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Sample records for genetic selection final

  1. A New Selectable Marker System for Genetic Studies of Bacteria: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Parsons, D; Tolmasky, M; Chain, P; Segelke, B W

    2011-03-18

    Genetic manipulations in bacteria currently rely on the introduction of antibiotic resistance genes into a bacterial strain; for those organisms that will be used for commercial or industrial applications, the genetic cassette encoding the antibiotic resistance is sometimes removed after selection. it is clear that if alternative technologies could obviate the need to introduce antibiotic resistance into bacteria, they would most certainly become a standard tool in molecular micriobiology for commercial, industrial as well as research applications. Here, they present the development of a novel genetic engineering technology based on toxin-antitoxin systems to modify bacterial genomes without the use of antibiotic resistance in the mutagenesis process. The primary goal is to develop antibiotic-free selection for genetically altered select agent pathogens. They are adapting the toxinc-antitoxin system to enable gene replacement in select agent pathogens since the NIH restrictions introducing antibiotic resistance into select agent pathogens have hindered research with select agent pathogens.

  2. Optimizing energy yields in black locust through genetic selection: final report

    Energy Technology Data Exchange (ETDEWEB)

    Bongarten, B.C.; Merkle, S.A. [Georgia Univ., Athens, GA (United States). School of Forest Resources

    1996-10-01

    The purpose of this work was to assess the magnitude of improvement in biomass yield of black locust possible through breeding, and to determine methods for efficiently capturing the yield improvement achievable from selective breeding. To meet this overall objective, six tasks were undertaken to determine: (1) the amount and geographic pattern of natural genetic variation, (2) the mating system of the species, (3) quantitative genetic parameters of relevant traits, (4) the relationship between nitrogen fixation and growth in black locust, (5) the viability of mass vegetative propagation, and (6) the feasibility of improvement through genetic transformation.

  3. Selected Readings in Genetic Engineering

    Science.gov (United States)

    Mertens, Thomas R.; Robinson, Sandra K.

    1973-01-01

    Describes different sources of readings for understanding issues and concepts of genetic engineering. Broad categories of reading materials are: concerns about genetic engineering; its background; procedures; and social, ethical and legal issues. References are listed. (PS)

  4. Genetic Inventory Task Final Report. Volume 2

    Science.gov (United States)

    Venkateswaran, Kasthuri; LaDuc, Myron T.; Vaishampayan, Parag

    2012-01-01

    Contaminant terrestrial microbiota could profoundly impact the scientific integrity of extraterrestrial life-detection experiments. It is therefore important to know what organisms persist on spacecraft surfaces so that their presence can be eliminated or discriminated from authentic extraterrestrial biosignatures. Although there is a growing understanding of the biodiversity associated with spacecraft and cleanroom surfaces, it remains challenging to assess the risk of these microbes confounding life-detection or sample-return experiments. A key challenge is to provide a comprehensive inventory of microbes present on spacecraft surfaces. To assess the phylogenetic breadth of microorganisms on spacecraft and associated surfaces, the Genetic Inventory team used three technologies: conventional cloning techniques, PhyloChip DNA microarrays, and 454 tag-encoded pyrosequencing, together with a methodology to systematically collect, process, and archive nucleic acids. These three analysis methods yielded considerably different results: Traditional approaches provided the least comprehensive assessment of microbial diversity, while PhyloChip and pyrosequencing illuminated more diverse microbial populations. The overall results stress the importance of selecting sample collection and processing approaches based on the desired target and required level of detection. The DNA archive generated in this study can be made available to future researchers as genetic-inventory-oriented technologies further mature.

  5. Studies in genetic discrimination. Final progress report

    Energy Technology Data Exchange (ETDEWEB)

    1994-06-01

    We have screened 1006 respondents in a study of genetic discrimination. Analysis of these responses has produced evidence of the range of institutions engaged in genetic discrimination and demonstrates the impact of this discrimination on the respondents to the study. We have found that both ignorance and policy underlie genetic discrimination and that anti-discrimination laws are being violated.

  6. Simulating natural selection in landscape genetics

    Science.gov (United States)

    E. L. Landguth; S. A. Cushman; N. Johnson

    2012-01-01

    Linking landscape effects to key evolutionary processes through individual organism movement and natural selection is essential to provide a foundation for evolutionary landscape genetics. Of particular importance is determining how spatially- explicit, individual-based models differ from classic population genetics and evolutionary ecology models based on ideal...

  7. Engineering development of selective agglomeration. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1993-04-01

    This report presents the findings of the project entitled ``Engineering Development of Selective Agglomeration.`` The purpose is to develop selective agglomeration technology to a commercially acceptable level by 1993. Engineering development included bench-scale process development, component development adaptation or modification of existing unit operations, proof-of-concept (POC) module design, fabrication, testing, data evaluation, and conceptual design of a commercial facility. The information obtained during POC operation resulted in a technical and economic design base sufficient to support construction and operation of a commercial plant. Throughout this project performance targets for the engineering development of selective agglomeration process were to achieve 85% or greater Btu recovery at 85% or greater pyritic sulfur rejection (PSR). Additional objectives included producing a final clean-coal product with an ash content of 6% or less which is suitable for conventional coal handling systems. The selective agglomeration process, as applied to coal cleaning, is based on differences in the surface chemistry of coal and its associated impurities. Coal particles are hydrophobic (i.e., repel water) while the majority of its impurities are hydrophilic (i.e., stabilized in water). During selective agglomeration, a liquid (the agglomerant) that is immiscible with water is introduced into a coal-water slurry and agitated to disperse it in the slurry, thereby allowing it to come into contact with all particles in the slurry. The coal particles, due to their hydrophobic nature, are attracted to the agglomerant phase. The hydrophilic mineral impurities remain in the water phase. Continued agitation of the agglomerant-coated coal particles causes them to coalesce to form agglomerates. Once the agglomerates are formed, they are separated from the mineral matter-bearing aqueous phase by subsequent processing steps.

  8. Genetic signatures of natural selection in a model invasive ascidian

    Science.gov (United States)

    Lin, Yaping; Chen, Yiyong; Yi, Changho; Fong, Jonathan J.; Kim, Won; Rius, Marc; Zhan, Aibin

    2017-03-01

    Invasive species represent promising models to study species’ responses to rapidly changing environments. Although local adaptation frequently occurs during contemporary range expansion, the associated genetic signatures at both population and genomic levels remain largely unknown. Here, we use genome-wide gene-associated microsatellites to investigate genetic signatures of natural selection in a model invasive ascidian, Ciona robusta. Population genetic analyses of 150 individuals sampled in Korea, New Zealand, South Africa and Spain showed significant genetic differentiation among populations. Based on outlier tests, we found high incidence of signatures of directional selection at 19 loci. Hitchhiking mapping analyses identified 12 directional selective sweep regions, and all selective sweep windows on chromosomes were narrow (~8.9 kb). Further analyses indentified 132 candidate genes under selection. When we compared our genetic data and six crucial environmental variables, 16 putatively selected loci showed significant correlation with these environmental variables. This suggests that the local environmental conditions have left significant signatures of selection at both population and genomic levels. Finally, we identified “plastic” genomic regions and genes that are promising regions to investigate evolutionary responses to rapid environmental change in C. robusta.

  9. Portfolio selection using genetic algorithms | Yahaya | International ...

    African Journals Online (AJOL)

    In this paper, one of the nature-inspired evolutionary algorithms – a Genetic Algorithms (GA) was used in solving the portfolio selection problem (PSP). Based on a real dataset from a popular stock market, the performance of the algorithm in relation to those obtained from one of the popular quadratic programming (QP) ...

  10. Genetic search feature selection for affective modeling

    DEFF Research Database (Denmark)

    Martínez, Héctor P.; Yannakakis, Georgios N.

    2010-01-01

    Automatic feature selection is a critical step towards the generation of successful computational models of affect. This paper presents a genetic search-based feature selection method which is developed as a global-search algorithm for improving the accuracy of the affective models built....... The method is tested and compared against sequential forward feature selection and random search in a dataset derived from a game survey experiment which contains bimodal input features (physiological and gameplay) and expressed pairwise preferences of affect. Results suggest that the proposed method...

  11. The joint effects of kin, multilevel selection and indirect genetic effects on response to genetic selection.

    Science.gov (United States)

    Bijma, P; Wade, M J

    2008-09-01

    Kin and levels-of-selection models are common approaches for modelling social evolution. Indirect genetic effect (IGE) models represent a different approach, specifying social effects on trait values rather than fitness. We investigate the joint effect of relatedness, multilevel selection and IGEs on response to selection. We present a measure for the degree of multilevel selection, which is the natural partner of relatedness in expressions for response. Response depends on both relatedness and the degree of multilevel selection, rather than only one or the other factor. Moreover, response is symmetric in relatedness and the degree of multilevel selection, indicating that both factors have exactly the same effect. Without IGEs, the key parameter is the product of relatedness and the degree of multilevel selection. With IGEs, however, multilevel selection without relatedness can explain evolution of social traits. Thus, next to relatedness and multilevel selection, IGEs are a key element in the genetical theory of social evolution.

  12. Selectable genetic markers for nematode transgenesis.

    Science.gov (United States)

    Giordano-Santini, Rosina; Dupuy, Denis

    2011-06-01

    The nematode Caenorhabditis elegans has been used to study genetics and development since the mid-1970s. Over the years, the arsenal of techniques employed in this field has grown steadily in parallel with the number of researchers using this model. Since the introduction of C. elegans transgenesis, nearly 20 years ago, this system has been extensively used in areas such as rescue experiments, gene expression studies, and protein localization. The completion of the C. elegans genome sequence paved the way for genome-wide studies requiring higher throughput and improved scalability than provided by traditional genetic markers. The development of antibiotic selection systems for nematode transgenesis addresses these requirements and opens the possibility to apply transgenesis to investigate biological functions in other nematode species for which no genetic markers had been developed to date.

  13. Natural selection and the genetics of adaptation in threespine stickleback.

    Science.gov (United States)

    Schluter, Dolph; Marchinko, Kerry B; Barrett, R D H; Rogers, Sean M

    2010-08-27

    Growing knowledge of the molecular basis of adaptation in wild populations is expanding the study of natural selection. We summarize ongoing efforts to infer three aspects of natural selection--mechanism, form and history--from the genetics of adaptive evolution in threespine stickleback that colonized freshwater after the last ice age. We tested a mechanism of selection for reduced bony armour in freshwater by tracking genotype and allele frequency changes at an underlying major locus (Ectodysplasin) in transplanted stickleback populations. We inferred disruptive selection on genotypes at the same locus in a population polymorphic for bony armour. Finally, we compared the distribution of phenotypic effect sizes of genes underlying changes in body shape with that predicted by models of adaptive peak shifts following colonization of freshwater. Studies of the effects of selection on genes complement efforts to identify the molecular basis of adaptive differences, and improve our understanding of phenotypic evolution.

  14. Morphological genetic markers for selection of broiler lines

    Directory of Open Access Journals (Sweden)

    Schmidt GS

    2003-01-01

    Full Text Available Two paternal broiler lines (LL and LLc, originated from the same stock in 1998 of Embrapa Suinos e Aves genetic program were used. Line LL had been selected for eight generations for rapid growth while LLc had been mated randomly, without selection, as a control line. In the last generation, 30 males and 240 females were used in hierarchical matings with pedigree control to determine sire effect. The same number of birds were used, but matings were at random for LLc. Eggs of both lines were incubated and embryos were collected in different development stages (40, 45, 50, 55 and 60 hours after setting in order to determine somite number (NOS. The number of evaluated embryos were 1,967 and 498 for LL and LLc, respectively. This study aimed to determine the changes in somite formation during embryonic development that resulted from artificial selection for heavier body weight. In the evaluated generation, the differences for body weight, feed conversion ratio, carcass and breast yields between LL and LLc were 546 g; 0.16 FC units, 2.20 and 2.19%, respectively. NOS was greater in the initial (40 h and in the final (60 h stages for LL and in the intermediary stages (45, 50 and 55 h for LLc, indicating significant differences in the mechanisms of somite formation and development. Considering that both lines had the same genetic origin, such deviation indicates genetic changes due to artificial selection for body weight. The heritability estimates indicated low additive genetic effect for NOS in the different stages. Since the alterations were due to artificial selection for body weight, one could consider the hypothesis of using such genetic marker throughout family selection.

  15. The joint effects of kin, multilevel selection and indirect genetic effects on response to genetic selection

    NARCIS (Netherlands)

    Bijma, P.; Wade, M.J.

    2008-01-01

    Kin and levels-of-selection models are common approaches for modelling social evolution. Indirect genetic effect (IGE) models represent a different approach, specifying social effects on trait values rather than fitness. We investigate the joint effect of relatedness, multilevel selection and IGEs

  16. Population Genetics and Natural Selection in Rheumatic Disease.

    Science.gov (United States)

    Ramos, Paula S

    2017-08-01

    Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Natural selection is an important influence on human genetic variation. Because immune and inflammatory function genes are enriched for signals of positive selection, the prevalence of rheumatic disease-risk alleles seen in different populations is partially the result of differing selective pressures (eg, due to pathogens). This review summarizes the genetic regions associated with susceptibility to different rheumatic diseases and concomitant evidence for natural selection, including known agents of selection exerting selective pressure in these regions. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Human fertility, molecular genetics, and natural selection in modern societies.

    Directory of Open Access Journals (Sweden)

    Felix C Tropf

    Full Text Available Research on genetic influences on human fertility outcomes such as number of children ever born (NEB or the age at first childbirth (AFB has been solely based on twin and family-designs that suffer from problematic assumptions and practical limitations. The current study exploits recent advances in the field of molecular genetics by applying the genomic-relationship-matrix based restricted maximum likelihood (GREML methods to quantify for the first time the extent to which common genetic variants influence the NEB and the AFB of women. Using data from the UK and the Netherlands (N = 6,758, results show significant additive genetic effects on both traits explaining 10% (SE = 5 of the variance in the NEB and 15% (SE = 4 in the AFB. We further find a significant negative genetic correlation between AFB and NEB in the pooled sample of -0.62 (SE = 0.27, p-value = 0.02. This finding implies that individuals with genetic predispositions for an earlier AFB had a reproductive advantage and that natural selection operated not only in historical, but also in contemporary populations. The observed postponement in the AFB across the past century in Europe contrasts with these findings, suggesting an evolutionary override by environmental effects and underscoring that evolutionary predictions in modern human societies are not straight forward. It emphasizes the necessity for an integrative research design from the fields of genetics and social sciences in order to understand and predict fertility outcomes. Finally, our results suggest that we may be able to find genetic variants associated with human fertility when conducting GWAS-meta analyses with sufficient sample size.

  18. The genetic consequences of selection in natural populations.

    Science.gov (United States)

    Thurman, Timothy J; Barrett, Rowan D H

    2016-04-01

    The selection coefficient, s, quantifies the strength of selection acting on a genetic variant. Despite this parameter's central importance to population genetic models, until recently we have known relatively little about the value of s in natural populations. With the development of molecular genetic techniques in the late 20th century and the sequencing technologies that followed, biologists are now able to identify genetic variants and directly relate them to organismal fitness. We reviewed the literature for published estimates of natural selection acting at the genetic level and found over 3000 estimates of selection coefficients from 79 studies. Selection coefficients were roughly exponentially distributed, suggesting that the impact of selection at the genetic level is generally weak but can occasionally be quite strong. We used both nonparametric statistics and formal random-effects meta-analysis to determine how selection varies across biological and methodological categories. Selection was stronger when measured over shorter timescales, with the mean magnitude of s greatest for studies that measured selection within a single generation. Our analyses found conflicting trends when considering how selection varies with the genetic scale (e.g., SNPs or haplotypes) at which it is measured, suggesting a need for further research. Besides these quantitative conclusions, we highlight key issues in the calculation, interpretation, and reporting of selection coefficients and provide recommendations for future research. © 2016 John Wiley & Sons Ltd.

  19. Selected genetic disorders affecting Ashkenazi Jewish families.

    Science.gov (United States)

    Weinstein, Lenore B

    2007-01-01

    Ashkenazi Jews of Central and Eastern European ancestry have a disproportionately high prevalence of several autosomal recessive genetic disorders. This article describes these 9 disorders and their genetic inheritance patterns: Bloom syndrome; Canavan disease; cystic fibrosis; familial dysautonomia; Fanconi anemia; Gaucher disease; Mucolipidosis IV; Niemann-Pick disease; and Tay-Sachs disease. Genetic testing, counseling, and family planning options for the at-risk population are described. The role of the community health nurse is addressed.

  20. The Ethics of Artificial Selection and Genetic Modification of Plants

    OpenAIRE

    Armstrong, Freya; Børgesen, Lasse Faber; Gierløff, Anders Pihl; Justesen, Louise; Niemeier, Sebastian; Sandgaard, Monica; Steensgaard, Ida Mathilde

    2013-01-01

    Artificial selection and genetic modification are both methods which are used to maximize crop profit. The recent years’ development in the genetic engineering sector has made it possible to transfer a specific trait from one organism to another. The development has caused a widespread ethical debate on the subject. This study examines two different cases based on genetic modification and artificial selection of plants respectively. The aim of this study is to determine, whi...

  1. The reliability of randomly selected final year pharmacy students in ...

    African Journals Online (AJOL)

    Employing ANOVA, factorial experimental analysis, and the theory of error, reliability studies were conducted on the assessment of the drug product chloroquine phosphate tablets. The G–Study employed equal numbers of the factors for uniform control, and involved three analysts (randomly selected final year Pharmacy ...

  2. The prospects of selection for social genetic effects to improve welfare and productivity in livestock

    Directory of Open Access Journals (Sweden)

    Esther D. Ellen

    2014-11-01

    Full Text Available Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects. It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. In our opinion, this review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock.

  3. Evolutionary genetics: 150 years of natural selection

    Indian Academy of Sciences (India)

    The study of morphology, along with comparative anatomy, played an important role in the develop- ment of evolutionary thinking in the decades before and ... for our understanding of ageing but also for our attempts at intervention in the process of human ageing. Journal of Genetics, Vol. 87, No. 4, December 2008. 319 ...

  4. Phenotypic and genetic parameters for selected production and ...

    African Journals Online (AJOL)

    Phenotypic and genetic parameters for selected production and reproduction traits of Mpwapwa cattle in low-input production systems. ... Genetic parameters were estimated using an animal model procedure with ASReml software. The heritability for LMY and 305LMY were moderately high (0.33 ± 0.11–0.44 ± 0.04) and ...

  5. Determination of genetic relatedness among selected rice ( Oryza ...

    African Journals Online (AJOL)

    For plant improvement programs, genetic variation information among different cultivars is very important. Genetic variation among 26 rice (Oryza sativa, L.) accessions, consisting of 13 Iranian and 13 Malaysian cultivars was investigated using microsatellite markers distributed across the rice genome. All the 21 selected ...

  6. Selection of okra parents based on performance and genetic ...

    African Journals Online (AJOL)

    A total of 200 okra accessions with wide variability and a potential for genetic improvement were stored in the Vegetables Germplasm Bank of the Federal University of Viçosa (UFV-BGH) in Viçosa, Minas Gerais State, Brazil. The objective of this work was to select parents by genetic divergence and behavior per se in 70 ...

  7. Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection.

    Science.gov (United States)

    Daetwyler, Hans D; Hayden, Matthew J; Spangenberg, German C; Hayes, Ben J

    2015-08-01

    Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selection, optimal haploid value (OHV) selection, which predicts the best doubled haploid that can be produced from a segregating plant. This method focuses selection on the haplotype and optimizes the breeding program toward its end goal of generating an elite fixed line. We rigorously tested OHV selection breeding programs, using computer simulation, and show that it results in up to 0.6 standard deviations more genetic gain than genomic selection. At the same time, OHV selection preserved a substantially greater amount of genetic diversity in the population than genomic selection, which is important to achieve long-term genetic gain in breeding populations. Copyright © 2015 by the Genetics Society of America.

  8. Genetic progress after cycles of upland rice recurrent selection

    Directory of Open Access Journals (Sweden)

    Odilon Peixoto de Morais Júnior

    2015-08-01

    Full Text Available Periodic assessment of the genetic progress made in recurrent selection programs is essential for assessing the evolution of the programs and identifying the main factors that have contributed to this progress. This study aimed to estimate genetic progress in grain yield, plant height and days-to-flowering achieved in the CNA6 population of upland rice (Oryza sativa L., after four cycles of recurrent selection; and evaluate the genetic potential of this population to generate superior inbred lines after each selection cycle. The experimental data were obtained from progeny yield trials of each recurrent selection cycle. These trials were carried out in two or three locations per cycle, and consisted of S0:2 progenies and at least three checks. Federer’s augmented block design, with one replication on location (the environment, was adopted. Results revealed genetic progress for grain yield and plant height, with total genetic gains of 375.87 kg ha−1 and -3.90 cm, respectively, during the four selection cycles. The annual relative gain observed for grain yield was 1.54 %. The genetic potential of the population was analysed by the expected proportion of superior inbred lines. The standard adopted as the limit for obtaining superior inbred lines was the average of the checks for each trait. The genetic potential for grain yield and plant height increased during the study period. For days-to-flowering, no genetic gain occurred; however, the genetic potential of the population to generate superior inbred lines for this trait was maintained after the selection cycles.

  9. Promiscuity, sexual selection, and genetic diversity: a reply to Spurgin.

    Science.gov (United States)

    Lifjeld, Jan T; Gohli, Jostein; Johnsen, Arild

    2013-10-01

    We recently reported a positive association between female promiscuity and genetic diversity across passerine birds, and launched the hypothesis that female promiscuity acts as a balancing selection, pressure maintaining genetic diversity in populations (Gohli et al.2013). Spurgin (2013) questions both our analyses and interpretations. While we agree that the hypothesis needs more comprehensive empirical testing, we find his specific points of criticism unjustified. In a more general perspective, we call for a more explicit recognition of female mating preferences as mechanisms of selection in population genetics theory. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  10. Genetic structure of natural populations: Final technical report

    International Nuclear Information System (INIS)

    Ayala, F.J.

    1987-01-01

    We determined the LD 50 for individuals with any one of four genetic constitutions. The LD 50 was in kR units (S and F refer to the two common alleles found in natural populations and N is a mull allele) S/S 5.31, F/F 4.61, S/F 4.19, N/N 3.16. These results are as expected under the hypothesis the SOD is involved in radio-resistance and the degree of protection is a function of SOD specific activity. S codes for an allozyme that has the highest in vitro specific activity while N reduces the amount of enzyme to 3.5% of the normal level. Natural selection experiments in population cages were carried out for 13 generations. In control populations, the frequency of the S allele decreases from the initial frequency of 0.50 to an equilibrium value 0.1 to 0.2 in about 10 generations. In populations with the larvae receiving 4 KR in each generation, s reaches an equilibrium frequency of 0.6; when the irradiation was no longer applied, the frequency of S started declining, eventually reaching 0.1 to 0.2. These results corroborate the hypothesis that SOD protects against irradiation and that the degree of protection is correlated by the in vitro specific activity of the allozymes. 29 refs., 4 tabs

  11. Exploiting a natural auxotrophy for genetic selection.

    Science.gov (United States)

    Ramage, Elizabeth; Gallagher, Larry; Manoil, Colin

    2012-08-01

    We exploited the natural histidine auxotrophy of Francisella species to develop hisD (encodes histidinol dehydrogenase) as a positive selection marker. A shuttle plasmid (pBR103) carrying Escherichia coli hisD and designed for cloning of PCR fragments replicated in both attenuated and highly virulent Francisella strains. During this work, we formulated a simplified defined growth medium for Francisella novicida.

  12. Response to family selection and genetic parameters in Japanese quail selected for four week breast weight

    DEFF Research Database (Denmark)

    Khaldari, Majid; Yeganeh, Hassan Mehrabani; Pakdel, Abbas

    2011-01-01

    An experiment was conducted to investigate the effect of short-term selection for 4 week breast weight (4wk BRW), and to estimate genetic parameters of body weight, and carcass traits. A selection (S) line and control (C) line was randomly selected from a base population. Data were collected over...

  13. Genetic selection increases parthenogenesis in Chinese painted quail (Coturnix chinensis).

    Science.gov (United States)

    Parker, H M; Kiess, A S; Wells, J B; Young, K M; Rowe, D; McDaniel, C D

    2010-07-01

    Parthenogenesis, embryonic development of an unfertilized egg, occurs naturally in turkey, chicken, and quail species. In fact, parthenogenesis in turkeys and chickens can be increased by genetic selection. However, it is unknown if genetic selection for parthenogenesis is effective in quail or if selection for parthenogenesis affects egg production. Therefore, the objectives of this study were to determine if the incidence of parthenogenesis in quail could be increased by genetic selection and if selection for this trait affects egg production. To prevent fertilization, 1,090 females were caged separately from males at 4 wk of age and then caged individually at 6 wk of age to monitor egg production. Eggs were collected daily, labeled, and stored for 0 to 3 d. After 10 d of incubation, 20 unfertilized eggs from each hen were examined for the occurrence of parthenogenesis and embryonic growth. In the parent (P) generation and subsequent generations (1 to 4), hens laying eggs containing parthenogenetic development and males whose sisters or mothers exhibited parthenogenesis were used for breeding. There was a linear increase in the percentage of hens exhibiting parthenogenesis as generation of selection increased. With each successive generation, there was a quadratic response in the percentage of eggs positive for parthenogenesis. When compared with the P generation, parthenogenesis was almost 3 times greater for eggs laid by the fourth generation (4.6 to 12.5%, respectively). Even when only hens exhibiting parthenogenesis were examined, the percentage of eggs demonstrating embryonic development responded quadratically with generation of selection. The embryonic size at 10 d of incubation was greater for each subsequent generation when compared with the P generation. There was a linear decrease in both egg production and the average position of an egg in a clutch as generation of selection increased. In conclusion, genetic selection for parthenogenesis increased the

  14. Genetic diversity and selection regulates evolution of infectious bronchitis virus.

    Science.gov (United States)

    Toro, Haroldo; van Santen, Vicky L; Jackwood, Mark W

    2012-09-01

    Conventional and molecular epidemiologic studies have confirmed the ability of infectious bronchitis virus (IBV) to rapidly evolve and successfully circumvent extensive vaccination programs implemented since the early 1950s. IBV evolution has often been explained as variation in gene frequencies as if evolution were driven by genetic drift alone. However, the mechanisms regulating the evolution of IBV include both the generation of genetic diversity and the selection process. IBV's generation of genetic diversity has been extensively investigated and ultimately involves mutations and recombination events occurring during viral replication. The relevance of the selection process has been further understood more recently by identifying genetic and phenotypic differences between IBV populations prior to, and during, replication in the natural host. Accumulating evidence suggests that multiple environmental forces within the host, including immune responses (or lack thereof) and affinity for cell receptors, as well as physical and biochemical conditions, are responsible for the selection process. Some scientists have used or adopted the related quasispecies frame to explain IBV evolution. The quasispecies frame, while providing a distinct explanation of the dynamics of populations in which mutation is a frequent event, exhibits relevant limitations which are discussed herein. Instead, it seems that IBV populations evolving by the generation of genetic variability and selection on replicons follow the evolutionary mechanisms originally proposed by Darwin. Understanding the mechanisms underlying the evolution of IBV is of basic relevance and, without doubt, essential to appropriately control and prevent the disease.

  15. The ethics of using genetic engineering for sex selection.

    Science.gov (United States)

    Liao, S Matthew

    2005-02-01

    It is quite likely that parents will soon be able to use genetic engineering to select the sex of their child by directly manipulating the sex of an embryo. Some might think that this method would be a more ethical method of sex selection than present technologies such as preimplantation genetic diagnosis (PGD) because, unlike PGD, it does not need to create and destroy "wrong gendered" embryos. This paper argues that those who object to present technologies on the grounds that the embryo is a person are unlikely to be persuaded by this proposal, though for different reasons.

  16. Improving Genetic Gain with Genomic Selection in Autotetraploid Potato

    Directory of Open Access Journals (Sweden)

    Anthony T. Slater

    2016-11-01

    Full Text Available Potato ( L. breeders consider a large number of traits during cultivar development and progress in conventional breeding can be slow. There is accumulating evidence that some of these traits, such as yield, are affected by a large number of genes with small individual effects. Recently, significant efforts have been applied to the development of genomic resources to improve potato breeding, culminating in a draft genome sequence and the identification of a large number of single nucleotide polymorphisms (SNPs. The availability of these genome-wide SNPs is a prerequisite for implementing genomic selection for improvement of polygenic traits such as yield. In this review, we investigate opportunities for the application of genomic selection to potato, including novel breeding program designs. We have considered a number of factors that will influence this process, including the autotetraploid and heterozygous genetic nature of potato, the rate of decay of linkage disequilibrium, the number of required markers, the design of a reference population, and trait heritability. Based on estimates of the effective population size derived from a potato breeding program, we have calculated the expected accuracy of genomic selection for four key traits of varying heritability and propose that it will be reasonably accurate. We compared the expected genetic gain from genomic selection with the expected gain from phenotypic and pedigree selection, and found that genetic gain can be substantially improved by using genomic selection.

