Showing papers on "Selection (genetic algorithm) published in 2002"
TL;DR: It is shown that the AU test is less biased than other methods in typical cases of tree selection, as well as in the analysis of mammalian mitochondrial protein sequences.
Abstract: An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce test bias. It was applied to maximum-likelihood tree selection for obtaining the confidence set of trees. The AU test is based on the theory of Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434; 1996), but the new method provides higher-order accuracy yet simpler implementation. The AU test, like the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap probability and Kishino-Hasegawa tests. The selection bias comes from comparing many trees at the same time and often leads to overconfidence in the wrong trees. The SH test, though safe to use, may exhibit another type of bias such that it appears conservative. Here I show that the AU test is less biased than other methods in typical cases of tree selection. These points are illustrated in a simulation study as well as in the analysis of mammalian mitochondrial protein sequences. The theoretical argument provides a simple formula that covers the bootstrap probability test, the Kishino-Hasegawa test, the AU test, and the Zharkikh-Li test. A practical suggestion is provided as to which test should be used under particular circumstances.
2,452 citations
TL;DR: It is demonstrated that when correction is made for the selection bias, the cross-validated error is no longer zero for a subset of only a few genes.
Abstract: In the context of cancer diagnosis and treatment, we consider the problem of constructing an accurate prediction rule on the basis of a relatively small number of tumor tissue samples of known type containing the expression data on very many (possibly thousands) genes. Recently, results have been presented in the literature suggesting that it is possible to construct a prediction rule from only a few genes such that it has a negligible prediction error rate. However, in these results the test error or the leave-one-out cross-validated error is calculated without allowance for the selection bias. There is no allowance because the rule is either tested on tissue samples that were used in the first instance to select the genes being used in the rule or because the cross-validation of the rule is not external to the selection process; that is, gene selection is not performed in training the rule at each stage of the cross-validation process. We describe how in practice the selection bias can be assessed and corrected for by either performing a cross-validation or applying the bootstrap external to the selection process. We recommend using 10-fold rather than leave-one-out cross-validation, and concerning the bootstrap, we suggest using the so-called .632+ bootstrap error estimate designed to handle overfitted prediction rules. Using two published data sets, we demonstrate that when correction is made for the selection bias, the cross-validated error is no longer zero for a subset of only a few genes.
1,387 citations
TL;DR: Improvements in genotyping technologies have led to the increased use of genetic polymorphism for inference about population phenomena, such as migration and selection, which presents a challenge in analysis of polymorphism data.
Abstract: Improvements in genotyping technologies have led to the increased use of genetic polymorphism for inference about population phenomena, such as migration and selection. Such inference presents a challenge, because polymorphism data reflect a unique, complex, non-repeatable evolutionary history. Traditional analysis methods do not take this into account. A stochastic process known as the 'coalescent' presents a coherent statistical framework for analysis of genetic polymorphisms.
677 citations
TL;DR: The genes and genetic markers that are being discovered can be used to enhance the genetic improvement of breeding stock through marker-assisted selection.
Abstract: Substantial advances have been made in the genetic improvement of agriculturally important animal and plant populations through artificial selection on quantitative traits. Most of this selection has been on the basis of observable phenotype, without knowledge of the genetic architecture of the selected characteristics. However, continuing molecular genetic analysis of traits in animal and plant populations is leading to a better understanding of quantitative trait genetics. The genes and genetic markers that are being discovered can be used to enhance the genetic improvement of breeding stock through marker-assisted selection.
669 citations
TL;DR: It is shown that the geographical context of speciation can be viewed as a form of assortative mating and this provides a framework for interpreting results from laboratory experiments, which are found to agree generally with theoretical predictions about conditions that are favorable to the evolution of prezygotic isolation.
Abstract: A large number of mathematical models have been developed that show how natural and sexual selection can cause prezygotic isolation to evolve. This article attempts to unify this literature by identifying five major elements that determine the outcome of speciation caused by selection: a form of disruptive selection, a form of isolating mechanism (assortment or a mating preference), a way to transmit the force of disruptive selection to the isolating mechanism (direct selection or indirect selection), a genetic basis for increased isolation (a one- or two-allele mechanism), and an initial condition (high or low initial divergence). We show that the geographical context of speciation (allopatry vs. sympatry) can be viewed as a form of assortative mating. These five elements appear to operate largely independently of each other and can be used to make generalizations about when speciation is most likely to happen. This provides a framework for interpreting results from laboratory experiments, which are found to agree generally with theoretical predictions about conditions that are favorable to the evolution of prezygotic isolation.
