When trees grow too long: Investigating the causes of highly inaccurate bayesian branch-length estimates

A surprising number of recent Bayesian phylogenetic analyses contain branch-length estimates that are several orders of magnitude longer than corresponding maximum-likelihood estimates. The levels of divergence implied by such branch lengths are unreasonable for studies using biological data and are known to be false for studies using simulated data. We conducted additional Bayesian analyses and studied approximate-posterior surfaces to investigate the causes underlying these large errors. We manipulated the starting parameter values of the Markov chain Monte Carlo (MCMC) analyses, the moves used by the MCMC analyses, and the prior-probability distribution on branch lengths. We demonstrate that inaccurate branch-length estimates result from either 1) poor mixing of MCMC chains or 2) posterior distributions with excessive weight at long tree lengths. Both effects are caused by a rapid increase in the volume of branch-length space as branches become longer. In the former case, both an MCMC move that scales all branch lengths in the tree simultaneously and the use of overdispersed starting branch lengths allow the chain to accurately sample the posterior distribution and should be used in Bayesian analyses of phylogeny. In the latter case, branch-length priors can have strong effects on resulting inferences and should be carefully chosen to reflect biological expectations. We provide a formula to calculate an exponential rate parameter for the branch-length prior that should eliminate inference of biased branch lengths in many cases. In any phylogenetic analysis, the biological plausibility of branch-length output must be carefully considered

The importance of data partitioning and the utility of bayes factors in bayesian phylogenetics

As larger, more complex data sets are being used to infer phylogenies, accuracy of these phylogenies increasingly requires models of evolution that accommodate heterogeneity in the processes of molecular evolution. We investigated the effect of improper data partitioning on phylogenetic accuracy, as well as the type I error rate and sensitivity of Bayes factors, a commonly used method for choosing among different partitioning strategies in Bayesian analyses. We also used Bayes factors to test empirical data for the need to divide data in a manner that has no expected biological meaning. Posterior probability estimates are misleading when an incorrect partitioning strategy is assumed. The error was greatest when the assumed model was underpartitioned. These results suggest that model partitioning is important for large data sets. Bayes factors performed well, giving a 5% type I error rate, which is remarkably consistent with standard frequentist hypothesis tests. The sensitivity of Bayes factors was found to be quite high when the across-class model heterogeneity reflected that of empirical data. These results suggest that Bayes factors represent a robust method of choosing among partitioning strategies. Lastly, results of tests for the inclusion of unexpected divisions in empirical data mirrored the simulation results, although the outcome of such tests is highly dependent on accounting for rate variation among classes. We conclude by discussing other approaches for partitioning data, as well as other applications of Bayes factors. Copyright © Society of Systematic Biologists

Alternative derivation of the relativistic contribution to perihelic precession

An alternative derivation of the first-order relativistic contribution to perihelic precession is presented. Orbital motion in the Schwarzschild geometry is considered in the Keplerian limit, and the orbit equation is derived for approximately elliptical motion. The method of solution makes use of coordinate transformations and the correspondence principle, rather than the standard perturbative approach. The form of the resulting orbit equation is similar to that derived from Newtonian mechanics and includes first-order corrections to Kepler's orbits due to general relativity. The associated relativistic contribution to perihelic precession agrees with established first-order results. The reduced radius for the circular orbit is in agreement to first-order with that calculated from the Schwarzschild effective potential. The method of solution is understandable by undergraduate students.Comment: 12 pages, 2 figures. Accepted for publication in the American Journal of Physic

Flow probe of symmetry energy in relativistic heavy-ion reactions

Flow observables in heavy-ion reactions at incident energies up to about 1 GeV per nucleon have been shown to be very useful for investigating the reaction dynamics and for determining the parameters of reaction models based on transport theory. In particular, the elliptic flow in collisions of neutron-rich heavy-ion systems emerges as an observable sensitive to the strength of the symmetry energy at supra-saturation densities. The comparison of ratios or differences of neutron and proton flows or neutron and hydrogen flows with predictions of transport models favors an approximately linear density dependence, consistent with ab-initio nuclear-matter theories. Extensive parameter searches have shown that the model dependence is comparable to the uncertainties of existing experimental data. Comprehensive new flow data of high accuracy, partly also through providing stronger constraints on model parameters, can thus be expected to improve our knowledge of the equation of state of asymmetric nuclear matter.Comment: 20 pages, 24 figures, review to appear in EPJA special volume on nuclear symmetry energ

Molecular Density Functional Theory of Water describing Hydrophobicity at Short and Long Length Scales

We present an extension of our recently introduced molecular density functional theory of water [G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619, 2013] to the solvation of hydrophobic solutes of various sizes, going from angstroms to nanometers. The theory is based on the quadratic expansion of the excess free energy in terms of two classical density fields, the particle density and the multipolar polarization density. Its implementation requires as input a molecular model of water and three measurable bulk properties, namely the structure factor and the k-dependent longitudinal and transverse dielectric susceptibilities. The fine three-dimensional water structure around small hydrophobic molecules is found to be well reproduced. In contrast the computed solvation free-energies appear overestimated and do not exhibit the correct qualitative behavior when the hydrophobic solute is grown in size. These shortcomings are corrected, in the spirit of the Lum-Chandler-Weeks theory, by complementing the functional with a truncated hard-sphere functional acting beyond quadratic order in density. It makes the resulting functional compatible with the Van-der-Waals theory of liquid-vapor coexistence at long range. Compared to available molecular simulations, the approach yields reasonable solvation structure and free energy of hard or soft spheres of increasing size, with a correct qualitative transition from a volume-driven to a surface-driven regime at the nanometer scale.Comment: 24 pages, 8 figure

Neutron Transfer Studied with a Radioactive beam of 24Ne, using TIARA at SPIRAL

A general experimental technique for high resolution studies of nucleon transfer reactions using radioactive beams is briefly described, together with the first new physics results that have been obtained with the new TIARA array. These first results from TIARA are for the reaction 24Ne(d,p)25Ne, studied in inverse kinematics with a pure radioactive beam of 100,000 pps from the SPIRAL facility at GANIL. The reaction probes the energies of neutron orbitals relevant to very neutron rich nuclei in this mass region and the results highlight the emergence of the N=16 magic number for neutrons and the associated disappearance of the N=20 neutron magic number for the very neutron rich neon isotopes.Comment: Proceedings of the Carpathian Summer School of Physics, Mamaia-Constanta, Romania, 13-24 June 200

Shape oscillations of a charged diamagnetically-levitated droplet

We investigate the effect of electrical charge on the normal mode frequencies of electrically-charged diamagnetically levitated water droplets with radii 4.5-7.5 mm using diamagnetic levitation. This technique allows us to levitate almost spherical droplets and therefore to directly compare the measured vibrational frequencies of the first seven modes of the charged droplet with theoretical values calculated by Lord Rayleigh, for which we find good agreement