Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement

BACKGROUND: When organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinforced in such multigene trees. Such approaches are valid only when the several markers indeed have identical phylogenies, an issue which many multigene methods (such as the use of concatenated gene sequences or the assembly of supertrees) do not directly address. Indeed, even when the true history is a mixture of vertical descent for some genes and lateral gene transfer (LGT) for others, such methods produce unique topologies. RESULTS: We have developed software that aims to extract evidence for vertical and lateral inheritance from a set of gene trees compared against an arbitrary reference tree. This evidence is then displayed as a synthesis showing support over the tree for vertical inheritance, overlaid with explicit lateral gene transfer (LGT) events inferred to have occurred over the history of the tree. Like splits-tree methods, one can thus identify nodes at which conflict occurs. Additionally one can make reasonable inferences about vertical and lateral signal, assigning putative donors and recipients. CONCLUSION: A tool such as ours can serve to explore the reticulated dimensionality of molecular evolution, by dissecting vertical and lateral inheritance at high resolution. By this, we mean that individual nodes can be examined not only for congruence, but also for coherence in light of LGT. We assert that our tools will facilitate the comparison of phylogenetic trees, and the interpretation of conflicting data

The Surface Brightness Fluctuations and Globular Cluster Populations of M87 and its Companions

Using the surface brightness fluctuations in HST WFPC-2 images, we determine that M87, NGC 4486B, and NGC 4478 are all at a distance of ~16 Mpc, while NGC 4476 lies in the background at ~21 Mpc. We also examine the globular clusters of M87 using archived HST fields. We detect the bimodal color distribution, and find that the amplitude of the red peak relative to the blue peak is greatest near the center. This feature is in good agreement with the merger model of elliptical galaxy formation, where some of the clusters originated in progenitor galaxies while other formed during mergers.Comment: 5 pages, 2 figure

The atmospheres of the hot-Jupiters Kepler-5b and Kepler-6b observed during occultations with Warm-Spitzer and Kepler

This paper reports the detection and the measurements of occultations of the two transiting hot giant exoplanets Kepler-5b and Kepler-6b by their parent stars. The observations are obtained in the near infrared with Spitzer Space Telescope and at optical wavelengths by combining more than a year of Kepler photometry. The investigation consists of constraining the eccentricities of these systems and of obtaining broad band emergent spectra for individual planets. For both targets, the occultations are detected at 3 sigma level at each wavelength with mid-occultation times consistent with circular orbits. The brightness temperatures of these planets are deduced from the infrared observations and reach T=1930+/-100K and T=1660+/-120K for Kepler-5b and Kepler-6b respectively. We measure optical geometric albedos A_g in the Kepler bandpass and find A_g=0.12+/-0.04 for Kepler-5b and A_g=0.11+/-0.04 for Kepler-6b leading to an upper limit for the Bond albedo of A_B < 0.17 in both cases. The observations for both planets are best described by models for which most of the incident energy is redistributed on the dayside, with only less than 10% of the absorbed stellar flux redistributed to the night side of these planets. The data for Kepler-5b favor a model without a temperature inversion, whereas for Kepler-6b they do not allow distinguishing between models with and without inversion.Comment: 26 pages, 18 figures, 3 tables, submitted to Ap

Architecture of Kepler's Multi-transiting Systems: II. New investigations with twice as many candidates

We report on the orbital architectures of Kepler systems having multiple planet candidates identified in the analysis of data from the first six quarters of Kepler data and reported by Batalha et al. (2013). These data show 899 transiting planet candidates in 365 multiple-planet systems and provide a powerful means to study the statistical properties of planetary systems. Using a generic mass-radius relationship, we find that only two pairs of planets in these candidate systems (out of 761 pairs total) appear to be on Hill-unstable orbits, indicating ~96% of the candidate planetary systems are correctly interpreted as true systems. We find that planet pairs show little statistical preference to be near mean-motion resonances. We identify an asymmetry in the distribution of period ratios near first-order resonances (e.g., 2:1, 3:2), with an excess of planet pairs lying wide of resonance and relatively few lying narrow of resonance. Finally, based upon the transit duration ratios of adjacent planets in each system, we find that the interior planet tends to have a smaller transit impact parameter than the exterior planet does. This finding suggests that the mode of the mutual inclinations of planetary orbital planes is in the range 1.0-2.2 degrees, for the packed systems of small planets probed by these observations.Comment: Accepted to Ap

Low False-Positive Rate of Kepler Candidates Estimated From A Combination Of Spitzer And Follow-Up Observations

