Showing papers on "Selection (genetic algorithm) published in 2005"

ProtTest: selection of best-fit models of protein evolution

Abstract: Summary: Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment. Availability: ProtTest is available under the GNU license from http://darwin.uvigo.es Contact: fabascal@uvigo.es

Molecular Signatures of Natural Selection

Abstract: There is an increasing interest in detecting genes, or genomic regions, that have been targeted by natural selection. The interest stems from a basic desire to learn more about evolutionary processes in humans and other organisms, and from the realization that inferences regarding selection may provide important functional information. This review provides a nonmathematical description of the issues involved in detecting selection from DNA sequences and SNP data and is intended for readers who are not familiar with population genetic theory. Particular attention is placed on issues relating to the analysis of large-scale genomic data sets.

Working Set Selection Using Second Order Information for Training Support Vector Machines

Abstract: Working set selection is an important step in decomposition methods for training support vector machines (SVMs). This paper develops a new technique for working set selection in SMO-type decomposition methods. It uses second order information to achieve fast convergence. Theoretical properties such as linear convergence are established. Experiments demonstrate that the proposed method is faster than existing selection methods using first order information.

Assignment methods: matching biological questions with appropriate techniques

Abstract: Assignment methods, which use genetic information to ascertain population membership of individuals or groups of individuals, have been used in recent years to study a wide range of evolutionary and ecological processes. In applied studies, the first step of articulating the biological question(s) to be addressed should be followed by selection of the method(s) best suited for the analysis. However, this first step often receives less attention than it should, and the recent proliferation of assignment methods has made the selection step challenging. Here, we review assignment methods and discuss how to match the appropriate methods with the underlying biological questions for several common problems in ecology and conservation (assessing population structure; measuring dispersal and hybridization; and forensics and mixture analysis). We also identify several topics for future research that should ensure that this field remains dynamic and productive.

Selection on heritable phenotypic plasticity in a wild bird population

Abstract: Theoretical and laboratory research suggests that phenotypic plasticity can evolve under selection. However, evidence for its evolutionary potential from the wild is lacking. We present evidence from a Dutch population of great tits (Parus major) for variation in individual plasticity in the timing of reproduction, and we show that this variation is heritable. Selection favoring highly plastic individuals has intensified over a 32-year period. This temporal trend is concurrent with climate change causing a mismatch between the breeding times of the birds and their caterpillar prey. Continued selection on plasticity can act to alleviate this mismatch.

Using genome scans of DNA polymorphism to infer adaptive population divergence.

Abstract: Elucidating the genetic basis of adaptive population divergence is a goal of central importance in evolutionary biology. In principle, it should be possible to identify chromosomal regions involved in adaptive divergence by screening genome-wide patterns of DNA polymorphism to detect the locus-specific signature of positive directional selection. In the case of spatially separated populations that inhabit different environments or sympatric populations that exploit different ecological niches, it is possible to identify loci that underlie divergently selected traits by comparing relative levels of differentiation among large numbers of unlinked markers. In this review I first address the question of whether diversifying selection on polygenic traits can be expected to produce predictable patterns of allelic variation at the underlying quantitative trait loci (QTL), and whether the locus-specific effects of selection can be reliably detected against the genome-wide backdrop of stochastic variability. I then review different approaches that have been developed to identify loci involved in adaptive population divergence and I discuss the relative merits of model-based approaches that rely on assumptions about population structure vs. model-free approaches that are based on empirical distributions of summary statistics. Finally, I consider the evolutionary and functional insights that might be gained by conducting genome scans for loci involved in adaptive population divergence.

Central tolerance: learning self-control in the thymus

Abstract: In the past few years, there has been a flurry of discoveries and advancements in our understanding of how the thymus prepares T cells to exist at peace in normal healthy tissue: that is, to be self-tolerant. In the thymus, one of the main mechanisms of T-cell central tolerance is clonal deletion, although the selection of regulatory T cells is also important and is gaining enormous interest. In this Review, we discuss the emerging consensus about which models of clonal deletion are most physiological, and we review recent data that define the molecular mechanisms of central tolerance.

