin clade, Pan is one such model and the only widely accepted extant hominid model for both interspecific and intraspecific variation. To explore the contributions of allometric scaling and meristic variation to molar variation in Pan, we applied geometric shape analysis to 3D landmarks collected from virtual replicas of chimpanzee and bonobo mandibular molars. Multivariate statistical analysis and 3D visualization of metameric and allometric shape vectors were used to characterize shape differences and test the hypothesis that species of Pan share patterns of metameric variation and molar shape allometry. Procrustes-based shape variables were found to effectively characterize crown shape, sorting molars into species and tooth-row positions with ≥ 95% accuracy. Chimpanzees and bonobos share a common pattern of M(1) -M(2) metameric variation, which is defined by differences in the relative position of the metaconid, size of the hypoconulid, curvature of the buccal wall, and proportions of the basins and foveae. Allometric scaling of molar shape is homogeneous for M(1) and M(2) within species, but bonobo and chimpanzee allometric vectors are significantly different. Nevertheless, the common allometric shape trend explains most molar-shape differences between P. paniscus and P. troglodytes. When allometric effects are factored out, chimpanzee and bonobo molars are not morphometrically distinguishable. Implications for hominid taxonomy and dietary reconstruction are discussed.

Quantifying mental foramen position in extant hominoids and Australopithecus: implications for its use in studies of human evolution.

The location of the mental foramen on the mandibular corpus has figured prominently in debates concerning the taxonomy of fossil hominins and Gorilla gorilla. In this study we quantify the antero/posterior (A/P) position of the mental foramen across great apes, modern humans and Australopithecus. Contrary to most qualitative assessments, we find significant differences between some extant hominoid species in mental foramen A/P position supporting its potential usefulness as a character for taxonomic and phylogenetic analyses of fossil hominoids. Gorilla gorilla, particularly the eastern subspecies, with a comparatively longer dental arcade and fossil and extant hominins with reduced canines and incisors tend to exhibit more anteriorly positioned mental foramina. Conversely, Pan troglodytes exhibits more posteriorly positioned mental foramina. Variation in this character among Gorilla gorilla subspecies supports recent taxonomic assessments that separate eastern and western populations. In all taxa other than Pan troglodytes the A/P position of the mental foramen is positively allometric with respect to dental arcade length. Thus, within each of these species, specimens with longer dental arcades tend to have more posteriorly positioned mental foramina. Those species with greater sexual dimorphism in canine size and dental arcade length (i.e., Gorilla gorilla and Pongo pygmaeus) exhibit more extreme differences between smaller and larger individuals. Moreover, among great apes those individuals with greater anterior convergence of the dental arcade tend to exhibit more posteriorly positioned mental foramina. Dental arcade length, canine crown area and anterior convergence are all significantly associated with mental foramen A/P position, suggesting that these traits may influence taxonomic variation in the A/P position of the mental foramen.

Recovery of benthic invertebrate communities from acidification in Killarney Park lakes.

Using a reference-condition comparison, recovery of benthic invertebrate communities from acidification was assessed in three lakes in Killarney Wilderness Park approximately 40-60 km from the massive metal smelters in Sudbury, Canada. Test site analyses (TSAs) were used to compare the park lakes to 20 reference lakes near Dorset Ontario, 200 km to the east. An extension of a previous survey (1997-2001) of two sensitive mayfly species (Stenonema femoratum and Stenacron interpunctatum) was conducted in one of the lakes. TSA results indicate that the three Killarney lakes remain significantly different from reference condition due primarily to higher abundances of a few acid-tolerant families and the presence of some less abundant sensitive families. Colonization rates differ greatly between the two mayfly species presumably because of competition for available habitat. Overall, this study suggests that early colonizers will gain an advantage to out-compete subsequent arrivals, and these competitive interactions will delay the return of communities to reference condition.