  17. Triangulating the genetic basis of adaptation to multifarious selection.

    Science.gov (United States)

    Pfrender, M E

    2012-05-01

    Understanding how natural populations adapt to their local environments is a major research theme for ecological genomics. This endeavour begins by sleuthing for shared genetic similarities among unrelated natural populations sharing adaptive traits to documented selective pressures. When the selective pressures have low dimensionality, and the genetic response is localized to a few genes of major effect, this detective work is relatively straightforward. However, in the real world, populations face a complex mixture of selective pressures and many adaptive responses are the result of changes in quantitative traits that have a polygenic genetic basis. This complex relationship between environment and adaptation presents a significant challenge. How can we begin to identify drivers of adaptation in natural settings? In this issue of Molecular Ecology, Orsini et al. (2012) take advantage of the biological attributes of the freshwater microcrustacean Daphnia (Fig. 1) to disentangle multidimensional selection's signature on the genome of populations that have repeatedly evolved adaptive responses to isolated selective pressures including predation, parasitism and anthropogenic changes in land use. Orsini et al. (2012) leverage a powerful combination of spatially structured populations in a geographic mosaic of environmental stressors, the historical archive of past genotypes preserved in lake-bottom sediments and selection experiments to identify sets of candidate genomic regions associated with adaptation in response to these three environmental stressors. This study provides a template for future investigation in ecological genomics, combining multiple experimental approaches with the genomic investigation of a well-studied ecological model species. © 2012 Blackwell Publishing Ltd.

  18. Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene.

    Science.gov (United States)

    Martin, Simon H; Möst, Markus; Palmer, William J; Salazar, Camilo; McMillan, W Owen; Jiggins, Francis M; Jiggins, Chris D

    2016-05-01

    A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects. Copyright © 2016 by the Genetics Society of America.

  19. Genetic diversity, phylogeographic structure and effect of selection ...

    Indian Academy of Sciences (India)

    Abdulhakeem B. Ajibike

    2017-12-11

    Dec 11, 2017 ... Abstract. In this study, the maternal genetic diversity, phylogenetic relationship and effect of natural selection on indigenous chickens from Nigeria were assessed. A total of 397-bp fragment of the mitochondrial DNA (mtDNA) D-loop region of 171 indigenous chickens from four populations of Nigeria and ...

  20. GMDH Method with Genetic Selection Algorithm and Cloning

    Czech Academy of Sciences Publication Activity Database

    Jiřina, Marcel; Jiřina jr., M.

    2013-01-01

    Roč. 23, č. 5 (2013), s. 451-464 ISSN 1210-0552 Institutional support: RVO:67985807 Keywords : multivariate data * GMDH * linear regression * Gauss-Markov conditions * cloning * genetic selection * classification Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 0.412, year: 2013

  1. Genetic diversity among selected genotypes of almond Prunus ...

    African Journals Online (AJOL)

    Average polymorphic information content (PIC) value of 16 selected primers was 0.684 and maximum and minimum PIC value was 0.8687 and 0.2551 for primers S073 and S081, respectively. Cophenetic correlation was found to be 0.89. RAPD data on genetic diversity matched classification of studied genotypes based on ...

  2. Genetic selection for coping style predicts stressor susceptibility

    NARCIS (Netherlands)

    Veenema, AH; Meijer, OC; de Kloet, ER; Koolhaas, JM

    Genetically selected aggressive (SAL) and nonaggressive (LAL) male wild house-mice which show distinctly different coping styles, also display a differential regulation of the hypothalamic-pituitary-adrenal axis after exposure to an acute stressor. To test the hypothesis that coping style predicts

  3. Growth performance, genetic parameters and selection index of ...

    African Journals Online (AJOL)

    As part of the ranking procedure, a selection index was constructed based on two major body components namely body weight (BWT) and heart girth (HGT) to objectively determine the genetic worth of the growing pure and crossbred progenies of Red Sokoto and West African Dwarf kids. The results showed that average ...

  4. Molecular genetics and livestock selection. Approaches, opportunities and risks

    International Nuclear Information System (INIS)

    Williams, J.L.

    2005-01-01

    Following domestication, livestock were selected both naturally through adaptation to their environments and by man so that they would fulfil a particular use. As selection methods have become more sophisticated, rapid progress has been made in improving those traits that are easily measured. However, selection has also resulted in decreased diversity. In some cases, improved breeds have replaced local breeds, risking the loss of important survival traits. The advent of molecular genetics provides the opportunity to identify the genes that control particular traits by a gene mapping approach. However, as with selection, the early mapping studies focused on traits that are easy to measure. Where molecular genetics can play a valuable role in livestock production is by providing the means to select effectively for traits that are difficult to measure. Identifying the genes underpinning particular traits requires a population in which these traits are segregating. Fortunately, several experimental populations have been created that have allowed a wide range of traits to be studied. Gene mapping work in these populations has shown that the role of particular genes in controlling variation in a given trait can depend on the genetic background. A second finding is that the most favourable alleles for a trait may in fact. be present in animals that perform poorly for the trait. In the long term, knowledge of -the genes controlling particular traits, and the way they interact with the genetic background, will allow introgression between breeds and the assembly of genotypes that are best suited to particular environments, producing animals with the desired characteristics. If used wisely, this approach will maintain genetic diversity while improving performance over a wide range of desired traits. (author)

  5. Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection

    OpenAIRE

    Daetwyler, Hans D.; Hayden, Matthew J.; Spangenberg, German C.; Hayes, Ben J.

    2015-01-01

    Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selec...

  6. Ontario Select Committee on Alternative Fuel Sources : Final Report

    International Nuclear Information System (INIS)

    Galt, D.

    2002-06-01

    On June 28, 2001, the Ontario Legislative Assembly appointed the Select Committee an Alternative Fuel Sources, comprised of representatives of all parties, with a broad mandate to investigate, report and offer recommendations with regard to the various options to support the development and application of environmentally sustainable alternatives to the fossil fuel sources already existing. The members of the Committee elected to conduct extensive public hearings, conduct site visits, attend relevant conferences, do some background research to examine a vast number of alternative fuel and energy sources that could be of relevance to the province of Ontario. A discussion paper (interim report) was issued by the Committee in November 2001, and the present document represents the final report, containing 141 recommendations touching 20 topics. The information contained in the report is expected to assist in the development and outline of policy and programs designed to specifically support alternative fuels and energy sources and applicable technologies. Policy issues were discussed in Part A of the report, along with the appropriate recommendations. The recommendations on specific alternative fuels and energy sources were included in Part B of the report. It is believed that the dependence of Ontario on traditional petroleum-based fuels and energy sources can be reduced through aggressive action on alternative fuels and energy. The benefits of such action would be felt in the area of air quality, with social, and economic benefits as well. 3 tabs

  7. Energy conservation in selected buildings, Gdansk. 1. final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-02-01

    This Final Report marks the end of the implementation stage of the project: `Energy Conservation in Selected Buildings in Gdansk, Poland` supported by the Danish Environment-related Energy Sector Programme for Poland under the Danish Energy Agency. The residential and commercial sectors together with public buildings account for 40-45% of the total energy consumption and are dominated by the use of space heating and hot water. The sector has a significant over-consumption of energy, which first of all is due to the lack of or too weak incentives for the individual tenants to decrease the energy consumption. Bad thermal insulation of buildings and inefficient central heating systems with a widespread lack of measurement and automatic control systems give cause for extensive heat losses. The objective of the project has been to document the effects of energy savings in 18 multi-family houses when different types of energy saving measures are applied. These measures include thermal insulation of buildings, refurbishment of the heating system and introduction of individual billing system for heating and hot tap water. Energy audits of 18 buildings were performed by combination of on-site inspection of all buildings and data collection from the available drawings, technical descriptions, etc. The on-site inspection was carried out by use of an energy audit scheme specially developed for this project. (EG)

  8. Plant Genetic Resources: Selected Issues from Genetic Erosion to Genetic Engineering

    Directory of Open Access Journals (Sweden)

    Karl Hammer

    2008-04-01

    Full Text Available Plant Genetic Resources (PGR continue to play an important role in the development of agriculture. The following aspects receive a special consideration:1. Definition. The term was coined in 1970. The genepool concept served as an important tool in the further development. Different approaches are discussed.2. Values of Genetic Resources. A short introduction is highlighting this problem and stressing the economic usfulness of PGR.3. Genetic Erosion. Already observed by E. Baur in 1914, this is now a key issue within PGR. The case studies cited include Ethiopia, Italy, China, S Korea, Greece and S. Africa. Modern approaches concentrate on allelic changes in varieties over time but neglect the landraces. The causes and consequences of genetic erosion are discussed.4. Genetic Resources Conservation. Because of genetic erosion there is a need for conservation. PGR should be consigned to the appropriate method of conservation (ex situ, in situ, on-farm according to the scientific basis of biodiversity (genetic diversity, species diversity, ecosystem diversity and the evolutionary status of plants (cultivated plants, weeds, related wild plants (crop wild relatives.5. GMO. The impact of genetically engineered plants on genetic diversity is discussed.6. The Conclusions and Recommendations stress the importance of PGR. Their conservation and use are urgent necessities for the present development and future survival of mankind.

  9. A molecular-genetic approach to studying source-sink interactions in Arabidopsis thalian. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Gibson, S. I.

    2000-06-01

    This is a final report describing the results of the research funded by the DOE Energy Biosciences Program grant entitled ''A Molecular-Genetic Approach to Studying Source-Sink Interactions in Arabidiopsis thaliana''.

  10. Genetic secrets: Protecting privacy and confidentiality in the genetic era. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Rothstein, M.A. [ed.

    1998-09-01

    Few developments are likely to affect human beings more profoundly in the long run than the discoveries resulting from advances in modern genetics. Although the developments in genetic technology promise to provide many additional benefits, their application to genetic screening poses ethical, social, and legal questions, many of which are rooted in issues of privacy and confidentiality. The ethical, practical, and legal ramifications of these and related questions are explored in depth. The broad range of topics includes: the privacy and confidentiality of genetic information; the challenges to privacy and confidentiality that may be projected to result from the emerging genetic technologies; the role of informed consent in protecting the confidentiality of genetic information in the clinical setting; the potential uses of genetic information by third parties; the implications of changes in the health care delivery system for privacy and confidentiality; relevant national and international developments in public policies, professional standards, and laws; recommendations; and the identification of research needs.

  11. Genetic gains in physic nut using selection indexes

    Directory of Open Access Journals (Sweden)

    Leonardo Lopes Bhering

    2012-03-01

    Full Text Available The objective of this work was to estimate genetic gains in physic nut (Jatropha curcas using selection indexes and to establish the best selection strategy for the species. Direct and indirect selection was carried out using different selection indexes, totalizing 14 strategies. One hundred and seventy five families from the active germplasm bank of Embrapa Agroenergy, Brasília, Brazil, were analyzed in a randomized complete block design with two replicates. The evaluated traits were: grain yield; seeds per fruit; endosperm/seed ratio; seed weight, length, width, and thickness; branches per plant at 0.5, 1.0, and 1.5 m; plant height; stem diameter; canopy projection on rows and between lines; canopy volume; juvenility (days to the first flowering; and height of the first inflorescence. Evaluations were done during the second year of cultivation. The use of selection indexes is relevant to maximize the genetic gains in physic nut, favoring a better distribution of desirable traits. The multiplicative and restrictive indexes are considered the most promising for selection.

  12. Integrating economic parameters into genetic selection for Large White pigs.

    Science.gov (United States)

    Dube, Bekezela; Mulugeta, Sendros D; Dzama, Kennedy

    2013-08-01

    The objective of the study was to integrate economic parameters into genetic selection for sow productivity, growth performance and carcass characteristics in South African Large White pigs. Simulation models for sow productivity and terminal production systems were performed based on a hypothetical 100-sow herd, to derive economic values for the economically relevant traits. The traits included in the study were number born alive (NBA), 21-day litter size (D21LS), 21-day litter weight (D21LWT), average daily gain (ADG), feed conversion ratio (FCR), age at slaughter (AGES), dressing percentage (DRESS), lean content (LEAN) and backfat thickness (BFAT). Growth of a pig was described by the Gompertz growth function, while feed intake was derived from the nutrient requirements of pigs at the respective ages. Partial budgeting and partial differentiation of the profit function were used to derive economic values, which were defined as the change in profit per unit genetic change in a given trait. The respective economic values (ZAR) were: 61.26, 38.02, 210.15, 33.34, -21.81, -68.18, 5.78, 4.69 and -1.48. These economic values indicated the direction and emphases of selection, and were sensitive to changes in feed prices and marketing prices for carcasses and maiden gilts. Economic values for NBA, D21LS, DRESS and LEAN decreased with increasing feed prices, suggesting a point where genetic improvement would be a loss, if feed prices continued to increase. The economic values for DRESS and LEAN increased as the marketing prices for carcasses increased, while the economic value for BFAT was not sensitive to changes in all prices. Reductions in economic values can be counterbalanced by simultaneous increases in marketing prices of carcasses and maiden gilts. Economic values facilitate genetic improvement by translating it to proportionate profitability. Breeders should, however, continually recalculate economic values to place the most appropriate emphases on the respective

  13. Combinatorial Optimization in Project Selection Using Genetic Algorithm

    Science.gov (United States)

    Dewi, Sari; Sawaluddin

    2018-01-01

    This paper discusses the problem of project selection in the presence of two objective functions that maximize profit and minimize cost and the existence of some limitations is limited resources availability and time available so that there is need allocation of resources in each project. These resources are human resources, machine resources, raw material resources. This is treated as a consideration to not exceed the budget that has been determined. So that can be formulated mathematics for objective function (multi-objective) with boundaries that fulfilled. To assist the project selection process, a multi-objective combinatorial optimization approach is used to obtain an optimal solution for the selection of the right project. It then described a multi-objective method of genetic algorithm as one method of multi-objective combinatorial optimization approach to simplify the project selection process in a large scope.

  14. The role of natural selection in circadian behaviour: a molecular-genetic approach.

    Science.gov (United States)

    Rosato, Ezio; Kyriacou, Charalambos P

    2011-06-30

    Circadian rhythms (~24 h) in biochemistry, physiology and behaviour are found in almost all eukaryotes and some bacteria. The elucidation of the molecular components of the 24 h circadian clock in a number of model organisms in recent years has provided an opportunity to assess the adaptive value of variation in clock genes. Laboratory experiments using artificially generated mutants reveal that the circadian period is adaptive in a 24 h world. Natural genetic variation can also be studied, and there are a number of ways in which the signature of natural selection can be detected. These include the study of geographical patterns of genetic variation, which provide a first indication that selection may be at work, and the use of sophisticated statistical neutrality tests, which examine whether the pattern of variation observed is consistent with a selective rather than a neutral (or drift) scenario. Finally, examining the probable selective agents and their differential effects on the circadian phenotype of the natural variants provides the final compelling evidence for selection. We present some examples of how these types of analyses have not only enlightened the evolutionary study of clocks, but have also contributed to a more pragmatic molecular understanding of the function of clock proteins.

  15. Variable selection in Logistic regression model with genetic algorithm.

    Science.gov (United States)

    Zhang, Zhongheng; Trevino, Victor; Hoseini, Sayed Shahabuddin; Belciug, Smaranda; Boopathi, Arumugam Manivanna; Zhang, Ping; Gorunescu, Florin; Subha, Velappan; Dai, Songshi

    2018-02-01

    Variable or feature selection is one of the most important steps in model specification. Especially in the case of medical-decision making, the direct use of a medical database, without a previous analysis and preprocessing step, is often counterproductive. In this way, the variable selection represents the method of choosing the most relevant attributes from the database in order to build a robust learning models and, thus, to improve the performance of the models used in the decision process. In biomedical research, the purpose of variable selection is to select clinically important and statistically significant variables, while excluding unrelated or noise variables. A variety of methods exist for variable selection, but none of them is without limitations. For example, the stepwise approach, which is highly used, adds the best variable in each cycle generally producing an acceptable set of variables. Nevertheless, it is limited by the fact that it commonly trapped in local optima. The best subset approach can systematically search the entire covariate pattern space, but the solution pool can be extremely large with tens to hundreds of variables, which is the case in nowadays clinical data. Genetic algorithms (GA) are heuristic optimization approaches and can be used for variable selection in multivariable regression models. This tutorial paper aims to provide a step-by-step approach to the use of GA in variable selection. The R code provided in the text can be extended and adapted to other data analysis needs.

  16. Genetic signature of natural selection in first Americans.

    Science.gov (United States)

    Amorim, Carlos Eduardo; Nunes, Kelly; Meyer, Diogo; Comas, David; Bortolini, Maria Cátira; Salzano, Francisco Mauro; Hünemeier, Tábita

    2017-02-28

    When humans moved from Asia toward the Americas over 18,000 y ago and eventually peopled the New World they encountered a new environment with extreme climate conditions and distinct dietary resources. These environmental and dietary pressures may have led to instances of genetic adaptation with the potential to influence the phenotypic variation in extant Native American populations. An example of such an event is the evolution of the fatty acid desaturases ( FADS ) genes, which have been claimed to harbor signals of positive selection in Inuit populations due to adaptation to the cold Greenland Arctic climate and to a protein-rich diet. Because there was evidence of intercontinental variation in this genetic region, with indications of positive selection for its variants, we decided to compare the Inuit findings with other Native American data. Here, we use several lines of evidence to show that the signal of FADS-positive selection is not restricted to the Arctic but instead is broadly observed throughout the Americas. The shared signature of selection among populations living in such a diverse range of environments is likely due to a single and strong instance of local adaptation that took place in the common ancestral population before their entrance into the New World. These first Americans peopled the whole continent and spread this adaptive variant across a diverse set of environments.

  17. 78 FR 54588 - Final Priorities, Requirements, Definitions, and Selection Criteria: Race to the Top-District...

    Science.gov (United States)

    2013-09-05

    ... CFR Subtitle A RIN 1810-AB17 Final Priorities, Requirements, Definitions, and Selection Criteria: Race... Education. ACTION: Final priorities, requirements, definitions, and selection criteria; correction. SUMMARY..., definitions, and selection criteria published in the Federal Register on August 6, 2013 (78 FR 47980), namely...

  18. Multilevel selection 2: Estimating the genetic parameters determining inheritance and response to selection.

    Science.gov (United States)

    Bijma, Piter; Muir, William M; Ellen, Esther D; Wolf, Jason B; Van Arendonk, Johan A M

    2007-01-01

    Interactions among individuals are universal, both in animals and in plants and in natural as well as domestic populations. Understanding the consequences of these interactions for the evolution of populations by either natural or artificial selection requires knowledge of the heritable components underlying them. Here we present statistical methodology to estimate the genetic parameters determining response to multilevel selection of traits affected by interactions among individuals in general populations. We apply these methods to obtain estimates of genetic parameters for survival days in a population of layer chickens with high mortality due to pecking behavior. We find that heritable variation is threefold greater than that obtained from classical analyses, meaning that two-thirds of the full heritable variation is hidden to classical analysis due to social interactions. As a consequence, predicted responses to multilevel selection applied to this population are threefold greater than classical predictions. This work, combined with the quantitative genetic theory for response to multilevel selection presented in an accompanying article in this issue, enables the design of selection programs to effectively reduce competitive interactions in livestock and plants and the prediction of the effects of social interactions on evolution in natural populations undergoing multilevel selection.

  19. Selecting an appropriate genetic evaluation model for selection in a developing dairy sector

    NARCIS (Netherlands)

    McGill, D.M.; Mulder, H.A.; Thomson, P.C.; Lievaart, J.J.

    2014-01-01

    This study aimed to identify genetic evaluation models (GEM) to accurately select cattle for milk production when only limited data are available. It is based on a data set from the Pakistani Sahiwal progeny testing programme which includes records from five government herds, each consisting of 100

  20. Genetic selection for temperament traits in dairy and beef cattle

    Directory of Open Access Journals (Sweden)

    Marie J Haskell

    2014-10-01

    Full Text Available Animal temperament can be defined as a response to environmental or social stimuli. There are a number of temperament traits in cattle that contribute to their welfare, including their response to handling or milking, response to challenge such as human approach or intervention at calving, and response to conspecifics. In a number of these areas, the genetic basis of the trait has been studied. Heritabilities have been estimated and in some cases quantitative trait loci (QTL have been identified. The variation is sometimes considerable and moderate heritabilities have been found for the major handling temperament traits, making them amenable to selection. Studies have also investigated the correlations between temperament and other traits, such as productivity and meat quality. Despite this, there are relatively few examples of temperament traits being used in selection programmes. Most often, animals are screened for aggression or excessive fear during handling or milking, with extreme animals being culled, or EBVs for temperament are estimated, but these traits are not commonly included routinely in selection indices, despite there being economic, welfare and human safety drivers for their. There may be a number of constraints and barriers. For some traits and breeds, there may be difficulties in collecting behavioral data on sufficiently large populations of animals to estimate genetic parameters. Most selection indices require estimates of economic values, and it is often difficult to assign an economic value to a temperament trait. The effects of selection primarily for productivity traits on temperament and welfare are discussed. Future opportunities include automated data collection methods and the wider use of genomic information in selection.

  1. Bacteriophage-based genetic system for selection of nonsplicing inteins.

    Science.gov (United States)

    Cann, Isaac K O; Amaya, Kensey R; Southworth, Maurice W; Perler, Francine B

    2004-05-01

    A genetic selection system that detects splicing and nonsplicing activities of inteins was developed based on the ability to rescue a T4 phage strain with a conditionally inactive DNA polymerase. This phage defect can be complemented by expression of plasmid-encoded phage RB69 DNA polymerase. Insertion of an intein gene into the active site of the RB69 DNA polymerase gene renders polymerase activity and phage viability dependent on protein splicing. The effectiveness of the system was tested by screening for thermosensitive splicing mutants. Development of genetic systems with the potential of identifying protein splicing inhibitors is a first step towards controlling proliferation of pathogenic microbes harboring inteins in essential proteins.

  2. Short communication: Genetic lag represents commercial herd genetic merit more accurately than the 4-path selection model.

    Science.gov (United States)

    Dechow, C D; Rogers, G W

    2018-05-01

    Expectation of genetic merit in commercial dairy herds is routinely estimated using a 4-path genetic selection model that was derived for a closed population, but commercial herds using artificial insemination sires are not closed. The 4-path model also predicts a higher rate of genetic progress in elite herds that provide artificial insemination sires than in commercial herds that use such sires, which counters other theoretical assumptions and observations of realized genetic responses. The aim of this work is to clarify whether genetic merit in commercial herds is more accurately reflected under the assumptions of the 4-path genetic response formula or by a genetic lag formula. We demonstrate by tracing the transmission of genetic merit from parents to offspring that the rate of genetic progress in commercial dairy farms is expected to be the same as that in the genetic nucleus. The lag in genetic merit between the nucleus and commercial farms is a function of sire and dam generation interval, the rate of genetic progress in elite artificial insemination herds, and genetic merit of sires and dams. To predict how strategies such as the use of young versus daughter-proven sires, culling heifers following genomic testing, or selective use of sexed semen will alter genetic merit in commercial herds, genetic merit expectations for commercial herds should be modeled using genetic lag expectations. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  3. Genetic variability and selection criteria in rice mutant lines as revealed by quantitative traits.

    Science.gov (United States)

    Oladosu, Yusuff; Rafii, M Y; Abdullah, Norhani; Abdul Malek, Mohammad; Rahim, H A; Hussin, Ghazali; Abdul Latif, Mohammad; Kareem, Isiaka

    2014-01-01

    Genetic based knowledge of different vegetative and yield traits play a major role in varietal improvement of rice. Genetic variation gives room for recombinants which are essential for the development of a new variety in any crop. Based on this background, this work was carried out to evaluate genetic diversity of derived mutant lines and establish relationships between their yield and yield components using multivariate analysis. To achieve this objective, two field trials were carried out on 45 mutant rice genotypes to evaluate their growth and yield traits. Data were taken on vegetative traits and yield and its components, while genotypic and phenotypic coefficients, variance components, expected genetic advance, and heritability were calculated. All the genotypes showed variations for vegetative traits and yield and its components. Also, there was positive relationship between the quantitative traits and the final yield with the exception of number of tillers. Finally, the evaluated genotypes were grouped into five major clusters based on the assessed traits with the aid of UPGMA dendrogram. So hybridization of group I with group V or group VI could be used to attain higher heterosis or vigour among the genotypes. Also, this evaluation could be useful in developing reliable selection indices for important agronomic traits in rice.

  4. Feature selection using genetic algorithms for fetal heart rate analysis

    International Nuclear Information System (INIS)

    Xu, Liang; Redman, Christopher W G; Georgieva, Antoniya; Payne, Stephen J

    2014-01-01

    The fetal heart rate (FHR) is monitored on a paper strip (cardiotocogram) during labour to assess fetal health. If necessary, clinicians can intervene and assist with a prompt delivery of the baby. Data-driven computerized FHR analysis could help clinicians in the decision-making process. However, selecting the best computerized FHR features that relate to labour outcome is a pressing research problem. The objective of this study is to apply genetic algorithms (GA) as a feature selection method to select the best feature subset from 64 FHR features and to integrate these best features to recognize unfavourable FHR patterns. The GA was trained on 404 cases and tested on 106 cases (both balanced datasets) using three classifiers, respectively. Regularization methods and backward selection were used to optimize the GA. Reasonable classification performance is shown on the testing set for the best feature subset (Cohen's kappa values of 0.45 to 0.49 using different classifiers). This is, to our knowledge, the first time that a feature selection method for FHR analysis has been developed on a database of this size. This study indicates that different FHR features, when integrated, can show good performance in predicting labour outcome. It also gives the importance of each feature, which will be a valuable reference point for further studies. (paper)

  5. Selective and genetic constraints on pneumococcal serotype switching.

    Directory of Open Access Journals (Sweden)

    Nicholas J Croucher

    2015-03-01

    Full Text Available Streptococcus pneumoniae isolates typically express one of over 90 immunologically distinguishable polysaccharide capsules (serotypes, which can be classified into "serogroups" based on cross-reactivity with certain antibodies. Pneumococci can alter their serotype through recombinations affecting the capsule polysaccharide synthesis (cps locus. Twenty such "serotype switching" events were fully characterised using a collection of 616 whole genome sequences from systematic surveys of pneumococcal carriage. Eleven of these were within-serogroup switches, representing a highly significant (p < 0.0001 enrichment based on the observed serotype distribution. Whereas the recombinations resulting in between-serogroup switches all spanned the entire cps locus, some of those that caused within-serogroup switches did not. However, higher rates of within-serogroup switching could not be fully explained by either more frequent, shorter recombinations, nor by genetic linkage to genes involved in β-lactam resistance. This suggested the observed pattern was a consequence of selection for preserving serogroup. Phenotyping of strains constructed to express different serotypes in common genetic backgrounds was used to test whether genotypes were physiologically adapted to particular serogroups. These data were consistent with epistatic interactions between the cps locus and the rest of the genome that were specific to serotype, but not serogroup, meaning they were unlikely to account for the observed distribution of capsule types. Exclusion of these genetic and physiological hypotheses suggested future work should focus on alternative mechanisms, such as host immunity spanning multiple serotypes within the same serogroup, which might explain the observed pattern.

  6. A fast multilocus test with adaptive SNP selection for large-scale genetic-association studies

    KAUST Repository

    Zhang, Han

    2013-09-11

    As increasing evidence suggests that multiple correlated genetic variants could jointly influence the outcome, a multilocus test that aggregates association evidence across multiple genetic markers in a considered gene or a genomic region may be more powerful than a single-marker test for detecting susceptibility loci. We propose a multilocus test, AdaJoint, which adopts a variable selection procedure to identify a subset of genetic markers that jointly show the strongest association signal, and defines the test statistic based on the selected genetic markers. The P-value from the AdaJoint test is evaluated by a computationally efficient algorithm that effectively adjusts for multiple-comparison, and is hundreds of times faster than the standard permutation method. Simulation studies demonstrate that AdaJoint has the most robust performance among several commonly used multilocus tests. We perform multilocus analysis of over 26,000 genes/regions on two genome-wide association studies of pancreatic cancer. Compared with its competitors, AdaJoint identifies a much stronger association between the gene CLPTM1L and pancreatic cancer risk (6.0 × 10(-8)), with the signal optimally captured by two correlated single-nucleotide polymorphisms (SNPs). Finally, we show AdaJoint as a powerful tool for mapping cis-regulating methylation quantitative trait loci on normal breast tissues, and find many CpG sites whose methylation levels are jointly regulated by multiple SNPs nearby.

  7. Genetic parameters and selection of soybean lines based on selection indexes.

    Science.gov (United States)

    Teixeira, F G; Hamawaki, O T; Nogueira, A P O; Hamawaki, R L; Jorge, G L; Hamawaki, C L; Machado, B Q V; Santana, A J O

    2017-09-21

    Defining selection criteria is important to obtain promising genotypes in a breeding program. The objective of this study was to estimate genetic parameters for agronomic traits and to perform soybean line selection using selection indices. The experiment was conducted at an experimental area located at Capim Branco farm, belonging to the Federal University of Uberlândia. A total of 37 soybean genotypes were evaluated in randomized complete block design with three replicates, in which twelve agronomic traits were evaluated. Analysis of variance, the Scott-Knott test at the 1 and 5% level of probability, and selection index analyses were performed. There was genetic variability for all agronomic traits, with medium to high levels of genotype determination coefficient. Twelve lines with a total cycle up to 110 days were observed and grouped with the cultivars MSOY 6101 and UFUS 7910. Three lines, UFUS FG 03, UFUS FG 20, and UFUS FG 31, were highlighted regarding grain yield with higher values than the national average of 3072 kg/ha. The direct selection enabled the highest trait individual gains. The Williams (1962) index and the Smith (1936) and Hazel (1943) index presented the highest selection gain for the grain yield character. The genotype-ideotype distance index and the index of the sum of ranks of Mulamba and Mock (1978) presented higher values of total selection gain. The lines UFUS FG 12, UFUS FG 14, UFUS FG 18, UFUS FG 25, and UFUS FG 31 were distinguished as superior genotypes by direct selection methods and selection indexes.

  8. Preimplantation genetic diagnosis for gender selection in the United States

    Energy Technology Data Exchange (ETDEWEB)

    Colls, P.; Silver, L.; Olivera, G.; Weier, J.; Escudero, T.; Goodall, N.; Tomkin, G.; Munne, S.