657 citations
TL;DR: This work investigated the patterns of genetic variation along a recombining chromosome by constructing ancestral recombination graphs that are modified to incorporate the effect of genetic hitchhiking, and proposed a statistical method to test the significance of a local reduction of variation and a skew of the frequency spectrum caused by a hitchhiker event.
Abstract: The theory of genetic hitchhiking predicts that the level of genetic variation is greatly reduced at the site of strong directional selection and increases as the recombinational distance from the site of selection increases. This characteristic pattern can be used to detect recent directional selection on the basis of DNA polymorphism data. However, the large variance of nucleotide diversity in samples of moderate size imposes difficulties in detecting such patterns. We investigated the patterns of genetic variation along a recombining chromosome by constructing ancestral recombination graphs that are modified to incorporate the effect of genetic hitchhiking. A statistical method is proposed to test the significance of a local reduction of variation and a skew of the frequency spectrum caused by a hitchhiking event. This method also allows us to estimate the strength and the location of directional selection from DNA sequence data.
657 citations
TL;DR: Three main issues that should be resolved to advance the understanding of postcopulatory sexual selection are identified: to determine the genetic basis of different male fertility traits and female traits that mediate sperm selection, and establish the coevolutionary trajectory of sexes.
Abstract: The female reproductive tract is where competition between the sperm of different males takes place, aided and abetted by the female herself Intense postcopulatory sexual selection fosters inter-sexual conflict and drives rapid evolutionary change to generate a startling diversity of morphological, behavioural and physiological adaptations We identify three main issues that should be resolved to advance our understanding of postcopulatory sexual selection We need to determine the genetic basis of different male fertility traits and female traits that mediate sperm selection; identify the genes or genomic regions that control these traits; and establish the coevolutionary trajectory of sexes
639 citations
Dissertation•
01 Jan 2002
554 citations
Patent•
12 Sep 2002
TL;DR: In this paper, a game with a bonus round with multiple selection groups is described. But the game does not end upon an "end-bonus" selection; rather, the bonus round ends upon the selection of a predetermined number of selections from the last or final selection group.
Abstract: A gaming device having a bonus round with multiple selection groups. The bonus round does not end upon an “end-bonus” selection; rather, the bonus round ends upon the selection of a predetermined number of selections from the last or final selection group. In one embodiment, the number of selections is determined from a selection group preceding the final selection group. Prior to determining the number of final selection group picks, the game provides the player with at least one selection group in which the player selects award indicators until selecting an indicator that advances the player to the next selection group. Player excitement and enjoyment is enhanced because the present invention provides the player with multiple opportunities to achieve game credits and because the player is guaranteed to have at least one opportunity to select from the final selection group. In one embodiment, the final selection group has larger values than the previous selection groups.
515 citations
TL;DR: In this article, the authors address micro-econometric evaluation by matching methods when the programs under consideration are heterogeneous, assuming that selection into the different sub-programs and the potential outcomes are independent given observable characteristics, estimators based on different propensity scores are compared and applied to the analysis of active labor market policies in the Swiss region of Zurich.
Abstract: Not available in German. This paper addresses microeconometric evaluation by matching methods when the programs under consideration are heterogeneous. Assuming that selection into the different sub-programs and the potential outcomes are independent given observable characteristics, estimators based on dif-ferent propensity scores are compared and applied to the analysis of active labor market policies in the Swiss region of Zurich. Furthermore, the issues of heterogeneous effects and aggregation are addressed. The results suggest that an approach that incorporates the possibility of having multiple programs can be an informative tool in applied work.
505 citations
TL;DR: In this paper, the authors compare analytic hierarchy process and total cost of ownership (COPO) for supplier selection and evaluation, and provide a comparison of the two approaches and their performance.