A reassessment of genetic limits to evolutionary change

Abstract: An absence of genetic variance in traits under selection is perhaps the oldest explanation for a limit to evolutionary change, but has also been the most easily dismissed. We review a range of theoretical and empirical results covering single traits to more complex multivariate systems, and show that an absence of genetic variance may be more common than is currently appreciated. From a single-trait perspective, we highlight that it is becoming clear that some trait types do not display significant levels of genetic variation, and we raise the possibility that species with restricted ranges may differ qualitatively from more widespread species in levels of genetic variance in ecologically important traits. A common misconception in many life-history studies is that a lack of genetic variance in single traits, and genetic constraints as a consequence of bivariate genetic correlations, are different causes of selection limits. We detail how interpretations of bivariate patterns are unlikely to demonstrate genetic limits to selection in many cases. We advocate a multivariate definition of genetic constraints that emphasizes the presence (or otherwise) of genetic variance in the multivariate direction of selection. For multitrait systems, recent results using longer term studies of organisms, in which more is understood concerning what traits may be under selection, have indicated that selection may exhaust genetic variance, resulting in a limit to the selection response.

Perspective:sign epistasis and genetic constraint on evolutionary trajectories

Abstract: Epistasis for fitness means that the selective effect of a mutation is conditional on the genetic background in which it appears. Although epistasis is widely observed in nature, our understanding of its consequences for evolution by natural selection remains incomplete. In particular, much attention focuses only on its influence on the instantaneous rate of changes in frequency of selected alleles via epistatic contribution to the additive genetic variance for fitness. Thus, in this framework epistasis only has evolutionary importance if the interacting loci are simultaneously segregating in the population. However, the selective accessibility of mutational trajectories to high fitness genotypes may depend on the genetic background in which novel mutations appear, and this effect is independent of population polymorphism at other loci. Here we explore this second influence of epistasis on evolution by natural selection. We show that it is the consequence of a particular form of epistasis, which we designate sign epistasis. Sign epistasis means that the sign of the fitness effect of a mutation is under epistatic control; thus, such a mutation is beneficial on some genetic backgrounds and deleterious on others. Recent experimental innovations in microbial systems now permit assessment of the fitness effects of individual mutations on multiple genetic backgrounds. We review this literature and identify many examples of sign epistasis, and we suggest that the implications of these results may generalize to other organisms. These theoretical and empirical considerations imply that strong genetic constraint on the selective accessibility of trajectories to high fitness genotypes may exist and suggest specific areas of investigation for future research.

Behavioral Causes and Consequences of Sexual Size Dimorphism

Abstract: (Invited Article) Abstract Sexual size dimorphism (SSD) is widespread and variable among animals. According to the differential equilibrium model, SSD in a given species is expected to result if opposing selection forces equilibrate differently in both sexes. Here I review the factors that affect the evolution of SSD specifically as they relate to behavior. Taking the approach that SSD results as an epiphenomenon from separate but related selection on male and female body size, the advantages and disadvantages of large size in terms of the standard components of individual fitness (mating success, fecundity, viability, growth, foraging success) are discussed to help guiding future research on the subject. This includes a discussion of intra-SSDs. The main conclusions are: (1) Evidence for disadvantages of large body size is still sparse and requires more research. In contrast, evidence for sexual or fecundity selection favoring large body size is overwhelming, so these mechanisms do no longer require special attention, but need to be documented nonetheless to acquire a complete picture. (2) Some hypotheses suggesting that small size is favored are not well investigated at all, because they apply only to some species or restricted situations, may be difficult to study, or have simply been disregarded. Evidence for these cryptic hypotheses is best revealed using experiments under multiple environmental (food, temperature, etc.) stresses with particularly well-suited model species. (3) The evolution of SSD ultimately depends on processes generating variation within as well as between the sexes, so studies should always investigate and report effects on both sexes separately, in addition to size-dependent effects within each sex; within sexes the key issue is whether small individuals under, over- or perfectly compensate their general fitness disadvantage. (4) Tests of several hypotheses should be integrated in case studies of well-suited model species to investigate selection on body size comprehensively. For example, all episodes of sexual selection (mate search, competition, pre- and post-copulatory choice) should be addressed in conjunction. Investigations of size-selective and sex-dependent predation should take the viewpoint of the prey rather than the predator to permit integration of effects throughout prey ontogeny generated by various predators with differing preferences. Comparative studies should also test multiple alternative hypotheses at the same time to permit stronger inference. (5) Experimental behavioral studies of sexual and natural selection should provide selection differentials using the available standard methods. This would allow integration with phenomenological studies of selection and facilitate subsequent meta-analyses, which are very valuable in evaluating general patterns. (6) Comparative phylogenetic studies identifying patterns and phenomenological and experimental studies of model species that investigate particular mechanisms should be integrated, so that macro-evolutionary patterns can be linked to micro-evolutionary processes, which is the central paradigm of evolutionary ecology. (7) A major problem is the general difficulty of separating causes generating a particular body size and SSD over evolutionary time and its consequences for behavior and ecology today, i.e. today's researchers cannot completely avoid this ‘ghost of SSD evolution past’.

