Detecting adaptive evolution in phylogenetic comparative analysis using the Ornstein-Uhlenbeck model

Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and more detailed evolutionary hypotheses, including adaptive hypotheses with multiple selective optima and hypotheses with rate variation within and across lineages. The statistical performance of these sophisticated models has received relatively little systematic attention, however. We conducted an extensive simulation study to quantify the statistical properties of a class of models toward the simpler end of the spectrum that model phenotypic evolution using Ornstein-Uhlenbeck processes. We focused on identifying where, how, and why these methods break down so that users can apply them with greater understanding of their strengths and weaknesses. Our analysis identifies three key determinants of performance: a discriminability ratio, a signal-to-noise ratio, and the number of taxa sampled. Interestingly, we find that model-selection power can be high even in regions that were previously thought to be difficult, such as when tree size is small. On the other hand, we find that model parameters are in many circumstances difficult to estimate accurately, indicating a relative paucity of information in the data relative to these parameters. Nevertheless, we note that accurate model selection is often possible when parameters are only weakly identified. Our results have implications for more sophisticated methods inasmuch as the latter are generalizations of the case we study.Comment: 38 pages, in press at Systematic Biolog

Systemic: A Testbed For Characterizing the Detection of Extrasolar Planets. I. The Systemic Console Package

We present the systemic Console, a new all-in-one, general-purpose software package for the analysis and combined multiparameter fitting of Doppler radial velocity (RV) and transit timing observations. We give an overview of the computational algorithms implemented in the Console, and describe the tools offered for streamlining the characterization of planetary systems. We illustrate the capabilities of the package by analyzing an updated radial velocity data set for the HD128311 planetary system. HD128311 harbors a pair of planets that appear to be participating in a 2:1 mean motion resonance. We show that the dynamical configuration cannot be fully determined from the current data. We find that if a planetary system like HD128311 is found to undergo transits, then self-consistent Newtonian fits to combined radial velocity data and a small number of timing measurements of transit midpoints can provide an immediate and vastly improved characterization of the planet's dynamical state.Comment: 10 pages, 5 figures, accepted for publication on PASP. Additional material at http://www.ucolick.org/~smeschia/systemic.ph

The Pitcher Plant Sarracenia purpurea Can Directly Acquire Organic Nitrogen and Short-Circuit the Inorganic Nitrogen Cycle

Background: Despite the large stocks of organic nitrogen in soil, nitrogen availability limits plant growth in many terrestrial ecosystems because most plants take up only inorganic nitrogen, not organic nitrogen. Although some vascular plants can assimilate organic nitrogen directly, only recently has organic nitrogen been found to contribute significantly to the nutrient budget of any plant. Carnivorous plants grow in extremely nutrient-poor environments and carnivory has evolved in these plants as an alternative pathway for obtaining nutrients. We tested if the carnivorous pitcher plant Sarracenia purpurea could directly take up intact amino acids in the field and compared uptake of organic and inorganic forms of nitrogen across a gradient of nitrogen deposition. We hypothesized that the contribution of organic nitrogen to the nitrogen budget of the pitcher plant would decline with increasing nitrogen deposition. Methodology and Principal Findings: At sites in Canada (low nitrogen deposition) and the United States (high nitrogen deposition), individual pitchers were fed two amino acids, glycine and phenylalanine, and inorganic nitrogen (as ammonium nitrate), individually and in mixture. Plants took up intact amino acids. Acquisition of each form of nitrogen provided in isolation exceeded uptake of the same form in mixture. At the high deposition site, uptake of organic nitrogen was higher than uptake of inorganic nitrogen. At the low deposition site, uptake of all three forms of nitrogen was similar. Completeness of the associated detritus-based food web that inhabits pitcher-plant leaves and breaks down captured prey had no effect on nitrogen uptake. Conclusions and Significance: By taking up intact amino acids, Sarracenia purpurea can short-circuit the inorganic nitrogen cycle, thus minimizing potential bottlenecks in nitrogen availability that result from the plant’s reliance for nitrogen mineralization on a seasonally reconstructed food web operating on infrequent and irregular prey capture.Other Research Uni

