An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary History

To understand biological diversification, it is important to account for large-scale processes that affect the evolutionary history of groups of co-distributed populations of organisms. Such events predict temporally clustered divergences times, a pattern that can be estimated using genetic data from co-distributed species. I introduce a new approximate-Bayesian method for comparative phylogeographical model-choice that estimates the temporal distribution of divergences across taxa from multi-locus DNA sequence data. The model is an extension of that implemented in msBayes. By reparameterizing the model, introducing more flexible priors on demographic and divergence-time parameters, and implementing a non-parametric Dirichlet-process prior over divergence models, I improved the robustness, accuracy, and power of the method for estimating shared evolutionary history across taxa. The results demonstrate the improved performance of the new method is due to (1) more appropriate priors on divergence-time and demographic parameters that avoid prohibitively small marginal likelihoods for models with more divergence events, and (2) the Dirichlet-process providing a flexible prior on divergence histories that does not strongly disfavor models with intermediate numbers of divergence events. The new method yields more robust estimates of posterior uncertainty, and thus greatly reduces the tendency to incorrectly estimate models of shared evolutionary history with strong support.Comment: 48 pages, 8 figures, 4 tables, 35 pages of supporting information with 1 supporting table and 33 supporting figure

Marginal likelihoods in phylogenetics: a review of methods and applications

By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marginal likelihoods are increasingly important. Here we try to provide an intuitive description of marginal likelihoods and why they are important in Bayesian model testing. We also categorize and review methods for estimating marginal likelihoods of phylogenetic models, highlighting several recent methods that provide well-behaved estimates. Furthermore, we review some empirical studies that demonstrate how marginal likelihoods can be used to learn about models of evolution from biological data. We discuss promising alternatives that can complement marginal likelihoods for Bayesian model choice, including posterior-predictive methods. Using simulations, we find one alternative method based on approximate-Bayesian computation (ABC) to be biased. We conclude by discussing the challenges of Bayesian model choice and future directions that promise to improve the approximation of marginal likelihoods and Bayesian phylogenetics as a whole.Comment: 33 pages, 3 figure

Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: A reply to Hickerson et al

Establishing that a set of population-splitting events occurred at the same time can be a potentially persuasive argument that a common process affected the populations. Oaks et al. (2013) assessed the ability of an approximate-Bayesian method (msBayes) to estimate such a pattern of simultaneous divergence across taxa, to which Hickerson et al. (2014) responded. Both papers agree the method is sensitive to prior assumptions and often erroneously supports shared divergences; the papers differ about the explanation and solution. Oaks et al. (2013) suggested the method's behavior is caused by the strong weight of uniform priors on divergence times leading to smaller marginal likelihoods of models with more divergence-time parameters (Hypothesis 1); they proposed alternative priors to avoid strongly weighted posteriors. Hickerson et al. (2014) suggested numerical approximation error causes msBayes analyses to be biased toward models of clustered divergences (Hypothesis 2); they proposed using narrow, empirical uniform priors. Here, we demonstrate that the approach of Hickerson et al. (2014) does not mitigate the method's tendency to erroneously support models of clustered divergences, and often excludes the true parameter values. Our results also show that the tendency of msBayes analyses to support models of shared divergences is primarily due to Hypothesis 1. This series of papers demonstrate that if our prior assumptions place too much weight in unlikely regions of parameter space such that the exact posterior supports the wrong model of evolutionary history, no amount of computation can rescue our inference. Fortunately, more flexible distributions that accommodate prior uncertainty about parameters without placing excessive weight in vast regions of parameter space with low likelihood increase the method's robustness and power to detect temporal variation in divergences.Comment: 24 pages, 4 figures, 1 table, 14 pages of supporting information with 10 supporting figure

Competitive Usability and the Catalogue: A Process for Justification and Selection of a Next-Generation Catalogue or Web-Scale Discovery System

This case study demonstrates how competitive usability testing informs the selection and purchase of a next-generation catalogue (NGC) or Web-scale discovery system (WSDS) to enhance a current library catalogue. Using competitive usability techniques, the authors explain how different NGCs and WSDSs solve issues that catalogue users may face when searching for materials in the online catalogue. The goal of this study is to provide a framework that identifies concrete evidence in support of purchase recommendations for an effective system that adequately addresses locally identified issues with catalogue searches. The process of selecting live system implementations from peer institutions is outlined. Steps include surveying library staff about their current library catalogue. Survey results and documented reference questions provided the foundation for user tasks created by testers for use in this study. This multifaceted research design resulted in a case study that captures current issues that users encounter in the discovery and access to library materials and shows how to include competitive usability techniques as part of a purchase rationale while assessing how well a variety of next-generation discovery and access systems address users’ issues.published or submitted for publicatio