Variation in the strength of selected codon usage bias among bacteria

Abstract: Among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. However, in other species selection appears to have been ineffective. Here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. The approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. The strength of selected codon usage bias, S, is found to vary substantially among species; in 30% of the genomes examined, there was no significant evidence that selection had been effective. Values of S are highly positively correlated with both the number of rRNA operons and the number of tRNA genes. These results are consistent with the hypothesis that species exposed to selection for rapid growth have more rRNA operons, more tRNA genes and more strongly selected codon usage bias. For example, Clostridium perfringens, the species with the highest value of S, can have a generation time as short as 7 min.

Bioaugmentation for bioremediation: the challenge of strain selection.

Abstract: Despite its long-term use in bioremediation, bioaugmentation of contaminated sites with microbial cells continues to be a source of controversy within environmental microbiology. This largely results from its notoriously unreliable performance record. In this article, we argue that the unpredictable nature of the approach comes from the initial strain selection step. Up until now, this has been dictated by the search for catabolically competent microorganisms, with little or no consideration given to other essential features that are required to be functionally active and persistent in target habitats. We describe how technical advances in molecular biology and analytical chemistry, now enable assessments of the functional diversity and spatial distribution of microbial communities to be made in situ. These advances now enable microbial populations, targeted for exploitation, to be differentiated to the cell level, an advance that is bound to improve microbial selection and exploitation. We argue that this information-based approach is already proving to be more effective than the traditional 'black-box' approach of strain selection. The future perspectives and opportunities for improving selection of effective microbial strains for bioaugmentation are also discussed.

Simultaneous inference of selection and population growth from patterns of variation in the human genome

Abstract: Natural selection and demographic forces can have similar effects on patterns of DNA polymorphism. Therefore, to infer selection from samples of DNA sequences, one must simultaneously account for demographic effects. Here we take a model-based approach to this problem by developing predictions for patterns of polymorphism in the presence of both population size change and natural selection. If data are available from different functional classes of variation, and a priori information suggests that mutations in one of those classes are selectively neutral, then the putatively neutral class can be used to infer demographic parameters, and inferences regarding selection on other classes can be performed given demographic parameter estimates. This procedure is more robust to assumptions regarding the true underlying demography than previous approaches to detecting and analyzing selection. We apply this method to a large polymorphism data set from 301 human genes and find (i) widespread negative selection acting on standing nonsynonymous variation, (ii) that the fitness effects of nonsynonymous mutations are well predicted by several measures of amino acid exchangeability, especially site-specific methods, and (iii) strong evidence for very recent population growth.

