Bayesian inference of natural selection from allele frequency time series

The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such direct observations of allele frequency dynamics are expected to be more powerful than inferences made using patterns of linked neutral variation obtained from modern individuals. We develop a Bayesian method to make use of allele frequency time series data and infer the parameters of general diploid selection, along with allele age, in non-equilibrium populations. We introduce a novel path augmentation approach, in which we use Markov chain Monte Carlo to integrate over the space of allele frequency trajectories consistent with the observed data. Using simulations, we show that this approach has good power to estimate selection coefficients and allele age. Moreover, when applying our approach to data on horse coat color, we find that ignoring a relevant demographic history can significantly bias the results of inference. Our approach is made available in a C++ software package.Comment: 27 page

Political Factors and the Adoption of the Merit System of Judicial Selection

There is widespread debate among politicians and academics as to the effectiveness and appropriateness of the merit system of judicial selection. Much of the literature on this subject is dedicated to the effects of the merit system after it has been adopted. The purpose of this paper was to examine the effects of certain political factors that may have created a political environment conducive to the adoption of the merit system. In this paper, three hypotheses were postulated and subsequently tested. The results of each test, while not as conclusive as anticipated, confirmed each of the hypotheses. The first conclusion of this study was that states are more likely than not to have the same party in control of both houses of the state legislature. The second conclusion was that states that adopted the merit system experienced a smaller amount of majority-party change in both houses of their legislatures prior to the adoption of the merit system than states that did not adopt the merit system. The final conclusion was that most states are more likely to adopt the merit system when they are bordered by other states that have the merit system

Semper Fi? The Infidelity of the Seventh Circuit in Applying a Good Moral Character Requirement to Naturalizing War Veterans

In a case of first impression, the Seventh Circuit misinterpreted naturalization statutes to hold that a good moral character requirement is applicable to aliens who served honorably in the military during times of war. The obligation of naturalizing aliens to show good moral character is listed among the residency requirements of 8 U.S.C.S. § 1427. However, 8 U.S.C.S. § 1440 excuses alien wartime veterans from making this showing by exempting them from the residency requirements in 8 U.S.C.S. § 1427. In supporting its position that alien wartime veterans must prove good moral character in order to naturalize, the Seventh Circuit misquoted a key naturalization statute and misinterpreted several others. The Seventh Circuit should have held that, based on a plain reading of 8 U.S.C.S. §§ 1427 and 1440, a showing of good moral character is not required from alien wartime veterans seeking to naturalize

Semper Fi? The Infidelity of the Seventh Circuit in Applying a Good Moral Character Requirement to Naturalizing War Veterans

In a case of first impression, the Seventh Circuit misinterpreted naturalization statutes to hold that a good moral character requirement is applicable to aliens who served honorably in the military during times of war. The obligation of naturalizing aliens to show good moral character is listed among the residency requirements of 8 U.S.C.S. § 1427. However, 8 U.S.C.S. § 1440 excuses alien wartime veterans from making this showing by exempting them from the residency requirements in 8 U.S.C.S. § 1427. In supporting its position that alien wartime veterans must prove good moral character in order to naturalize, the Seventh Circuit misquoted a key naturalization statute and misinterpreted several others. The Seventh Circuit should have held that, based on a plain reading of 8 U.S.C.S. §§ 1427 and 1440, a showing of good moral character is not required from alien wartime veterans seeking to naturalize

Fixing a Non-Existent Problem with an Ineffective Solution: Doe v. Snyder and Michigan\u27s Punitive Sex Offender Registration and Notification Laws