KMC modeling of helium bubble clustering and evolution in BCC iron

The effect of helium in iron is an important issue in nuclear systems, as iron and iron alloys (steels) are the primary materials used for structural elements. Helium is known to cause embrittlement and decrease fatigue life, as well as aid creep and promote swelling. These effects can significantly alter the mechanical properties of the reactor materials, and generally lead to early failure and decreased part lifetimes. This is a concern in both fission and fusion systems. The precise role that helium, helium-vacancy clusters, and helium bubbles play in the material degradation processes described above are still only partially understood. Further understanding into the role helium plays in these phenomena is essential to predicting the lifetime of iron and steels in nuclear reactors. This work was motivated by the results found earlier by Okuniewski. Said work was primarily experimental work studying the effects of helium concentration on cluster size distribution. KMC simulations were run for comparison, but the results were inconsistent. Both with and without helium present, the results showed the KMC simulation resulted in a significant shift compared to the experimental results. The KMC simulations predicted a high density of small sized clusters, while the experimental results showed a lower density of larger sized clusters. This inconsistency was believed to be a result of the various parameters chosen in the KMC model. This work focused on two primary goals: first, to develop a flexible KMC code capable of simulating the desired models, and second, to explore the modeling assumptions made in the previous KMC simulations in an attempt to come closer to experimental results. Several different models for cluster interaction range, dissociation energy, and migration energy were considered, and a KMC code was designed and built to accommodate these and other models. The code design will be presented, along with performance benchmarking results. Both annealing and damage simulations were then performed with varying combinations of parameter models. The results of these simulations are compared and discussed

Submicrosecond comparisons of time standards via the Navigation Technology Satellites (NTS)

An interim demonstration was performed of the time transfer capability of the NAVSTAR GPS system using a single NTS satellite. Measurements of time difference (pseudo-range) are made from the NTS tracking network and at the participating observatories. The NTS network measurements are used to compute the NTS orbit trajectory. The central NTS tracking station has a time link to the Naval Observatory UTC (USNO,MC1) master clock. Measurements are used with the NTS receiver at the remote observatory, the time transfer value UTC (USNO,MC1)-UTC (REMOTE, VIA NTS) is calculated. Intercomparisons were computed using predicted values of satellite clock offset and ephemeus

A "Closed-Circuit" Flume for Suspended-Load Studies

Scope of suspended-load study—One phase of the study of fundamental problems of dynamics of stream-flow which confronts the Cooperative Laboratory of the Soil Conservation Service is the determination of the influence of suspended load upon flow-characteristics of a stream. Some of the aspects to be considered are: (a) The effect of suspended load on mean velocity, velocity-distribution, entrainment-force, competence, and capacity; and (b) variations of vertical distribution of suspended load with variations of change, variations of grain, and variations of material

Submicrosecond comparison of international clock synchronization by VLBI and the NTS satellite

The intercontinental clock synchronization capabilities of Very Long Baseline Interferometry (VLBI) and the Navigation Technology Satellite (NTS) were compared using both methods to synchronize the Cesium clocks at the NASA Deep Space Net complexes at Madrid, Spain and Goldstone, California. Verification of the accuracy of both systems was examined. The VLBI experiments used the Wideband VLBI Data Acquisition System developed at the NASA Jet Propulsion Laboratory. The NTS Satellites were designed and built by the Naval Research Laboratory used with NTS Timing Receivers developed by the Goddard Space Flight Center. The two methods agreed at about the one-half microsecond level

Al-Hawārī’s commentary on Ibn al-Bannā’’s Talkhīs: Contents and influences

In 1305 al-Hawārī completed his commentary on Ibn al-Bannā’’s famous arithmetic book Talkhī½ṣ aþmāl al-¬isāb . This is the only commentary, apart from Ibn al-Bannā’’s own, to have been written during the author’s lifetime. What distinguishes al-Hawārī’s book from the numerous later commentaries is its focus on numerical examples of the rules of calculation. We present here what we know about the author, his book, its salient features, and its influences