    2009-08-20

    Preimplantation genetic diagnosis (PGD) of gender selection for non medical reasons has been considered an unethical procedure by several authors and agencies in the Western society on the basis of disrupting the sex ratio, being discriminatory againsts women and disposal of normal embryos of the non desired gender. In this study, the analysis of a large series of PGD procedures for gender selection from a wide geographical area in the United States, shows that in general there is no deviation in preference towards any specific gender except for a preference of males in some ethnic populations of Chinese, Indian and Middle Eastern origin that represent a small percentage of the US population. In cases where only normal embryos of the non-desired gender are available, 45.5% of the couples elect to cancel the transfer, while 54.5% of them are open to have transferred embryos of the non-desired gender, this fact being strongly linked to cultural and ethnical background of the parents. In addition this study adds some evidence to the proposition that in couples with previous children of a given gender there is no biological predisposition towards producing embryos of that same gender. Based on these facts, it seems that objections to gender selection formulated by ethics committees and scientific societies are not well-founded.

  9. Genetic architecture and balancing selection: the life and death of differentiated variants.

    Science.gov (United States)

    Llaurens, Violaine; Whibley, Annabel; Joron, Mathieu

    2017-05-01

    Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems. © 2017 John Wiley & Sons Ltd.

  10. Divergent selection on intramuscular fat in rabbits: Responses to selection and genetic parameters.

    Science.gov (United States)

    Martínez-Álvaro, M; Hernández, P; Blasco, A

    2016-12-01

    A divergent selection experiment on intramuscular fat (IMF) was performed in rabbits. The aim of this study is to estimate the response to selection, the correlated responses in carcass and meat quality traits, and their genetic parameters. Selection criterion was the averaged phenotypic value of IMF measured at 9 wk of age in 2 full-sibs of the candidate. Traits considered were IMF, BW, chilled carcass weight, reference carcass weight, scapular and perirenal fat weights, carcass and meat color, pH, protein and fatty acid composition of meat. Total direct response to selection for IMF was 2.6 phenotypic SD of the trait, around 5% of the mean (1.09 g/100 g) per generation, with both lines following a symmetrical trend. Heritability of IMF was high (0.54), and in general, all traits related to carcass fat depots and IMF fatty acid composition showed high heritabilities (dissectible fat of the carcass, 0.70; MUFA percentage, 0.61; PUFA percentage, 0.45; and PUFA:SFA ratio, 0.42), except SFA percentage (0.09). The other carcass and meat quality traits showed moderate to low heritabilities. Intramuscular fat and dissectible fat percentage showed a low genetic correlation (0.34). Intramuscular fat was positively correlated with MUFA percentage (0.95) and negatively correlated with PUFA percentage (-0.89) and PUFA:SFA ratio (-0.98), corroborated with high correlated responses to selection. The rest of the traits did not show any substantial correlated response except protein content, which was greater in the high-IMF line than in the low-IMF line.

  11. A weight based genetic algorithm for selecting views

    Science.gov (United States)

    Talebian, Seyed H.; Kareem, Sameem A.

    2013-03-01

    Data warehouse is a technology designed for supporting decision making. Data warehouse is made by extracting large amount of data from different operational systems; transforming it to a consistent form and loading it to the central repository. The type of queries in data warehouse environment differs from those in operational systems. In contrast to operational systems, the analytical queries that are issued in data warehouses involve summarization of large volume of data and therefore in normal circumstance take a long time to be answered. On the other hand, the result of these queries must be answered in a short time to enable managers to make decisions as short time as possible. As a result, an essential need in this environment is in improving the performances of queries. One of the most popular methods to do this task is utilizing pre-computed result of queries. In this method, whenever a new query is submitted by the user instead of calculating the query on the fly through a large underlying database, the pre-computed result or views are used to answer the queries. Although, the ideal option would be pre-computing and saving all possible views, but, in practice due to disk space constraint and overhead due to view updates it is not considered as a feasible choice. Therefore, we need to select a subset of possible views to save on disk. The problem of selecting the right subset of views is considered as an important challenge in data warehousing. In this paper we suggest a Weighted Based Genetic Algorithm (WBGA) for solving the view selection problem with two objectives.

  12. 78 FR 53963 - Final Priorities, Requirements, Definitions, and Selection Criteria; Race to the Top-Early...

    Science.gov (United States)

    2013-08-30

    ... be disaggregated by race and ethnicity to selection criterion (A)(1). We amended the list of... grant funds on these efforts. Finally, to address any perceived inequalities in the application process...

  13. Genetic counselor attitudes towards fetal sex identification and selective abortion.

    Science.gov (United States)

    Burke, B M

    1992-06-01

    Thirty-four prenatal genetic counselors (all but one non-M.D.s) in seven American cities were interviewed on attitudes which might plausibly affect counselor-client interchanges. They overwhelmingly endorse both non-directive counseling and the pro-choice ethos which supports a woman's absolute right to abortion in the early stages of pregnancy. However, they also overwhelmingly condemn using prenatal diagnosis for sex selection purposes. Therefore, counselors experience continual stress from clients who evoke the conflict inherent between these two stances. Counselors use a variety of coping mechanisms to minimize this cognitive dissonance. Avoidance through out-referral or invoking institutional policies forbidding prenatal diagnosis for sex selection purposes is a diminishing option and not possible with clients who have or offer a medical indication. More common is the use of psychological coping mechanisms. By elevating the ideals of non-directiveness and female autonomy counselors better tolerate client values in conflict with their own. Some redefine the category of 'unwanted pregnancy' to include fetuses of the 'wrong sex'; others redefine the problem as their own ethnocentricism. Empowering counselors to set the protocols they use to screen applicants for prenatal diagnosis would not remove these conflicts. Many counselors believe a ban on releasing fetal sex information while abortion is still a legal option would be organizationally or legally unacceptable, or a violation of patient automony. A complicating factor is that 60% of the counselors interviewed would prefer to know fetal sex in their own pregnancies. Counselors reflect the ambivalence of American society in balancing conflicting social goals.(ABSTRACT TRUNCATED AT 250 WORDS)

  14. Engineering complex riboswitch regulation by dual genetic selection.

    Science.gov (United States)

    Sharma, Vandana; Nomura, Yoko; Yokobayashi, Yohei

    2008-12-03

    The recent discovery of riboswitches in diverse species of bacteria and few eukaryotes added metabolite-responsive gene regulation to the growing list of RNA functions in biology. The natural riboswitches have inspired several designs of synthetic analogues capable of gene regulation in response to a small molecule trigger. In this work, we describe our efforts to engineer complex riboswitches capable of sensing and responding to two small molecules according to Boolean logics AND and NAND. Two aptamers that recognize theophylline and thiamine pyrophosphate were embedded in tandem in the 5' UTR of bacterial mRNA, and riboswitches that function as logic gates were isolated by dual genetic selection. The diverse phenotype of the engineered logic gates supports the versatility of RNA-based gene regulation which may have preceded the modern protein-based gene regulators. Additionally, our design strategy advances our ability to harness the versatile capacities of RNA to program complex behavior in bacteria without the use of engineered proteins.

  15. Route Selection with Unspecified Sites Using Knowledge Based Genetic Algorithm

    Science.gov (United States)

    Kanoh, Hitoshi; Nakamura, Nobuaki; Nakamura, Tomohiro

    This paper addresses the problem of selecting a route to a given destination that traverses several non-specific sites (e.g. a bank, a gas station) as requested by a driver. The proposed solution uses a genetic algorithm that includes viral infection. The method is to generate two populations of viruses as domain specific knowledge in addition to a population of routes. A part of an arterial road is regarded as a main virus, and a road that includes a site is regarded as a site virus. An infection occurs between two points common to a candidate route and the virus, and involves the substitution of the intersections carried by the virus for those on the existing candidate route. Crossover and infection determine the easiest-to-drive and quasi-shortest route through the objective landmarks. Experiments using actual road maps show that this infection-based mechanism is an effective way of solving the problem. Our strategy is general, and can be effectively used in other optimization problems.

  16. Genetic biases for showy males: are some genetic systems especially conducive to sexual selection?

    Science.gov (United States)

    Reeve, Hudson Kern; Pfennig, David W

    2003-02-04

    Male secondary sexual characters (conspicuous ornaments, signals, colors) are among nature's most striking features. Yet, it is unclear why certain groups of organisms are more likely than others to evolve these traits. One explanation for such taxonomic biases is that some genetic systems may be especially conducive to sexual selection. Here, we present theory and simulation results demonstrating that rare alleles encoding either male ornaments or female preferences for those ornaments are better protected against random loss in species with ZZZW or ZZZO sex chromosome systems (male homogamety) than in species with XXXY or XXXO systems (male heterogamety). Moreover, this protection is much stronger in diploid than haplodiploid species. We also present empirical data showing that male secondary sexual characters are better developed in diploid than haplodiploid species and in diploid species with male homogamety than in those with male heterogamety. Thus, taxonomic biases for showy males may stem from differences in sex chromosome systems.

  17. Phenotypic and genetic characterization of circulating tumor cells by combining immunomagnetic selection and FICTION techniques.

    Science.gov (United States)

    Campos, María; Prior, Celia; Warleta, Fernando; Zudaire, Isabel; Ruíz-Mora, Jesús; Catena, Raúl; Calvo, Alfonso; Gaforio, José J

    2008-07-01

    The presence of circulating tumor cells (CTCs) in breast cancer patients has been proven to have clinical relevance. Cytogenetic characterization of these cells could have crucial relevance for targeted cancer therapies. We developed a method that combines an immunomagnetic selection of CTCs from peripheral blood with the fluorescence immunophenotyping and interphase cytogenetics as a tool for investigation of neoplasm (FICTION) technique. Briefly, peripheral blood (10 ml) from healthy donors was spiked with a predetermined number of human breast cancer cells. Nucleated cells were separated by double density gradient centrifugation of blood samples. Tumor cells (TCs) were immunomagnetically isolated with an anti-cytokeratin antibody and placed onto slides for FICTION analysis. For immunophenotyping and genetic characterization of TCs, a mixture of primary monoclonal anti-pancytokeratin antibodies was used, followed by fluorescent secondary antibodies, and finally hybridized with a TOP2A/HER-2/CEP17 multicolor probe. Our results show that TCs can be efficiently isolated from peripheral blood and characterized by FICTION. Because genetic amplification of TOP2A and ErbB2 (HER-2) in breast cancer correlates with response to anthracyclines and herceptin therapies, respectively, this novel methodology could be useful for a better classification of patients according to the genetic alterations of CTCs and for the application of targeted therapies.

  18. Experimental evolution reveals natural selection on standing genetic variation

    OpenAIRE

    Teotónio, H; Chelo, IM; Bradic, M; Rose, MR; Long, AD

    2009-01-01

    Evolution depends on genetic variation generated by mutation or recombination from standing genetic variation. In sexual organisms, little is known about the molecular population genetics of adaptation and reverse evolution(1-11). We carry out 50 generations of experimental reverse evolution in populations of Drosophila melanogaster, previously differentiated by forward evolution, and follow changes in the frequency of SNPs in both arms of the third chromosome. We characterize the effects of ...

  19. Area program in population genetics. Final report, November 1, 1975-August 31, 1982

    International Nuclear Information System (INIS)

    Chu, E.H.Y.; Gershowitz, H.; Meisler, M.H.; Mohrenweiser, H.W.; Neel, J.V.; Rothman, E.D.; Sing, C.S.

    1982-01-01

    Research results are summarized for the following task areas: (1) Amerindian mutation rates; (2) pilot study of monitoring populations for the frequency of mutation; (3) interdigitation with the biochemical genetics study of the Radiation Effects Research Foundation (Hiroshima, Japan); (4) intraindividual variation in erythrocyte blood group antigens as indicators of somatic mutation; (5) in vitro studies of somatic cell mutation rates; (6) development of approaches to the study of mutation rates; and (7) statistical problems associated with the study of mutation and selection

  20. A Paradox of Genetic Variance in Epigamic Traits: Beyond "Good Genes" View of Sexual Selection.

    Science.gov (United States)

    Radwan, Jacek; Engqvist, Leif; Reinhold, Klaus

    Maintenance of genetic variance in secondary sexual traits, including bizarre ornaments and elaborated courtship displays, is a central problem of sexual selection theory. Despite theoretical arguments predicting that strong sexual selection leads to a depletion of additive genetic variance, traits associated with mating success show relatively high heritability. Here we argue that because of trade-offs associated with the production of costly epigamic traits, sexual selection is likely to lead to an increase, rather than a depletion, of genetic variance in those traits. Such trade-offs can also be expected to contribute to the maintenance of genetic variation in ecologically relevant traits with important implications for evolutionary processes, e.g. adaptation to novel environments or ecological speciation. However, if trade-offs are an important source of genetic variation in sexual traits, the magnitude of genetic variation may have little relevance for the possible genetic benefits of mate choice.

  1. Individual-based simulation of sexual selection: A quantitative genetic approach

    NARCIS (Netherlands)

    van Dijk, D.; Sloot, P.M.A.; Tay, J.C.; Schut, M.C.

    2010-01-01

    Sexual selection has been mathematically modeled using quantitative genetics as well as population genetics. Two-locus simulation models have been used to study the evolution of male display and female preference. We present an individual-based simulation model of sexual selection in a quantitative

  2. Selection for uniformity in livestock by exploiting genetic heterogeneity of environmental variance

    NARCIS (Netherlands)

    Mulder, H.A.; Bijma, P.; Hill, W.G.

    2008-01-01

    In some situations, it is worthwhile to change not only the mean, but also the variability of traits by selection. Genetic variation in residual variance may be utilised to improve uniformity in livestock populations by selection. The objective was to investigate the effects of genetic parameters,

  3. Selection for uniformity in livestock by exploiting genetic heterogeneity of residual variance

    NARCIS (Netherlands)

    Mulder, H.A.; Veerkamp, R.F.; Vereijken, A.; Bijma, P.; Hill, W.G.

    2008-01-01

    some situations, it is worthwhile to change not only the mean, but also the variability of traits by selection. Genetic variation in residual variance may be utilised to improve uniformity in livestock populations by selection. The objective was to investigate the effects of genetic parameters,

  4. Genetic evidence for natural selection in humans in the contemporary United States

    OpenAIRE

    Beauchamp, Jonathan P.

    2016-01-01

    I leverage recent advances in molecular genetics to test directly whether genetic variants associated with a number of phenotypes have been under natural selection in the contemporary United States. My finding that natural selection has been slowly occurring for genetic variants associated with educational attainment and (suggestively, in females) for variants associated with age at menarche provides additional evidence that humans are still evolving—albeit slowly and at a rate that cannot ac...

  5. Paternity reconstruction and phenotypic pre-selection for genetic ...

    Indian Academy of Sciences (India)

    For decades, forest tree breeders have used controlled crossing approach for genetic parameter estimation to ... However, number of controlled crosses needed for genetic analysis in a forest breeding program is usuallyhigh. ..... The unassigned progeniescould be due to the fact that the true father is possibly not present in ...

  6. Assessment of genetic variation of selected spiderplant (Cleome ...

    African Journals Online (AJOL)

    were differentiated. Nei's genetic identity value calculated from the RAPD data ranged from 0.3 to 0.6 indicating the degree of genetic identity between the morphotypes. Dendrograms constructed from a matrix calculated on the basis of UPGMA clustering algorithm revealed that the 4 morphotypes formed 3 groups .

  7. Is genetic selection for skin nodule traits of ostriches feasible ...

    African Journals Online (AJOL)

    Preliminary genetic parameters for nodule traits of ostrich skins were estimated to examine whether genetic improvement of skin quality is feasible. Average nodule size and density per dmยฒ were determined on five localities on each of 439 ostrich skins. An animal model with random animal and skin permanent ...

  8. Optimization of genomic selection training populations with a genetic algorithm

    Science.gov (United States)

    In this article, we derive a computationally efficient statistic to measure the reliability of estimates of genetic breeding values for a fixed set of genotypes based on a given training set of genotypes and phenotypes. We adopt a genetic algorithm scheme to find a training set of certain size from ...

  9. Enzyme assays: high-throughput screening, genetic selection, and fingerprinting

    National Research Council Canada - National Science Library

    Reymond, Jean-Louis

    2006-01-01

    ... (Testing Many Substrates Toward Hydrolase) Comparison with Other Methods 26 Estimating and Measuring Selectivity 27 Estimating Selectivity without a Reference Compound 28 Quantitative Measure of Se...

  10. The effects of stress and sex on selection, genetic covariance, and the evolutionary response.

    Science.gov (United States)

    Holman, L; Jacomb, F

    2017-10-01

    The capacity of a population to adapt to selection (evolvability) depends on whether the structure of genetic variation permits the evolution of fitter trait combinations. Selection, genetic variance and genetic covariance can change under environmental stress, and males and females are not genetically independent, yet the combined effects of stress and dioecy on evolvability are not well understood. Here, we estimate selection, genetic (co)variance and evolvability in both sexes of Tribolium castaneum flour beetles under stressful and benign conditions, using a half-sib breeding design. Although stress uncovered substantial latent heritability, stress also affected genetic covariance, such that evolvability remained low under stress. Sexual selection on males and natural selection on females favoured a similar phenotype, and there was positive intersex genetic covariance. Consequently, sexual selection on males augmented adaptation in females, and intralocus sexual conflict was weak or absent. This study highlights that increased heritability does not necessarily increase evolvability, suggests that selection can deplete genetic variance for multivariate trait combinations with strong effects on fitness, and tests the recent hypothesis that sexual conflict is weaker in stressful or novel environments. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  11. Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster.

    Science.gov (United States)

    Svetec, Nicolas; Zhao, Li; Saelao, Perot; Chiu, Joanna C; Begun, David J

    2015-03-13

    Drosophila melanogaster often shows correlations between latitude and phenotypic or genetic variation on different continents, which suggests local adaptation with respect to a heterogeneous environment. Previous phenotypic analyses of latitudinal clines have investigated mainly physiological, morphological, or life-history traits. Here, we studied latitudinal variation in sleep in D. melanogaster populations from North and Central America. In parallel, we used RNA-seq to identify interpopulation gene expression differences. We found that in D. melanogaster the average nighttime sleep bout duration exhibits a latitudinal cline such that sleep bouts of equatorial populations are roughly twice as long as those of temperate populations. Interestingly, this pattern of latitudinal variation is not observed for any daytime measure of activity or sleep. We also found evidence for geographic variation for sunrise anticipation. Our RNA-seq experiment carried out on heads from a low and high latitude population identified a large number of gene expression differences, most of which were time dependent. Differentially expressed genes were enriched in circadian regulated genes and enriched in genes potentially under spatially varying selection. Our results are consistent with a mechanistic and selective decoupling of nighttime and daytime activity. Furthermore, the present study suggests that natural selection plays a major role in generating transcriptomic variation associated with circadian behaviors. Finally, we identified genomic variants plausibly causally associated with the observed behavioral and transcriptomic variation.

  12. An introduction to genetic quality in the context of sexual selection.

    Science.gov (United States)

    Pitcher, Trevor E; Mays, Herman L

    2008-09-01

    This special issue of Genetica brings together empirical researchers and theoreticians to present the latest on the evolutionary ecology of genetic quality in the context of sexual selection. The work comes from different fields of study including behavioral ecology, quantitative genetics and molecular genetics on a diversity of organisms using different approaches from comparative studies, mathematical modeling, field studies and laboratory experiments. The papers presented in this special issue primarily focus on genetic quality in relation to (1) sources of genetic variation, (2) polyandry, (3) new theoretical developments and (4) comprehensive reviews.

  13. Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae).

    Science.gov (United States)

    Muir, Christopher D; Pease, James B; Moyle, Leonie C

    2014-12-01

    Adaptive evolution requires both raw genetic material and an accessible path of high fitness from one fitness peak to another. In this study, we used an introgression line (IL) population to map quantitative trait loci (QTL) for leaf traits thought to be associated with adaptation to precipitation in wild tomatoes (Solanum sect. Lycopersicon; Solanaceae). A QTL sign test showed that several traits likely evolved under directional natural selection. Leaf traits correlated across species do not share a common genetic basis, consistent with a scenario in which selection maintains trait covariation unconstrained by pleiotropy or linkage disequilibrium. Two large effect QTL for stomatal distribution colocalized with key genes in the stomatal development pathway, suggesting promising candidates for the molecular bases of adaptation in these species. Furthermore, macroevolutionary transitions between vastly different stomatal distributions may not be constrained when such large-effect mutations are available. Finally, genetic correlations between stomatal traits measured in this study and data on carbon isotope discrimination from the same ILs support a functional hypothesis that the distribution of stomata affects the resistance to CO2 diffusion inside the leaf, a trait implicated in climatic adaptation in wild tomatoes. Along with evidence from previous comparative and experimental studies, this analysis indicates that leaf traits are an important component of climatic niche adaptation in wild tomatoes and demonstrates that some trait transitions between species could have involved few, large-effect genetic changes, allowing rapid responses to new environmental conditions. Copyright © 2014 by the Genetics Society of America.

  14. Natural selection affects multiple aspects of genetic variation at putatively peutral sites across the human genome

    DEFF Research Database (Denmark)

    Lohmueller, Kirk E; Albrechtsen, Anders; Li, Yingrui

    2011-01-01

    A major question in evolutionary biology is how natural selection has shaped patterns of genetic variation across the human genome. Previous work has documented a reduction in genetic diversity in regions of the genome with low recombination rates. However, it is unclear whether other summaries...... and that human diversity, human-chimp divergence, and average minor allele frequency are reduced near genes. Population genetic simulations show that either positive natural selection acting on favorable mutations or negative natural selection acting against deleterious mutations can explain these correlations...... throughout the genome. Further, we show that the widespread presence of weakly deleterious alleles, rather than a small number of strongly positively selected mutations, is responsible for the correlation between neutral genetic diversity and recombination rate. This work suggests that natural selection has...

  15. 78 FR 12955 - Final Requirements, Definitions, and Selection Criteria-Native American Career and Technical...

    Science.gov (United States)

    2013-02-26

    ... in the Indian Self-Determination and Education Assistance Act (ISDEA) (25 U.S.C. 450b(l)), the term... DEPARTMENT OF EDUCATION 34 CFR Chapter IV [Docket ID ED-2012-OVAE-0053] Final Requirements, Definitions, and Selection Criteria--Native American Career and Technical Education Program (NACTEP) [Catalog...

  16. PhysicsGP: A Genetic Programming Approach to Event Selection

    CERN Document Server

    Cranmer, K S; Cranmer, Kyle

    2005-01-01

    We present a novel multivariate classification technique based on Genetic Programming. The technique is distinct from Genetic Algorithms and offers several advantages compared to Neural Networks and Support Vector Machines. The technique optimizes a set of human-readable classifiers with respect to some user-defined performance measure. We calculate the Vapnik-Chervonenkis dimension of this class of learning machines and consider a practical example: the search for the Standard Model Higgs Boson at the LHC. The resulting classifier is very fast to evaluate, human-readable, and easily portable. The software may be downloaded at: http://cern.ch/~cranmer/PhysicsGP.html

  17. Site selection - siting of the final repository for spent nuclear fuel

    International Nuclear Information System (INIS)

    2011-03-01

    SKB has selected Forsmark as the site for the final repository for spent nuclear fuel. The site selection is the end result of an extensive siting process that began in the early 1990s. The strategy and plan for the work was based on experience from investigations and development work over a period of more than ten years prior to then. This document describes the siting work and SKB's choice of site for the final repository. It also presents the information on which the choice was based and the reasons for the decisions made along the way. The document comprises Appendix PV to applications under the Nuclear Activities Act and the Environmental Code for licences to build and operate an encapsulation plant adjacent to the central interim storage facility for spent nuclear fuel in Oskarshamn, and to build and operate a final repository for spent nuclear fuel in Forsmark in Oesthammar Municipality

  18. Site selection - siting of the final repository for spent nuclear fuel

    Energy Technology Data Exchange (ETDEWEB)

    2011-03-15

    SKB has selected Forsmark as the site for the final repository for spent nuclear fuel. The site selection is the end result of an extensive siting process that began in the early 1990s. The strategy and plan for the work was based on experience from investigations and development work over a period of more than ten years prior to then. This document describes the siting work and SKB's choice of site for the final repository. It also presents the information on which the choice was based and the reasons for the decisions made along the way. The document comprises Appendix PV to applications under the Nuclear Activities Act and the Environmental Code for licences to build and operate an encapsulation plant adjacent to the central interim storage facility for spent nuclear fuel in Oskarshamn, and to build and operate a final repository for spent nuclear fuel in Forsmark in Oesthammar Municipality

  19. Ecological genetics of the Bromus tectorum (Poaceae) - Ustilago Bullata (Ustilaginaceae): A role for frequency dependent selection?

    Science.gov (United States)

    Susan E. Meyer; David L. Nelson; Suzette Clement; Alisa Ramakrishnan

    2010-01-01

    Evolutionary processes that maintain genetic diversity in plants are likely to include selection imposed by pathogens. Negative frequency-dependent selection is a mechanism for maintenance of resistance polymorphism in plant - pathogen interactions. We explored whether such selection operates in the Bromus tectorum - Ustilago bullata pathosystem. Gene-for-gene...

  20. Paternity reconstruction and phenotypic pre-selection for genetic ...

    Indian Academy of Sciences (India)

    ITC Life Sciences and Technology Centre,Peenya Industrial Area Phase I, Bangalore - 560058. *Corrseponding Author: anand.kullan@itc.in. Running title: Paternity reconstruction and genetic parameter estimation in Eucalyptus. Key words: Eucalyptus, seed orchard and parentage analysis. Abstract. Pedigree construction ...

  1. Genetic diversity in selected stud and commercial herds of the ...

    African Journals Online (AJOL)

    Martina

    2014-08-29

    Aug 29, 2014 ... The Afrikaner cattle breed (Bos taurus africanus) is an indigenous South African breed of the “Sanga” type. Sanga cattle are generally found in Southern Africa and are a mixture of the Bos indicus and Bos taurus breeds (Payne & Wilson, 1999). Sanga cattle therefore contain genetic material that has been.

  2. Genetic diversity, phylogeographic structure and effect of selection ...

    Indian Academy of Sciences (India)

    Department of Animal Health and Production, Oyo State College of Agriculture and Technology, P.M.B 10, Igbo-Ora 201103, Oyo, Nigeria; Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Abeokuta 110124, Ogun State, Nigeria; Department of Animal Production and Health, ...

  3. Genetic divergence in selected durum wheat genotypes of Ethiopian ...

    African Journals Online (AJOL)

    genotypes of diverse origin, and clustering them into homogenous groups for the hybridisation programme. Genetic divergence analysis was done based on multivariate analysis using Mahalanobis's D2 statistic, which grouped the durum wheat genotypes into ten clusters. The highest inter-cluster distance was between ...

  4. The effect of selection on genetic parameter estimates

    African Journals Online (AJOL)

    Unknown

    the herd the following information was recorded: cow number, fixed effect level at first lactation, production ... obtain pseudo-random values from a normal distribution with a mean of zero and variance of one, and is similar to a ... The genetic and error components were obtained by generating random numbers from a normal.

  5. Differences in exam performance between pupils attending selective and non-selective schools mirror the genetic differences between them

    Science.gov (United States)

    Smith-Woolley, Emily; Pingault, Jean-Baptiste; Selzam, Saskia; Rimfeld, Kaili; Krapohl, Eva; von Stumm, Sophie; Asbury, Kathryn; Dale, Philip S.; Young, Toby; Allen, Rebecca; Kovas, Yulia; Plomin, Robert

    2018-03-01

    On average, students attending selective schools outperform their non-selective counterparts in national exams. These differences are often attributed to value added by the school, as well as factors schools use to select pupils, including ability, achievement and, in cases where schools charge tuition fees or are located in affluent areas, socioeconomic status. However, the possible role of DNA differences between students of different schools types has not yet been considered. We used a UK-representative sample of 4814 genotyped students to investigate exam performance at age 16 and genetic differences between students in three school types: state-funded, non-selective schools (`non-selective'), state-funded, selective schools (`grammar') and private schools, which are selective (`private'). We created a genome-wide polygenic score (GPS) derived from a genome-wide association study of years of education (EduYears). We found substantial mean genetic differences between students of different school types: students in non-selective schools had lower EduYears GPS compared to those in grammar (d = 0.41) and private schools (d = 0.37). Three times as many students in the top EduYears GPS decile went to a selective school compared to the bottom decile. These results were mirrored in the exam differences between school types. However, once we controlled for factors involved in pupil selection, there were no significant genetic differences between school types, and the variance in exam scores at age 16 explained by school type dropped from 7% to <1%. These results show that genetic and exam differences between school types are primarily due to the heritable characteristics involved in pupil admission.

  6. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    Science.gov (United States)

    Yabe, Shiori; Yamasaki, Masanori; Ebana, Kaworu; Hayashi, Takeshi; Iwata, Hiroyoshi

    2016-01-01

    Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of genomic

  7. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    Directory of Open Access Journals (Sweden)

    Shiori Yabe

    Full Text Available Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS, which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the

  8. Invited review: Genetics and claw health: Opportunities to enhance claw health by genetic selection

    Science.gov (United States)

    Routine recording of claw health status at claw trimming of dairy cattle have been established in several countries, providing valuable data for genetic evaluation. In this review, issues related to genetic evaluation of claw health are examined, data sources, trait definitions and data validation p...

  9. Experimental designs for evaluation of genetic variability and selection of ancient grapevine varieties: a simulation study.

