Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum

The sample frequency spectrum (SFS) of DNA sequences from a collection of individuals is a summary statistic which is commonly used for parametric inference in population genetics. Despite the popularity of SFS-based inference methods, currently little is known about the information-theoretic limit on the estimation accuracy as a function of sample size. Here, we show that using the SFS to estimate the size history of a population has a minimax error of at least $O(1/\log s)$, where $s$ is the number of independent segregating sites used in the analysis. This rate is exponentially worse than known convergence rates for many classical estimation problems in statistics. Another surprising aspect of our theoretical bound is that it does not depend on the dimension of the SFS, which is related to the number of sampled individuals. This means that, for a fixed number $s$ of segregating sites considered, using more individuals does not help to reduce the minimax error bound. Our result pertains to populations that have experienced a bottleneck, and we argue that it can be expected to apply to many populations in nature.Comment: 17 pages, 1 figur

Multi-locus analysis of genomic time series data from experimental evolution.

Genomic time series data generated by evolve-and-resequence (E&R) experiments offer a powerful window into the mechanisms that drive evolution. However, standard population genetic inference procedures do not account for sampling serially over time, and new methods are needed to make full use of modern experimental evolution data. To address this problem, we develop a Gaussian process approximation to the multi-locus Wright-Fisher process with selection over a time course of tens of generations. The mean and covariance structure of the Gaussian process are obtained by computing the corresponding moments in discrete-time Wright-Fisher models conditioned on the presence of a linked selected site. This enables our method to account for the effects of linkage and selection, both along the genome and across sampled time points, in an approximate but principled manner. We first use simulated data to demonstrate the power of our method to correctly detect, locate and estimate the fitness of a selected allele from among several linked sites. We study how this power changes for different values of selection strength, initial haplotypic diversity, population size, sampling frequency, experimental duration, number of replicates, and sequencing coverage depth. In addition to providing quantitative estimates of selection parameters from experimental evolution data, our model can be used by practitioners to design E&R experiments with requisite power. We also explore how our likelihood-based approach can be used to infer other model parameters, including effective population size and recombination rate. Then, we apply our method to analyze genome-wide data from a real E&R experiment designed to study the adaptation of D. melanogaster to a new laboratory environment with alternating cold and hot temperatures

Reformation of the EC Competition Policy on Vertical Restraints

In the present article, I present the main issues surrounding the reform process, its reasoning and the result it brought to the European Community\u27s ( EC ) competition policy on vertical restraints. Furthermore, I summarize some of the reactions by other bodies of the EC and industry sectors toward this reform process. Finally, I will discuss the responses by business toward these changes in the EC rules to vertical restraints and the way enterprises will operate in the Member States of the EC

A stratigraphic concept for Middle Pleistocene Quaternary sequences in Upper Austria

Auf den mittelpleistozänen fluvioglazialen Terrassen der Traun-Enns-Platte in der Region um Wels (Oberösterreich) wurden drei Löss-/Paläobodensequenzen untersucht. Jedes dieser Profile ist für mittelpleistozäne Abfolgen im nordöstlichen Alpenvorland charakteristisch. Die Profile umfassen mächtige Pedokomplexe, welche eine Differenzierung und Einstufung von interglazialen Paläoböden erlauben. Die Löss-/Paläobodensequenz von Oberlaab ist auf der fluvioglazialen Terrasse des Mindel-Glazials im klassischen Sinne entwickelt (Jüngere Deckenschotter) und weist vier interglaziale Paläoböden auf. Diese Tatsache macht eine Einstufung der Jüngeren Deckenschotter mindestens in die fünftletzte Kaltzeit wahrscheinlich (MIS 12). Die Deckschichten auf den Günz-Deckenschottern im klassischen Sinn (Ältere Deckenschotter) beinhalten fünf Paläoböden. Beide Lokalitäten weisen eine sehr intensive Pedogenese in ihrem basalen Pedokomplex auf, die wesentlich ausgeprägter ist, als in den überlagernden Paläoböden. Die pedostratigraphischen Ergebnisse lassen eine Einstufung der Älteren Deckenschotter mindestens ins MIS 16 zu

Reformation of the EC Competition Policy on Vertical Restraints

In the present article, I present the main issues surrounding the reform process, its reasoning and the result it brought to the European Community\u27s ( EC ) competition policy on vertical restraints. Furthermore, I summarize some of the reactions by other bodies of the EC and industry sectors toward this reform process. Finally, I will discuss the responses by business toward these changes in the EC rules to vertical restraints and the way enterprises will operate in the Member States of the EC

