Mutation-biased adaptation in Andean house wrens

Genes, proteins, and genomes are pervasively shaped by biases in mutation that exert their influence by biasing rates of evolutionary change. Indeed, methods of phylogeny inference routinely assume that evolutionary rates will reflect transition–transversion bias and other common mutational biases. This influence is typically attributed to neutral evolution, presuming that mutation is a weak force easily overcome by selection, so that any noticeable effect of mutation must signal a lack of selection. However, in PNAS Galen et al. (1) propose a case of mutation-biased adaptation, in which the course of evolution reflects both a bias in mutation and a fitness benefit. How important are mutational biases in shaping adaptation? Are internal sources of orientation or direction in evolution—once dismissed as improbable (2)—more important than previously imagined

Minimum Epistasis Interpolation for Sequence-Function Relationships

Massively parallel phenotyping assays have provided unprecedented insight into how multiple mutations combine to determine biological function. While such assays can measure phenotypes for thousands to millions of genotypes in a single experiment, in practice these measurements are not exhaustive, so that there is a need for techniques to impute values for genotypes whose phenotypes have not been directly assayed. Here, we present an imputation method based on inferring the least epistatic possible sequence-function relationship compatible with the data. In particular, we infer the reconstruction where mutational effects change as little as possible across adjacent genetic backgrounds. The resulting models can capture complex higher-order genetic interactions near the data, but approach additivity where data is sparse or absent. We apply the method to high-throughput transcription factor binding assays and use it to explore a fitness landscape for protein G

Transcriptional errors and the drift barrier

Population genetics predicts that the balance between natural selection and genetic drift is determined by the population size. Species with large population sizes are predicted to have properties governed mainly by selective forces; whereas species with small population sizes should exhibit features governed by mutational processes alone. This “drift-barrier hypothesis” has been successful in explaining extensive variation in genome size, mutation rate, transposable element abundance, and other molecular features across diverse taxa (1⇓–3). However, in PNAS Traverse and Ochman (4) report a striking exception to this theory by showing that transcriptional error rates are nearly equal across several bacterial species with very different population sizes

E-Voting in an ubicomp world: trust, privacy, and social implications

The advances made in technology have unchained the user from the desktop into interactions where access is anywhere, anytime. In addition, the introduction of ubiquitous computing (ubicomp) will see further changes in how we interact with technology and also socially. Ubicomp evokes a near future in which humans will be surrounded by “always-on,” unobtrusive, interconnected intelligent objects where information is exchanged seamlessly. This seamless exchange of information has vast social implications, in particular the protection and management of personal information. This research project investigates the concepts of trust and privacy issues specifically related to the exchange of e-voting information when using a ubicomp type system

Predicting evolution and visualizing high-dimensional fitness landscapes

The tempo and mode of an adaptive process is strongly determined by the structure of the fitness landscape that underlies it. In order to be able to predict evolutionary outcomes (even on the short term), we must know more about the nature of realistic fitness landscapes than we do today. For example, in order to know whether evolution is predominantly taking paths that move upwards in fitness and along neutral ridges, or else entails a significant number of valley crossings, we need to be able to visualize these landscapes: we must determine whether there are peaks in the landscape, where these peaks are located with respect to one another, and whether evolutionary paths can connect them. This is a difficult task because genetic fitness landscapes (as opposed to those based on traits) are high-dimensional, and tools for visualizing such landscapes are lacking. In this contribution, we focus on the predictability of evolution on rugged genetic fitness landscapes, and determine that peaks in such landscapes are highly clustered: high peaks are predominantly close to other high peaks. As a consequence, the valleys separating such peaks are shallow and narrow, such that evolutionary trajectories towards the highest peak in the landscape can be achieved via a series of valley crossingsComment: 12 pages, 7 figures. To appear in "Recent Advances in the Theory and Application of Fitness Landscapes" (A. Engelbrecht and H. Richter, eds.). Springer Series in Emergence, Complexity, and Computation, 201

Perineal Assessment and Repair Longitudinal Study (PEARLS): a matched-pair cluster randomized trial.

Perineal trauma during childbirth affects millions of women worldwide every year. The aim of the Perineal Assessment and Repair Longitudinal Study (PEARLS) was to improve maternal clinical outcomes following childbirth through an enhanced cascaded multiprofessional training program to support implementation of evidence-based perineal management

How individuals change language

Languages emerge and change over time at the population level though interactions between individual speakers. It is, however, hard to directly observe how a single speaker's linguistic innovation precipitates a population-wide change in the language, and many theoretical proposals exist. We introduce a very general mathematical model that encompasses a wide variety of individual-level linguistic behaviours and provides statistical predictions for the population-level changes that result from them. This model allows us to compare the likelihood of empirically-attested changes in definite and indefinite articles in multiple languages under different assumptions on the way in which individuals learn and use language. We find that accounts of language change that appeal primarily to errors in childhood language acquisition are very weakly supported by the historical data, whereas those that allow speakers to change incrementally across the lifespan are more plausible, particularly when combined with social network effects

The interpretations and uses of fitness landscapes in the social sciences

__Abstract__ This working paper precedes our full article entitled “The evolution of Wright’s (1932) adaptive field to contemporary interpretations and uses of fitness landscapes in the social sciences” as published in the journal Biology & Philosophy (http://link.springer.com/article/10.1007/s10539-014-9450-2). The working paper features an extended literature overview of the ways in which fitness landscapes have been interpreted and used in the social sciences, for which there was not enough space in the full article. The article features an in-depth philosophical discussion about the added value of the various ways in which fitness landscapes are used in the social sciences. This discussion is absent in the current working paper. Th

Hybrid nanoparticles based on sulfides, oxides, and carbides

The methods for synthesis of hybrid nanoparticles based on sulfides, oxides, and carbides of heavy and transition metals were considered. The problem of the influence of the method of synthesis of the hybrid nanoparticles on their atomic structure, morphology of the nanomaterials, and functional properties was analyzed. The areas of practical use of the hybrid nanoparticles were proposed. © 2013 Springer Science+Business Media New York