    Science.gov (United States)

    Gonçalves, E; St Aubyn, A; Martins, A

    2010-06-01

    Classical methodologies for grapevine selection used in the vine-growing world are generally based on comparisons among a small number of clones. This does not take advantage of the entire genetic variability within ancient varieties, and therefore limits selection challenges. Using the general principles of plant breeding and of quantitative genetics, we propose new breeding strategies, focussed on conservation and quantification of genetic variability by performing a cycle of mass genotypic selection prior to clonal selection. To exploit a sufficiently large amount of genetic variability, initial selection trials must be generally very large. The use of experimental designs adequate for those field trials has been intensively recommended for numerous species. However, their use in initial trials of grapevines has not been studied. With the aim of identifying the most suitable experimental designs for quantification of genetic variability and selection of ancient varieties, a study was carried out to assess through simulation the comparative efficiency of various experimental designs (randomized complete block design, alpha design and row-column (RC) design). The results indicated a greater efficiency for alpha and RC designs, enabling more precise estimates of genotypic variance, greater precision in the prediction of genetic gain and consequently greater efficiency in genotypic mass selection.

  10. Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background.

    Science.gov (United States)

    Dykhuizen, D; Hartl, D L

    1980-12-01

    We have used gluconate-limited chemostats to study selective differences between isogenic strains of Escherichia coli K12 into which four naturally occurring alleles coding for allozymes of 6-phosphogluconate dehydrogenase (6PGD) had been transferred. The limit of detectability of selection with our procedures is a selection coefficient of 0.5%. In the normal E. coli K12 genetic background, all alleles are selectively neutral or nearly neutral. The absence of detectable selection does, however, depend on genetic background and on such environmental factors as cell density. In a genetic background containing a mutation that cuts off the alternative metabolic route for 6-phosphogluconate, selection between allozymes can be detected, and the selection is in the direction expected from the measured apparent Km values of the allozymes. Even when the alternative metabolic route is not blocked by mutation, one of the 6PGD allozymes has a detrimental, but density-dependent, interaction with a mutation conferring resistance to bacteriophage T5. In all cases, the observed selection is due to the allozymes themselves (or to associated regulatory elements), as the selection disappears when the chemostats are limited by a different carbon source (ribose plus succinate). Nevertheless, the four alleles do seem to be selectively neutral or nearly neutral in the normal E. coli K12 genetic background. Moreover, the distribution of allele frequencies in natural populations of E. coli is in accord with the expectations of selective neutrality.

  11. Response to selection and genetic parameters of body and carcass weights in Japanese quail selected for 4-week body weight

    DEFF Research Database (Denmark)

    Khaldari, M; Pakdel, A; Yegane, H Mehrabani

    2010-01-01

    dams were used as parents for the next generation. Data were collected over 2 consecutive hatches for 4 generations, and 1,554 records from 151 sires and 285 dams were used to estimate the genetic parameters. The genetic improvement of 4-wk BW was 9.6, 8.8, and 8.2 g in generations 2, 3, and 4...... to improve carcass traits. Also, intense selection resulting in high rates of inbreeding might result in decreased response to selection due to inbreeding depression....

  12. Genetic parameters and consequences of selection for short-term ...

    African Journals Online (AJOL)

    toshiba

    2013-03-20

    Mar 20, 2013 ... Quail chicks in the control were reared intermingled with the population under selection throughout generations of selection to also minimize environmental variation. At six weeks of age, female quails were moved into individual laying cages for egg production study. During egg production, the birds were ...

  13. 77 FR 25470 - Final Revision to Selection Criteria-Enhanced Assessment Instruments; CFDA Number: 84.368

    Science.gov (United States)

    2012-04-30

    ... Final Revision to Selection Criteria--Enhanced Assessment Instruments; CFDA Number: 84.368 AGENCY... Assistant Secretary for Elementary and Secondary Education amends the selection criteria under the Enhanced... in the notice of final priorities, requirements, definitions, and selection criteria published in the...

  14. Island selection on mammalian life-histories: genetic differentiation in offspring size.

    Science.gov (United States)

    Mappes, Tapio; Grapputo, Alessandro; Hakkarainen, Harri; Huhta, Esa; Koskela, Esa; Saunanen, Raimo; Suorsa, Petri

    2008-10-27

    Since Darwin's pioneering work, evolutionary changes in isolated island populations of vertebrates have continued to provide the strongest evidence for the theory of natural selection. Besides macro-evolutionary changes, micro-evolutionary changes and the relative importance of natural selection vs. genetic drift are under intense investigation. Our study focuses on the genetic differentiation in morphological and life-history traits in insular populations of a small mammal the bank vole Myodes glareolus. Our results do not support the earlier findings for larger adult size or lower reproductive effort in insular populations of small mammals. However, the individuals living on islands produced larger offspring than individuals living on the mainland. Genetic differentiation in offspring size was further confirmed by the analyses of quantitative genetics in lab. In insular populations, genetic differentiation in offspring size simultaneously decreases the additive genetic variation (VA) for that trait. Furthermore, our analyses of differentiation in neutral marker loci (Fst) indicate that VA is less than expected on the basis of genetic drift alone, and thus, a lower VA in insular populations could be caused by natural selection. We believe that different selection pressures (e.g. higher intraspecific competition) in an insular environment might favour larger offspring size in small mammals. Island selection for larger offspring could be the preliminary mechanism in a process which could eventually lead to a smaller litter size and lower reproductive effort frequently found in insular vertebrates.

  15. Island selection on mammalian life-histories: genetic differentiation in offspring size

    Directory of Open Access Journals (Sweden)

    Saunanen Raimo

    2008-10-01

    Full Text Available Abstract Background Since Darwin's pioneering work, evolutionary changes in isolated island populations of vertebrates have continued to provide the strongest evidence for the theory of natural selection. Besides macro-evolutionary changes, micro-evolutionary changes and the relative importance of natural selection vs. genetic drift are under intense investigation. Our study focuses on the genetic differentiation in morphological and life-history traits in insular populations of a small mammal the bank vole Myodes glareolus. Results Our results do not support the earlier findings for larger adult size or lower reproductive effort in insular populations of small mammals. However, the individuals living on islands produced larger offspring than individuals living on the mainland. Genetic differentiation in offspring size was further confirmed by the analyses of quantitative genetics in lab. In insular populations, genetic differentiation in offspring size simultaneously decreases the additive genetic variation (VA for that trait. Furthermore, our analyses of differentiation in neutral marker loci (Fst indicate that VA is less than expected on the basis of genetic drift alone, and thus, a lower VA in insular populations could be caused by natural selection. Conclusion We believe that different selection pressures (e.g. higher intraspecific competition in an insular environment might favour larger offspring size in small mammals. Island selection for larger offspring could be the preliminary mechanism in a process which could eventually lead to a smaller litter size and lower reproductive effort frequently found in insular vertebrates.

  16. Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies.

    Directory of Open Access Journals (Sweden)

    Joseph P Jarvis

    Full Text Available African Pygmy groups show a distinctive pattern of phenotypic variation, including short stature, which is thought to reflect past adaptation to a tropical environment. Here, we analyze Illumina 1M SNP array data in three Western Pygmy populations from Cameroon and three neighboring Bantu-speaking agricultural populations with whom they have admixed. We infer genome-wide ancestry, scan for signals of positive selection, and perform targeted genetic association with measured height variation. We identify multiple regions throughout the genome that may have played a role in adaptive evolution, many of which contain loci with roles in growth hormone, insulin, and insulin-like growth factor signaling pathways, as well as immunity and neuroendocrine signaling involved in reproduction and metabolism. The most striking results are found on chromosome 3, which harbors a cluster of selection and association signals between approximately 45 and 60 Mb. This region also includes the positional candidate genes DOCK3, which is known to be associated with height variation in Europeans, and CISH, a negative regulator of cytokine signaling known to inhibit growth hormone-stimulated STAT5 signaling. Finally, pathway analysis for genes near the strongest signals of association with height indicates enrichment for loci involved in insulin and insulin-like growth factor signaling.

  17. Genetic parameters estimates and visual selection for leaves production in Ilex paraguariensis

    Directory of Open Access Journals (Sweden)

    José Alfredo Sturion

    2017-08-01

    Full Text Available ABSTRACT The selection of yerba mate superior genotypes, based on each plant leaf weight, is based on genetic parameters obtained from experimental plantations and it is practically impossible from the fourth year of age. Therefore, we estimate genetic parameters and check the feasibility of selection through notes and weight estimates of each tree at 18.5 years of age. The genetic material consists of a combined trial of provenances and progenies of half-sibs with 140 progenies from 7 provenances, installed in Ivaí, Paraná, Brazil, in a randomized block design with 10 repetitions. The genetic control of leaf production is of low magnitude (ĥ2a= 0.175042 ± 0.0393 revealing high influence of the environment. The additive genetic correlations between the real weight of leaves × notes and real weight of leaves × visually estimated weight were of high magnitude (higher than 88%. Thus, the selection based on the leaves weight can be carried out without major losses in genetic gains by both methodologies when the purpose is the sexual selection, in which case the sort order has no importance. In the case of vegetative propagation, aiming clonal plantations, in which only the plants with the highest genotypic values should be selected, the selection by means of notes and leaves weight estimates proved to be inefficient.

  18. Unexpected consequences of genetic selection in broilers and turkeys: problems and solutions.

    Science.gov (United States)

    Hocking, P M

    2014-02-01

    1. Genetic theory leads to the expectation that unexpected consequences of genetic selection for production traits will inevitably occur and that these changes are likely to be undesirable. 2. Both artificial selection for production efficiency and "natural" selection for adaptation to the production environment result in selection sweeps that increase the frequencies of rare recessive alleles that have a negative effect on fitness. 3. Fitness is broadly defined as any trait that affects the ability to survive, reproduce and contribute to the next generation, such as musculoskeletal disease in growing broiler chickens and multiple ovulation in adult broiler parents. 4. Welfare concerns about the negative effects of genetic selection on bird welfare are sometimes exaggerated but are nevertheless real. Breeders have paid increasing attention to these traits over several decades and have demonstrated improvement in pedigree flocks. There is an urgent need to monitor changes in commercial flocks to ensure that genetic change is accompanied by improvements in that target population. 5. New technologies for trait measurement, whole genome selection and targeted genetic modification hold out the promise of efficient and rapid improvement of welfare traits in future breeding of broiler chickens and turkeys. The potential of targeted genetic modification for enhancing welfare traits is considerable, but the goal of achieving public acceptability for the progeny of transgenic poultry will be politically challenging.

  19. Genetic Gain Increases by Applying the Usefulness Criterion with Improved Variance Prediction in Selection of Crosses.

    Science.gov (United States)

    Lehermeier, Christina; Teyssèdre, Simon; Schön, Chris-Carolin

    2017-12-01

    A crucial step in plant breeding is the selection and combination of parents to form new crosses. Genome-based prediction guides the selection of high-performing parental lines in many crop breeding programs which ensures a high mean performance of progeny. To warrant maximum selection progress, a new cross should also provide a large progeny variance. The usefulness concept as measure of the gain that can be obtained from a specific cross accounts for variation in progeny variance. Here, it is shown that genetic gain can be considerably increased when crosses are selected based on their genomic usefulness criterion compared to selection based on mean genomic estimated breeding values. An efficient and improved method to predict the genetic variance of a cross based on Markov chain Monte Carlo samples of marker effects from a whole-genome regression model is suggested. In simulations representing selection procedures in crop breeding programs, the performance of this novel approach is compared with existing methods, like selection based on mean genomic estimated breeding values and optimal haploid values. In all cases, higher genetic gain was obtained compared with previously suggested methods. When 1% of progenies per cross were selected, the genetic gain based on the estimated usefulness criterion increased by 0.14 genetic standard deviation compared to a selection based on mean genomic estimated breeding values. Analytical derivations of the progeny genotypic variance-covariance matrix based on parental genotypes and genetic map information make simulations of progeny dispensable, and allow fast implementation in large-scale breeding programs. Copyright © 2017 by the Genetics Society of America.

  20. Genetic grouping strategies in selection efficiency of composite beef cattle ( × ).

    Science.gov (United States)

    Petrini, J; Pertile, S F N; Eler, J P; Ferraz, J B S; Mattos, E C; Figueiredo, L G G; Mourão, G B

    2015-02-01

    The inclusion of genetic groups in sire evaluation has been widely used to represent genetic differences among animals not accounted for by the absence of parentage data. However, the definition of these groups is still arbitrary, and studies assessing the effects of genetic grouping strategies on the selection efficiency are rare. Therefore, the aim in this study was to compare genetic grouping strategies for animals with unknown parentage in prediction of breeding values (EBV). The total of 179,302 records of weaning weight (WW), 29,825 records of scrotal circumference (SC), and 70,302 records of muscling score (MUSC) from Montana Tropical animals, a Brazilian composite beef cattle population, were used. Genetic grouping strategies involving year of birth, sex of the unknown parent, birth farm, breed composition, and their combinations were evaluated. Estimated breeding values were predicted for each approach simulating a loss of genealogy data. Thereafter, these EBV were compared to those obtained in an analysis involving a real relationship matrix to estimate selection efficiency and correlations between EBV and animal rankings. The analysis model included the fixed effects of contemporary groups and class of the dam age at calving, the covariates of additive and nonadditive genetic effects, and age, and the additive genetic effect of animal as random effects. A second model also included the fixed effects of genetic group. The use of genetic groups resulted in means of selection efficiency and correlation of 70.4 to 97.1% and 0.51 to 0.94 for WW, 85.8 to 98.8% and 0.82 to 0.98 for SC, and 85.1 to 98.6% and 0.74 to 0.97 for MUSC, respectively. High selection efficiencies were observed for year of birth and breed composition strategies. The maximum absolute difference in annual genetic gain estimated through the use of complete genealogy and genetic groups were 0.38 kg for WW, 0.02 cm for SC, and 0.01 for MUSC, with lower differences obtained when year of birth

  1. Sexual selection modulates genetic conflicts and patterns of genomic imprinting.

    Science.gov (United States)

    Faria, Gonçalo S; Varela, Susana A M; Gardner, Andy

    2017-03-01

    Recent years have seen a surge of interest in linking the theories of kin selection and sexual selection. In particular, there is a growing appreciation that kin selection, arising through demographic factors such as sex-biased dispersal, may modulate sexual conflicts, including in the context of male-female arms races characterized by coevolutionary cycles. However, evolutionary conflicts of interest need not only occur between individuals, but may also occur within individuals, and sex-specific demography is known to foment such intragenomic conflict in relation to social behavior. Whether and how this logic holds in the context of sexual conflict-and, in particular, in relation to coevolutionary cycles-remains obscure. We develop a kin-selection model to investigate the interests of different genes involved in sexual and intragenomic conflict, and we show that consideration of these conflicting interests yields novel predictions concerning parent-of-origin specific patterns of gene expression and the detrimental effects of different classes of mutation and epimutation at loci underpinning sexually selected phenotypes. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  2. Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat.

    Science.gov (United States)

    Bertin, Angeline; Gouin, Nicolas; Baumel, Alex; Gianoli, Ernesto; Serratosa, Juan; Osorio, Rodomiro; Manel, Stephanie

    2017-01-01

    Positive species-genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non-neutral mechanisms have not been explored. Here, we investigate the impact of non-neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens from five species (three common aquatic macroinvertebrate and two dominant plant species) that were genotyped for 396 amplified fragment length polymorphism loci. We also appraise the importance of neutral processes on SGDCs by investigating the influence of habitat fragmentation features. Significant positive SGDCs were detected for all five species (mean SGDC = 0.52 ± 0.05). While only a few outlier loci were detected in each species, they resulted in significant decreases in GD and in SGDCs. This supports the hypothesis that neutral processes drive species-genetic diversity relationships in high Andean wetlands. Unexpectedly, the effects on genetic diversity GD of the habitat fragmentation characteristics in this study increased with the presence of outlier loci in two species. Overall, our results reveal pitfalls in using habitat features to infer processes driving SGDCs and show that a few loci potentially under selection are enough to cause a significant downward bias in SGDC. Investigating confounding effects of outlier loci thus represents a useful approach to evidence the contribution of neutral processes on species-genetic diversity relationships. © 2016 John Wiley & Sons Ltd.

  3. Genetic diversity among selected genotypes of almond Prunus ...

    African Journals Online (AJOL)

    rohit

    2012-10-16

    Oct 16, 2012 ... introductions, as well as indigenous selections (Table 1). Genomic. DNA was isolated from freshly collected leaves following modified. CTAB method (Doyle and Doyle, 1987, 1990). Phenolics and tannins were removed by repeated purification of DNA following phenol and chloroform treatment. Also during ...

  4. instability and reversal of genetic correlations during selection on ...

    Indian Academy of Sciences (India)

    Unknown

    rate displayed a strong net negative evolutionary correlation with weight at eclosion across all selection treatments, consistent with the existence of a .... loss of variation and second because functional traits may vary in the degree to which .... increases in either desiccation or starvation resistance al- ways lead to increased ...

  5. Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome.

    Science.gov (United States)

    Lohmueller, Kirk E; Albrechtsen, Anders; Li, Yingrui; Kim, Su Yeon; Korneliussen, Thorfinn; Vinckenbosch, Nicolas; Tian, Geng; Huerta-Sanchez, Emilia; Feder, Alison F; Grarup, Niels; Jørgensen, Torben; Jiang, Tao; Witte, Daniel R; Sandbæk, Annelli; Hellmann, Ines; Lauritzen, Torsten; Hansen, Torben; Pedersen, Oluf; Wang, Jun; Nielsen, Rasmus

    2011-10-01

    A major question in evolutionary biology is how natural selection has shaped patterns of genetic variation across the human genome. Previous work has documented a reduction in genetic diversity in regions of the genome with low recombination rates. However, it is unclear whether other summaries of genetic variation, like allele frequencies, are also correlated with recombination rate and whether these correlations can be explained solely by negative selection against deleterious mutations or whether positive selection acting on favorable alleles is also required. Here we attempt to address these questions by analyzing three different genome-wide resequencing datasets from European individuals. We document several significant correlations between different genomic features. In particular, we find that average minor allele frequency and diversity are reduced in regions of low recombination and that human diversity, human-chimp divergence, and average minor allele frequency are reduced near genes. Population genetic simulations show that either positive natural selection acting on favorable mutations or negative natural selection acting against deleterious mutations can explain these correlations. However, models with strong positive selection on nonsynonymous mutations and little negative selection predict a stronger negative correlation between neutral diversity and nonsynonymous divergence than observed in the actual data, supporting the importance of negative, rather than positive, selection throughout the genome. Further, we show that the widespread presence of weakly deleterious alleles, rather than a small number of strongly positively selected mutations, is responsible for the correlation between neutral genetic diversity and recombination rate. This work suggests that natural selection has affected multiple aspects of linked neutral variation throughout the human genome and that positive selection is not required to explain these observations.

  6. Genetic trends of selection for pelt traits in Karakul sheep I. Direct ...

    African Journals Online (AJOL)

    Genetic trends owing to selection for an increase in pattern and hair quality and a decrease in hair length and curl development in the Karakul Wereestimated with the Animal Model in four selection lines and in a control flock over. 12 years (3.6 generations). The objective was, firstly, to determine whether the control flock ...

  7. Postcopulatory sexual selection reduces genetic diversity in experimental populations of Caenorhabditis elegans.

    Science.gov (United States)

    LaMunyon, Craig W; Bouban, Oussama; Cutter, Asher D

    2007-01-01

    Postcopulatory sexual selection affects the evolution of numerous features ranging from mating behavior to seminal fluid toxicity to the size of gametes. In an earlier study of the effect of sperm competition risk on sperm size evolution, experimental populations of the nematode Caenorhabditis elegans were maintained either by outcrossing (sperm competition present) or by selfing (no sperm competition), and after 60 generations, significantly larger sperm had evolved in the outcrossing populations. To determine the effects of this selection on population genetic variation, we assessed genetic diversity in a large number of loci using random amplification of polymorphic DNA-PCR. Nearly 80% of the alleles present in parental strain populations persisted in the 6 experimental populations after the 60 generations and, despite a 2.2-fold difference in expected heterozygosity, the resulting levels of genetic variation were equivalent between the outcrossing and selfing experimental populations. By inference, we conclude that genetic hitchhiking due to sexual selection in the experimental populations dramatically reduced genetic diversity. We use the levels of variation in the selfing populations as a control for the effects of drift, and estimate the strength of sexual selection to be strong in obligatorily outcrossing populations. Although sequential hermaphrodites like C. elegans probably experience little sexual selection in nature, these data suggest that sexual selection can profoundly affect diversity in outcrossing taxa.

  8. The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus.

    Science.gov (United States)

    Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

    2014-01-01

    Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a QST/FST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (QST) was compared with divergence at eight neutral microsatellite loci (FST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had QST values significantly lower than FST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (QST>FST). Estimates of heritability were high for all traits (means ranging between 0.55-0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.

  9. Pathways and barriers to genetic testing and screening: Molecular genetics meets the high-risk family. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Duster, T.

    1998-11-01

    The proliferation of genetic screening and testing is requiring increasing numbers of Americans to integrate genetic knowledge and interventions into their family life and personal experience. This study examines the social processes that occur as families at risk for two of the most common autosomal recessive diseases, sickle cell disease (SC) and cystic fibrosis (CF), encounter genetic testing. Each of these diseases is found primarily in a different ethnic/racial group (CF in Americans of North European descent and SC in Americans of West African descent). This has permitted them to have a certain additional lens on the role of culture in integrating genetic testing into family life and reproductive planning. A third type of genetic disorder, the thalassemias was added to the sample in order to extent the comparative frame and to include other ethnic and racial groups.

  10. QUANTITATIVE GENETICS OF MORPHOLOGICAL DIFFERENTIATION IN PEROMYSCUS. II. ANALYSIS OF SELECTION AND DRIFT.

    Science.gov (United States)

    Lofsvold, David

    1988-01-01

    The hypothesis that the morphological divergence of local populations of Peromyscus is due to random genetic drift was evaluated by testing the proportionality of the among-locality covariance matrix, L, and the additive genetic covariance matrix, G. Overall, significant proportionality of L̂ and Ĝ was not observed, indicating the evolutionary divergence of local populations does not result from random genetic drift. The forces of selection needed to differentiate three taxa of Peromyscus were reconstructed to examine the divergence of species and subspecies. The selection gradients obtained illustrate the inadequacy of univariate analyses of selection by finding that some characters evolve in the direction opposite to the force of selection acting directly on them. A retrospective selection index was constructed using the estimated selection gradients, and truncation selection on this index was used to estimate the minimum selective mortality per generation required to produce the observed change. On any of the time scales used, the proportion of the population that would need to be culled was quite low, the greatest being of the same order of magnitude as the selective intensities observed in extant natural populations. Thus, entirely plausible intensities of directional natural selection can produce species-level differences in a period of time too short to be resolved in the fossil record. © 1988 The Society for the Study of Evolution.

  11. Genetic structure and signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos).

    Science.gov (United States)

    Momigliano, P; Harcourt, R; Robbins, W D; Jaiteh, V; Mahardika, G N; Sembiring, A; Stow, A

    2017-09-01

    With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Using samples from Australia, Indonesia and oceanic reefs in the Indian Ocean, we established that large oceanic distances represent barriers to gene flow, whereas genetic differentiation on continental shelves follows an isolation by distance model. In Australia and Indonesia differentiation at nuclear SNPs was weak, with coral reefs acting as stepping stones maintaining connectivity across large distances. Differentiation of mtDNA was stronger, and more pronounced in females, suggesting sex-biased dispersal. Four independent tests identified a set of loci putatively under selection, indicating that grey reef sharks in eastern Australia are likely under different selective pressures to those in western Australia and Indonesia. Genetic distances averaged across all loci were uncorrelated with genetic distances calculated from outlier loci, supporting the conclusion that different processes underpin genetic divergence in these two data sets. This pattern of heterogeneous genomic differentiation, suggestive of local adaptation, has implications for the conservation of grey reef sharks; furthermore, it highlights that marine species showing little genetic differentiation at neutral loci may exhibit patterns of cryptic genetic structure driven by local selection.

  12. Genetic association of marbling score with intragenic nucleotide variants at selection signals of the bovine genome.

    Science.gov (United States)

    Ryu, J; Lee, C

    2016-04-01

    Selection signals of Korean cattle might be attributed largely to artificial selection for meat quality. Rapidly increased intragenic markers of newly annotated genes in the bovine genome would help overcome limited findings of genetic markers associated with meat quality at the selection signals in a previous study. The present study examined genetic associations of marbling score (MS) with intragenic nucleotide variants at selection signals of Korean cattle. A total of 39 092 nucleotide variants of 407 Korean cattle were utilized in the association analysis. A total of 129 variants were selected within newly annotated genes in the bovine genome. Their genetic associations were analyzed using the mixed model with random polygenic effects based on identical-by-state genetic relationships among animals in order to control for spurious associations produced by population structure. Genetic associations of MS were found (P<3.88×10-4) with six intragenic nucleotide variants on bovine autosomes 3 (cache domain containing 1, CACHD1), 5 (like-glycosyltransferase, LARGE), 16 (cell division cycle 42 binding protein kinase alpha, CDC42BPA) and 21 (snurportin 1, SNUPN; protein tyrosine phosphatase, non-receptor type 9, PTPN9; chondroitin sulfate proteoglycan 4, CSPG4). In particular, the genetic associations with CDC42BPA and LARGE were confirmed using an independent data set of Korean cattle. The results implied that allele frequencies of functional variants and their proximity variants have been augmented by directional selection for greater MS and remain selection signals in the bovine genome. Further studies of fine mapping would be useful to incorporate favorable alleles in marker-assisted selection for MS of Korean cattle.

  13. Testing for a genetic response to sexual selection in a wild Drosophila population.

    Science.gov (United States)

    Gosden, T P; Thomson, J R; Blows, M W; Schaul, A; Chenoweth, S F

    2016-06-01

    In accordance with the consensus that sexual selection is responsible for the rapid evolution of display traits on macroevolutionary scales, microevolutionary studies suggest sexual selection is a widespread and often strong form of directional selection in nature. However, empirical evidence for the contemporary evolution of sexually selected traits via sexual rather than natural selection remains weak. In this study, we used a novel application of quantitative genetic breeding designs to test for a genetic response to sexual selection on eight chemical display traits from a field population of the fly, Drosophila serrata. Using our quantitative genetic approach, we were able to detect a genetically based difference in means between groups of males descended from fathers who had either successfully sired offspring or were randomly collected from the same wild population for one of these display traits, the diene (Z,Z)-5,9-C27 : 2 . Our experimental results, in combination with previous laboratory studies on this system, suggest that both natural and sexual selection may be influencing the evolutionary trajectories of these traits in nature, limiting the capacity for a contemporary evolutionary response. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  14. Feature Selection and Classification of Electroencephalographic Signals: An Artificial Neural Network and Genetic Algorithm Based Approach.

    Science.gov (United States)

    Erguzel, Turker Tekin; Ozekes, Serhat; Tan, Oguz; Gultekin, Selahattin

    2015-10-01

    Feature selection is an important step in many pattern recognition systems aiming to overcome the so-called curse of dimensionality. In this study, an optimized classification method was tested in 147 patients with major depressive disorder (MDD) treated with repetitive transcranial magnetic stimulation (rTMS). The performance of the combination of a genetic algorithm (GA) and a back-propagation (BP) neural network (BPNN) was evaluated using 6-channel pre-rTMS electroencephalographic (EEG) patterns of theta and delta frequency bands. The GA was first used to eliminate the redundant and less discriminant features to maximize classification performance. The BPNN was then applied to test the performance of the feature subset. Finally, classification performance using the subset was evaluated using 6-fold cross-validation. Although the slow bands of the frontal electrodes are widely used to collect EEG data for patients with MDD and provide quite satisfactory classification results, the outcomes of the proposed approach indicate noticeably increased overall accuracy of 89.12% and an area under the receiver operating characteristic (ROC) curve (AUC) of 0.904 using the reduced feature set. © EEG and Clinical Neuroscience Society (ECNS) 2014.

  15. Direct multitrait selection realizes the highest genetic response for ratio traits.

    Science.gov (United States)

    Zetouni, L; Henryon, M; Kargo, M; Lassen, J

    2017-05-01

    For a number of traits the phenotype considered to be the goal trait is a combination of 2 or more traits, like methane (CH) emission (CH/kg of milk). Direct selection on CH4 emission defined as a ratio is problematic, because it is uncertain whether the improvement comes from an improvement in milk yield, a decrease in CH emission or both. The goal was to test different strategies on selecting for 2 antagonistic traits- improving milk yield while decreasing methane emissions. The hypothesis was that to maximize genetic gain for a ratio trait, the best approach is to select directly for the component traits rather than using a ratio trait or a trait where 1 trait is corrected for the other as the selection criteria. Stochastic simulation was used to mimic a dairy cattle population. Three scenarios were tested, which differed in selection criteria but all selecting for increased milk yield: 1) selection based on a multitrait approach using the correlation structure between the 2 traits, 2) the ratio of methane to milk and 3) gross methane phenotypically corrected for milk. Four correlation sets were tested in all scenarios, to access robustness of the results. An average genetic gain of 66 kg of milk per yr was obtained in all scenarios, but scenario 1 had the best response for decreased methane emissions, with a genetic gain of 24.8 l/yr, while scenarios 2 and 3 had genetic gains of 27.1 and 27.3 kg/yr. The results found were persistent across correlation sets. These results confirm the hypothesis that to obtain the highest genetic gain a multitrait selection is a better approach than selecting for the ratio directly. The results are exemplified for a methane and milk scenario but can be generalized to other situations where combined traits need to be improved.

  16. Genetic variation but weak genetic covariation between pre- and post-copulatory episodes of sexual selection in Drosophila melanogaster.