Evolution of antifungal-drug resistance: mechanisms and pathogen fitness

Abstract: Like other microorganisms, fungi exist in populations that are adaptable. Under the selection imposed by antifungal drugs, drug-sensitive fungal pathogens frequently evolve resistance. Although the molecular mechanisms of resistance are well-characterized, there are few measurements of the impact of these mechanisms on pathogen fitness in different environments. To predict resistance before a new drug is prescribed in the clinic, the full spectrum of potential resistance mutations and the interactions among combinations of divergent mechanisms can be determined in evolution experiments. In the search for new strategies to manage drug resistance, measuring the limits of adaptation might reveal methods for trapping fungal pathogens in evolutionary dead ends.

Portfolio Selection with Monotone Mean-Variance Preferences

Abstract: We propose a portfolio selection model based on a class of preferences that coincide with mean-variance preferences on their domain of monotonicity, but differ where mean-variance preferences fail to be monotone.

A Meta‐Analysis of the Effect of Common Currencies on International Trade*

Abstract: . Thirty-four recent studies have investigated the effect of currency union on trade, resulting in 754 point estimates of this effect. This paper uses meta-analysis to combine, explain, and to summarize these disparate estimates of common currency trade effects. The hypothesis that there is no effect of currency union on trade is easily and robustly rejected at standard significance levels. Combining these estimates implies that a currency union increases bilateral trade by between 30 and 90%. Although there is evidence of publication selection, there is also evidence of a genuine positive trade effect beyond publication bias.

The Evolution of Infidelity in Socially Monogamous Passerines: The Strength of Direct and Indirect Selection on Extrapair Copulation Behavior in Females

Abstract: Many studies have been aimed at understanding the maintenance of female infidelity in socially monogamous birds. Because engaging in extrapair copulations (EPCs) is believed to be costly for females, it has been argued that EPC behavior must bring indirect benefits to females by elevating offspring fitness. We use empirical data from the literature to assess the relative strength of indirect and direct selection on female EPC behavior, using quantitative genetic approximations of selection. This analysis confirmed that there is generally negative direct selection on EPC behavior caused by depressed paternal investment by social males. In contrast, there was no significant positive indirect selection on EPC behavior in females. A comparison between the two types of selection suggests that the force of direct negative selection is generally much stronger than that of indirect positive selection. Indirect selection is thus unlikely to maintain EPC behavior in the face of direct selection against it. We suggest that EPCs may instead be the result of antagonistic selection on loci influencing the outcome of male-female encounters and that EPC behavior per se may not be adaptive for females but may reflect sexual conflict due to strong selection in males to achieve extrapair copulations.

Selection and breeding programs in aquaculture

Abstract: Preface * Contributors * 1. Status and scope of aquaculture - T. Gjedrem * 2. Basic genetics - T.Gjedrem and O.Andersen * 3. Population genetics - O. Andersen and B. Hayes * 4. Polygenic inheritance - H.B. Bentsen * 5. Basic statistical parameters - T. Gjedrem and I. Olesen * 6. Kinship, relationship and inbreeding - A. K. Sonesson, J.A. Woolliams and Th.H.E. Meuwissen * 7. Selection - T. Gjedrem and J. Thodesen * 8. Reproductive traits in aquatic animals - T. Refstie and T. Gjedrem * 9. Methods for estimating phenotypic and genetic parameters - K. Kolstad * 10. Breeding strategies - K.T. Fjalestad * 11. Selection methods - K.T. Fjalestad * 12. Design of breeding programs - B. Gjerde * 13. Prediction of breeding values - B. Gjerde * 14. Genotype - environment interaction - T. Gjedrem * 15. Measuring genetic change - M. Rye and T. Gjedrem * 16. Breeding plans - T. Gjedrem * 17. Organising breeding programs - T. Gjedrem and T. Refstie * 18. Chromosome engineering - T. Refstie and T. Gjedrem * 19. Modern biotechnolgoy and aquaculture - B. Hayes and O. Andersen * 20. Genetic interactions between farmed and wild fish, with examples from the Atlantic salmon case in Norway - H.B. Bentsen and J. Thodesen * Appendix * References * Index