Abstract: Supplier selection and evaluation are arguably one of the most critical functions for the success of an organization. Several approaches exist in the literature to objectively evaluate suppliers, including analytic hierarchy process and total cost of ownership. Analytic hierarchy process provides a framework to cope with multiple criteria situations involving supplier selection, while the total cost of ownership is a methodology and philosophy, which look beyond just the price of a purchase to better understand and manage costs in selecting and maintaining relationships with suppliers. This paper illustrates the two approaches and provides a comparison.
Patent•
02 Apr 2002
TL;DR: In this paper, the success or failure of a current selection directly affects the player's chances for success in a later selection and the players chances for obtaining the highest bonus award possible.
Abstract: A gaming device wherein the success or failure of a current selection directly affects the player's chances for success in a later selection and the player's chances for obtaining the highest bonus award possible.
TL;DR: It is argued that frequency-dependent biotic interactions that have ‘Red Queen dynamics’ (eg, host-parasite interactions, predator-prey relationships or intraspecific arms races) often fuel chronic correlational selection, which is strong enough to maintain adaptive genetic correlations of the kind the authors describe.
Abstract: We review and discuss the importance of correlational selection (selection for optimal character combinations) in natural populations If two or more traits subject to multivariate selection are heritable, correlational selection builds favourable genetic correlations through the formation of linkage disequilibrium at underlying loci governing the traits However, linkage disequilibria built up by correlational selection are expected to decay rapidly (ie, within a few generations), unless correlational selection is strong and chronic We argue that frequency-dependent biotic interactions that have 'Red Queen dynamics' (eg, host-parasite interactions, predator-prey relationships or intraspecific arms races) often fuel chronic correlational selection, which is strong enough to maintain adaptive genetic correlations of the kind we describe We illustrate these processes and phenomena using empirical examples from various plant and animal systems, including our own recent work on the evolutionary dynamics of a heritable throat colour polymorphism in the side-blotched lizard Uta stansburiana In particular, male and female colour morphs of side-blotched lizards cycle on five- and two-generation (year) timescales under the force of strong frequency-dependent selection Each morph refines the other morph in a Red Queen dynamic Strong correlational selection gradients among life history, immunological and morphological traits shape the genetic correlations of the side-blotched lizard polymorphism We discuss the broader evolutionary consequences of the buildup of co-adapted trait complexes within species, such as the implications for speciation processes
12 Jul 2002
TL;DR: In this article, a comprehensive organization of the materials selection process includes analytical approaches to materials selection and extensive information about materials available in the marketplace, sources of properties data, procurement and data management, properties testing procedures and equipment, analysis of failure modes, manufacturing processes and assembly techniques, and applications.
Abstract: This comprehensive organization of the materials selection process includes analytical approaches to materials selection and extensive information about materials available in the marketplace, sources of properties data, procurement and data management, properties testing procedures and equipment, analysis of failure modes, manufacturing processes and assembly techniques, and applications. Throughout the handbook, an international roster of contributors with a broad range of experience conveys practical knowledge about materials and illustrates in detail how they are used in a wide variety of industries.
TL;DR: The authors generalizes Vuong (1989) asymptotically normal tests for model selection in several important directions, such as allowing incompletely parametrized models such as econometric models defined by moment conditions.
Abstract: This paper generalizes Vuong (1989) asymptotically normal tests for model selection in several important directions. First, it allows for incompletely parametrized models such as econometric models defined by moment conditions. Second, it allows for a broad class of estimation methods that includes most estimators currently used in practice. Third, it considers model selection criteria other than the models’ likelihoods such as the mean squared errors of prediction. Fourth, the proposed tests are applicable to possibly misspecified nonlinear dynamic models with weakly dependent heterogeneous data. Cases where the estimation methods optimize the model selection criteria are distinguished from cases where they do not. We also consider the estimation of the asymptotic variance of the difference between the competing models’ selection criteria, which is necessary to our tests. Finally, we discuss conditions under which our tests are valid. It is seen that the competing models must be essentially nonnested.
TL;DR: To evaluate the impact of selection across an agronomically important pathway, nucleotide diversity at six major genes involved in starch metabolism is surveyed and found unusually low genetic diversity and strong evidence of selection.
