Natural selection. II. Developmental variability and evolutionary rate

In classical evolutionary theory, genetic variation provides the source of heritable phenotypic variation on which natural selection acts. Against this classical view, several theories have emphasized that developmental variability and learning enhance nonheritable phenotypic variation, which in turn can accelerate evolutionary response. In this paper, I show how developmental variability alters evolutionary dynamics by smoothing the landscape that relates genotype to fitness. In a fitness landscape with multiple peaks and valleys, developmental variability can smooth the landscape to provide a directly increasing path of fitness to the highest peak. Developmental variability also allows initial survival of a genotype in response to novel or extreme environmental challenge, providing an opportunity for subsequent adaptation. This initial survival advantage arises from the way in which developmental variability smooths and broadens the fitness landscape. Ultimately, the synergism between developmental processes and genetic variation sets evolutionary rate

Localization of adaptive variants in human genomes using averaged one-dependence estimation.

Statistical methods for identifying adaptive mutations from population genetic data face several obstacles: assessing the significance of genomic outliers, integrating correlated measures of selection into one analytic framework, and distinguishing adaptive variants from hitchhiking neutral variants. Here, we introduce SWIF(r), a probabilistic method that detects selective sweeps by learning the distributions of multiple selection statistics under different evolutionary scenarios and calculating the posterior probability of a sweep at each genomic site. SWIF(r) is trained using simulations from a user-specified demographic model and explicitly models the joint distributions of selection statistics, thereby increasing its power to both identify regions undergoing sweeps and localize adaptive mutations. Using array and exome data from 45 ‡Khomani San hunter-gatherers of southern Africa, we identify an enrichment of adaptive signals in genes associated with metabolism and obesity. SWIF(r) provides a transparent probabilistic framework for localizing beneficial mutations that is extensible to a variety of evolutionary scenarios

Adaptive foveated single-pixel imaging with dynamic super-sampling

As an alternative to conventional multi-pixel cameras, single-pixel cameras enable images to be recorded using a single detector that measures the correlations between the scene and a set of patterns. However, to fully sample a scene in this way requires at least the same number of correlation measurements as there are pixels in the reconstructed image. Therefore single-pixel imaging systems typically exhibit low frame-rates. To mitigate this, a range of compressive sensing techniques have been developed which rely on a priori knowledge of the scene to reconstruct images from an under-sampled set of measurements. In this work we take a different approach and adopt a strategy inspired by the foveated vision systems found in the animal kingdom - a framework that exploits the spatio-temporal redundancy present in many dynamic scenes. In our single-pixel imaging system a high-resolution foveal region follows motion within the scene, but unlike a simple zoom, every frame delivers new spatial information from across the entire field-of-view. Using this approach we demonstrate a four-fold reduction in the time taken to record the detail of rapidly evolving features, whilst simultaneously accumulating detail of more slowly evolving regions over several consecutive frames. This tiered super-sampling technique enables the reconstruction of video streams in which both the resolution and the effective exposure-time spatially vary and adapt dynamically in response to the evolution of the scene. The methods described here can complement existing compressive sensing approaches and may be applied to enhance a variety of computational imagers that rely on sequential correlation measurements.Comment: 13 pages, 5 figure

A fast patch-dictionary method for whole image recovery

Various algorithms have been proposed for dictionary learning. Among those for image processing, many use image patches to form dictionaries. This paper focuses on whole-image recovery from corrupted linear measurements. We address the open issue of representing an image by overlapping patches: the overlapping leads to an excessive number of dictionary coefficients to determine. With very few exceptions, this issue has limited the applications of image-patch methods to the local kind of tasks such as denoising, inpainting, cartoon-texture decomposition, super-resolution, and image deblurring, for which one can process a few patches at a time. Our focus is global imaging tasks such as compressive sensing and medical image recovery, where the whole image is encoded together, making it either impossible or very ineffective to update a few patches at a time. Our strategy is to divide the sparse recovery into multiple subproblems, each of which handles a subset of non-overlapping patches, and then the results of the subproblems are averaged to yield the final recovery. This simple strategy is surprisingly effective in terms of both quality and speed. In addition, we accelerate computation of the learned dictionary by applying a recent block proximal-gradient method, which not only has a lower per-iteration complexity but also takes fewer iterations to converge, compared to the current state-of-the-art. We also establish that our algorithm globally converges to a stationary point. Numerical results on synthetic data demonstrate that our algorithm can recover a more faithful dictionary than two state-of-the-art methods. Combining our whole-image recovery and dictionary-learning methods, we numerically simulate image inpainting, compressive sensing recovery, and deblurring. Our recovery is more faithful than those of a total variation method and a method based on overlapping patches