Resolving the genetic paradox in invasive species

Abstract: A recent paper in Nature helps to solve a genetic dilemma in invasion biology. That is, how bottlenecked populations that typically have low genetic diversity, low evolutionary potential and perhaps low reproductive fitness can become invasive. Potential solutions to the dilemma include being asexual or self-fertilising, having high reproductive rates, purging deleterious alleles that cause inbreeding depression, or having high migration rates where repeated introductions occur to overcome low genetic diversity and inbreeding. New work by Kolbe et al (2004) provides evidence for the latter scenario with an invasive lizard species. Many invasive species are asexual or self-fertilising and may escape inbreeding depression (Sakai et al, 2001) and invasive species may have higher than normal reproductive rates. Purging of deleterious alleles by natural selection in small populations does not remove the problem, as two recent studies in birds and Drosophila have demonstrated that bottlenecked populations typically suffer lowered reproductive fitness (Reed et al, 2003; Briskie and MacIntosh, 2004). Kolbe et al (2004) investigated this genetic dilemma by surveying mtDNA diversity in 71 native and 59 introduced populations of the invasive brown inole lizard (Anolis sagrei) from Cuba. They found that the populations that had established in Florida from the sources in Cuba had higher genetic diversity than individual populations, due to at least eight migration events. Further, these Florida populations seem to have been the main source for other recent introductions of the lizard to Hawaii and Taiwan. Related evidence of multiple introductions being associated with invasiveness exists for European starlings (Sturnus vulgaris) and house sparrows (Passer domesticus) in North America, and for a range of plants (Sakai et al, 2001). A similar situation has also been found in some house mouse (Mus musculus) populations (Frankham, 1997). Several subspecies of mice exist, and island populations with genetic diversity higher than mainland populations occur on major trade routes. Further, fire ants around Brisbane, Australia have been founded by multiple introductions before they were discovered and eradication efforts begun (Henshaw et al, 2004). Thus, at least some invasive species have elevated genetic diversity and enhanced ability to evolve when they invade new places. It is important that follow-up studies be carried out in such cases to establish whether greater evolutionary changes have actually occurred in invasive populations than in noninvasive ones. Not all introduced populations of brown anole have low genetic diversity. Of 57 introduced populations worldwide, 27 have reduced genetic diversity compared with the average level found in native Cuban populations, and 11 have lower genetic diversity than any of the Cuban populations (Kolbe et al, 2004). Information on multiple nuclear loci, such as microsatellites, would improve the precision of such comparisons. Population bottlenecks do not stop evolution or necessarily doom populations (Frankham et al, 2002). Even a single pair bottleneck in an outbreeding species only reduces heterozygosity by 25%, provided the population then grows rapidly in numbers. The inbreeding effect of such a bottleneck in a natural outbreeding species is likely to reduce the population growth rate, but as long as it remains positive the population will still grow. Many introduced species exhibit a lag before undergoing rapid expansion. This may be due to the early stage of exponential growth, stochastic extinctions of propagules, or genetic adaptation to the new environment (Sakai et al, 2001). The Kolbe et al (2004) study provides evidence that genetic adaptation may well be involved in invasiveness, but it remains to be seen whether this is generally true. Genotypes of introduced populations certainly influence introduction and reintroduction success in fish, plants, rabbits, starlings and invertebrates; in particular, populations adapted to captivity do poorly (Frankham et al, 2002). The Kolbe et al (2004) work has implications for controlling invasive species and for predicting the risk of introducing species that become invasive. It is clearly desirable to eliminate invasive species as soon as possible after the invasion, before they adapt to the local environment and before additional invasions occur. Unfortunately, this is rarely the case. With free trade agreements, increased trade is likely to both increase the number of introduction sites and the number of multiple introductions at individual sites. If the Kolbe et al (2004) story is general, then we are likely to face increased risks of invasive outbreaks from introduced populations in the future, both from multiple introductions to a site and from source populations being from trade centres with multiple source populations. R Frankham is at the Department of Biological Sciences, Key Centre for Biodiversity and Bioresources, Macquarie University, New South Wales 2109, Australia.