    Science.gov (United States)

    Travers, L M; Garcia-Gonzalez, F; Simmons, L W

    2016-08-01

    When females mate polyandrously, male reproductive success depends both on the male's ability to attain matings and on his ability to outcompete rival males in the fertilization of ova post-copulation. Increased investment in  ejaculate components may trade off with investment in precopulatory traits due to resource allocation. Alternatively, pre- and post-copulatory traits could be positively related if individuals can afford to invest heavily in traits advantageous at both episodes of selection. There is empirical evidence for both positive and negative associations between pre- and post-copulatory episodes, but little is known about the genetic basis of these correlations. In this study, we measured morphological, chemical and behavioural precopulatory male traits and investigated their relationship with measures of male fitness (male mating success, remating inhibition and offensive sperm competitiveness) across 40 isofemale lines of Drosophila melanogaster. We found significant variation among isofemale lines, indicating a genetic basis for most of the traits investigated. However, we found weak evidence for genetic correlations between precopulatory traits and our indices of male fitness. Moreover, pre- and post-copulatory episodes of selection were uncorrelated, suggesting selection may act independently at the different episodes to maximize male reproductive success. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  17. Site-selection studies for final disposal of spent fuel in Finland

    International Nuclear Information System (INIS)

    Vuorela, P.; Aeikaes, T.

    1984-02-01

    In the management of waste by the Industrial Power Company Ltd. (TVO) preparations are being made for the final disposal of unprocessed spent fuel into the Finnish bedrock. The site selection program will advance in three phases. The final disposal site must be made at the latest by the end of the year 2000, in accordance with a decision laid down by the Finnish Government. In the first phase, 1983-85, the main object is to find homogeneous stable bedrock blocks surrounded by fracture zones located at a safe distance from the planned disposal area. The work usually starts with a regional structural analysis of mosaics of Landsat-1 winter and summer imagery. Next an assortment of different maps, which cover the whole country, is used. Technical methods for geological and hydrogeological site investigations are being developed during the very first phase of the studies, and a borehole 1000 meters deep will be made in southwestern Finland. Studies for the final disposal of spent fuel or high-level reprocessing waste have been made since 1974 in Finland. General suitability studies of the bedrock have been going on since 1977. The present results indicate that suitable investigation areas for the final disposal of highly active waste can be found in Finland

  18. Sports selection of volley-ball players: genetic criteria to define motor endowments (information 2)

    OpenAIRE

    Ablikovа, Alisa; Serhiyenko, Leonid

    2016-01-01

    Purpose: to define genetic criteria which can be used while selecting gifted volley-ball players. Material & Methods: the study involved 50 high class volley-ball players and 50 women at the age of 20–29 years old. There were used methods of theoretical analysis and general conclusion, systematic analysis, genealogic methods of genetics, methods of dermatoglyphic and serologic analyses. Results: family gift for going in for sport was detected. At was revealed that gifted volley-ball playe...

  19. Hybrid Model Based on Genetic Algorithms and SVM Applied to Variable Selection within Fruit Juice Classification

    Science.gov (United States)

    Fernandez-Lozano, C.; Canto, C.; Gestal, M.; Andrade-Garda, J. M.; Rabuñal, J. R.; Dorado, J.; Pazos, A.

    2013-01-01

    Given the background of the use of Neural Networks in problems of apple juice classification, this paper aim at implementing a newly developed method in the field of machine learning: the Support Vector Machines (SVM). Therefore, a hybrid model that combines genetic algorithms and support vector machines is suggested in such a way that, when using SVM as a fitness function of the Genetic Algorithm (GA), the most representative variables for a specific classification problem can be selected. PMID:24453933

  20. Global patterns of genetic diversity and signals of natural selection for human ADME genes.

    Science.gov (United States)

    Li, Jing; Zhang, Luyong; Zhou, Hang; Stoneking, Mark; Tang, Kun

    2011-02-01

    Genetic polymorphisms in many genes related to drug absorption, distribution, metabolism and excretion (ADME genes) contribute to the high heterogeneity of drug responses in humans. However, the extent to which genetic variation in ADME genes may contribute to differences among human populations in drug responses has not been studied. In this work, we investigate the global distribution of genetic diversity for 31 core and 252 extended ADME genes. We find that many important ADME genes are highly differentiated across continental regions. Additionally, we analyze the genetic differentiation associated with clinically relevant, functional polymorphism alleles, which is important for evaluating potential among-population heterogeneity in drug treatment effects. We find that ADME genes show significantly greater variation in levels of population differentiation, and we find numerous signals of recent positive selection on ADME genes. These results suggest that genetic differentiation at ADME genes could contribute to population heterogeneity in drug responses.

  1. Chemical Variation in a Dominant Tree Species: Population Divergence, Selection and Genetic Stability across Environments

    Science.gov (United States)

    O’Reilly-Wapstra, Julianne M.; Miller, Alison M.; Hamilton, Matthew G.; Williams, Dean; Glancy-Dean, Naomi; Potts, Brad M.

    2013-01-01

    Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E). We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs) in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h2op = 0.24) to high (e.g., macrocarpal G h2op = 0.48) narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal) and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes. PMID:23526981

  2. Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments.

    Directory of Open Access Journals (Sweden)

    Julianne M O'Reilly-Wapstra

    Full Text Available Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E. We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h(2op = 0.24 to high (e.g., macrocarpal G h(2op = 0.48 narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.

  3. Persistency of Prediction Accuracy and Genetic Gain in Synthetic Populations Under Recurrent Genomic Selection.

    Science.gov (United States)

    Müller, Dominik; Schopp, Pascal; Melchinger, Albrecht E

    2017-03-10

    Recurrent selection (RS) has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents [Formula: see text] but little is known about how [Formula: see text] affects genomic selection (GS) in RS, especially the persistency of prediction accuracy ([Formula: see text]) and genetic gain. Synthetics were simulated by intermating [Formula: see text]= 2-32 parent lines from an ancestral population with short- or long-range linkage disequilibrium ([Formula: see text]) and subjected to multiple cycles of GS. We determined [Formula: see text] and genetic gain across 30 cycles for different training set ( TS ) sizes, marker densities, and generations of recombination before model training. Contributions to [Formula: see text] and genetic gain from pedigree relationships, as well as from cosegregation and [Formula: see text] between QTL and markers, were analyzed via four scenarios differing in (i) the relatedness between TS and selection candidates and (ii) whether selection was based on markers or pedigree records. Persistency of [Formula: see text] was high for small [Formula: see text] where predominantly cosegregation contributed to [Formula: see text], but also for large [Formula: see text] where [Formula: see text] replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing [Formula: see text] > 4, given long-range LD A in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to [Formula: see text] for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size ([Formula: see text]) and higher marker density improved persistency of

  4. Persistency of Prediction Accuracy and Genetic Gain in Synthetic Populations Under Recurrent Genomic Selection

    Directory of Open Access Journals (Sweden)

    Dominik Müller

    2017-03-01

    Full Text Available Recurrent selection (RS has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents ( Np , but little is known about how Np affects genomic selection (GS in RS, especially the persistency of prediction accuracy (rg , g ^ and genetic gain. Synthetics were simulated by intermating Np= 2–32 parent lines from an ancestral population with short- or long-range linkage disequilibrium (LDA and subjected to multiple cycles of GS. We determined rg , g ^ and genetic gain across 30 cycles for different training set (TS sizes, marker densities, and generations of recombination before model training. Contributions to rg , g ^ and genetic gain from pedigree relationships, as well as from cosegregation and LDA between QTL and markers, were analyzed via four scenarios differing in (i the relatedness between TS and selection candidates and (ii whether selection was based on markers or pedigree records. Persistency of rg , g ^ was high for small Np , where predominantly cosegregation contributed to rg , g ^ , but also for large Np , where LDA replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing Np > 4, given long-range LDA in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to rg , g ^ for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size (NTS and higher marker density improved persistency of rg , g ^ and hence genetic gain, but additional recombinations could not increase genetic gain.

  5. Hitting times of local and global optima in genetic algorithms with very high selection pressure

    Directory of Open Access Journals (Sweden)

    Eremeev Anton V.

    2017-01-01

    Full Text Available The paper is devoted to upper bounds on the expected first hitting times of the sets of local or global optima for non-elitist genetic algorithms with very high selection pressure. The results of this paper extend the range of situations where the upper bounds on the expected runtime are known for genetic algorithms and apply, in particular, to the Canonical Genetic Algorithm. The obtained bounds do not require the probability of fitness-decreasing mutation to be bounded by a constant which is less than one.

  6. Optimal Genetic Contribution Selection in Danish Holstein Depends on Pedigree Qualtiy

    DEFF Research Database (Denmark)

    Sørensen, M K; Sørensen, A C; Baumung, R

    2008-01-01

    .D. units at the total merit index. This reduction was obtained when selection was only on reduction of average relationship compared to selection only on genetic merit. Optimal genetic contribution selection is a promising tool for managing breeding schemes for populations facing inbreeding problems....... In the analyses earlier breeding decisions were considered by including all AI waiting- and young bulls and contract matings. Twenty potential sires, 2169 potential dams, 1421 AI-bulls and 754 contract matings plus pedigree animals were included. Results showed that the outcome was very dependent on quality...... of pedigree, also for information going more than 25 years (5-7 generations) back. The analyses showed that EVA works satisfactorily as a management tool for planning of breeding schemes with respect to contributions of sires of sons at population level in maximising the genetic gain, while controlling...

  7. Recognition of genetic predisposition in pediatric cancer patients: An easy-to-use selection tool.

    Science.gov (United States)

    Jongmans, Marjolijn C J; Loeffen, Jan L C M; Waanders, Esmé; Hoogerbrugge, Peter M; Ligtenberg, Marjolijn J L; Kuiper, Roland P; Hoogerbrugge, Nicoline

    2016-03-01

    Genetic predisposition for childhood cancer is under diagnosed. Identifying these patients may lead to therapy adjustments in case of syndrome-related increased toxicity or resistant disease and syndrome-specific screening programs may lead to early detection of a further independent malignancy. Cancer surveillance might also be warranted for affected relatives and detection of a genetic mutation can allow for reproductive counseling. Here we present an easy-to-use selection tool, based on a systematic review of pediatric cancer predisposing syndromes, to identify patients who may benefit from genetic counseling. The selection tool involves five questions concerning family history, the type of malignancy, multiple primary malignancies, specific features and excessive toxicity, which results in the selection of those patients that may benefit from referral to a clinical geneticist. Copyright © 2016 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

  8. Differing patterns of selection and geospatial genetic diversity within two leading Plasmodium vivax candidate vaccine antigens.

    Directory of Open Access Journals (Sweden)

    Christian M Parobek

    2014-04-01

    Full Text Available Although Plasmodium vivax is a leading cause of malaria around the world, only a handful of vivax antigens are being studied for vaccine development. Here, we investigated genetic signatures of selection and geospatial genetic diversity of two leading vivax vaccine antigens--Plasmodium vivax merozoite surface protein 1 (pvmsp-1 and Plasmodium vivax circumsporozoite protein (pvcsp. Using scalable next-generation sequencing, we deep-sequenced amplicons of the 42 kDa region of pvmsp-1 (n = 44 and the complete gene of pvcsp (n = 47 from Cambodian isolates. These sequences were then compared with global parasite populations obtained from GenBank. Using a combination of statistical and phylogenetic methods to assess for selection and population structure, we found strong evidence of balancing selection in the 42 kDa region of pvmsp-1, which varied significantly over the length of the gene, consistent with immune-mediated selection. In pvcsp, the highly variable central repeat region also showed patterns consistent with immune selection, which were lacking outside the repeat. The patterns of selection seen in both genes differed from their P. falciparum orthologs. In addition, we found that, similar to merozoite antigens from P. falciparum malaria, genetic diversity of pvmsp-1 sequences showed no geographic clustering, while the non-merozoite antigen, pvcsp, showed strong geographic clustering. These findings suggest that while immune selection may act on both vivax vaccine candidate antigens, the geographic distribution of genetic variability differs greatly between these two genes. The selective forces driving this diversification could lead to antigen escape and vaccine failure. Better understanding the geographic distribution of genetic variability in vaccine candidate antigens will be key to designing and implementing efficacious vaccines.

  9. The joint regulation of genetic gain and inbreeding under mate selection.

    Science.gov (United States)

    Klieve, H M; Kinghorn, B P; Barwick, S A

    1994-01-12

    Stochastic simulation was used to evaluate a range of selection strategies with respect to both additive genetic response and inbreeding. Strategies involving selection on BLUP ebvs or individual phenotype, followed by random mating, were compared with mate selection strategies which used portfolio analysis to give joint consideration to genetic merit and inbreeding. An adapted Mean Of Total Absolute Deviations (MOTAD) method was used in a mate selection model to define optimal matings with regard to aggregate genetic merit and inbreeding for a base population h(2) of 0.2. Compared with random mating following selection on BLUP ebvs, inbreeding levels after 10 years of selection were able to be reduced under BLUP plus mate selection from ∼.23 to as little as .11. Additive genetic gain was either little compromised or increased. The results suggest that information linking expected levels of genetic merit and inbreeding can be used to find the preferred selection strategy. ZUSAMMENFASSUNG: Gemeinsame Kontrolle von Zuchtfortschritt und Inzucht bei Partnerselektion Es wurde stochastische Simulation zur Auswertung einer Reihe von Selektionsstrategien hinsichtlich Zuchtwertzuwachs und Inzucht verwendet. Strategien mit Selektion auf der Basis von BLUP ebvs oder individuellem Phänotyp mit nachfolgender Zufallspaarung wurden mit Partnerselektionsstrategien verglichen, die Portfolioanalyse zur gemeinsamen Beachtung von Zuchtwert und Inzucht verwendeten. Eine Methode adaptierter MITTELWERTE TOTALER ABSOLUTER ABWEICHUNGEN (MOTAD) Methode wurde beim Partnerselektionsmodell zur Definition optimaler Paarungen in Hinblick auf Gesamtzuchtwert und Inzucht bei einer Populationsheritabilität von 0,2 verwendet. Verglichen mit Zufallspaarung nach Selektion auf BLUP ebvs waren die Inzuchtgrade nach 10 Selektionsjahren von 0,23 auf 0,11 reduziert und additiver Zuchtfortschritt war dabei wenig beeinträchtigt oder nahm sogar zu. Die Ergebnisse weisen darauf hin, daß Information, die

  10. Resource allocation for maximizing prediction accuracy and genetic gain of genomic selection in plant breeding: a simulation experiment.

    Science.gov (United States)

    Lorenz, Aaron J

    2013-03-01

    Allocating resources between population size and replication affects both genetic gain through phenotypic selection and quantitative trait loci detection power and effect estimation accuracy for marker-assisted selection (MAS). It is well known that because alleles are replicated across individuals in quantitative trait loci mapping and MAS, more resources should be allocated to increasing population size compared with phenotypic selection. Genomic selection is a form of MAS using all marker information simultaneously to predict individual genetic values for complex traits and has widely been found superior to MAS. No studies have explicitly investigated how resource allocation decisions affect success of genomic selection. My objective was to study the effect of resource allocation on response to MAS and genomic selection in a single biparental population of doubled haploid lines by using computer simulation. Simulation results were compared with previously derived formulas for the calculation of prediction accuracy under different levels of heritability and population size. Response of prediction accuracy to resource allocation strategies differed between genomic selection models (ridge regression best linear unbiased prediction [RR-BLUP], BayesCπ) and multiple linear regression using ordinary least-squares estimation (OLS), leading to different optimal resource allocation choices between OLS and RR-BLUP. For OLS, it was always advantageous to maximize population size at the expense of replication, but a high degree of flexibility was observed for RR-BLUP. Prediction accuracy of doubled haploid lines included in the training set was much greater than of those excluded from the training set, so there was little benefit to phenotyping only a subset of the lines genotyped. Finally, observed prediction accuracies in the simulation compared well to calculated prediction accuracies, indicating these theoretical formulas are useful for making resource allocation

  11. The genomic signature of sexual selection in the genetic diversity of the sex chromosomes and autosomes.

    Science.gov (United States)

    Corl, Ammon; Ellegren, Hans

    2012-07-01

    Genomic levels of variation can help reveal the selective and demographic forces that have affected a species during its history. The relative amount of genetic diversity observed on the sex chromosomes as compared to the autosomes is predicted to differ among monogamous and polygynous species. Many species show departures from the expectation for monogamy, but it can be difficult to conclude that this pattern results from variation in mating system because forces other than sexual selection can act upon sex chromosome genetic diversity. As a critical test of the role of mating system, we compared levels of genetic diversity on the Z chromosome and autosomes of phylogenetically independent pairs of shorebirds that differed in their mating systems. We found general support for sexual selection shaping sex chromosome diversity because most polygynous species showed relatively reduced genetic variation on their Z chromosomes as compared to monogamous species. Differences in levels of genetic diversity between the sex chromosomes and autosomes may therefore contribute to understanding the long-term history of sexual selection experienced by a species. © 2012 The Author(s).

  12. Selection and genetic gain in rubber tree (Hevea populations using a mixed mating system

    Directory of Open Access Journals (Sweden)

    Costa Reginaldo Brito da

    2000-01-01

    Full Text Available The components of genetic variation and genetic gain obtained with three selection methods - individual, combined and multi-effect index selection - were compared in rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss. Muell. Arg.] progenies. The rubber tree is a cross pollinating species with a mixed reproductive system in which the self pollination rate is 22%. Twenty-two half sib progenies were planted at experimental stations at Pindorama, Votuporanga and Jaú, in São Paulo State, using a randomized and complete block design, with five replications and ten plants per plot. Dry rubber production was assessed when the plants were three years old. Based on the genetic variability of the populations, Pindorama was the best environment for the expression of variability. At the individual level, heritability was seriously affected when random progenies from an open pollinating population were considered as half sib progenies. Considerable overestimation of genetic gains occurred during individual, combined and multi-effect index selection when the rubber tree reproductive system was not considered as mixed. Selection based on the multi-effect index maximizes genetic progress and should be used more in rubber tree breeding programs.

  13. Female promiscuity is positively associated with neutral and selected genetic diversity in passerine birds.

    Science.gov (United States)

    Gohli, Jostein; Anmarkrud, Jarl A; Johnsen, Arild; Kleven, Oddmund; Borge, Thomas; Lifjeld, Jan T

    2013-05-01

    Passerine birds show large interspecific variation in extrapair paternity rates. There is accumulating evidence that such promiscuous behavior is driven by indirect, genetic benefits to females. Sexual selection theory distinguishes between two types of genetic benefits, additive and nonadditive effects, mediated by preferences for good and compatible genes, respectively. Good genes preferences should imply directional selection and mating skew among males, and thus reduced genetic diversity in the population. In contrast, compatible genes preferences should give balancing selection that retains genetic diversity. Here, we test how well these predictions fit with patterns of variation in genetic diversity and promiscuity levels among passerine birds. We found that more promiscuous species had higher nucleotide diversity at autosomal introns, but not at Z-chromosome introns. We also found that major histocompatibility complex (MHC) class IIB alleles had higher sequence diversity, and therefore should recognize a broader spectrum of pathogens, in more promiscuous species. Our results suggest that female promiscuity targets a multitude of autosomal genes for their nonadditive, compatibility benefits. Also, as immunity genes seem to be of particular importance, we hypothesize that interspecific variation in female promiscuity among passerine birds has arisen in response to the strength of pathogen-mediated selection. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  14. Genetic parameters and selection gains for Euterpe oleracea in juvenile phase

    Directory of Open Access Journals (Sweden)

    João Tomé de Farias Neto

    2012-09-01

    Full Text Available Genetics parameters and selection gains, obtained 36 months after planting, are presented and discussed for progenies of open pollinated population of açai palm for plant height (AP, plant diameter (DPC, number of live leaves ( NFV and tiller number (NP, based on the linear mixed model methodology (REML / BLUP. The thirty progenies were evaluated in a randomized blocks design with three replications and plots of five plants, spaced at 6m x 4m. The values obtained for individual heritability (0.55, 0.44, 0.38 and 0.43 and for progeny means (0.64, 0.54, 0.58 and 0.64 for AP, DPC, NFV and NP, respectively, were expressives, which indicates the possibility of genetic progress with the selection. The accuracy among the genetics values predicted and the true were of 0.802 for height, 0.736 for diameter, 0.760 for number of live leaves and 0.797 for tiller number. With the exception of NFV character, the coefficients of individual genetic variation were high (>10%, confirming the potential of the population for selection. Predicted genetic gains of 89.3% were obtained for the character AP and 2.1% for DCP, with the selection of the twenty top individuals. Correlation was found between height and diameter of the plant. Among ages, for the same characters, positive correlations of mean magnitudes were found.

  15. Performance Enhancement of Data Classification using Selectively Cloned Genetic Algorithm for Neural Network

    Directory of Open Access Journals (Sweden)

    Devinder Kaur

    2010-12-01

    to compare the selective cloning technique with the conventional GA and the back-propagation algorithm. For comparative analysis, same neural network architecture is used for both the back propagation and the genetic algorithms. The selective cloning approach is based on the schema theorem. By using selective cloning, it has been shown that GA is 27.78% more efficient than the conventional GA and 83.33% more efficient than the back propagation approach. The results of selective cloning on other data sets are also discussed.

  16. Genetic parameters for two selection criteria for feed efficiency in rabbits.

    Science.gov (United States)

    Drouilhet, L; Gilbert, H; Balmisse, E; Ruesche, J; Tircazes, A; Larzul, C; Garreau, H

    2013-07-01

    Improvement of feed efficiency can be achieved by genetic selection directly on feed to BW gain ratio or for alternative traits. In the present study, 2 different traits were explored in the growing rabbit and their heritability and genetic correlations with traits recorded between weaning (30 d) and 63 d of age: i) residual feed intake (RFI), to select animals having low ad libitum feed intake independently from their production level, and ii) ADG under restricted feeding (ADGR; with a restriction level of 80% compared with ad libitum feeding of a control group), to select animals having high growth rate despite limited feed intake. To study these traits, 2 rabbit lines were established named i) ConsoResidual line and ii) ADGrestrict line. Under ad libitum or restricted feeding, it comes to select animals that waste less energy for maintenance, metabolism, or activity and retain more for tissue deposition. The selection process was similar in both lines. Data comprised records from generations 0 to 6 for about 1,800 rabbits per line measured for their BW at weaning and 63 d of age (BW63) and their individual feed consumption. Under ad libitum feeding, the heritability estimates were moderate for RFI (0.16 ± 0.05), ADG (0.19 ± 0.05), and feed conversion ratio (FCR; 0.22 ± 0.05). The high genetic correlation estimated between RFI and FCR (0.96 ± 0.03) was in accordance with the literature. The genetic correlation between RFI and ADG traits was not significant. Thus, selection for low RFI with ad libitum feeding was confirmed as a potential trait to improve FCR and reduce feed intake, with little effect on ADG. To our knowledge, there is no previous selection experiment on growing rabbits with restricted feeding. Our heritability estimates for ADGR and feed conversion ratio under restricted feeding (FCRR) were moderate (0.22 ± 0.06 and 0.23 ± 0.07, respectively) and had very high negative genetic correlation. Both selection criteria were found with high and

  17. Sexually antagonistic selection on genetic variation underlying both male and female same-sex sexual behavior.

    Science.gov (United States)

    Berger, David; You, Tao; Minano, Maravillas R; Grieshop, Karl; Lind, Martin I; Arnqvist, Göran; Maklakov, Alexei A

    2016-05-13

    Intralocus sexual conflict, arising from selection for different alleles at the same locus in males and females, imposes a constraint on sex-specific adaptation. Intralocus sexual conflict can be alleviated by the evolution of sex-limited genetic architectures and phenotypic expression, but pleiotropic constraints may hinder this process. Here, we explored putative intralocus sexual conflict and genetic (co)variance in a poorly understood behavior with near male-limited expression. Same-sex sexual behaviors (SSBs) generally do not conform to classic evolutionary models of adaptation but are common in male animals and have been hypothesized to result from perception errors and selection for high male mating rates. However, perspectives incorporating sex-specific selection on genes shared by males and females to explain the expression and evolution of SSBs have largely been neglected. We performed two parallel sex-limited artificial selection experiments on SSB in male and female seed beetles, followed by sex-specific assays of locomotor activity and male sex recognition (two traits hypothesized to be functionally related to SSB) and adult reproductive success (allowing us to assess fitness consequences of genetic variance in SSB and its correlated components). Our experiments reveal both shared and sex-limited genetic variance for SSB. Strikingly, genetically correlated responses in locomotor activity and male sex-recognition were associated with sexually antagonistic fitness effects, but these effects differed qualitatively between male and female selection lines, implicating intralocus sexual conflict at both male- and female-specific genetic components underlying SSB. Our study provides experimental support for the hypothesis that widespread pleiotropy generates pervasive intralocus sexual conflict governing the expression of SSBs, suggesting that SSB in one sex can occur due to the expression of genes that carry benefits in the other sex.

  18. Bayesian inference of selection in a heterogeneous environment from genetic time-series data.

    Science.gov (United States)

    Gompert, Zachariah

    2016-01-01

    Evolutionary geneticists have sought to characterize the causes and molecular targets of selection in natural populations for many years. Although this research programme has been somewhat successful, most statistical methods employed were designed to detect consistent, weak to moderate selection. In contrast, phenotypic studies in nature show that selection varies in time and that individual bouts of selection can be strong. Measurements of the genomic consequences of such fluctuating selection could help test and refine hypotheses concerning the causes of ecological specialization and the maintenance of genetic variation in populations. Herein, I proposed a Bayesian nonhomogeneous hidden Markov model to estimate effective population sizes and quantify variable selection in heterogeneous environments from genetic time-series data. The model is described and then evaluated using a series of simulated data, including cases where selection occurs on a trait with a simple or polygenic molecular basis. The proposed method accurately distinguished neutral loci from non-neutral loci under strong selection, but not from those under weak selection. Selection coefficients were accurately estimated when selection was constant or when the fitness values of genotypes varied linearly with the environment, but these estimates were less accurate when fitness was polygenic or the relationship between the environment and the fitness of genotypes was nonlinear. Past studies of temporal evolutionary dynamics in laboratory populations have been remarkably successful. The proposed method makes similar analyses of genetic time-series data from natural populations more feasible and thereby could help answer fundamental questions about the causes and consequences of evolution in the wild. © 2015 John Wiley & Sons Ltd.

  19. The role of protozoa-driven selection in shaping human genetic variability.

    Science.gov (United States)

    Pozzoli, Uberto; Fumagalli, Matteo; Cagliani, Rachele; Comi, Giacomo P; Bresolin, Nereo; Clerici, Mario; Sironi, Manuela

    2010-03-01

    Protozoa exert a strong selective pressure in humans. The selection signatures left by these pathogens can be exploited to identify genetic modulators of infection susceptibility. We show that protozoa diversity in different geographic locations is a good measure of protozoa-driven selective pressure; protozoa diversity captured selection signatures at known malaria resistance loci and identified several selected single nucleotide polymorphisms in immune and hemolytic anemia genes. A genome-wide search enabled us to identify 5180 variants mapping to 1145 genes that are subjected to protozoa-driven selective pressure. We provide a genome-wide estimate of protozoa-driven selective pressure and identify candidate susceptibility genes for protozoa-borne diseases. Copyright 2010 Elsevier Ltd. All rights reserved.

  20. Genetic diversity and selection gain in the physic nut (Jatropha curcas).

    Science.gov (United States)

    Brasileiro, B P; Silva, S A; Souza, D R; Santos, P A; Oliveira, R S; Lyra, D H

    2013-07-08

    The use of efficient breeding methods depends on knowledge of genetic control of traits to be improved. We estimated genetic parameters, selection gain, and genetic diversity in physic nut half-sib families, in order to provide information for breeding programs of this important biofuel species. The progeny test included 20 half-sib families in 4 blocks and 10 plants per plot. The mean progeny heritability values were: 50% for number of bunches, 47% for number of fruits, 35% for number of seeds, 6% for stem diameter, 26% for number of primary branches, 14% for number of secondary branches, 66% for plant height, and 25% for survival of the plants, demonstrating good potential for early selection in plant height, number of branches, and number of fruits per plant. In the analysis of genetic diversity, genotypes were divided into 4 groups. Genotypes 18, 19, 20, and 8 clustered together and presented the highest means for the vegetative and production. Lower means were observed in the 17, 12, 13, and 9 genotypes from the same group. We detected genetic variability in this population, with high heritability estimates and accuracy, demonstrating the possibility of obtaining genetic gains for vegetative characters and production at 24 months after planting.

  1. Expanding Possibilities for Intervention against Small Ruminant Lentiviruses through Genetic Marker-Assisted Selective Breeding

    Directory of Open Access Journals (Sweden)

    Donald P. Knowles

    2013-06-01

    Full Text Available Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus and goats (caprine arthritis encephalitis virus [CAEV]. Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions.

  2. Expanding Possibilities for Intervention against Small Ruminant Lentiviruses through Genetic Marker-Assisted Selective Breeding

    Science.gov (United States)

    White, Stephen N.; Knowles, Donald P.

    2013-01-01

    Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus) and goats (caprine arthritis encephalitis virus [CAEV]). Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS) has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions. PMID:23771240

  3. Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy.

    Science.gov (United States)

    Byars, Sean G; Huang, Qin Qin; Gray, Lesley-Ann; Bakshi, Andrew; Ripatti, Samuli; Abraham, Gad; Stearns, Stephen C; Inouye, Michael

    2017-06-01

    Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD.