Sex offender registration and notification laws (SORAs) in the United States apply not only to those who commit sex offenses after the enactment of such laws, but also to those who committed sex offenses before those laws were enacted. However, the Ex Post Facto Clause of the Constitution prevents the retroactive application of a punitive law; this means that a person cannot be punished for a bad act that the person committed before the law punishing that act was enacted. Importantly, the Ex Post Facto Clause does not prohibit the retroactive application of a civil, regulatory—i.e., non-punitive—law. Thus, to survive constitutional scrutiny, SORAs must be deemed civil, regulatory measures that are designed to achieve a non-punitive goal. The federal courts—including the United States Supreme Court—have consistently characterized SORAs as just that: non-punitive, civil, regulatory measures designed to protect the innocent from dangerous sex offenders by deterring the commission of subsequent sex offenses. Thus, the constitutionality of SORAs rests on two fundamental assumptions: (1) that sex offenders recidivate at very high rates; and (2) that restrictive SORAs actually reduce recidivism. The Sixth Circuit, in its Doe v. Snyder decision, which reviewed the constitutionality of Michigan’s SORA, carefully examined these assumptions and found that both were false. Federal government recidivism data and social science studies show that sex offenders—a category that includes not just those convicted of rape, but also includes a high school senior convicted of statutory rape because he slept with his underage high school girlfriend—do not recidivate at high rates. In fact, most sex offenders recidivate at low rates. Moreover, SORAs do not reduce recidivism; some studies even indicate that such laws may be causing recidivism rates to increase. Thus, the Sixth Circuit found that Michigan’s SORA unconstitutionally violated the Ex Post Facto Clause, in large part because it lacked a rational connection to a non-punitive purpose. This Article carefully examines the available data on sex offender recidivism rates, as well as the failure of the federal courts (prior to the Sixth Circuit’s Doe v. Snyder decision) to give much more than a passing glance at that data. This Article proposes that other federal courts should follow the Sixth Circuit’s example and carefully examine the factual justifications upon which the constitutionality of SORAs rests. Only then will the federal courts be able to protect the rights of United States’ citizens to be free from unconstitutional ex post facto punishment

Using Urban Farmer Perceptions of Urban Agricultural Resources to Inform Extension Programming: A Q Methodology Study

Urban farmers face challenges as they work among traditionally underserved populations, are new to farming, and may not recognize the resources available to them. The United States Department of Agriculture (USDA) prioritizes urban food production research and has recognized the unique challenges faced by urban farmers. The purpose of this study was to better understand the perspectives of urban farmers toward urban agricultural resources. Using the USDA Urban Agricultural Toolkit (2016) as a conceptual framework, this study found three perspectives of Oklahoma agricultural producers regarding urban agricultural resource challenges: The Visionary Farmer, The Business-minded Farmer, and The Learning Farmer. Visionary Farmers emphasize the application of urban agriculture toward urban social and community-building needs. Business-minded Farmers recognize the need for economic and financial education and resources for urban farmers. Learning Farmers highlight the need for continued agricultural education in urban agricultural operations. The findings suggest an opportunity for Extension and farmer-serving agencies to provide innovative communication, programming and support designed to address the unique struggles of urban farmers

Temporal data fusion approaches to remote sensing-based wetland classification

This thesis investigates the ecology of wetlands and associated classification in prairie and boreal environments of Alberta, Canada, using remote sensing technology to enhance classification of wetlands in the province. Objectives of the thesis are divided into two case studies, 1) examining how satellite borne Synthetic Aperture Radar (SAR), optical (RapidEye & SPOT) can be used to evaluate surface water trends in a prairie pothole environment (Shepard Slough); and 2) investigating a data fusion methodology combining SAR, optical and Lidar data to characterize wetland vegetation and surface water attributes in a boreal environment (Utikuma Regional Study Area (URSA)). Surface water extent and hydroperiod products were derived from SAR data, and validated using optical imagery with high accuracies (76-97% overall) for both case studies. High resolution Lidar Digital Elevation Models (DEM), Digital Surface Models (DSM), and Canopy Height Model (CHM) products provided the means for data fusion to extract riparian vegetation communities and surface water; producing model accuracies of (R2 0.90) for URSA, and RMSE of 0.2m to 0.7m at Shepard Slough when compared to field and optical validation data. Integration of Alberta and Canadian wetland classifications systems used to classify and determine economic value of wetlands into the methodology produced thematic maps relevant for policy and decision makers for potential wetland monitoring and policy development.Funding for this thesis was provided by the NSERC CREATE AMETHYST Program, and the Government of Alberta (Economic Development and Trade, Environment and Parks), Campus Alberta Innovates Program

Can Foot Exercises Alter Foot Posture, Strength, and Walking Foot Pressure Patterns in People with Severe Flat Foot?

Introduction/Purpose: Muscle training muscle control for barefoot running (i.e. doming seated[DS] and standing[DSt]) and post foot and ankle injury (i.e. seated plantar flexion and inversion[SPFI]) are common. Although studies demonstrated improvement in foot posture (validated foot posture index [FPI]) immediately following a 4-week exercise program this was not assessed in people with flatfoot. Also, more rigorous assessment of foot function is lacking (i.e. foot posture, strength, and plantar pressure during walking). There is clearly a need for more rigorous clinical data on the effect of foot exercises. The purpose of this pilot study was to assess the immediate effect of a 4-week exercise program on a comprehensive assessment of foot function to evaluate the potential for a more rigorous clinical trial