Selective Sampling with Drift

Recently there has been much work on selective sampling, an online active learning setting, in which algorithms work in rounds. On each round an algorithm receives an input and makes a prediction. Then, it can decide whether to query a label, and if so to update its model, otherwise the input is discarded. Most of this work is focused on the stationary case, where it is assumed that there is a fixed target model, and the performance of the algorithm is compared to a fixed model. However, in many real-world applications, such as spam prediction, the best target function may drift over time, or have shifts from time to time. We develop a novel selective sampling algorithm for the drifting setting, analyze it under no assumptions on the mechanism generating the sequence of instances, and derive new mistake bounds that depend on the amount of drift in the problem. Simulations on synthetic and real-world datasets demonstrate the superiority of our algorithms as a selective sampling algorithm in the drifting setting

Concepts of Drift and Selection in “The Great Snail Debate” of the 1950s and Early 1960s

Recently, much philosophical discussion has centered on the best way to characterize the concepts of random drift and natural selection, and, in particular, on the question of whether selection and drift can be conceptually distinguished (Beatty 1984; Brandon 2005; Hodge 1983, 1987; Millstein 2002, 2005; Pfeifer 2005; Shanahan 1992; Stephens 2004). These authors all contend, to a greater or lesser degree, that their concepts make sense of biological practice. So, it should be instructive to see how the concepts of drift and selection were distinguished by the disputants in a high-profile debate; debates such as these often force biologists to take a more philosophical turn, discussing the concepts at issue in greater detail than usual. A prime candidate for just such a case study is what William Provine (1986) has termed “The Great Snail Debate,” that is, the debate over the highly polymorphic land snails Cepaea nemoralis and Cepaea hortensis in the 1950s and early 1960s. This study will reveal that much of the present-day confusion over the concepts of drift and selection is rooted in confusions of the past. Nonetheless, there are lessons that can be learned about nonadaptiveness, indiscriminate sampling, and causality with respect to these two concepts. In particular, this paper will shed light on the following questions: 1) What is “drift”? Is “drift” a purely mathematical construct, a physical process analogous to the indiscriminate sampling of balls from an urn, or the outcome of a sampling process? 2) What is “nonadaptiveness,” and is a proponent of drift committed to claims that organisms’ traits are nonadaptive? 3) Can disputes concerning selection and drift be settled by statistics alone, or is causal information essential? If causal information is essential, what does that say about the concepts of “drift” and “selection” themselves

Session 4: Evolutionary Indeterminism

Proceedings of the Pittsburgh Workshop in History and Philosophy of Biology, Center for Philosophy of Science, University of Pittsburgh, March 23-24 2001 Session 4: Evolutionary Indeterminis

Coalescence 2.0: a multiple branching of recent theoretical developments and their applications

Population genetics theory has laid the foundations for genomics analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species. Identifying SNPs under natural selection and underpinning species adaptation relies on disentangling the respective contribution of random processes (mutation, drift, migration) from that of selection on nucleotide variability. Most theory and statistical tests have been developed using the Kingman coalescent theory based on the Wright-Fisher population model. However, these theoretical models rely on biological and life-history assumptions which may be violated in many prokaryote, fungal, animal or plant species. Recent theoretical developments of the so called multiple merger coalescent models are reviewed here ({\Lambda}-coalescent, beta-coalescent, Bolthausen-Snitzman, {\Xi}-coalescent). We explicit how these new models take into account various pervasive ecological and biological characteristics, life history traits or life cycles which were not accounted in previous theories such as 1) the skew in offspring production typical of marine species, 2) fast adapting microparasites (virus, bacteria and fungi) exhibiting large variation in population sizes during epidemics, 3) the peculiar life cycles of fungi and bacteria alternating sexual and asexual cycles, and 4) the high rates of extinction-recolonization in spatially structured populations. We finally discuss the relevance of multiple merger models for the detection of SNPs under selection in these species, for population genomics of very large sample size and advocate to potentially examine the conclusion of previous population genetics studies.Comment: 3 Figure

The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data.

Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. These approaches have been motivated by the intuition that properly accounting for the population size history can significantly improve estimates of selective strengths. However, the improvement in inference accuracy that can be attained by modeling drift has not been characterized. Here, by comparing maximum likelihood estimates of selection coefficients that account for the true population size history with estimates that ignore drift by assuming allele frequencies evolve deterministically in a population of infinite size, we address the following questions: how much can modeling the population size history improve estimates of selection coefficients? How much can mis-inferred population sizes hurt inferences of selection coefficients? We conduct our analysis under the discrete Wright-Fisher model by deriving the exact probability of an allele frequency trajectory in a population of time-varying size and we replicate our results under the diffusion model. For both models, we find that ignoring drift leads to estimates of selection coefficients that are nearly as accurate as estimates that account for the true population history, even when population sizes are small and drift is high. This result is of interest because inference methods that ignore drift are widely used in evolutionary studies and can be many orders of magnitude faster than methods that account for population sizes

Inferring the Distribution of Selective Effects from a Time Inhomogeneous Model

We have developed a Poisson random field model for estimating the distribution of selective effects of newly arisen nonsynonymous mutations that could be observed as polymorphism or divergence in samples of two related species under the assumption that the two species populations are not at mutation-selection-drift equilibrium. The model is applied to 91Drosophila genes by comparing levels of polymorphism in an African population of D. melanogaster with divergence to a reference strain of D. simulans. Based on the difference of gene expression level between testes and ovaries, the 91 genes were classified as 33 male-biased, 28 female-biased, and 30 sex-unbiased genes. Under a Bayesian framework, Markov chain Monte Carlo simulations are implemented to the model in which the distribution of selective effects is assumed to be Gaussian with a mean that may differ from one gene to the other to sample key parameters. Based on our estimates, the majority of newly-arisen nonsynonymous mutations that could contribute to polymorphism or divergence in Drosophila species are mildly deleterious with a mean scaled selection coefficient of -2.81, while almost 86% of the fixed differences between species are driven by positive selection. There are only 16.6% of the nonsynonymous mutations observed in sex-unbiased genes that are under positive selection in comparison to 30% of male-biased and 46% of female-biased genes that are beneficial. We also estimated that D. melanogaster and D. simulans may have diverged 1.72 million years ago

Directional selection effects on patterns of phenotypic (co)variation in wild populations.

Phenotypic (co)variation is a prerequisite for evolutionary change, and understanding how (co)variation evolves is of crucial importance to the biological sciences. Theoretical models predict that under directional selection, phenotypic (co)variation should evolve in step with the underlying adaptive landscape, increasing the degree of correlation among co-selected traits as well as the amount of genetic variance in the direction of selection. Whether either of these outcomes occurs in natural populations is an open question and thus an important gap in evolutionary theory. Here, we documented changes in the phenotypic (co)variation structure in two separate natural populations in each of two chipmunk species (Tamias alpinus and T. speciosus) undergoing directional selection. In populations where selection was strongest (those of T. alpinus), we observed changes, at least for one population, in phenotypic (co)variation that matched theoretical expectations, namely an increase of both phenotypic integration and (co)variance in the direction of selection and a re-alignment of the major axis of variation with the selection gradient

Tradeoff between short-term and long-term adaptation in a changing environment

We investigate the competition dynamics of two microbial or viral strains that live in an environment that switches periodically between two states. One of the strains is adapted to the long-term environment, but pays a short-term cost, while the other is adapted to the short-term environment and pays a cost in the long term. We explore the tradeoff between these alternative strategies in extensive numerical simulations, and present a simple analytic model that can predict the outcome of these competitions as a function of the mutation rate and the time scale of the environmental changes. Our model is relevant for arboviruses, which alternate between different host species on a regular basis.Comment: 9 pages, 3 figures, PRE in pres