  4. Artificial Selection Response due to Polygenic Adaptation from a Multilocus, Multiallelic Genetic Architecture.

    Science.gov (United States)

    Zan, Yanjun; Sheng, Zheya; Lillie, Mette; Rönnegård, Lars; Honaker, Christa F; Siegel, Paul B; Carlborg, Örjan

    2017-10-01

    The ability of a population to adapt to changes in their living conditions, whether in nature or captivity, often depends on polymorphisms in multiple genes across the genome. In-depth studies of such polygenic adaptations are difficult in natural populations, but can be approached using the resources provided by artificial selection experiments. Here, we dissect the genetic mechanisms involved in long-term selection responses of the Virginia chicken lines, populations that after 40 generations of divergent selection for 56-day body weight display a 9-fold difference in the selected trait. In the F15 generation of an intercross between the divergent lines, 20 loci explained >60% of the additive genetic variance for the selected trait. We focused particularly on fine-mapping seven major QTL that replicated in this population and found that only two fine-mapped to single, bi-allelic loci; the other five contained linked loci, multiple alleles or were epistatic. This detailed dissection of the polygenic adaptations in the Virginia lines provides a deeper understanding of the range of different genome-wide mechanisms that have been involved in these long-term selection responses. The results illustrate that the genetic architecture of a highly polygenic trait can involve a broad range of genetic mechanisms, and that this can be the case even in a small population bred from founders with limited genetic diversity. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Final Report: The DNA Files: Unraveling the mysteries of genetics, January 1, 1998-March 31, 1999

    Energy Technology Data Exchange (ETDEWEB)

    Scott, Bari

    1999-05-01

    The DNA Files is an award-winning radio documentary series on genetics created by SoundVision Productions. The DNA Files was hosted by John Hockenberry and was presented in documentary and discussion format. The programs covered a range of topics from prenatal and predictive gene testing, gene therapy, and commercialization of genetic information to new evolutionary genetic evidence, transgenic vegetables and use of DNA in forensics.

  6. Ethical and legal issues arising from complex genetic disorders. DOE final report

    Energy Technology Data Exchange (ETDEWEB)

    Andrews, Lori

    2002-10-09

    The project analyzed the challenges raised by complex genetic disorders in genetic counselling, for clinical practice, for public health, for quality assurance, and for protection against discrimination. The research found that, in some settings, solutions created in the context of single gene disorders are more difficult to apply to complex disorders. In other settings, the single gene solutions actually backfired and created additional problems when applied to complex genetic disorders. The literature of five common, complex genetic disorders--Alzheimer's, asthma, coronary heart disease, diabetes, and psychiatric illnesses--was evaluated in depth.

  7. Multiple-Trait Genomic Selection Methods Increase Genetic Value Prediction Accuracy

    Science.gov (United States)

    Jia, Yi; Jannink, Jean-Luc

    2012-01-01

    Genetic correlations between quantitative traits measured in many breeding programs are pervasive. These correlations indicate that measurements of one trait carry information on other traits. Current single-trait (univariate) genomic selection does not take advantage of this information. Multivariate genomic selection on multiple traits could accomplish this but has been little explored and tested in practical breeding programs. In this study, three multivariate linear models (i.e., GBLUP, BayesA, and BayesCπ) were presented and compared to univariate models using simulated and real quantitative traits controlled by different genetic architectures. We also extended BayesA with fixed hyperparameters to a full hierarchical model that estimated hyperparameters and BayesCπ to impute missing phenotypes. We found that optimal marker-effect variance priors depended on the genetic architecture of the trait so that estimating them was beneficial. We showed that the prediction accuracy for a low-heritability trait could be significantly increased by multivariate genomic selection when a correlated high-heritability trait was available. Further, multiple-trait genomic selection had higher prediction accuracy than single-trait genomic selection when phenotypes are not available on all individuals and traits. Additional factors affecting the performance of multiple-trait genomic selection were explored. PMID:23086217

  8. Application of multi-objective optimization based on genetic algorithm for sustainable strategic supplier selection under fuzzy environment

    Directory of Open Access Journals (Sweden)

    Muhammad Hashim

    2017-05-01

    Full Text Available Purpose:  The incorporation of environmental objective into the conventional supplier selection practices is crucial for corporations seeking to promote green supply chain management (GSCM. Challenges and risks associated with green supplier selection have been broadly recognized by procurement and supplier management professionals. This paper aims to solve a Tetra “S” (SSSS problem based on a fuzzy multi-objective optimization with genetic algorithm in a holistic supply chain environment. In this empirical study, a mathematical model with fuzzy coefficients is considered for sustainable strategic supplier selection (SSSS problem and a corresponding model is developed to tackle this problem. Design/methodology/approach: Sustainable strategic supplier selection (SSSS decisions are typically multi-objectives in nature and it is an important part of green production and supply chain management for many firms. The proposed uncertain model is transferred into deterministic model by applying the expected value mesurement (EVM and genetic algorithm with weighted sum approach for solving the multi-objective problem. This research focus on a multi-objective optimization model for minimizing lean cost, maximizing sustainable service and greener product quality level. Finally, a mathematical case of textile sector is presented to exemplify the effectiveness of the proposed model with a sensitivity analysis. Findings: This study makes a certain contribution by introducing the Tetra ‘S’ concept in both the theoretical and practical research related to multi-objective optimization as well as in the study of sustainable strategic supplier selection (SSSS under uncertain environment. Our results suggest that decision makers tend to select strategic supplier first then enhance the sustainability. Research limitations/implications: Although the fuzzy expected value model (EVM with fuzzy coefficients constructed in present research should be helpful for

  9. Application of multi-objective optimization based on genetic algorithm for sustainable strategic supplier selection under fuzzy environment

    Energy Technology Data Exchange (ETDEWEB)

    Hashim, M.; Nazam, M.; Yao, L.; Baig, S.A.; Abrar, M.; Zia-ur-Rehman, M.

    2017-07-01

    The incorporation of environmental objective into the conventional supplier selection practices is crucial for corporations seeking to promote green supply chain management (GSCM). Challenges and risks associated with green supplier selection have been broadly recognized by procurement and supplier management professionals. This paper aims to solve a Tetra “S” (SSSS) problem based on a fuzzy multi-objective optimization with genetic algorithm in a holistic supply chain environment. In this empirical study, a mathematical model with fuzzy coefficients is considered for sustainable strategic supplier selection (SSSS) problem and a corresponding model is developed to tackle this problem. Design/methodology/approach: Sustainable strategic supplier selection (SSSS) decisions are typically multi-objectives in nature and it is an important part of green production and supply chain management for many firms. The proposed uncertain model is transferred into deterministic model by applying the expected value mesurement (EVM) and genetic algorithm with weighted sum approach for solving the multi-objective problem. This research focus on a multi-objective optimization model for minimizing lean cost, maximizing sustainable service and greener product quality level. Finally, a mathematical case of textile sector is presented to exemplify the effectiveness of the proposed model with a sensitivity analysis. Findings: This study makes a certain contribution by introducing the Tetra ‘S’ concept in both the theoretical and practical research related to multi-objective optimization as well as in the study of sustainable strategic supplier selection (SSSS) under uncertain environment. Our results suggest that decision makers tend to select strategic supplier first then enhance the sustainability. Research limitations/implications: Although the fuzzy expected value model (EVM) with fuzzy coefficients constructed in present research should be helpful for solving real world

  10. Application of multi-objective optimization based on genetic algorithm for sustainable strategic supplier selection under fuzzy environment

    International Nuclear Information System (INIS)

    Hashim, M.; Nazam, M.; Yao, L.; Baig, S.A.; Abrar, M.; Zia-ur-Rehman, M.

    2017-01-01

    The incorporation of environmental objective into the conventional supplier selection practices is crucial for corporations seeking to promote green supply chain management (GSCM). Challenges and risks associated with green supplier selection have been broadly recognized by procurement and supplier management professionals. This paper aims to solve a Tetra “S” (SSSS) problem based on a fuzzy multi-objective optimization with genetic algorithm in a holistic supply chain environment. In this empirical study, a mathematical model with fuzzy coefficients is considered for sustainable strategic supplier selection (SSSS) problem and a corresponding model is developed to tackle this problem. Design/methodology/approach: Sustainable strategic supplier selection (SSSS) decisions are typically multi-objectives in nature and it is an important part of green production and supply chain management for many firms. The proposed uncertain model is transferred into deterministic model by applying the expected value mesurement (EVM) and genetic algorithm with weighted sum approach for solving the multi-objective problem. This research focus on a multi-objective optimization model for minimizing lean cost, maximizing sustainable service and greener product quality level. Finally, a mathematical case of textile sector is presented to exemplify the effectiveness of the proposed model with a sensitivity analysis. Findings: This study makes a certain contribution by introducing the Tetra ‘S’ concept in both the theoretical and practical research related to multi-objective optimization as well as in the study of sustainable strategic supplier selection (SSSS) under uncertain environment. Our results suggest that decision makers tend to select strategic supplier first then enhance the sustainability. Research limitations/implications: Although the fuzzy expected value model (EVM) with fuzzy coefficients constructed in present research should be helpful for solving real world

  11. Studying the Genetics of Behavior and Evolution by Adaptation and Natural Selection.

    Science.gov (United States)

    Silverman, Jules

    1998-01-01

    Provides an exercise designed to give students an appreciation for the genetic basis of behavior. Employs the phenomenon of glucose aversion as an example of evolution by mutation and accelerated natural selection, thereby revealing one of the ways in which organisms adapt to human interference. (DDR)

  12. Genetic trends of selection for pelt traits in Karakul sheep I. Direct ...

    African Journals Online (AJOL)

    selection based on traits measured subjectively in Merino sheep was questioned by Laubser (1961), Roux (1961) ... ment, hair quality, hair thickness, hair length, lustre, pattern and hair stiffness, data of the control flock were .... type flock from a predominantly pipe curl type flock. Differences in genetic response are also a ...

  13. Genetically heterogeneous and selected lines of rats: behavioral and reproductive comparison.

    Science.gov (United States)

    Satinder, K P

    1980-03-01

    Avoidance learning, open-field, and reproductive behaviors of a genetically heterogeneous stock (derived from a four-way cross of selected lines) were compared with the corresponding behaviors of the parental lines. The heterogeneous stock showed heterosis on the body development, fertility rate, litter size at birth and at weaning, and directional dominance on the avoidance learning and open-field measures.

  14. Genetic Counseling Supervisors' Self-Efficacy for Select Clinical Supervision Competencies.

    Science.gov (United States)

    Finley, Sabra Ledare; Veach, Pat McCarthy; MacFarlane, Ian M; LeRoy, Bonnie S; Callanan, Nancy

    2016-04-01

    Supervision is a primary instructional vehicle for genetic counseling student clinical training. Approximately two-thirds of genetic counselors report teaching and education roles, which include supervisory roles. Recently, Eubanks Higgins and colleagues published the first comprehensive list of empirically-derived genetic counseling supervisor competencies. Studies have yet to evaluate whether supervisors possess these competencies and whether their competencies differ as a function of experience. This study investigated three research questions: (1) What are genetic counselor supervisors' perceptions of their capabilities (self-efficacy) for a select group of supervisor competencies?, (2) Are there differences in self-efficacy as a function of their supervision experience or their genetic counseling experience, and 3) What training methods do they use and prefer to develop supervision skills? One-hundred thirty-one genetic counselor supervisors completed an anonymous online survey assessing demographics, self-efficacy (self-perceived capability) for 12 goal setting and 16 feedback competencies (Scale: 0-100), competencies that are personally challenging, and supervision training experiences and preferences (open-ended). A MANOVA revealed significant positive effects of supervision experience but not genetic counseling experience on participants' self-efficacy. Although mean self-efficacy ratings were high (>83.7), participant comments revealed several challenging competencies (e.g., incorporating student's report of feedback from previous supervisors into goal setting, and providing feedback about student behavior rather than personal traits). Commonly preferred supervision training methods included consultation with colleagues, peer discussion, and workshops/seminars.

  15. Parametric and nonparametric statistical methods for genomic selection of traits with additive and epistatic genetic architectures.

    Science.gov (United States)

    Howard, Réka; Carriquiry, Alicia L; Beavis, William D

    2014-04-11

    Parametric and nonparametric methods have been developed for purposes of predicting phenotypes. These methods are based on retrospective analyses of empirical data consisting of genotypic and phenotypic scores. Recent reports have indicated that parametric methods are unable to predict phenotypes of traits with known epistatic genetic architectures. Herein, we review parametric methods including least squares regression, ridge regression, Bayesian ridge regression, least absolute shrinkage and selection operator (LASSO), Bayesian LASSO, best linear unbiased prediction (BLUP), Bayes A, Bayes B, Bayes C, and Bayes Cπ. We also review nonparametric methods including Nadaraya-Watson estimator, reproducing kernel Hilbert space, support vector machine regression, and neural networks. We assess the relative merits of these 14 methods in terms of accuracy and mean squared error (MSE) using simulated genetic architectures consisting of completely additive or two-way epistatic interactions in an F2 population derived from crosses of inbred lines. Each simulated genetic architecture explained either 30% or 70% of the phenotypic variability. The greatest impact on estimates of accuracy and MSE was due to genetic architecture. Parametric methods were unable to predict phenotypic values when the underlying genetic architecture was based entirely on epistasis. Parametric methods were slightly better than nonparametric methods for additive genetic architectures. Distinctions among parametric methods for additive genetic architectures were incremental. Heritability, i.e., proportion of phenotypic variability, had the second greatest impact on estimates of accuracy and MSE. Copyright © 2014 Howard et al.

  16. Helping Couples Fulfill the "Highest of Life's Goals": Mate Selection, Marriage Counselling, and Genetic Counseling in United States.

    Science.gov (United States)

    Stillwell, Devon

    2016-02-01

    This article traces the history of modern genetic counseling to mate selection and marriage counselling practices of the early-20th century. Mate selection revolved around a belief that human heredity could be improved and genetic diseases eradicated through better breeding. Marriage counselling, though interested in reproduction, was also concerned with the emotional and psychological well-being of couples. These two practices coalesced most obviously in the work of well-known geneticist Sheldon Reed. Even as marriage and genetic counselling diverged in the post-WWII period, vestiges of these practices remain in contemporary counseling experiences with family planning and genetic screening programs. Emphasizing points of continuity between "positive" eugenic ideologies and modern genetic practices elaborates the diverse origins of genetic counseling. It also exposes how genetic counselors have become involved in genetic enterprises beyond standard clinical settings, and prods at key issues in the interaction between genetic science and social values.

  17. BREEDING AND GENETICS SYMPOSIUM: Climate change and selective breeding in aquaculture.

    Science.gov (United States)

    Sae-Lim, P; Kause, A; Mulder, H A; Olesen, I

    2017-04-01

    Aquaculture is the fastest growing food production sector and it contributes significantly to global food security. Based on Food and Agriculture Organization (FAO) of the United Nations, aquaculture production must increase significantly to meet the future global demand for aquatic foods in 2050. According to Intergovernmental Panel on Climate Change (IPCC) and FAO, climate change may result in global warming, sea level rise, changes of ocean productivity, freshwater shortage, and more frequent extreme climate events. Consequently, climate change may affect aquaculture to various extents depending on climatic zones, geographical areas, rearing systems, and species farmed. There are 2 major challenges for aquaculture caused by climate change. First, the current fish, adapted to the prevailing environmental conditions, may be suboptimal under future conditions. Fish species are often poikilothermic and, therefore, may be particularly vulnerable to temperature changes. This will make low sensitivity to temperature more important for fish than for livestock and other terrestrial species. Second, climate change may facilitate outbreaks of existing and new pathogens or parasites. To cope with the challenges above, 3 major adaptive strategies are identified. First, general 'robustness' will become a key trait in aquaculture, whereby fish will be less vulnerable to current and new diseases while at the same time thriving in a wider range of temperatures. Second, aquaculture activities, such as input power, transport, and feed production contribute to greenhouse gas emissions. Selection for feed efficiency as well as defining a breeding goal that minimizes greenhouse gas emissions will reduce impacts of aquaculture on climate change. Finally, the limited adoption of breeding programs in aquaculture is a major concern. This implies inefficient use of resources for feed, water, and land. Consequently, the carbon footprint per kg fish produced is greater than when fish from

  18. Hydrogen selective membrane for the natural gas system. Development of CO{sub 2}-selective biogas membrane. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Vestboe, A.P.

    2012-02-15

    The project started as a literature study and technology development project for a hydrogen selective membrane for the natural gas system. The introduction of hydrogen (for example produced from wind turbines by surplus electricity) in the gas system makes it possible to store energy which can be selectively used with high energy conversion in fuel cells directly located at the end users. In order to make this possible, it is necessary to have a separating unit that can selectively remove hydrogen from the gas mixture and deliver it as fuel to the electrical generator (a fuel cell). In the project, several existing technologies were evaluated with regard to the application in view. It was concluded that while other technologies are ripe, they are costly in energy and unsuitable for the relatively low capacity application that are in question close to the end users. Membrane technology was evaluated to be the most suitable, although the technology is still under development in many cases. In the project it was found that metallic membranes in the form of palladium coated stainless discs would answer the needs for the high purity needed. Laboratory development yielded discs that could separate hydrogen from natural gas, however, the flux was low compared to the needs of the application. It was found that at least 2 bar pressure difference of hydrogen would be needed to get a high enough flux. The way to achieve this pressure would necessitate a compressor which would consume an energy amount high enough to invalidate the concept. When concluding on the results and the study it was found that the direction of the project could be changed towards developing CO{sub 2}-selective membranes with the goal of developing membrane technology that could upgrade biogas by removing CO{sub 2}. The laboratory equipment and setup that were developed in the first part of the project could be used directly in this second part of the project. In this second part of the project it was

  19. Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes. Final Report

    International Nuclear Information System (INIS)

    Lidstrom, Mary E.

    2003-01-01

    Aqueous mixed low level wastes (MLLW) containing radionuclides, solvents, and/or heavy metals represent a serious current and future problem for DOE environmental management and cleanup. In order to provide low-cost treatment alternatives under mild conditions for such contained wastes, we have proposed to use the radiation-resistant bacterium, Deinococcus radiodurans. This project has focused on developing D. radiodurans strains for dual purpose processes: cometabolic treatment of haloorganics and other solvents and removal of heavy metals from waste streams in an above-ground reactor system. The characteristics of effective treatment strains that must be attained are: (a) high biodegradative and metal binding activity; (b) stable treatment characteristics in the absence of selection and in the presence of physiological stress; (c) survival and activity under harsh chemical conditions, including radiation. The result of this project has been a suite of strains with high biodegradative capabilities that are candidates for pilot stage treatment systems. In addition, we have determined how to create conditions to precipitate heavy metals on the surface of the bacterium, as the first step towards creating dual-use treatment strains for contained mixed wastes of importance to the DOE. Finally, we have analyzed stress response in this bacterium, to create the foundation for developing treatment processes that maximize degradation while optimizing survival under high stress conditions

  20. Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes--Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Mary E. Lidstrom

    2003-12-26

    Aqueous mixed low level wastes (MLLW) containing radionuclides, solvents, and/or heavy metals represent a serious current and future problem for DOE environmental management and cleanup. In order to provide low-cost treatment alternatives under mild conditions for such contained wastes, we have proposed to use the radiation-resistant bacterium, Deinococcus radiodurans. This project has focused on developing D. radiodurans strains for dual purpose processes: cometabolic treatment of haloorganics and other solvents and removal of heavy metals from waste streams in an above-ground reactor system. The characteristics of effective treatment strains that must be attained are: (a) high biodegradative and metal binding activity; (b) stable treatment characteristics in the absence of selection and in the presence of physiological stress; (c) survival and activity under harsh chemical conditions, including radiation. The result of this project has been a suite of strains with high biodegradative capabilities that are candidates for pilot stage treatment systems. In addition, we have determined how to create conditions to precipitate heavy metals on the surface of the bacterium, as the first step towards creating dual-use treatment strains for contained mixed wastes of importance to the DOE. Finally, we have analyzed stress response in this bacterium, to create the foundation for developing treatment processes that maximize degradation while optimizing survival under high stress conditions.

  1. Broiler meat quality: effect of selection for increased carcass quality and estimates of genetic parameters.

    Science.gov (United States)

    Le Bihan-Duval, E; Millet, N; Remignon, H

    1999-06-01

    Ultimate pH (pHu), color measurements, and water holding capacity of the chicken Pectoralis major muscle were compared between birds of an experimental line selected for 13 generations for increased BW and breast meat yield and reduced abdominal fat percentage and its control line. Ultimate pH differed slightly between lines after selection, with values of 5.78 +/- 0.10 and 5.68 +/- 0.12 in the selected and control birds, respectively. Drip loss was significantly lower in the selected birds. Although selection did not modify lightness L*, it led to paler meat, as redness a* and yellowness b* were significantly lower in the selected line than in the control line. Ultimate pH of the meat was related to lightness and drip loss (with mean correlations over both lines of -0.59 and -0.40, respectively). Storage of the meat resulted in similar color variation in both lines, with a significant increase in a* and b* until 3 d postslaughter and in L* after 6 d postslaughter. Estimates of the genetic parameters of the criteria of meat quality were calculated in the selected line. The estimates suggested that there is a predominant role of genetics in the control of these traits, with heritability estimates of 0.49 +/- 0.11 for pHu, 0.75 +/- 0.08 for L*, 0.81 +/- 0.04 for a*, and 0.64 +/- 0.06 for b*. A significant negative genetic correlation (-0.65) was found between pHu and L*. The genetic correlation between a* and b* measurements was estimated at 0.72.

  2. Multilevel selection 2: Estimating the genetic parameters determing inheritance and response to selection

    NARCIS (Netherlands)

    Bijma, P.; Muir, W.M.; Ellen, E.D.; Wolf, J.B.; Arendonk, van J.A.M.

    2007-01-01

    Interactions among individuals are universal, both in animals and in plants and in natural as well as domestic populations. Understanding the consequences of these interactions for the evolution of populations by either natural or artificial selection requires knowledge of the heritable components

  3. The procedure of alternative site selection within the report of the study group on the radioactive waste final repository selection process (AKEnd)

    International Nuclear Information System (INIS)

    Nies, A.

    2005-01-01

    The study group on the selection procedures of radioactive waste final repository sites has presented the report in December 2002. The author dicusses the consequences of this report with respect to the site selection focussing on two topics: the serach for the best possible site and the prevention of prejudices

  4. Maintenance of a genetic polymorphism with disruptive natural selection in stickleback.

    Science.gov (United States)

    Marchinko, Kerry B; Matthews, Blake; Arnegard, Matthew E; Rogers, Sean M; Schluter, Dolph

    2014-06-02

    The role of natural selection in the maintenance of genetic variation in wild populations remains a major problem in evolution. The influence of disruptive natural selection on genetic variation is especially interesting because it might lead to the evolution of assortative mating or dominance [1, 2]. In theory, variation can persist at a gene under disruptive natural selection, but the process is little studied and there are few examples [3, 4]. We report a stable polymorphism in the bony armor of threespine stickleback maintained with a deficit of heterozygotes at the major underlying gene, Ectodysplasin (Eda) [5]. The deficit vanishes at the embryo life stage only to re-emerge in adults, indicating that disruptive natural selection, rather than nonrandom mating, is the cause. The mechanism enabling long-term persistence of the polymorphism is unknown, but disruptive selection is predicted to be frequency dependent, favoring homozygous genotypes when they become rare. Further research on the ecological and evolutionary processes affecting individual genes will ultimately lead to a better understanding of the causes of genetic variation in populations. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. High temperature size selective membranes. Final report, September 1992--March 1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-02-01

    Availability of a high temperature size selective membrane capable of separating hydrogen from carbon dioxide and other gases is seen as highly desirable from an economic perspective. Preparation of such a membrane is technically very difficult due to the limitations that the high temperature places on materials selection. We have prepared high temperature membranes as thin film composites of a porous Blackglas{trademark} support and a carbon molecular sieve selective film. Porous Blackglail{trademark} supports have been prepared by pyrolysis of a formed mixture of Blackglas{trademark} B-staged precursor and short Carbon fibers. Such supports have the necessary smoothness for use as a membrane support, good mechanical properties, and an appropriate pore size distribution. These supports can be made either in flat sheet form or in a tubular configuration. A carbon molecular sieve layer can be added to the support by repeated coating/pyrolysis with a dilute solution of precursor polymer. The preferred precursors are polyimide or polyamic acid. Crack formation is observed after the first pyrolyses, but these cracks are repaired during later pyrolyses. The final membrane thickness is only 2.5 {mu}m. The permeation flux of the membrane for hydrogen ranges from 8.1 x 10{sup -5} at room temperature to 3.0 x 10{sup -3} cm{sup 3} (STP) cm{sup -2} sec{sup -1} cmHg{sup -1} at 717{degrees}C, and the selectivity for hydrogen over nitrogen from 2.8 to 3.8, and a selectivity for hydrogen over carbon dioxide of 2.4. This selectivity is close to the Knudsen diffusion limit. In a companion study, unsupported carbon molecular sieve films were also prepared under pyrolysis conditions similar to those used for the supported film. Hydrogen adsorption porosimetry at 19.7{degrees}K was used to show that, under appropriate activation or pyrolysis conditions, such films can be prepared which adsorb hydrogen to a much greater extent than carbon dioxide.

  6. Procedures for selecting and buying district heating equipment. Sofia district heating. Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    The aim of this Final Report, prepared for the project `Procedures for Selecting and Buying DistRict Heating Equipment - Sofia District Heating Company`, is to establish an overview of the activities accomplished, the outputs delivered and the general experience gained as a result of the project. The main objective of the project is to enable Sofia District Heating Company to prepare specifications and tender documents, identify possible suppliers, evaluate offers, etc. in connection with purchase of district heating equipment. This objective has been reached by using rehabilitation of sub-stations as an example requested by Sofia DH. The project was originally planned to be finalized end of 1995, but due to the extensions of the scope of work, the project has been prolonged until end 1997. The following main activities were accomplished: Preparation of a detailed work plan; Collection of background information; Discussion and advice about technical specifications and tender documents for sub-station rehabilitation; Input to terms of reference for a master plan study; Input to technical specification for heat meters; Collection of ideas for topics and examples related to dissemination of information to consumers about matters related to district heating consumption. (EG)

  7. Comparison of designs for estimating genetic parameters and obtaining response to selection for social interaction traits in aquaculture

    NARCIS (Netherlands)

    Sae-Lim, P.; Bijma, P.

    2016-01-01

    Social interactions among individuals may affect individual productivity and welfare in aquaculture. Since social effects may have a genetic component, known as an indirect genetic effect (IGE), genetic selection may be a promising tool to simultaneously improve welfare and productivity in

  8. Selection Transforms the Landscape of Genetic Variation Interacting with Hsp90.

    Science.gov (United States)

    Geiler-Samerotte, Kerry A; Zhu, Yuan O; Goulet, Benjamin E; Hall, David W; Siegal, Mark L

    2016-10-01

    The protein-folding chaperone Hsp90 has been proposed to buffer the phenotypic effects of mutations. The potential for Hsp90 and other putative buffers to increase robustness to mutation has had major impact on disease models, quantitative genetics, and evolutionary theory. But Hsp90 sometimes contradicts expectations for a buffer by potentiating rapid phenotypic changes that would otherwise not occur. Here, we quantify Hsp90's ability to buffer or potentiate (i.e., diminish or enhance) the effects of genetic variation on single-cell morphological features in budding yeast. We corroborate reports that Hsp90 tends to buffer the effects of standing genetic variation in natural populations. However, we demonstrate that Hsp90 tends to have the opposite effect on genetic variation that has experienced reduced selection pressure. Specifically, Hsp90 tends to enhance, rather than diminish, the effects of spontaneous mutations and recombinations. This result implies that Hsp90 does not make phenotypes more robust to the effects of genetic perturbation. Instead, natural selection preferentially allows buffered alleles to persist and thereby creates the false impression that Hsp90 confers greater robustness.

  9. Genomic data illuminates demography, genetic structure and selection of a popular dog breed.

    Science.gov (United States)

    Wiener, Pamela; Sánchez-Molano, Enrique; Clements, Dylan N; Woolliams, John A; Haskell, Marie J; Blott, Sarah C

    2017-08-14

    Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever. We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and also with coat colour (i.e. black, yellow, brown). There was little evidence of geographical differentiation. Highly differentiated genomic regions contained genes and markers associated with skull shape, suggesting that at least some of the differentiation is related to human-imposed selection on this trait. We also found that the total length of homozygous segments (runs of homozygosity, ROHs) was highly correlated with inbreeding coefficient. This study demonstrates that high-density genomic data can be used to quantify genetic diversity and to decipher demographic and selection processes. Analysis of genetically differentiated regions in the UK Labrador Retriever population suggests the possibility of human-imposed selection on craniofacial characteristics. The high correlation between estimates of inbreeding from genomic and pedigree data for this breed demonstrates that genomic approaches can be used to quantify inbreeding levels in dogs, which will be particularly useful where pedigree information is missing.

  10. Genetics, mental illness, and complex disease: development and distribution of an interactive CD-ROM for genetic counselors. Final report for period 15 August 2000 - 31 December 2002

    Energy Technology Data Exchange (ETDEWEB)

    McInerney, Joseph D.

    2003-03-31

    "Genetics and Major Psychiatric Disorders: A Program for Genetic Counselors" provides an introduction to psychiatric genetics, with a focus on the genetics of common complex disease, for genetics professionals. The program is available as a CD-ROM and an online educational resource. The on-line version requires a direct internet connection. Each educational module begins with an interactive case study that raises significant issues addressed in each module. In addition, case studies provided throughout the educational materials support teaching of major concepts. Incorporated throughout the content are expert video clips, video clips from individuals affected by psychiatric illness, and optional "learn more" materials that offer greater depth about a particular topic. The structure of the CD-ROM permits self-navigation, but we have suggested a sequence that allows materials to build upon each other. At any point in the materials, users may pause and look up terms in the glossary or review the DSM-IV criteria for selected psychiatric disorders. A detailed site map is available for those who choose to self navigate through the content.