Periodic Optical Variability of Radio Detected Ultracool Dwarfs

A fraction of very low mass stars and brown dwarfs are known to be radio active, in some cases producing periodic pulses. Extensive studies of two such objects have also revealed optical periodic variability and the nature of this variability remains unclear. Here we report on multi-epoch optical photometric monitoring of six radio detected dwarfs, spanning the $\sim$M8 - L3.5 spectral range, conducted to investigate the ubiquity of periodic optical variability in radio detected ultracool dwarfs. This survey is the most sensitive ground-based study carried out to date in search of periodic optical variability from late-type dwarfs, where we obtained 250 hours of monitoring, delivering photometric precision as low as $\sim$0.15%. Five of the six targets exhibit clear periodicity, in all cases likely associated with the rotation period of the dwarf, with a marginal detection found for the sixth. Our data points to a likely association between radio and optical periodic variability in late-M/early-L dwarfs, although the underlying physical cause of this correlation remains unclear. In one case, we have multiple epochs of monitoring of the archetype of pulsing radio dwarfs, the M9 TVLM 513-46546, spanning a period of 5 years, which is sufficiently stable in phase to allow us to establish a period of 1.95958 $\pm$ 0.00005 hours. This phase stability may be associated with a large-scale stable magnetic field, further strengthening the correlation between radio activity and periodic optical variability. Finally, we find a tentative spin-orbit alignment of one component of the very low mass binary LP 349-25.Comment: Accepted to The Astrophysical Journal; 22 pages; 12 figure

A determination of the spin-orbit alignment of the anomalously dense planet orbiting HD 149026

We report 35 radial velocity measurements of HD 149026 taken with the Keck Telescope. Of these measurements, 15 were made during the transit of the companion planet HD 149026b, which occurred on 2005 June 25. These velocities provide a high-cadence observation of the Rossiter-McLaughlin effect, the shifting of photospheric line profiles that occurs when a planet occults a portion of the rotating stellar surface. We combine these radial velocities with previously published radial velocity and photometric data sets and derive a composite best-fit model for the star-planet system. This model confirms and improves previously published orbital parameters, including the remarkably small planetary radius, the planetary mass, and the orbital inclination, found to be Rp/RJup = 0.718 ± 0.065, Mp/MJup = 0.352 ± 0.025, and I = 86.1° ± 1.4°, respectively. Together the planetary mass and radius determinations imply a mean planetary density of 1.18(-0.30)(+0.38)g cm(-3). The new data also allow for the determination of the angle between the apparent stellar equator and the orbital plane, which we constrain to be λ = -12° ± 15°

Software Validation via Model Animation

This paper explores a new approach to validating software implementations that have been produced from formally-verified algorithms. Although visual inspection gives some confidence that the implementations faithfully reflect the formal models, it does not provide complete assurance that the software is correct. The proposed approach, which is based on animation of formal specifications, compares the outputs computed by the software implementations on a given suite of input values to the outputs computed by the formal models on the same inputs, and determines if they are equal up to a given tolerance. The approach is illustrated on a prototype air traffic management system that computes simple kinematic trajectories for aircraft. Proofs for the mathematical models of the system's algorithms are carried out in the Prototype Verification System (PVS). The animation tool PVSio is used to evaluate the formal models on a set of randomly generated test cases. Output values computed by PVSio are compared against output values computed by the actual software. This comparison improves the assurance that the translation from formal models to code is faithful and that, for example, floating point errors do not greatly affect correctness and safety properties

The Primary Volatile Composition of Comet C/2015 ER61 (PANSTARRS)

In the outer edges of the solar system exist two regions: the Kuiper belt and Oort cloud. These two regions have a high amount of icy bodies (comets) orbiting the Sun. Comets located within the Oort cloud and Kuiper belt contain an ancient codex to the solar systems contents, before the formation of our solar system. Presented are near-infrared, high-resolution (λ/Δλ ~40000) data obtained from the immersion-grating echelle spectrograph iSHELL at the 3m NASA Infrared Telescope Facility (IRTF) in Maunakea, Hawaii of the Oort cloud comet C/2015 ER61 (PANSTARRS). Observations took place on April 15 and 17 in 2017 while the comet was declining after a dramatic outburst. We used two settings (LCustom and LP1) to measure the production rates and abundances (or upper limits) of H2O, CH3OH, C2H2, C2H6, HCN, and H2CO. We found the comet to be enriched in C2H2, normal in H2CO, and depleted in other detected volatiles compared to other Oort cloud comets