The Kalmanson Complex

Let X be a finite set of cardinality n. The Kalmanson complex K_n is the simplicial complex whose vertices are non-trivial X-splits, and whose facets are maximal circular split systems over X. In this paper we examine K_n from three perspectives. In addition to the T-theoretic description, we show that K_n has a geometric realization as the Kalmanson conditions on a finite metric. A third description arises in terms of binary matrices which possess the circular ones property. We prove the equivalence of these three definitions. This leads to a simplified proof of the well-known equivalence between Kalmanson and circular decomposable metrics, as well as a partial description of the f-vector of K_n.Comment: Improved exposition. 24 pages, 2 figures, 1 tabl

Academic Barriers for Migrant Middle School Students in Salinas, California

The educational barriers facing migrant students are examined in this research based on the experiences of teachers and Mexican migrant middle school students in Salinas, California. Through the research, I ask if academic barriers for migrant students differ from obstacles of their peers and if so, what are those differences? The barriers to migrant students’ education were explored through a literature review, examining themes of parental involvement, teacher–student relationships, student self-esteem, and the use of educational programs. Through snowball sampling, semi-structured interviews, and surveys, data were collected from four teachers and 18 migrant students to understand how these themes manifested and affected educational experiences. Research results have shown that positive teacher–student relationships were dependent on respect and understanding of one’s cultural background. Both academic and migration stresses affected student self-esteem and attitude towards schooling. Educational programs organized by various educational institutions helped students develop skills needed to meet state testing requirements despite outside social and cultural factors. Interviews demonstrated parents’ inability to support their children academically due to educational, language, or working restrictions. This research contributes to an increased understanding of migrant education by identifying and analyzing consistent experiences of migrant students within the American educational system

Systemic infection induced by Campylobacter jejuni: Development of a mouse model and elucidation of molecular mechanisms

Campylobacter jejuni clone SA has emerged as the predominant cause of Campylobacter-associated ovine abortion in the U.S., and this clone is highly pathogenic in pregnant sheep and guinea pigs. To induce abortion, orally ingested Campylobacter must be able to translocate across the intestinal epithelium and spread systemically. To understand the pathogenic mechanisms and immune protection of C. jejuni-induced abortion, it is necessary to develop a cost-effective animal model to evaluate systemic infection induced by this pathogenic clone. In this study, two different breeds of female mice (BALB/c and CD-1) were orally inoculated with C. jejuni IA3902, a clinical clone SA isolate whose complete genome sequence has been determined, to evaluate the induction of bacteremia and hepatic infection. Our results revealed that CD-1 mice were more susceptible than BALB/c mice to infection by IA3902. In CD-1 mice, C. jejuni IA3902 induced bacteremia and hepatic infection within 1 hour after oral inoculation, and bacteremia peaked at 8 and/or 12 hours after inoculation. Compared with IA3902, the magnitude and duration of bacteremia and hepatic infection induced by C. jejuni strains NCTC 11168 and 81-176 were significantly less prominent, indicating that IA3902 is more virulent than the other strains tested with regard to systemic spread. Mutagenesis in IA3902 showed that the loss of the capsule (ÄkpsS) completely prevented the organism from causing bacteremia and hepatic infection, while the loss of pVir plasmid did not affect systemic spread. These findings indicate that the CD-1 mouse model is suitable for examining critical steps of Campylobacter pathogenesis and identify the capsule as a key virulence factor of this pathogenic organism to induce bacteremia

Inference of Population History using Coalescent HMMs: Review and Outlook

Studying how diverse human populations are related is of historical and anthropological interest, in addition to providing a realistic null model for testing for signatures of natural selection or disease associations. Furthermore, understanding the demographic histories of other species is playing an increasingly important role in conservation genetics. A number of statistical methods have been developed to infer population demographic histories using whole-genome sequence data, with recent advances focusing on allowing for more flexible modeling choices, scaling to larger data sets, and increasing statistical power. Here we review coalescent hidden Markov models, a powerful class of population genetic inference methods that can effectively utilize linkage disequilibrium information. We highlight recent advances, give advice for practitioners, point out potential pitfalls, and present possible future research directions.Comment: 12 pages, 2 figure