A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.Comment: 30 pages, 1 table, 4 figures, 1 supplementary table, 3 supplementary figure

Universal trapping scaling on the unstable manifold for a collisionless electrostatic mode

An amplitude equation for an unstable mode in a collisionless plasma is derived from the dynamics on the two-dimensional unstable manifold of the equilibrium. The mode amplitude $\rho(t)$ decouples from the phase due to the spatial homogeneity of the equilibrium, and the resulting one-dimensional dynamics is analyzed using an expansion in $\rho$. As the linear growth rate $\gamma$ vanishes, the expansion coefficients diverge; a rescaling $\rho(t)\equiv\gamma^2\,r(\gamma t)$ of the mode amplitude absorbs these singularities and reveals that the mode electric field exhibits trapping scaling $|E_1|\sim\gamma^2$ as $\gamma\rightarrow0$. The dynamics for $r(\tau)$ depends only on the phase $e^{i\xi}$ where $d\epsilon_{{k}} /dz=|{\epsilon_{{k}}}|e^{-i\xi/2}$ is the derivative of the dielectric as $\gamma\rightarrow0$.Comment: 11 pages (Latex/RevTex), 2 figures available in hard copy from the Author ([email protected]); paper accepted by Physical Review Letter

THE RELATIONSHIP BETWEEN MUSCULOSKELETAL STRENGTH, PHYSIOLOGICAL CHARACTERISTICS, AND KNEE KINESTHESIA FOLLOWING FATIGUING EXERCISE

Fatiguing exercise may result in impaired functional joint stability and increased risk of unintentional injury. While there are several musculoskeletal and physiological characteristics related to fatigue onset, their relationship with proprioceptive changes following fatigue has not been examined. The purpose of this study was to establish the relationship between musculoskeletal and physiological characteristics and changes in proprioception, measured by threshold to detect passive motion (TTDPM), following fatiguing exercise. Twenty, physically active females participated (age: 28.65 ± 5.6 years, height: 165.6 ± 4.3 cm, weight: 61.8 ± 8.0 kg, BMI: 22.5± 2.3 kg/m2, BF: 23.3 ± 5.4%). During Visit 1, subjects completed an exercise history and 24-hour dietary questionnaire, and body composition, TTDPM familiarization, isokinetic knee strength, and maximal oxygen uptake/lactate threshold assessments. During Visit 2, subjects completed TTDPM and isometric knee strength testing prior to and following a fatiguing exercise protocol. Wilcoxon signed rank tests determined TTDPM and isometric knee strength changes from pre- to post- fatigue. Spearman’s rho correlation coefficients determined the relationship between strength and physiological variables with pre- to post-fatigue changes in TTDPM and with pre-fatigue and post-fatigue TTDPM in extension and flexion (α=0.05). No significant differences were demonstrated from pre-fatigue to post-fatigue TTDPM despite a significant decrease in isometric knee flexion strength (P<0.01) and flexion/extension ratio (P<0.05) following fatigue. No significant correlations were observed between strength or physiological variables and changes in TTDPM from pre- to post-fatigue in extension or flexion. Flexion/extension ratio was significantly correlated with pre-fatigue TTDPM in extension (r=-0.231, P<0.05). Peak oxygen uptake was significantly correlated with pre-fatigue (r=-0.500, P<0.01) and post-fatigue (r=-0.520, P<0.05) TTDPM in extension. No significant relationships were demonstrated between musculoskeletal and physiological characteristics and changes in TTDPM following fatigue. The results suggest that highly trained individuals may have better proprioception, and that the high fitness level of subjects in this investigation may have contributed to absence of TTDPM deficits following fatigue despite reaching a high level of perceptual and physiological fatigue. Future studies should consider various subject populations, other musculoskeletal strength characteristics, and different modalities of proprioception to determine the most important contributions to proprioceptive changes following fatigue