  11. Final report on implementation of energy conservation practices training in selected public housing developments

    Energy Technology Data Exchange (ETDEWEB)

    1991-10-01

    This report on the implementation of energy conservation practices training in selected public housing developments represents an initiative of the Research and Education Division, Office of Minority Economic Impact, US Department of Energy. The Office of Minority Economic Impact (MI) was created by Congress in 1979, within the US Department of Energy, to afford the Secretary advice on the effect policies, regulations and other actions of DOE respecting minority participation in energy programs. The Director of MI is responsible for the conduct of ongoing research into the effects, including socio-economic and environmental, of national energy programs, policies, and regulations of the Department of minorities. Public housing in the United States is dominated by minorities, public housing is a large consumer of residential energy. Consequently, this project is a logical merging of these two factors and an attempt to somehow influence energy savings through improving public housing residents` energy-consumption practices. This final report attempts to capture the results of this current demonstration, and incorporate the historical basis for today`s results by renewing the efforts that preceded the implementation of energy conservation practices training in selected public housing developments.

  12. Final report on implementation of energy conservation practices training in selected public housing developments

    Energy Technology Data Exchange (ETDEWEB)

    1991-10-01

    This report on the implementation of energy conservation practices training in selected public housing developments represents an initiative of the Research and Education Division, Office of Minority Economic Impact, US Department of Energy. The Office of Minority Economic Impact (MI) was created by Congress in 1979, within the US Department of Energy, to afford the Secretary advice on the effect policies, regulations and other actions of DOE respecting minority participation in energy programs. The Director of MI is responsible for the conduct of ongoing research into the effects, including socio-economic and environmental, of national energy programs, policies, and regulations of the Department of minorities. Public housing in the United States is dominated by minorities, public housing is a large consumer of residential energy. Consequently, this project is a logical merging of these two factors and an attempt to somehow influence energy savings through improving public housing residents' energy-consumption practices. This final report attempts to capture the results of this current demonstration, and incorporate the historical basis for today's results by renewing the efforts that preceded the implementation of energy conservation practices training in selected public housing developments.

  13. Signatures of natural selection on genetic variants affecting complex human traits.

    Science.gov (United States)

    Zhang, Ge; Muglia, Louis J; Chakraborty, Ranajit; Akey, Joshua M; Williams, Scott M

    2013-12-01

    It has recently been hypothesized that polygenic adaptation, resulting in modest allele frequency changes at many loci, could be a major mechanism behind the adaptation of complex phenotypes in human populations. Here we leverage the large number of variants that have been identified through genome-wide association (GWA) studies to comprehensively study signatures of natural selection on genetic variants associated with complex traits. Using population differentiation based methods, such as F ST and phylogenetic branch length analyses, we systematically examined nearly 1300 SNPs associated with 38 complex phenotypes. Instead of detecting selection signatures at individual variants, we aimed to identify combined evidence of natural selection by aggregating signals across many trait associated SNPs. Our results have revealed some general features of polygenic selection on complex traits associated variants. First, natural selection acting on standing variants associated with complex traits is a common phenomenon. Second, characteristics of selection for different polygenic traits vary both temporarily and geographically. Third, some studied traits (e.g. height and urate level) could have been the primary targets of selection, as indicated by the significant correlation between the effect sizes and the estimated strength of selection in the trait associated variants; however, for most traits, the allele frequency changes in trait associated variants might have been driven by the selection on other correlated phenotypes. Fourth, the changes in allele frequencies as a result of selection can be highly stochastic, such that, polygenic adaptation may accelerate differentiation in allele frequencies among populations, but generally does not produce predictable directional changes. Fifth, multiple mechanisms (pleiotropy, hitchhiking, etc) may act together to govern the changes in allele frequencies of genetic variants associated with complex traits.

  14. Short-Term Genetic Selection for Adolescent Locomotor Sensitivity to Delta9-Tetrahydrocannabinol (THC).

    Science.gov (United States)

    Kasten, Chelsea R; Zhang, Yanping; Mackie, Ken; Boehm, Stephen L

    2018-03-17

    Cannabis use is linked to positive and negative outcomes. Identifying genetic targets of susceptibility to the negative effects of cannabinoid use is of growing importance. The current study sought to complete short-term selective breeding for adolescent sensitivity and resistance to the locomotor effects of a single 10 mg/kg THC dose in the open field. Selection for THC-locomotor sensitivity was moderately heritable, with the greatest estimates of heritability seen in females from the F2 to S3 generations. Selection for locomotor sensitivity also resulted in increased anxiety-like activity in the open field. These results are the first to indicate that adolescent THC-locomotor sensitivity can be influenced via selective breeding. Development of lines with a genetic predisposition for THC-sensitivity or resistance to locomotor effects allow for investigation of risk factors, differences in consequences of THC use, identification of correlated behavioral responses, and detection of genetic targets that may contribute to heightened cannabinoid sensitivity.

  15. Genetic gain for body weight, feed conversion and carcass traits in selected broiler strains

    Directory of Open Access Journals (Sweden)

    GS Schmidt

    2006-03-01

    Full Text Available The Brazilian Swine and Poultry Research Center (Embrapa Suínos e Aves maintains a chicken breeding program for meat production since 1985. Two control lines (LLc and PPc are maintained, whereas two male lines (TT and ZZ and three female lines (PP, VV and KK have been selected. This paper reports the genetic gain after 15 generations of combined selection (mass and independent culling levels in order to develop the commercial broiler stocks Embrapa 021 and Embrapa 022. Selection pressure has been exerted on weight gain, carcass traits and fertility. In addition, female lines have also been selected for egg production, whereas males have been selected for feed efficiency since 1992. All lines have been selected for breast area instead of carcass traits since 1999. The genetic gain was estimated as the deviation between selected lines and the respective unselected lines at 42 days of age. In female lines, body weight improved 504, 548 and 587 g; average breast area increased 27.60; 16.99 and 26.43 cm²; adjusted feed conversion (42-49 d improved -1.46; -0.97 and 1.76 units, and egg production varied 6.99; 7.12 and -3.43% units for PP, VV and KK, respectively. In male lines, body weight improved 758 and 408 g; average breast area increased 31.95 and 19.38 cm², and adjusted feed conversion improved (42-49 d -0.99 and 1.26 for TT and ZZ, respectively. This breeding program has been effective to generate genetic gain and to develop two commercial products, Embrapa 021 (standard and Embrapa 022 (high yield. Nevertheless, feed efficiency is still not satisfactory.

  16. Genetic and Genomic Response to Selection for Food Consumption in Drosophila melanogaster

    Science.gov (United States)

    Garlapow, Megan E.; Everett, Logan J.; Zhou, Shanshan; Gearhart, Alexander W.; Fay, Kairsten A.; Huang, Wen; Morozova, Tatiana V.; Arya, Gunjan H.; Turlapati, Lavanya; Armour, Genevieve St.; Hussain, Yasmeen N.; McAdams, Sarah E.; Fochler, Sophia; Mackay, Trudy F. C.

    2016-01-01

    Food consumption is an essential component of animal fitness; however, excessive food intake in humans increases risk for many diseases. The roles of neuroendocrine feedback loops, food sensing modalities, and physiological state in regulating food intake are well understood, but not the genetic basis underlying variation in food consumption. Here, we applied ten generations of artificial selection for high and low food consumption in replicate populations of Drosophila melanogaster. The phenotypic response to selection was highly asymmetric, with significant responses only for increased food consumption and minimal correlated responses in body mass and composition. We assessed the molecular correlates of selection responses by DNA and RNA sequencing of the selection lines. The high and low selection lines had variants with significantly divergent allele frequencies within or near 2,081 genes and 3,526 differentially expressed genes in one or both sexes. A total of 519 genes were both genetically divergent and differentially expressed between the divergent selection lines. We performed functional analyses of the effects of RNAi suppression of gene expression and induced mutations for 27 of these candidate genes that have human orthologs and the strongest statistical support, and confirmed that 25 (93%) affected the mean and/or variance of food consumption. PMID:27704301

  17. Genetic evidence for natural selection in humans in the contemporary United States.

    Science.gov (United States)

    Beauchamp, Jonathan P

    2016-07-12

    Recent findings from molecular genetics now make it possible to test directly for natural selection by analyzing whether genetic variants associated with various phenotypes have been under selection. I leverage these findings to construct polygenic scores that use individuals' genotypes to predict their body mass index, educational attainment (EA), glucose concentration, height, schizophrenia, total cholesterol, and (in females) age at menarche. I then examine associations between these scores and fitness to test whether natural selection has been occurring. My study sample includes individuals of European ancestry born between 1931 and 1953 who participated in the Health and Retirement Study, a representative study of the US population. My results imply that natural selection has been slowly favoring lower EA in both females and males, and are suggestive that natural selection may have favored a higher age at menarche in females. For EA, my estimates imply a rate of selection of about -1.5 mo of education per generation (which pales in comparison with the increases in EA observed in contemporary times). Although they cannot be projected over more than one generation, my results provide additional evidence that humans are still evolving-albeit slowly, especially compared with the rapid changes that have occurred over the past few generations due to cultural and environmental factors.

  18. Genetic structure and evidence of putative Darwinian diversifying selection in the Potato yellow vein virus (PYVV

    Directory of Open Access Journals (Sweden)

    Giovanni Chaves-Bedoya

    2013-08-01

    Full Text Available The population structure and genetic variation of Potato yellow vein virus (PYVV were estimated by analysis of the nucleotide and deduced amino acid sequence of the coat protein of 69 isolates, reported in GenBank, from Solanum tuberosum (ST and Solanum phureja (SP hosts from different regions; predominantly Cundinamarca, Antioquia and Nariño, located in central and southwestern Colombia. Bioinformatics analysis revealed that despite the wide geographic distribution of different hosts and different collecting years, PYVV maintains a genetic similarity between 97.1 to 100.0%, indicating high spatial and temporal genetic stability of the major coat protein. No recombination events were found, but evidence was seen for the first time that this protein could be undergoing Darwinian diversifying selection

  19. Sports selection of volley-ball players: genetic criteria to define motor endowments (information 2

    Directory of Open Access Journals (Sweden)

    Alisa Ablikova

    2016-04-01

    Full Text Available Purpose: to define genetic criteria which can be used while selecting gifted volley-ball players. Material & Methods: the study involved 50 high class volley-ball players and 50 women at the age of 20–29 years old. There were used methods of theoretical analysis and general conclusion, systematic analysis, genealogic methods of genetics, methods of dermatoglyphic and serologic analyses. Results: family gift for going in for sport was detected. At was revealed that gifted volley-ball players had peculiar finger tips prints and distribution of blood groups: the system AB0 in comparison with the total population. Conclusions: the obtained quantitative characteristics of finger dermatoglyphic, some blood groups and rhesus-factor as genetic markers of motor endowments of volley-ball players are proposed.

  20. Genetic tests in work place from the preventive selection to selective prevention

    International Nuclear Information System (INIS)

    Poissonnet, C.M.; Veron, M.

    2004-01-01

    The research in this area allows to better understand the mechanisms of illness trigger, to improve the knowledge in the relation exposure-illness, to detect the risk associated to low exposure among some particularly sensitive persons and to define the validity criteria. Inevitably these researches reach to define the most vulnerable persons. This designation could be a factor favorable to the prevention and to give a better sense of responsibility. The worker, well informed, can be particularly concerned by wearing the individual protections, and the person in charge of the installation by looking to reduce exposure. It can be also deviate and corresponds to a real discrimination with rejection of sensitive persons and selection of resistant individuals with which it could be possible to work in non optimal conditions. The problem is at this level the conflicts of interest exist between these ones that dream to use this possibility wisely and that ones for which the interests are elsewhere. (N.C.)

  1. Direct benefits of genetic mosaicism and intraorganismal selection: modeling coevolution between a long-lived tree and a short-lived herbivore.

    Science.gov (United States)

    Folse, Henry J; Roughgarden, Joan

    2012-04-01

    We model direct fitness benefits of genetic mosaicism for a long-lived tree in coevolution with a short-lived herbivore to test four hypotheses: that mosaicism reduces selection on the herbivore for resistance to plant defenses; that module-level selection allows the individual tree to adapt to its herbivore; and that this benefits the tree population, increasing average tree fitness and reducing local adaptation of the herbivore. We show that: mosaicism does not sufficiently reduce selection for resistance in the herbivore to benefit the tree; that individual trees do benefit from module-level selection when somatic mutation introduces new defenses; and that mosaicism does reduce local adaptation in the herbivore, which increases average tree fitness. These results are robust to varying genetic assumptions of dominance and the somatic mutation rate, but only hold for sufficiently long-lived trees with relatively strong selection. We also show that a mixed reproductive strategy of primarily asexual reproduction interspersed with occasional sexual reproduction is effective in coevolving with the herbivore, as it maintains beneficial allele combinations. Finally, we argue that intraorganismal genetic heterogeneity need not threaten the integrity of the individual and may be adaptive when selection acts concordantly between levels. © 2011 The Author. Evolution© 2011 The Society for the Study of Evolution.

  2. Genetic drift and selection effects of modified recurrent full-sib selection programs in two F2 populations of European flint maize.

    Science.gov (United States)

    Flachenecker, C; Frisch, M; Falke, K C; Melchinger, A E

    2006-10-01

    Selection response of a modified recurrent full-sib (FS) selection scheme conducted in two European flint F(2) maize (Zea mays L.) populations was re-evaluated. Our objectives were to (1) determine the selection response for per se and testcross performance in both populations and (2) separate genetic effects due to selection from those due to random genetic drift. Modified recurrent FS selection was conducted at three locations using an effective population size N(e) = 32 and a selection rate of 25% for a selection index, based on grain yield and grain moisture. Recombination was performed according to a pseudo-factorial mating scheme. Selection response was assessed using a population diallel including the source population and advanced selection cycles, as well as testcrosses with unrelated inbred line testers and the parental F(1) generation. Selection response per cycle was significant for grain yield and grain moisture in both populations. Effects of random genetic drift caused only a small reduction in the selection response. No significant selection response was observed for testcrosses, suggesting that for heterotic traits, such as grain yield, a high frequency of favorable alleles in the elite tester masked the effects of genes segregating in the populations. We conclude that our modified recurrent FS selection is an alternative to other commonly applied intrapopulation recurrent selection schemes, and some of its features may also be useful for increasing the efficiency of interpopulation recurrent selection programs.

  3. Genetic Selection to Enhance Animal Welfare Using Meat Inspection Data from Slaughter Plants.

    Science.gov (United States)

    Mathur, Pramod K; Vogelzang, Roos; Mulder, Herman A; Knol, Egbert F

    2018-01-24

    Animal health and welfare are monitored during meat inspection in many slaughter plants around the world. Carcasses are examined by meat inspectors and remarks are made with respect to different diseases, injuries, and other abnormalities. This is a valuable data resource for disease prevention and enhancing animal welfare, but it is rarely used for this purpose. Records on carcass remarks on 140,375 finisher pigs were analyzed to investigate the possibility of genetic selection to reduce the risk of the most prevalent diseases and indicators of suboptimal animal welfare. As part of this, effects of some non-genetic factors such as differences between farms, sexes, and growth rates were also examined. The most frequent remarks were pneumonia (15.4%), joint disorders (9.8%), pleuritis (4.7%), pericarditis (2.3%), and liver lesions (2.2%). Joint disorders were more frequent in boars than in gilts. There were also significant differences between farms. Pedigree records were available for 142,324 pigs from 14 farms and were used for genetic analysis. Heritability estimates for pneumonia, pleuritis, pericarditis, liver lesions, and joint disorders were 0.10, 0.09, 0.14, 0.24, and 0.17 on the liability scale, respectively, suggesting the existence of substantial genetic variation. This was further confirmed though genome wide associations using deregressed breeding values as phenotypes. The genetic correlations between these remarks and finishing traits were small but mostly negative, suggesting the possibility of enhancing pig health and welfare simultaneously with genetic improvement in finishing traits. A selection index based on the breeding values for these traits and their economic values was developed. This index is used to enhance animal welfare in pig farms.

  4. Animal genetic resources in Brazil: result of five centuries of natural selection.

    Science.gov (United States)

    Mariante, A da S; Egito, A A

    2002-01-01

    Brazil has various species of domestic animals, which developed from breeds brought by the Portuguese settlers soon after their discovery. For five centuries, these breeds have been subjected to natural selection in specific environments. Today, they present characteristics adapted to the specific Brazilian environmental conditions. These breeds developed in Brazil are known as "Crioulo," "local," or naturalized. From the beginning of the 20th century, some exotic breeds, selected in temperate regions, have begun to be imported. Although more productive, these breeds do not have adaptive traits, such as resistance to disease and parasites found in breeds considered to be "native." Even so, little by little, they replaced the native breeds, to such an extent that the latter are in danger of extinction. In 1983, to avoid the loss of this important genetic material, the National Research Center for Genetic Resources and Biotechnology (Cenargen) of the Brazilian Agricultural Research Corporation (Embrapa) decided to include conservation of animal genetic resources in its research program Conservation and Utilization of Genetic Resources. Until this time, they were only concerned with conservation of native plants. Conservation has been carried out by various research centers of Embrapa, universities, state research corporations, and private farmers, with a single coordinator at the national level, Cenargen. Specifically, conservation is being carried out by conservation nuclei, which are specific herds in which the animals are being conserved, situated in the habitats where the animals have been subjected to natural selection. This involves storage of semen and embryos from cattle, horses, buffaloes, donkeys, goats, sheep, and pigs. The Brazilian Animal Germplasm Bank is kept at Cenargen, which is responsible for the storage of semen and embryos of various breeds of domestic animals threatened with extinction, where almost 45,000 doses of semen and more than 200

  5. Improvement in genetic characteristics and oil yield of selected soybean progenies from octuple crosses

    Directory of Open Access Journals (Sweden)

    Hamawaki Osvaldo Toshiyuki

    2000-01-01

    Full Text Available The objective of the present study was to evaluate 44 soybean octuple crosses in the F4:3[8] and F5:3[8] generations in order to select progenies superior for seed oil yield (OY and other important agronomic characteristics. Octuple crosses were hybridized in a chain mating system. In one group, crosses were carried out for three generations with the adapted x exotic parents until octuple crosses with 75% adapted genes and 25% exotic genes were obtained. In a second group, hybridization of adapted x adapted parents originated crosses with 100% adapted genes. During the growing season 1994/95, the progenies F4:3[8] were evaluated by using the augmented block design. The progenies F5:3[8] were evaluated during the growing season 1995/96 in three experiments using augmented block design without repetition. The octuple crosses gave origin to superior progenies for all the characters studied. In the C22 cross, OY values were 707 kg/ha. The estimates of heritability in relation to the crosses average resulted in the following mean, minimum and maximum values, respectively: number of days to maturity (52.35%, 3.71%, 84.23%; agronomic value (26.69%, 1.62%, 61.28% and grain yield (29.28%, 1.52%, 61.06%. The observed genetic gains for grain yield in the early, intermediate and late F5:3[8] progenies were superior to the expected genetic gains and the observed genetic gains for OY were more expressive in the early and late F5:[8] progenies. The genetic variability remaining in the selected progenies of some crosses suggests that further genetic gains for grain yield and OY might be possible with advanced selection cycles.

  6. Genetic Gain from Phenotypic and Genomic Selection for Quantitative Resistance to Stem Rust of Wheat

    Directory of Open Access Journals (Sweden)

    J. Rutkoski

    2015-07-01

    Full Text Available Stem rust of wheat ( L. caused by f. sp. Eriks. and E. Henn. is a globally important disease that can cause severe yield loss. Breeding for quantitative stem rust resistance (QSRR is important for developing cultivars with durable resistance. Genomic selection (GS could increase rates of genetic gain for quantitative traits, but few experiments comparing GS and phenotypic selection (PS have been conducted. Our objectives were to (i compare realized gain from GS based on markers only with that of PS for QSRR in spring wheat using equal selection intensities; (ii determine if gains agree with theoretical expectations; and (iii compare the impact of GS and PS on inbreeding, genetic variance, and correlated response for pseudo-black chaff (PBC, a correlated trait. Over 2 yr, two cycles of GS were performed in parallel with one cycle of PS, with each method replicated twice. For GS, markers were generated using genotyping-by-sequencing, the prediction model was initially trained using historical data, and the model was updated before the second GS cycle. Overall, GS and PS led to a 31 ± 11 and 42 ± 12% increase in QSRR and a 138 ± 22 and 180 ± 70% increase in PBC, respectively. Genetic gains were not significant but were in agreement with expectations. Per year, gains from GS and PS were equal, but GS led to significantly lower genetic variance. This shows that while GS and PS can lead to equal rates of short-term gains, GS can reduce genetic variance more rapidly. Further work to develop efficient GS implementation strategies in spring wheat is warranted.

  7. A comparison of regression methods for model selection in individual-based landscape genetic analysis.

    Science.gov (United States)

    Shirk, Andrew J; Landguth, Erin L; Cushman, Samuel A

    2018-01-01

    Anthropogenic migration barriers fragment many populations and limit the ability of species to respond to climate-induced biome shifts. Conservation actions designed to conserve habitat connectivity and mitigate barriers are needed to unite fragmented populations into larger, more viable metapopulations, and to allow species to track their climate envelope over time. Landscape genetic analysis provides an empirical means to infer landscape factors influencing gene flow and thereby inform such conservation actions. However, there are currently many methods available for model selection in landscape genetics, and considerable uncertainty as to which provide the greatest accuracy in identifying the true landscape model influencing gene flow among competing alternative hypotheses. In this study, we used population genetic simulations to evaluate the performance of seven regression-based model selection methods on a broad array of landscapes that varied by the number and type of variables contributing to resistance, the magnitude and cohesion of resistance, as well as the functional relationship between variables and resistance. We also assessed the effect of transformations designed to linearize the relationship between genetic and landscape distances. We found that linear mixed effects models had the highest accuracy in every way we evaluated model performance; however, other methods also performed well in many circumstances, particularly when landscape resistance was high and the correlation among competing hypotheses was limited. Our results provide guidance for which regression-based model selection methods provide the most accurate inferences in landscape genetic analysis and thereby best inform connectivity conservation actions. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

  8. Genetic inheritance of pulp colour and selected traits of cassava (Manihot esculenta Crantz) at early generation selection.

    Science.gov (United States)

    Nduwumuremyi, Athanase; Melis, Rob; Shanahan, Paul; Theodore, Asiimwe

    2017-12-12

    The early generation selection of cassava quantitative and qualitative traits saves breeding resources as it can shorten breeding schemes. Inheritance analysis provides important breeding information for developing new improved varieties. This study aimed at developing an F1 segregating cassava population and determining mode of gene action of pulp colour and selected traits at early generation selection (F1 seedling and clones). The 15 families exhibited significant (P < 0.05) phenotypic variation between offspring. The general combining ability (GCA) was significant for all traits except cassava brown streak disease on leaves, whereas specific combining ability (SCA) was significant for all evaluated traits. The Garukansubire and Gitamisi genotypes were the best general combiners for improving fresh storage root yield, while G1 and G2 were the best general combiners for improved carotenoid (yellow/orange pulp colour) and delayed physiological postharvest deterioration. The pulp colour had the highest GCA/SCA ratio and percent sum of squares due to GCA. The 15 F1 families exhibited essential genetic diversity for cassava improvement. The expression of most cassava traits was controlled by both additive and non-additive gene action. The study elucidated the role of dominance effects over the additive effects for the evaluated traits. However, the pulp colour was predominantly controlled by additive gene action. This implies the possibility of improving cassava through conventional breeding using recurrent selection for most traits. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  9. Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates.

    Science.gov (United States)

    Herrmann, Doris; Poncet, Bénédicte N; Manel, Stéphanie; Rioux, Delphine; Gielly, Ludovic; Taberlet, Pierre; Gugerli, Felix

    2010-04-01

    A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.

  10. Red Cell Genetic Markers in Malarial Susceptibility and Selective Advantage Hypothesis

    Directory of Open Access Journals (Sweden)

    RS Balgir

    2014-02-01

    Full Text Available Malaria is still a serious public health challenge in many parts of the world including India. Human genetic susceptibility to malaria varies from individual to individual depending upon the genetic constitution and from region to region based on geo-ecological and climatic conditions. In the present study, intravenous 334 random blood samples of unrelated adult individuals belonging to Mongoloid ethnic stock were taken after informed consent from the endemic localities of Arunachal Pradesh, Assam and Nagaland to find out the relationship between the abnormal hemoglobin and G6PD enzyme deficiency, and susceptibility to malaria. Abnormal hemoglobin E and G6PD enzyme deficiency seem to interact with malarial parasite in such a way that they probably provide decreased susceptibility or inhibitory effect or increased resistance. Genetic alterations in human genome are maintained in the specific population by natural selection to protect the host against the malarial infection. These findings are consistent with those studies which support the notion of selective genetic advantage hypothesis against the malaria infection.

  11. Genetic diversity and natural selection footprints of the glycine amidinotransferase gene in various human populations.

    Science.gov (United States)

    Khan, Asifullah; Tian, Lei; Zhang, Chao; Yuan, Kai; Xu, Shuhua

    2016-01-05

    The glycine amidinotransferase gene (GATM) plays a vital role in energy metabolism in muscle tissues and is associated with multiple clinically important phenotypes. However, the genetic diversity of the GATM gene remains poorly understood within and between human populations. Here we analyzed the 1,000 Genomes Project data through population genetics approaches and observed significant genetic diversity across the GATM gene among various continental human populations. We observed considerable variations in GATM allele frequencies and haplotype composition among different populations. Substantial genetic differences were observed between East Asian and European populations (FST = 0.56). In addition, the frequency of a distinct major GATM haplotype in these groups was congruent with population-wide diversity at this locus. Furthermore, we identified GATM as the top differentiated gene compared to the other statin drug response-associated genes. Composite multiple analyses identified signatures of positive selection at the GATM locus, which was estimated to have occurred around 850 generations ago in European populations. As GATM catalyzes the key step of creatine biosynthesis involved in energy metabolism, we speculate that the European prehistorical demographic transition from hunter-gatherer to farming cultures was the driving force of selection that fulfilled creatine-based metabolic requirement of the populations.

  12. Genetic variation and selection of MHC class I loci differ in two congeneric frogs.

    Science.gov (United States)

    Kiemnec-Tyburczy, Karen M; Tracy, Karen E; Lips, Karen R; Zamudio, Kelly R

    2018-04-01

    Major histocompatibility complex (MHC) genes encode proteins in the acquired immune response pathway that often show distinctive selection-driven patterns in wild vertebrate populations. We examined genetic variation and signatures of selection in the MHC class I alpha 1 (A1)- and alpha 2 (A2)-domain encoding exons of two frog congeners [Agalychnis callidryas (n = 20) and A. lemur (n = 20)] from a single locality in Panama. We also investigated how historical demographic processes may have impacted MHC genetic diversity by analyzing a neutral mitochondrial marker. We found that both MHC domains were highly variable in both species, with both species likely expressing three loci. Our analyses revealed different signatures of selection between the two species, most notably that the A. callidryas A2 domain had experienced positive selection while the A2 domain of A. lemur had not. Diversifying selection acted on the same number of A1 and A2 allelic lineages, but on a higher percentage of A1 sites compared to A2 sites. Neutrality tests of mitochondrial haplotypes predominately indicated that the two species were at genetic equilibrium when the samples were collected. In addition, two historical tests of demography indicated both species have had relatively stable population sizes over the past 100,000 years; thus large population size changes are unlikely to have greatly influenced MHC diversity in either species during this time period. In conclusion, our results suggest that the impact of selection on MHC diversity varied between these two closely related species, likely due to a combination of distinct ecological conditions and past pathogenic pressures.

  13. Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.).

    Science.gov (United States)

    Sim, S-C; Robbins, M D; Van Deynze, A; Michel, A P; Francis, D M

    2011-06-01

    Tomato (Solanum lycopersicum L.) has undergone intensive selection during and following domestication. We investigated population structure and genetic differentiation within a collection of 70 tomato lines representing contemporary (processing and fresh-market) varieties, vintage varieties and landraces. The model-based Bayesian clustering software, STRUCTURE, was used to detect subpopulations. Six independent analyses were conducted using all marker data (173 markers) and five subsets of markers based on marker type (single-nucleotide polymorphisms, simple sequence repeats and insertion/deletions) and location (exon and intron sequences) within genes. All of these analyses consistently separated four groups predefined by market niche and age into distinct subpopulations. Furthermore, we detected at least two subpopulations within the processing varieties. These subpopulations correspond to historical patterns of breeding conducted for specific production environments. We found no subpopulation within fresh-market varieties, vintage varieties and landraces when using all marker data. High levels of admixture were shown in several varieties representing a transition in the demarcation between processing and fresh-market breeding. The genetic clustering detected by using the STRUCTURE software was confirmed by two statistics, pairwise F(st) (θ) and Nei's standard genetic distance. We also identified a total of 19 loci under positive selection between processing, fresh-market and vintage germplasm by using an F(st)-outlier method based on the deviation from the expected distribution of F(st) and heterozygosity. The markers and genome locations we identified are consistent with known patterns of selection and linkage to traits that differentiate the market classes. These results demonstrate how human selection through breeding has shaped genetic variation within cultivated tomato.