Abstract: Maize is both phenotypically and genetically diverse. Sequence studies generally confirm the extensive genetic variability in modern maize is consistent with a lack of selection. For more than 6,000 years, Native Americans and modern breeders have exploited the tremendous genetic diversity of maize (Zea mays ssp. mays) to create the highest yielding grain crop in the world. Nonetheless, some loci have relatively low levels of genetic variation, particularly loci that have been the target of artificial selection, like c1 and tb1. However, there is limited information on how selection may affect an agronomically important pathway for any crop. These pathways may retain the signature of artificial selection and may lack genetic variation in contrast to the rest of the genome. To evaluate the impact of selection across an agronomically important pathway, we surveyed nucleotide diversity at six major genes involved in starch metabolism and found unusually low genetic diversity and strong evidence of selection. Low diversity in these critical genes suggests that a paradigm shift may be required for future maize breeding. Rather than relying solely on the diversity within maize or on transgenics, future maize breeding would perhaps benefit from the incorporation of alleles from maize's wild relatives.
TL;DR: Through the design of decomposition methods for bound-constrained SVM formulations, it is demonstrated that the working set selection is not a trivial task and a simple selection is proposed which leads to faster convergences for difficult cases.
Abstract: The decomposition method is currently one of the major methods for solving support vector machines. An important issue of this method is the selection of working sets. In this paper through the design of decomposition methods for bound-constrained SVM formulations we demonstrate that the working set selection is not a trivial task. Then from the experimental analysis we propose a simple selection of the working set which leads to faster convergences for difficult cases. Numerical experiments on different types of problems are conducted to demonstrate the viability of the proposed method.
TL;DR: A new fuzzy programming method is proposed for assessment of uncertain weights of partnership selection criteria and uncertain scores of alternative partners, in the basic framework of the Analytic Hierarchy Process, which can derive priorities from inconsistent interval comparison matrices, thus eliminating the drawbacks of the existing interval prioritisation methods.
Abstract: The main objective of this paper is to present a new fuzzy approach to partnership selection in the formation of virtual enterprises. The phases of the virtual enterprise life cycle are briefly described and it is shown that the partnership selection is a key factor in the formation of such complex organisations. It is justified that the partnership selection process should be formulated as a multiple criteria decision-making problem under uncertainty. A new fuzzy programming method is proposed for assessment of uncertain weights of partnership selection criteria and uncertain scores of alternative partners, in the basic framework of the Analytic Hierarchy Process. The proposed fuzzy prioritisation method uses interval pairwise comparison judgements rather than exact numerical values of the comparison ratios and transforms the initial prioritisation problem into a linear program. The method can derive priorities from inconsistent interval comparison matrices, thus eliminating the drawbacks of the existing interval prioritisation methods. Moreover, the method generalises the known prioritisation methods, since it can be used for deriving priorities from exact, interval or mixed comparison matrices, regardless of their consistency. A numerical example, illustrating the application of this method to partnership selection process is given.
TL;DR: It is shown that natural selection was the dominant diversifying agent in the evolution of the quantitative traits in isolated populations of grayling that originated from a common source 80–120 years ago.
Abstract: The relative importance of natural selection and random drift in phenotypic evolution has been discussed since the introduction of the first population genetic models. The empirical evidence used to evaluate the evolutionary theories of Fisher and Wright remains obscure because formal tests for neutral divergence or sensitive attempts to separate the effects of selection and drift are scarce, subject to error, and have not been interpreted in the light of well-known population demography. We combined quantitative genetic and microsatellite DNA analyses to investigate the determinants of contemporary life-history evolution in isolated populations of grayling (Thymallus thymallus, Salmonidae) that originated from a common source 80-120 years ago. Here we show that natural selection was the dominant diversifying agent in the evolution of the quantitative traits. However, the populations were founded by a small number of individuals, exhibit very low microsatellite-based effective sizes and show genetic imprints of severe 'bottlenecks'; which are conditions often suggested to constrain selection and favour drift. This study demonstrates a very clear case of fisherian evolution in small natural populations across a contemporary timescale.
