Trees of Unusual Size: Biased Inference of Early Bursts from Large Molecular Phylogenies

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive radiations. One often-overlooked source of bias in these studies is that of sampling at the level of whole clades, as researchers tend to choose large, speciose clades to study. In this paper, we investigate the performance of common methods across the distribution of clade sizes that can be generated by a constant-rate birth-death process. Clades which are larger than expected for a given constant-rate branching process tend to show a pattern of an early burst even when both speciation and extinction rates are constant through time. All methods evaluated were susceptible to detecting this false signature when extinction was low. Under moderate extinction, both the gamma-statistic and diversity-dependent models did not detect such a slowdown but only because the signature of a slowdown was masked by subsequent extinction. Some models which estimate time-varying speciation rates are able to detect early bursts under higher extinction rates, but are extremely prone to sampling bias. We suggest that examining clades in isolation may result in spurious inferences that rates of diversification have changed through time.Comment: 17 pages, 5 figure

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

<p>Abstract</p> <p>Background</p> <p>One of the main explanations for the stunning diversity of teleost fishes (~29,000 species, nearly half of all vertebrates) is that a fish-specific whole-genome duplication event (FSGD) in the ancestor to teleosts triggered their subsequent radiation. However, one critical assumption of this hypothesis, that diversification rates in teleosts increased soon after the acquisition of a duplicated genome, has never been tested.</p> <p>Results</p> <p>Here we show that one of three major diversification rate shifts within ray-finned fishes occurred at the base of the teleost radiation, as predicted by the FSGD hypothesis. We also find evidence for two rate increases that are much younger than the inferred age of the FSGD: one in the common ancestor of most ostariophysan fishes, and a second one in the common ancestor of percomorphs. The biodiversity contained within these two clades accounts for more than 88% of living fish species.</p> <p>Conclusion</p> <p>Teleosts diversified explosively in their early history and this burst of diversification may have been caused by genome duplication. However, the FSGD itself may be responsible for a little over 10% of living teleost biodiversity. ~88% of species diversity is derived from two relatively recent radiations of freshwater and marine fishes where genome duplication is not suspected. Genome duplications are a common event on the tree of life and have been implicated in the diversification of major clades like flowering plants, vertebrates, and gnathostomes. However our results suggest that the causes of diversification in large clades are likely to be complex and not easily ascribed to a single event, even a dramatic one such as a whole genome duplication.</p

AC Power Monitoring System Provides Individual Circuit Energy Consumption Data

Motivated by high energy costs, people and organizations want to cut back on their energy consumption. However, the only feedback consumers typically receive is a monthly bill listing their total electricity usage (in kWh). Some companies have begun developing systems that allow households and organizations to monitor their energy usage for individual circuits. Available systems are expensive so a CU engineering senior design team has designed, fabricated, and tested a system for use at Cedarville University. The AC power monitoring system has the ability to measure energy consumption for each individual circuit in the breaker panel, store the data, and then provide the user with visual feedback on energy usage behavior. The basic system provides the proof of concept for future senior design teams. After more testing is completed, further development of this product will be needed by other senior design teams. Eventually, this energy monitoring system could be expanded to include larger loads such as HVAC systems and refrigeration units. It is also envisioned that future projects might be able to provide the user with suggestions for changing and improving energy usage behavior. Failure prediction of equipment on individual circuits could also stem from this initial project. For this project, it has been clearly shown that the concept is feasible, expandable, and cost-effective

AC Power Monitoring System

Motivated by high energy costs, people and organizations want to cut back on their energy consumption. However, the only feedback consumers typically receive is a monthly bill listing their total electricity usage (in kWh). Some companies have begun developing systems that allow households and organizations to monitor their energy usage for individual circuits. Available systems are expensive so a CU engineering senior design team has designed, fabricated, and tested a system for use at Cedarville University. The AC power monitoring system has the ability to measure energy consumption for each individual circuit in the breaker panel, store the data, and then provide the user with visual feedback on energy usage behavior. The basic system provides the proof of concept for future senior design teams. After more testing is completed, further development of this product will be needed by other senior design teams. Eventually, this energy monitoring system could be expanded to include larger loads such as HVAC systems and refrigeration units. It is also envisioned that future projects might be able to provide the user with suggestions for changing and improving energy usage behavior. Failure prediction of equipment on individual circuits could also stem from this initial project. For this project, it has been clearly shown that the concept is feasible, expandable, and cost-effective

HERatio: Homomorphic Encryption of Rationals using Laurent Polynomials

In this work we present $\mathsf{HERatio}$, a homomorphic encryption scheme that builds on the scheme of Brakerski, and Fan and Vercauteren. Our scheme naturally accepts Laurent polynomials as inputs, allowing it to work with rationals via their bounded base-$b$ expansions. This eliminates the need for a specialized encoder and streamlines encryption, while maintaining comparable efficiency to BFV. To achieve this, we introduce a new variant of the Polynomial Learning With Errors (PLWE) problem which employs Laurent polynomials instead of the usual ``classic\u27\u27 polynomials, and provide a reduction to the PLWE problem

Inference of evolutionary jumps in large phylogenies using Lévy processes

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson’s hypothesis

PIE: pp-adic Encoding for High-Precision Arithmetic in Homomorphic Encryption

A large part of current research in homomorphic encryption (HE) aims towards making HE practical for real-world applications. In any practical HE, an important issue is to convert the application data (type) to the data type suitable for the HE. The main purpose of this work is to investigate an efficient HE-compatible encoding method that is generic, and can be easily adapted to apply to the HE schemes over integers or polynomials. $p$-adic number theory provides a way to transform rationals to integers, which makes it a natural candidate for encoding rationals. Although one may use naive number-theoretic techniques to perform rational-to-integer transformations without reference to $p$-adic numbers, we contend that the theory of $p$-adic numbers is the proper lens to view such transformations. In this work we identify mathematical techniques (supported by $p$-adic number theory) as appropriate tools to construct a generic rational encoder which is compatible with HE. Based on these techniques, we propose a new encoding scheme PIE, that can be easily combined with both AGCD-based and RLWE-based HE to perform high precision arithmetic. After presenting an abstract version of PIE, we show how it can be attached to two well-known HE schemes: the AGCD-based IDGHV scheme and the RLWE-based (modified) Fan-Vercauteren scheme. We also discuss the advantages of our encoding scheme in comparison with previous works