(Abridged) NASA's Kepler mission has provided several thousand transiting planet candidates, yet only a small subset have been confirmed as true planets. Therefore, the most fundamental question about these candidates is the fraction of bona fide planets. Estimating the rate of false positives of the overall Kepler sample is necessary to derive the planet occurrence rate. We present the results from two large observational campaigns that were conducted with the Spitzer telescope during the the Kepler mission. These observations are dedicated to estimating the false positive rate (FPR) amongst the Kepler candidates. We select a sub-sample of 51 candidates, spanning wide ranges in stellar, orbital and planetary parameter space, and we observe their transits with Spitzer at 4.5 microns. We use these observations to measures the candidate's transit depths and infrared magnitudes. A bandpass-dependent depth alerts us to the potential presence of a blending star that could be the source of the observed eclipse: a false-positive scenario. For most of the candidates (85%), the transit depths measured with Kepler are consistent with the depths measured with Spitzer as expected for planetary objects, while we find that the most discrepant measurements are due to the presence of unresolved stars that dilute the photometry. The Spitzer constraints on their own yield FPRs between 5-40%, depending on the KOIs. By considering the population of the Kepler field stars, and by combining follow-up observations (imaging) when available, we find that the overall FPR of our sample is low. The measured upper limit on the FPR of our sample is 8.8% at a confidence level of 3 sigma. This observational result, which uses the achromatic property of planetary transit signals that is not investigated by the Kepler observations, provides an independent indication that Kepler's false positive rate is low.Comment: 33 pages, 16 figures, 3 tables; accepted for publication in ApJ on February 7, 201

Validation of Kepler's Multiple Planet Candidates. III: Light Curve Analysis & Announcement of Hundreds of New Multi-planet Systems

The Kepler mission has discovered over 2500 exoplanet candidates in the first two years of spacecraft data, with approximately 40% of them in candidate multi-planet systems. The high rate of multiplicity combined with the low rate of identified false-positives indicates that the multiplanet systems contain very few false-positive signals due to other systems not gravitationally bound to the target star (Lissauer, J. J., et al., 2012, ApJ 750, 131). False positives in the multi- planet systems are identified and removed, leaving behind a residual population of candidate multi-planet transiting systems expected to have a false-positive rate less than 1%. We present a sample of 340 planetary systems that contain 851 planets that are validated to substantially better than the 99% confidence level; the vast majority of these have not been previously verified as planets. We expect ~2 unidentified false-positives making our sample of planet very reliable. We present fundamental planetary properties of our sample based on a comprehensive analysis of Kepler light curves and ground-based spectroscopy and high-resolution imaging. Since we do not require spectroscopy or high-resolution imaging for validation, some of our derived parameters for a planetary system may be systematically incorrect due to dilution from light due to additional stars in the photometric aperture. None the less, our result nearly doubles the number of verified exoplanets.Comment: 138 pages, 8 Figures, 5 Tables. Accepted for publications in the Astrophysical Journa

Calpain system regulates muscle mass and glucose transporter GLUT4 turnover

The experiments in this study were undertaken to determine whether inhibition of calpain activity in skeletal muscle is associated with alterations in muscle metabolism. Transgenic mice that overexpress human calpastatin, an endogenous calpain inhibitor, in skeletal muscle were produced. Compared with wild type controls, muscle calpastatin mice demonstrated normal glucose tolerance. Levels of the glucose transporter GLUT4 were increased more than 3-fold in the transgenic mice by Western blotting while mRNA levels for GLUT4 and myocyte enhancer factors, MEF 2A and MEF 2D, protein levels were decreased. We found that GLUT4 can be degraded by calpain-2, suggesting that diminished degradation is responsible for the increase in muscle GLUT4 in the calpastatin transgenic mice. Despite the increase in GLUT4, glucose transport into isolated muscles from transgenic mice was not increased in response to insulin. The expression of protein kinase B was decreased by approximately 60% in calpastatin transgenic muscle. This decrease could play a role in accounting for the insulin resistance relative to GLUT4 content of calpastatin transgenic muscle. The muscle weights of transgenic animals were substantially increased compared with controls. These results are consistent with the conclusion that calpain-mediated pathways play an important role in the regulation of GLUT4 degradation in muscle and in the regulation of muscle mass. Inhibition of calpain activity in muscle by overexpression of calpastatin is associated with an increase in GLUT4 protein without a proportional increase in insulin-stimulated glucose transport. These findings provide evidence for a physiological role for calpains in the regulation of muscle glucose metabolism and muscle mass