The Properties of Poor Groups of Galaxies: II. X-ray and Optical Comparisons

We use ROSAT PSPC data to study the X-ray properties of a sample of twelve poor groups that have extensive membership information (Zabludoff and Mulchaey 1997; Paper I). Diffuse X-ray emission is detected in nine of these groups. In all but one of the X-ray detected groups, the X-ray emission is centered on a luminous elliptical galaxy. Fits to the surface brightness profiles of the X-ray emission suggest the presence of two X-ray components in these groups. The first component is centered on the central elliptical galaxy. The location and extent of this component, combined with its X-ray temperature and luminosity, favor an origin in the interstellar medium of the central galaxy. Alternatively, the central component may be the result of a large-scale cooling flow. The second X-ray component is detected out to a radius of at least 100-300 kpc. This component follows the same relationships found among the X-ray temperature, X-ray luminosity and optical velocity dispersion of rich clusters. This result suggests that the X-ray detected groups are low-mass versions of clusters and that the extended gas component can properly be called the intragroup medium, in analogy to the intracluster medium in clusters. We also find a trend for the position angle of the optical light in the central elliptical galaxy to align with the position angle of the large-scale X-ray emission. (Abridged)Comment: 38 pages, AASLaTeX with 16 PS figures. Figure 1a-1l available in gzipped postscript format at ftp://corvus.ociw.edu/pub/mulchae

Scaling and singularities in the entrainment of globally-coupled oscillators

The onset of collective behavior in a population of globally coupled oscillators with randomly distributed frequencies is studied for phase dynamical models with arbitrary coupling. The population is described by a Fokker-Planck equation for the distribution of phases which includes the diffusive effect of noise in the oscillator frequencies. The bifurcation from the phase-incoherent state is analyzed using amplitude equations for the unstable modes with particular attention to the dependence of the nonlinearly saturated mode $|\alpha_\infty|$ on the linear growth rate $\gamma$. In general we find $|\alpha_\infty|\sim \sqrt{\gamma(\gamma+l^2D)}$ where $D$ is the diffusion coefficient and $l$ is the mode number of the unstable mode. The unusual $(\gamma+l^2D)$ factor arises from a singularity in the cubic term of the amplitude equation.Comment: 11 pages (Revtex); paper submitted to Phys. Rev. Let

Extreme Precipitation in the Eastern Canadian Arctic and Greenland: An Evaluation of Atmospheric Reanalyses

Extreme precipitation events are becoming more common in the Arctic as the climate warms, but characterizing these events is notoriously challenging. Atmospheric reanalyses have become popular tools for climate studies in data-sparse regions such as the Arctic. While modern reanalyses have been shown to perform reasonably well at reproducing Arctic climate, their ability to represent extreme precipitation events has not been investigated in depth. In this study, three of the most recent reanalyses, ERA-5, MERRA-2, and CFSR, are compared to surface precipitation observations in the Eastern Canadian Arctic and Greenland from 1980 to 2016 to assess how well they represent the most intense observed events. Overall, the reanalyses struggled to match observed accumulations from individual events (−0.11 ≤ r ≤ 0.47) but matched the observed seasonality of precipitation extremes. The region with the strongest match between observations and reanalyses was Southwest Greenland. Performance varies by event, and the best match between reanalyses and station observations may have a spatial/temporal offset (up to one grid cell or 1 day). The three products saw similar performance in general; however, ERA-5 tends to see slightly higher correlations and lower biases than MERRA-2 or CFSR. Considering the limitations of in situ observations, these results suggest that the reanalyses are capable of representing aggregate extreme precipitation (e.g., seasonal or annual time scales), but struggle to consistently match the timing and location of specific observed events

Effects of carbon dioxide on the searching behaviour of the root-feeding clover weevil <i>Sitona lepidus</i> (Coleoptera: Curculionidae)

The respiratory emission of CO2 from roots is frequently proposed as an attractant that allows soil-dwelling insects to locate host plant roots, but this role has recently become less certain. CO2 is emitted from many sources other than roots, so does not necessarily indicate the presence of host plants, and because of the high density of roots in the upper soil layers, spatial gradients may not always be perceptible by soil-dwelling insects. The role of CO2 in host location was investigated using the clover root weevil Sitona lepidus Gyllenhall and its host plant white clover (Trifolium repens L.) as a model system. Rhizochamber experiments showed that CO2 concentrations were approximately 1000 ppm around the roots of white clover, but significantly decreased with increasing distance from roots. In behavioural experiments, no evidence was found for any attraction by S. lepidus larvae to point emissions of CO2, regardless of emission rates. Fewer than 15% of larvae were attracted to point emissions of CO2, compared with a control response of 17%. However, fractal analysis of movement paths in constant CO2 concentrations demonstrated that searching by S. lepidus larvae significantly intensified when they experienced CO2 concentrations similar to those found around the roots of white clover (i.e. 1000 ppm). It is suggested that respiratory emissions of CO2 may act as a ‘search trigger’ for S. lepidus, whereby it induces larvae to search a smaller area more intensively, in order to detect location cues that are more specific to their host plant.<br/