19 Aug 2002
TL;DR: By modelling variability and dependency between requirements using propositional connectives, a logical expression can be developed for the model and this approach can be used to validate the model as a whole.
Abstract: Product line models are used to drive the generation of requirements for single systems in the product line. They are difficult to validate because they are large and complex. By modelling variability and dependency between requirements using propositional connectives, a logical expression can be developed for the model. Validation of the selection of requirements from the model can be achieved by satisfying the logical expression. This approach can be used to validate the model as a whole. A detailed worked example is presented, and the computational aspects of the approach are discussed.
TL;DR: Presents a discussion of some important and unresolved issues related to previous work to provide a more comprehensive understanding of the practicability of wavelet-based denoising.
Abstract: Presents a discussion of some important and unresolved issues related to previous work to provide a more comprehensive understanding of the practicability of wavelet-based denoising.
Patent•
22 Sep 2002
TL;DR: In this article, the player selectable selections are arranged or grouped into a plurality of associated or related selection sets and the related plurality of selection sets are arranged adjacent to each other to enable each player's pick in each selection set limits the available selections in the subsequent selection sets.
Abstract: A gaming device having a bonus game with an adjacent selection feature. In one embodiment of the present invention, the gaming device provides a plurality of adjacent player selectable selections. An award is associated with each player selectable selection. The award associated with each selectable selection is not initially displayed or revealed to the player. The player selectable selections are arranged or grouped into a plurality of associated or related selection sets. In one embodiment, each selection set has a different number of player selectable selections. In one embodiment, the related plurality of selection sets are arranged adjacent to each other to enable each player selectable selection in one set to be adjacent to at least one player selectable selection from another selection set. The player's pick in each selection set limits the available selections in the subsequent selection sets.
TL;DR: The framework for recursions to describe the evolution of multilocus systems under arbitrary forms of selection is extended to allow for arbitrary modes of inheritance, including diploidy, polyploidsy, sex linkage, cytoplasmic inheritance, and genomic imprinting.
Abstract: In 1991, Barton and Turelli developed recursions to describe the evolution of multilocus systems under arbitrary forms of selection. This article generalizes their approach to allow for arbitrary modes of inheritance, including diploidy, polyploidy, sex linkage, cytoplasmic inheritance, and genomic imprinting. The framework is also extended to allow for other deterministic evolutionary forces, including migration and mutation. Exact recursions that fully describe the state of the population are presented; these are implemented in a computer algebra package (available on the Web at http://helios.bto.ed.ac.uk/evolgen). Despite the generality of our framework, it can describe evolutionary dynamics exactly by just two equations. These recursions can be further simplified using a "quasi-linkage equilibrium" (QLE) approximation. We illustrate the methods by finding the effect of natural selection, sexual selection, mutation, and migration on the genetic composition of a population.
TL;DR: Fecundity selection and sexual selection work in concert to drive the evolution of sexual dimorphism in trunk length in snow skinks.
Abstract: Sexual dimorphism is widespread in lizards, with the most consistently dimorphic traits being head size (males have larger heads) and trunk length (the distance between the front and hind legs is greater in females). These dimorphisms have generally been interpreted as follows: (1) large heads in males evolve through male-male rivalry (sexual selection); and (2) larger interlimb lengths in females provide space for more eggs (fecundity selection). In an Australian lizard (the snow skink, Niveoscincus microlepidotus), we found no evidence for ongoing selection on head size. Trunk length, however, was under positive fecundity selection in females and under negative sexual selection in males. Thus, fecundity selection and sexual selection work in concert to drive the evolution of sexual dimorphism in trunk length in snow skinks.
TL;DR: It is found that bias caused by environmental covariances appears mainly to affect quantitative estimates of the strength of selection based on phenotypic data and that the magnitude of these biases is large.
Abstract: Measuring natural selection has been a fundamental goal of evolutionary biology for more than a century, and techniques developed in the last 20 yr have provided relatively simple means for biologists to do so. Many of these techniques, however, share a common limitation: when applied to phenotypic data, environmentally induced covariances between traits and fitness can lead to biased estimates of selection and misleading predictions about evolutionary change. Utilizing estimates of breeding values instead of phenotypic data with these methods can eliminate environmentally induced bias, although this approach is more difficult to implement. Despite this potential limitation to phenotypic methods and the availability of a potential solution, little empirical evidence exists on the extent of environmentally induced bias in phenotypic estimates of selection. In this article, we present a method for detecting bias in phenotypic estimates of selection and demonstrate its use with three independent da...