The Role of Systematic International Market Selection on Small Firms’ Export Performance

Abstract: This article hypothesizes that, on average, small and medium-sized enterprises (SMEs) that use a systematic methodology in selecting foreign target markets (what we call systematic market selection) perform better than SMEs using an ad hoc international market selection methodology. Using a sample of Greek exporting firms, we found that systematic international market selection is a significant determinant of export performance, even when controlling for decision-maker and firm-specific characteristics previous studies found to be related to export success. Implications for managers, trade promotion agencies, and future research are discussed.

A useful evaluation design, and effects of the Olweus Bullying Prevention Program

Abstract: The article presents the logic and other characteristics of an “extended selection cohorts” quasi-experimental design. Possible threats to the validity of conclusions based on this kind of design a...

A Large-Scale Screen for Artificial Selection in Maize Identifies Candidate Agronomic Loci for Domestication and Crop Improvement

Abstract: Maize (Zea mays subsp mays) was domesticated from teosinte (Z. mays subsp parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties, which were spread throughout the Americas by Native Americans and adapted to a wide range of environmental conditions. Starting with landraces, 20th century plant breeders selected inbred lines of maize for use in hybrid maize production. Both domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. Here, we sequenced 1095 maize genes from a sample of 14 inbred lines and chose 35 genes with zero sequence diversity as potential targets of selection. These 35 genes were then sequenced in a sample of diverse maize landraces and teosintes and tested for selection. Using two statistical tests, we identified eight candidate genes. Extended gene sequencing of these eight candidate loci confirmed that six were selected throughout the gene, and the remaining two exhibited evidence of selection in the 3' portion of each gene. The selected genes have functions consistent with agronomic selection for nutritional quality, maturity, and productivity. Our large-scale screen for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown.

Marker assisted selection in crop plants

Abstract: Genetic mapping of major genes and quantitative traits loci (QTLs) for many important agricultural traits is increasing the integration of biotechnology with the conventional breeding process. Exploitation of the information derived from the map position of traits with agronomical importance and of the linked molecular markers, can be achieved through marker assisted selection (MAS) of the traits during the breeding process. However, empirical applications of this procedure have shown that the success of MAS depends upon several factors, including the genetic base of the trait, the degree of the association between the molecular marker and the target gene, the number of individuals that can be analyzed and the genetic background in which the target gene has to be transferred. MAS for simply inherited traits is gaining increasing importance in breeding programs, allowing an acceleration of the breeding process. Traits related to disease resistance to pathogens and to the quality of some crop products are offering some important examples of a possible routinary application of MAS. For more complex traits, like yield and abiotic stress tolerance, a number of constraints have determined severe limitations on an efficient utilization of MAS in plant breeding, even if there are a few successful applications in improving quantitative traits. Recent advances in genotyping technologies together with comparative and functional genomic approaches are providing useful tools for the selection of genotypes with superior agronomical performancies.

Broadcast advertisement adapting method and apparatus

Abstract: Techniques of adapting an advertisement previously broadcast or in the process of being broadcast are disclosed. An advertisement selection factor is generated in order to adapt ads to a particular recipient. The advertisement selection factor can be derived from a database of information concerning the recipient and/or from data input by the recipient. The ad may be adapted in a variety of ways including replacing a broadcast ad segment with another segment. The replacement ad segment may be stored in a local device such as a set-top box or hardware card of a TV or PC and selected according to the advertisement selection factor. The replacement ad segment is synchronized with the on-going broadcast to produce a seamless ad. Alternatively, an ad processing can change audio or visual characteristics of the ad according to the ad selection factor. Such ad processing also includes dynamical texture mapping, object replacement, object addition, and audio/video data layering. The ad processing may also be combined with ad segment replacement. The result is a broadcast advertisement specifically targeted for a recipient and thereby likely to have a greater impact on that recipient's buying patterns. These techniques may also be applied to a variety of content such as sitcoms and sports shows to adapt the content to a particular recipient.