TL;DR: The rate of protein adaptation is reduced in regions of low recombination, and evolution at strongly selected amino acid sites interferes with optimal codon usage at weakly selected, tightly linked synonymous sites, suggesting that linkage limits the rate and degree of adaptation even in recombining genomes.
Abstract: Population genetic theory shows that the efficacy of natural selection is limited by linkage-selection at one site interferes with selection at linked sites. Such interference slows adaptation in asexual genomes and may explain the evolutionary advantage of sex. Here, we test for two signatures of constraint caused by linkage in a sexual genome, by using sequence data from 255 Drosophila melanogaster and Drosophila simulans loci. We find that (i) the rate of protein adaptation is reduced in regions of low recombination, and (ii) evolution at strongly selected amino acid sites interferes with optimal codon usage at weakly selected, tightly linked synonymous sites. Together these findings suggest that linkage limits the rate and degree of adaptation even in recombining genomes.
TL;DR: Analysis of QTL effects for 572 traits from 86 studies revealed significantly fewer antagonistic QTLs than expected under neutrality, a result that validates Darwin's claim that phenotypic diversification is caused mainly by selection.
Abstract: Selection is widely accepted as the principal force shaping phenotypic variation within populations. Its importance in speciation and macroevolution has been questioned, however, because phenotypic differences between species or higher taxa sometimes appear to be nonadaptive. Here, we use the quantitative trait locus (QTL) sign test to evaluate the importance of directional selection in phenotypic divergence. If a trait has a history of directional selection, QTL effects should be mostly in the same direction; otherwise QTLs with antagonistic effects should be common. Analysis of QTL effects for 572 traits from 86 studies revealed significantly fewer antagonistic QTLs than expected under neutrality, a result that validates Darwin's claim that phenotypic diversification is caused mainly by selection. Moreover, interspecific trait differences were more strongly or consistently selected than intraspecific differences, strengthening a growing consensus among students of speciation that directional selection is the primary cause of speciation. Contrary to studies of selection in contemporary populations, life history traits appear to be selected more strongly than morphological traits, but traits related to the timing of development are weakly selected relative to most other traits.
TL;DR: It is claimed that the dynamical conception of evolutionary theory as a theory of forces is mistaken and only the statistical interpretation preserves the presumed relation between natural selection and drift.
Abstract: We distinguish dynamical and statistical interpretations of evolutionary theory. We argue that only the statistical interpretation preserves the presumed relation between natural selection and drift. On these grounds we claim that the dynamical conception of evolutionary theory as a theory of forces is mistaken. Selection and drift are not forces. Nor do selection and drift explanations appeal to the (sub‐population‐level) causes of population level change. Instead they explain by appeal to the statistical structure of populations. We briefly discuss the implications of the statistical interpretation of selection for various debates within the philosophy of biology—the ‘explananda of selection’ debate and the ‘units of selection’ debate.
TL;DR: Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and strongly significant, association with recombination--as expected if recombination allows natural selection to act more efficiently when multiple linked sites segregate functional variation.
Abstract: In Drosophila, as in many organisms, natural selection leads to high levels of codon bias in genes that are highly expressed. Thus codon bias is an indicator of the intensity of one kind of selection that is experienced by genes and can be used to assess the impact of other genomic factors on natural selection. Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and strongly significant, association with recombination--as expected if recombination allows natural selection to act more efficiently when multiple linked sites segregate functional variation. The same reasoning leads to the expectation that the efficiency of selection, and thus average codon bias, should decline with gene density. However, this prediction is not confirmed. Levels of codon bias and gene expression are highest for those genes in an intermediate range of gene density, a pattern that may be the result of a tradeoff between the advantages for gene expression of close gene spacing and disadvantages arising from regulatory conflicts among tightly packed genes. These factors appear to overlay the more subtle effect of linkage among selected sites that gives rise to the association between recombination rate and codon bias.