  14. Elucidating the role of genetic drift and natural selection in cork oak differentiation regarding drought tolerance.

    Science.gov (United States)

    Ramírez-Valiente, J A; Lorenzo, Z; Soto, A; Valladares, F; Gil, L; Aranda, I

    2009-09-01

    Drought is the main selection agent in Mediterranean ecosystems and it has been suggested as an important evolutionary force responsible for population diversification in these types of environments. However, population divergence in quantitative traits can be driven by either natural selection, genetic drift or both. To investigate the roles of these forces on among-population divergence in ecophysiological traits related to drought tolerance (carbon isotope discrimination, specific leaf area, leaf size and leaf nitrogen content), we compared molecular and quantitative genetic differentiation in a common garden experiment including thirteen cork oak (Quercus suber L.) populations across a gradient of rainfall and temperature. Population differentiation for height, specific leaf area, leaf size and nitrogen leaf content measured during a dry year far exceeded the molecular differentiation measured by six nuclear microsatellites. Populations from dry-cool sites showed the lowest nitrogen leaf content and the smallest and thickest leaves contrasting with those from humid-warm sites. These results suggest (i) these traits are subjected to divergence selection and (ii) the genetic differences among populations are partly due to climate adaptation. By contrast, the low among-population divergence found in basal diameter, annual growth and carbon isotopic discrimination (a surrogate for water use efficiency) suggests low or no divergence selection for these traits. Among-population differentiation for neutral markers was not a good predictor for differentiation regarding the quantitative traits studied here, except for leaf size. The correlation observed between the genetic differentiation for leaf size and that for molecular markers was exclusively due to the association between leaf size and the microsatellite QpZAG46, which suggests a possible linkage between QpZAG46 and genes encoding for leaf size.

  15. Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups

    OpenAIRE

    Cesconeto, Robson Jose; Joost, Stéphane; McManus, Concepta Margaret; Paiva, Samuel Rezende; Cobuci, Jaime Araujo; Braccini, Jose

    2017-01-01

    Abstract Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as FST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in b...

  16. Selective harmonic elimination of new family of multilevel inverters using genetic algorithms

    International Nuclear Information System (INIS)

    El-Naggar, Khaled; Abdelhamid, Tamer H.

    2008-01-01

    Selective harmonic elimination has been a widely researched alternative to traditional PWM techniques. This paper presents the selective harmonic elimination of a new family of multilevel inverters using genetic algorithms. The new topology has the advantage of a reduced number of devices compared to traditional configurations and can be extended to any number of levels. The presented system reduces both the implementation complexity and the computational time. The GA technique finds the optimal solution set of switching angles, if it exists, for each required harmonic profile. Both simulation results and experimental verification of the proposed inverter topology for different numbers of levels and different harmonic profiles are presented

  17. Information and (co)variances in discrete evolutionary genetics involving solely selection

    International Nuclear Information System (INIS)

    Huillet, Thierry E

    2009-01-01

    The purpose of this paper is twofold. First, we introduce the general formalism of evolutionary genetics dynamics involving fitnesses, under both the deterministic and stochastic setups, and chiefly in discrete time. In the process, we particularize it to a one-parameter model where only a selection parameter is unknown. Then and in a parallel manner, we discuss the problems of estimation of the selection parameter on the basis of a single-generation frequency distribution shift under both deterministic and stochastic evolutionary dynamics. In the stochastics, we consider both the celebrated Wright–Fisher and Moran models

  18. Comparison of Naive Bayes and Decision Tree on Feature Selection Using Genetic Algorithm for Classification Problem

    Science.gov (United States)

    Rahmadani, S.; Dongoran, A.; Zarlis, M.; Zakarias

    2018-03-01

    This paper discusses the problem of feature selection using genetic algorithms on a dataset for classification problems. The classification model used is the decicion tree (DT), and Naive Bayes. In this paper we will discuss how the Naive Bayes and Decision Tree models to overcome the classification problem in the dataset, where the dataset feature is selectively selected using GA. Then both models compared their performance, whether there is an increase in accuracy or not. From the results obtained shows an increase in accuracy if the feature selection using GA. The proposed model is referred to as GADT (GA-Decision Tree) and GANB (GA-Naive Bayes). The data sets tested in this paper are taken from the UCI Machine Learning repository.

  19. Genetic transformation of Nannochloropsis oculata with a bacterial phleomycin resistance gene as dominant selective marker

    Science.gov (United States)

    Ma, Xiaolei; Pan, Kehou; Zhang, Lin; Zhu, Baohua; Yang, Guanpin; Zhang, Xiangyang

    2016-04-01

    The gene ble from Streptoalloteichus hindustanus is widely used as a selective antibiotic marker. It can control the phleomycin resistance, and significantly increase the tolerance of hosts to zeocin. The unicellular marine microalga Nannochloropsis oculata is extremely sensitive to zeocin. We selected ble as the selective marker for the genetic transformation of N. oculata. After the algal cells at a density of 2×107 cells mL-1 was digested with 4% hemicellulase and 2% driselase for 1 h, the protoplasts accounted for 90% of the total. The ble was placed at the downstream of promoter HSP70A-RUBS2 isolated from Chlamydomonas reinhardtii, yielding a recombinant expression construct pMS188. The construct was transferred into the protoplasts through electroporation (1 kV, 15 μS). The transformed protoplasts were cultured in fresh f/2 liquid medium, and selected on solid f/2 medium supplemented with 500 ng mL-1 zeocin. The PCR result proved that ble existed in the transformants. Three transformants had been cultured for at least 5 generations without losing ble. Southern blotting analysis showed that the ble has been integrated into the genome of N. oculata. The ble will serve as a new dominant selective marker in genetic engineering N. oculata.

  20. Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes.

    Science.gov (United States)

    Sutton, Jolene T; Nakagawa, Shinichi; Robertson, Bruce C; Jamieson, Ian G

    2011-11-01

    The major histocompatibility complex (MHC) forms an integral component of the vertebrate immune response and, due to strong selection pressures, is one of the most polymorphic regions of the entire genome. Despite over 15 years of research, empirical studies offer highly contradictory explanations of the relative roles of different evolutionary forces, selection and genetic drift, acting on MHC genes during population bottlenecks. Here, we take a meta-analytical approach to quantify the results of studies into the effects of bottlenecks on MHC polymorphism. We show that the consequences of selection acting on MHC loci prior to a bottleneck event, combined with drift during the bottleneck, will result in overall loss of MHC polymorphism that is ∼15% greater than loss of neutral genetic diversity. These results are counter to general expectations that selection should maintain MHC polymorphism, but do agree with the results of recent simulation models and at least two empirical studies. Notably, our results suggest that negative frequency-dependent selection could be more important than overdominance for maintaining high MHC polymorphism in pre-bottlenecked populations. © 2011 Blackwell Publishing Ltd.

  1. Is preimplantation genetic diagnosis the ideal embryo selection method in aneuploidy screening?

    Science.gov (United States)

    Sahin, Levent; Bozkurt, Murat; Sahin, Hilal; Gürel, Aykut; Yumru, Ayse Ender

    2014-10-01

    To select cytogenetically normal embryos, preimplantation genetic diagnosis (PGD) aneuploidy screening (AS) is used in numerous centers around the world. Chromosomal abnormalities lead to developmental problems, implantation failure, and early abortion of embryos. The usefulness of PGD in identifying single-gene diseases, human leukocyte antigen typing, X-linked diseases, and specific genetic diseases is well-known. In this review, preimplantation embryo genetics, PGD research studies, and the European Society of Human Reproduction and Embryology PGD Consortium studies and reports are examined. In addition, criteria for embryo selection, technical aspects of PGD-AS, and potential noninvasive embryo selection methods are described. Indications for PGD and possible causes of discordant PGD results between the centers are discussed. The limitations of fluorescence in situ hybridization, and the advantages of the array comparative genomic hybridization are included in this review. Although PGD-AS for patients of advanced maternal age has been shown to improve in vitro fertilization outcomes in some studies, to our knowledge, there is not sufficient evidence to use advanced maternal age as the sole indication for PGD-AS. PGD-AS might be harmful and may not increase the success rates of in vitro fertilization. At the same time PGD, is not recommended for recurrent implantation failure and unexplained recurrent pregnancy loss. Copyright © 2014. Published by Elsevier Taiwan.

  2. Sardinians genetic background explained by runs of homozygosity and genomic regions under positive selection.

    Science.gov (United States)

    Di Gaetano, Cornelia; Fiorito, Giovanni; Ortu, Maria Francesca; Rosa, Fabio; Guarrera, Simonetta; Pardini, Barbara; Cusi, Daniele; Frau, Francesca; Barlassina, Cristina; Troffa, Chiara; Argiolas, Giuseppe; Zaninello, Roberta; Fresu, Giovanni; Glorioso, Nicola; Piazza, Alberto; Matullo, Giuseppe

    2014-01-01

    The peculiar position of Sardinia in the Mediterranean sea has rendered its population an interesting biogeographical isolate. The aim of this study was to investigate the genetic population structure, as well as to estimate Runs of Homozygosity and regions under positive selection, using about 1.2 million single nucleotide polymorphisms genotyped in 1077 Sardinian individuals. Using four different methods--fixation index, inflation factor, principal component analysis and ancestry estimation--we were able to highlight, as expected for a genetic isolate, the high internal homogeneity of the island. Sardinians showed a higher percentage of genome covered by RoHs>0.5 Mb (F(RoH%0.5)) when compared to peninsular Italians, with the only exception of the area surrounding Alghero. We furthermore identified 9 genomic regions showing signs of positive selection and, we re-captured many previously inferred signals. Other regions harbor novel candidate genes for positive selection, like TMEM252, or regions containing long non coding RNA. With the present study we confirmed the high genetic homogeneity of Sardinia that may be explained by the shared ancestry combined with the action of evolutionary forces.

  3. Is preimplantation genetic diagnosis the ideal embryo selection method in aneuploidy screening?

    Directory of Open Access Journals (Sweden)

    Levent Sahin

    2014-10-01

    Full Text Available To select cytogenetically normal embryos, preimplantation genetic diagnosis (PGD aneuploidy screening (AS is used in numerous centers around the world. Chromosomal abnormalities lead to developmental problems, implantation failure, and early abortion of embryos. The usefulness of PGD in identifying single-gene diseases, human leukocyte antigen typing, X-linked diseases, and specific genetic diseases is well-known. In this review, preimplantation embryo genetics, PGD research studies, and the European Society of Human Reproduction and Embryology PGD Consortium studies and reports are examined. In addition, criteria for embryo selection, technical aspects of PGD-AS, and potential noninvasive embryo selection methods are described. Indications for PGD and possible causes of discordant PGD results between the centers are discussed. The limitations of fluorescence in situ hybridization, and the advantages of the array comparative genomic hybridization are included in this review. Although PGD-AS for patients of advanced maternal age has been shown to improve in vitro fertilization outcomes in some studies, to our knowledge, there is not sufficient evidence to use advanced maternal age as the sole indication for PGD-AS. PGD-AS might be harmful and may not increase the success rates of in vitro fertilization. At the same time PGD, is not recommended for recurrent implantation failure and unexplained recurrent pregnancy loss.

  4. Population genetics inference for longitudinally-sampled mutants under strong selection.

    Science.gov (United States)

    Lacerda, Miguel; Seoighe, Cathal

    2014-11-01

    Longitudinal allele frequency data are becoming increasingly prevalent. Such samples permit statistical inference of the population genetics parameters that influence the fate of mutant variants. To infer these parameters by maximum likelihood, the mutant frequency is often assumed to evolve according to the Wright-Fisher model. For computational reasons, this discrete model is commonly approximated by a diffusion process that requires the assumption that the forces of natural selection and mutation are weak. This assumption is not always appropriate. For example, mutations that impart drug resistance in pathogens may evolve under strong selective pressure. Here, we present an alternative approximation to the mutant-frequency distribution that does not make any assumptions about the magnitude of selection or mutation and is much more computationally efficient than the standard diffusion approximation. Simulation studies are used to compare the performance of our method to that of the Wright-Fisher and Gaussian diffusion approximations. For large populations, our method is found to provide a much better approximation to the mutant-frequency distribution when selection is strong, while all three methods perform comparably when selection is weak. Importantly, maximum-likelihood estimates of the selection coefficient are severely attenuated when selection is strong under the two diffusion models, but not when our method is used. This is further demonstrated with an application to mutant-frequency data from an experimental study of bacteriophage evolution. We therefore recommend our method for estimating the selection coefficient when the effective population size is too large to utilize the discrete Wright-Fisher model. Copyright © 2014 by the Genetics Society of America.

  5. A paradox of genetic variance in epigamic traits: beyond „good genes” view of sexual selection

    OpenAIRE

    Radwan, Jacek; Engqvist, Leif Martin; Reinhold, Klaus

    2016-01-01

    Maintenance of genetic variance in secondary sexual traits, including bizarre ornaments and elaborated courtship displays, is a central problem of sexual selection theory. Despite theoretical arguments predicting that strong sexual selection leads to a depletion of additive genetic variance, traits associated with mating success show relatively high heritability. Here we argue that because of trade-offs associated with the production of costly epigamic traits, sexual selection is likely to le...

  6. A Regionalization Approach to select the final watershed parameter set among the Pareto solutions

    Science.gov (United States)

    Park, G. H.; Micheletty, P. D.; Carney, S.; Quebbeman, J.; Day, G. N.

    2017-12-01

    The calibration of hydrological models often results in model parameters that are inconsistent with those from neighboring basins. Considering that physical similarity exists within neighboring basins some of the physically related parameters should be consistent among them. Traditional manual calibration techniques require an iterative process to make the parameters consistent, which takes additional effort in model calibration. We developed a multi-objective optimization procedure to calibrate the National Weather Service (NWS) Research Distributed Hydrological Model (RDHM), using the Nondominant Sorting Genetic Algorithm (NSGA-II) with expert knowledge of the model parameter interrelationships one objective function. The multi-objective algorithm enables us to obtain diverse parameter sets that are equally acceptable with respect to the objective functions and to choose one from the pool of the parameter sets during a subsequent regionalization step. Although all Pareto solutions are non-inferior, we exclude some of the parameter sets that show extremely values for any of the objective functions to expedite the selection process. We use an apriori model parameter set derived from the physical properties of the watershed (Koren et al., 2000) to assess the similarity for a given parameter across basins. Each parameter is assigned a weight based on its assumed similarity, such that parameters that are similar across basins are given higher weights. The parameter weights are useful to compute a closeness measure between Pareto sets of nearby basins. The regionalization approach chooses the Pareto parameter sets that minimize the closeness measure of the basin being regionalized. The presentation will describe the results of applying the regionalization approach to a set of pilot basins in the Upper Colorado basin as part of a NASA-funded project.

  7. The joint effects of background selection and genetic recombination on local gene genealogies.

    Science.gov (United States)

    Zeng, Kai; Charlesworth, Brian

    2011-09-01

    Background selection, the effects of the continual removal of deleterious mutations by natural selection on variability at linked sites, is potentially a major determinant of DNA sequence variability. However, the joint effects of background selection and genetic recombination on the shape of the neutral gene genealogy have proved hard to study analytically. The only existing formula concerns the mean coalescent time for a pair of alleles, making it difficult to assess the importance of background selection from genome-wide data on sequence polymorphism. Here we develop a structured coalescent model of background selection with recombination and implement it in a computer program that efficiently generates neutral gene genealogies for an arbitrary sample size. We check the validity of the structured coalescent model against forward-in-time simulations and show that it accurately captures the effects of background selection. The model produces more accurate predictions of the mean coalescent time than the existing formula and supports the conclusion that the effect of background selection is greater in the interior of a deleterious region than at its boundaries. The level of linkage disequilibrium between sites is elevated by background selection, to an extent that is well summarized by a change in effective population size. The structured coalescent model is readily extendable to more realistic situations and should prove useful for analyzing genome-wide polymorphism data.

  8. Genetic engineering of sulfur-degrading Sulfolobus. Final technical report, September 1, 1990--August 31, 1991

    Energy Technology Data Exchange (ETDEWEB)

    Ho, N.W.Y.

    1991-12-31

    The objectives of the proposed research is to first establish a plasmid-mediated genetic transformation system for the sulfur degrading Sulfolobus, and then to clone and overexpress the genes encoding the organic-sulfur-degrading enzymes from Sulfolobus- as well as from other microorganisms, to develop a Sulfolobus-based microbial process for the removal of both organic and inorganic sulfur from coal.

  9. Columbia River Stock Identification Study; Validation of Genetic Method, 1980-1981 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Milner, George B.; Teel, David J.; Utter, Fred M. (Northwest and Alaska Fisheries Science Center, Coastal Zone and Estuarine Studies Division, Seattle, WA)

    1981-06-01

    The reliability of a method for obtaining maximum likelihood estimate of component stocks in mixed populations of salmonids through the frequency of genetic variants in a mixed population and in potentially contributing stocks was tested in 1980. A data base of 10 polymorphic loci from 14 hatchery stocks of spring chinook salmon of the Columbia River was used to estimate proportions of these stocks in four different blind'' mixtures whose true composition was only revealed subsequent to obtaining estimates. The accuracy and precision of these blind tests have validated the genetic method as a valuable means for identifying components of stock mixtures. Properties of the genetic method were further examined by simulation studies using the pooled data of the four blind tests as a mixed fishery. Replicated tests with samples sizes between 100 and 1,000 indicated that actual standard deviations on estimated contributions were consistently lower than calculated standard deviations; this difference diminished as sample size increased. It is recommended that future applications of the method be preceded by simulation studies that will identify appropriate levels of sampling required for acceptable levels of accuracy and precision. Variables in such studies include the stocks involved, the loci used, and the genetic differentiation among stocks. 8 refs., 6 figs., 4 tabs.

  10. The uses of alternative dispute resolution to resolve genetic disputes. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Stein, Robert E.

    2003-01-01

    The report sets out lessons learned while carrying out the study. It concludes that genetic disputes will increase in number and that ADR processes including mediation, arbitration, the use of independent experts and court-appointed masters can be helpful in resolving them. It suggests additional effort on bioremediation, and workplace disputes and training for ADR neutrals.

  11. THE EFFECT OF INDIVIDUAL SELECTION FOR GENETIC DIVERSITY OF Acacia mangium SEEDLING SEED ORCHARD USING AFLP MARKERS

    Directory of Open Access Journals (Sweden)

    A. Y.P.B.C. Widyatmoko

    2006-07-01

    Full Text Available Establishment of seed orchard is aimed at producing good quality seeds which is an important activity for breeding program. Seed orchard is also a base population, thus its genetic diversity is depending on its design and composition (provenance, family and individual tree. Selection of an individual tree in seed orchard is needed for the enhancement of  retaining good-character trees. However, selection of individual tree can change the genetic diversity of seed orchard, and the degrees to which the genetic diversity will change depend on the used selection methods. In order to investigate the effects of selection methods, 4 simulations of selection methods based on height, diameter and stem performance of individual trees were used. The differences among the 4 methods were the ranking of individual trees those selected, and families and provenances those have been represented. Seedling seed orchard of Acacia mangium in Wonogiri, Central Java was used as materials. Analysis of genetic diversity was carried out using AFLP markers. Nine primer combinations were used to produce 1025 AFLP banding patterns. Among those banding patterns, only 109 were polymorphic markers. No significant effect of individual tree selection was revealed in this study. Even though the selection was done intensively, only 7.1% of genetic diversity was reduced. In other words, the selection activity did not reduce the genetic diversity of seed orchard significantly. The result is important for developing future tree improvement of A. mangium, including development of hybrid between A. mangium and A. auriculiformis.

  12. Population genetic structure and natural selection of apical membrane antigen-1 in Plasmodium vivax Korean isolates.

    Science.gov (United States)

    Kang, Jung-Mi; Lee, Jinyoung; Cho, Pyo-Yun; Moon, Sung-Ung; Ju, Hye-Lim; Ahn, Seong Kyu; Sohn, Woon-Mok; Lee, Hyeong-Woo; Kim, Tong-Soo; Na, Byoung-Kuk

    2015-11-16

    Plasmodium vivax apical membrane antigen-1 (PvAMA-1) is a leading candidate antigen for blood stage malaria vaccine. However, antigenic variation is a major obstacle in the development of an effective vaccine based on this antigen. In this study, the genetic structure and the effect of natural selection of PvAMA-1 among Korean P. vivax isolates were analysed. Blood samples were collected from 66 Korean patients with vivax malaria. The entire PvAMA-1 gene was amplified by polymerase chain reaction and cloned into a TA cloning vector. The PvAMA-1 sequence of each isolate was sequenced and the polymorphic characteristics and effect of natural selection were analysed using the DNASTAR, MEGA4, and DnaSP programs. Thirty haplotypes of PvAMA-1, which were further classified into seven different clusters, were identified in the 66 Korean P. vivax isolates. Domain II was highly conserved among the sequences, but substantial nucleotide diversity was observed in domains I and III. The difference between the rates of non-synonymous and synonymous mutations suggested that the gene has evolved under natural selection. No strong evidence indicating balancing or positive selection on PvAMA-1 was identified. Recombination may also play a role in the resulting genetic diversity of PvAMA-1. This study is the first comprehensive analysis of nucleotide diversity across the entire PvAMA-1 gene using a single population sample from Korea. Korean PvAMA-1 had limited genetic diversity compared to PvAMA-1 in global isolates. The overall pattern of genetic polymorphism of Korean PvAMA-1 differed from other global isolates and novel amino acid changes were also identified in Korean PvAMA-1. Evidences for natural selection and recombination event were observed, which is likely to play an important role in generating genetic diversity across the PvAMA-1. These results provide useful information for the understanding the population structure of P. vivax circulating in Korea and have important

  13. Seasonal Genetic Changes of Aedes aegypti (Diptera: Culicidae) Populations in Selected Sites of Cebu City, Philippines.

    Science.gov (United States)

    Sayson, S L; Gloria-Soria, A; Powell, J R; Edillo, F E

    2015-07-01

    Aedes aegypti (L.) is the primary vector of dengue virus in the Philippines, where dengue is endemic. We examined the genetic changes of Ae. aegypti collected from three selected sites in Cebu city, Philippines, during the relatively wet (2011-2012) and dry seasons (2012 and 2013). A total of 493 Ae. aegypti adults, reared in the laboratory from field-collected larvae, were analyzed using 11 microsatellite loci. Seasonal variation was observed in allele frequencies and allelic richness. Average genetic differentiation (DEST=0.018; FST=0.029) in both dry seasons was higher, due to reduced Ne, than in the wet season (DEST=0.006; FST=0.009). Thus, average gene flow was higher in the wet season than in the dry seasons. However, the overall FST estimate (0.02) inclusive of the two seasons showed little genetic differentiation as supported by Bayesian clustering analysis. Results suggest that during the dry season the intense selection that causes a dramatic reduction of population size favors heterozygotes, leading to small pockets of mosquitoes (refuges) that exhibit random genetic differentiation. During the wet season, the genetic composition of the population is reconstituted by the expansion of the refuges that survived the preceding dry season. Source reduction of mosquitoes during the nonepidemic dry season is thus recommended to prevent dengue re-emergence in the subsequent wet season. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  14. Quantifying selection in evolving populations using time-resolved genetic data

    Science.gov (United States)

    Illingworth, Christopher J. R.; Mustonen, Ville

    2013-01-01

    Methods which uncover the molecular basis of the adaptive evolution of a population address some important biological questions. For example, the problem of identifying genetic variants which underlie drug resistance, a question of importance for the treatment of pathogens, and of cancer, can be understood as a matter of inferring selection. One difficulty in the inference of variants under positive selection is the potential complexity of the underlying evolutionary dynamics, which may involve an interplay between several contributing processes, including mutation, recombination and genetic drift. A source of progress may be found in modern sequencing technologies, which confer an increasing ability to gather information about evolving populations, granting a window into these complex processes. One particularly interesting development is the ability to follow evolution as it happens, by whole-genome sequencing of an evolving population at multiple time points. We here discuss how to use time-resolved sequence data to draw inferences about the evolutionary dynamics of a population under study. We begin by reviewing our earlier analysis of a yeast selection experiment, in which we used a deterministic evolutionary framework to identify alleles under selection for heat tolerance, and to quantify the selection acting upon them. Considering further the use of advanced intercross lines to measure selection, we here extend this framework to cover scenarios of simultaneous recombination and selection, and of two driver alleles with multiple linked neutral, or passenger, alleles, where the driver pair evolves under an epistatic fitness landscape. We conclude by discussing the limitations of the approach presented and outlining future challenges for such methodologies.

  15. Preimplantation Genetic Diagnosis: Prenatal Testing for Embryos Finally Achieving Its Potential

    Science.gov (United States)

    Stern, Harvey J.

    2014-01-01

    Preimplantation genetic diagnosis was developed nearly a quarter-century ago as an alternative form of prenatal diagnosis that is carried out on embryos. Initially offered for diagnosis in couples at-risk for single gene genetic disorders, such as cystic fibrosis, spinal muscular atrophy and Huntington disease, preimplantation genetic diagnosis (PGD) has most frequently been employed in assisted reproduction for detection of chromosome aneuploidy from advancing maternal age or structural chromosome rearrangements. Major improvements have been seen in PGD analysis with movement away from older, less effective technologies, such as fluorescence in situ hybridization (FISH), to newer molecular tools, such as DNA microarrays and next generation sequencing. Improved results have also started to be seen with decreasing use of Day 3 blastomere biopsy in favor of polar body or Day 5 trophectoderm biopsy. Discussions regarding the scientific, ethical, legal and social issues surrounding the use of sequence data from embryo biopsy have begun and must continue to avoid concern regarding eugenic or inappropriate use of this technology. PMID:26237262

  16. Preimplantation Genetic Diagnosis: Prenatal Testing for Embryos Finally Achieving Its Potential

    Directory of Open Access Journals (Sweden)

    Harvey J. Stern

    2014-03-01

    Full Text Available Preimplantation genetic diagnosis was developed nearly a quarter-century ago as an alternative form of prenatal diagnosis that is carried out on embryos. Initially offered for diagnosis in couples at-risk for single gene genetic disorders, such as cystic fibrosis, spinal muscular atrophy and Huntington disease, preimplantation genetic diagnosis (PGD has most frequently been employed in assisted reproduction for detection of chromosome aneuploidy from advancing maternal age or structural chromosome rearrangements. Major improvements have been seen in PGD analysis with movement away from older, less effective technologies, such as fluorescence in situ hybridization (FISH, to newer molecular tools, such as DNA microarrays and next generation sequencing. Improved results have also started to be seen with decreasing use of Day 3 blastomere biopsy in favor of polar body or Day 5 trophectoderm biopsy. Discussions regarding the scientific, ethical, legal and social issues surrounding the use of sequence data from embryo biopsy have begun and must continue to avoid concern regarding eugenic or inappropriate use of this technology.

  17. Genetic parameters for predicted methane production and potential for reducing enteric emissions through genomic selection.

    Science.gov (United States)

    Haas, Y de; Windig, J J; Calus, M P L; Dijkstra, J; Haan, M de; Bannink, A; Veerkamp, R F

    2011-12-01

    Mitigation of enteric methane (CH₄) emission in ruminants has become an important area of research because accumulation of CH₄ is linked to global warming. Nutritional and microbial opportunities to reduce CH₄ emissions have been extensively researched, but little is known about using natural variation to breed animals with lower CH₄ yield. Measuring CH₄ emission rates directly from animals is difficult and hinders direct selection on reduced CH₄ emission. However, improvements can be made through selection on associated traits (e.g., residual feed intake, RFI) or through selection on CH₄ predicted from feed intake and diet composition. The objective was to establish phenotypic and genetic variation in predicted CH₄ output, and to determine the potential of genetics to reduce methane emissions in dairy cattle. Experimental data were used and records on daily feed intake, weekly body weights, and weekly milk production were available from 548 heifers. Residual feed intake (MJ/d) is the difference between net energy intake and calculated net energy requirements for maintenance as a function of body weight and for fat- and protein-corrected milk production. Predicted methane emission (PME; g/d) is 6% of gross energy intake (Intergovernmental Panel on Climate Change methodology) corrected for energy content of methane (55.65 kJ/g). The estimated heritabilities for PME and RFI were 0.35 and 0.40, respectively. The positive genetic correlation between RFI and PME indicated that cows with lower RFI have lower PME (estimates ranging from 0.18 to 0.84). Hence, it is possible to decrease the methane production of a cow by selecting more-efficient cows, and the genetic variation suggests that reductions in the order of 11 to 26% in 10 yr are theoretically possible, and could be even higher in a genomic selection program. However, several uncertainties are discussed; for example, the lack of true methane measurements (and the key assumption that methane

  18. Selected Area Fishery Evaluation Project Economic Analysis Study Final Report, Final Draft Revision 4: November 10, 2006.

    Energy Technology Data Exchange (ETDEWEB)

    Bonneville Power Administration; Washington Department of Fish and Wildlife; Oregon Department of Fish and Wildlife

    2006-11-01

    The purpose of this Study is to provide an economic review of current and proposed changes to the Select Area Fishery Evaluation Project (SAFE or Project). The Study results are the information requested in comments made on the Project by a joint review dated March 2005 by the Northwest Power and Conservation Council (NPCC) Independent Scientific Review Panel (ISRP) and Independent Economic Analysis Board (IEAB). North et al. (2006) addressed technical questions about operations and plans, and this report contains the response information for comments concerning Project economics. This report can be considered an economic feasibility review meeting guidelines for cost-effective analysis developed by the IEAB (2003). It also contains other economic measurement descriptions to illustrate the economic effects of SAFE. The SAFE is an expansion of a hatchery project (locally called the Clatsop Economic Development Council Fisheries Project or CEDC) started in 1977 that released an early run coho (COH) stock into the Youngs River. The Youngs River entrance to the Columbia River at River Mile 12 is called Youngs Bay, which is located near Astoria, Oregon. The purpose of the hatchery project was to provide increased fishing opportunities for the in-river commercial fishing gillnet fleet. Instead of just releasing fish at the hatchery, a small scale net pen acclimation project in Youngs Bay was tried in 1987. Hirose et al. (1998) found that 1991-1992 COH broodstock over-wintered at the net pens had double the smolt-to-adult return rate (SAR) of traditional hatchery release, less than one percent stray rates, and 99 percent fishery harvests. It was surmised that smolts from other Columbia River hatcheries could be hauled to the net pens for acclimation and release to take advantage of the SAR's and fishing rates. Proposals were tendered to Bonneville Power Administration (BPA) and other agencies to fund the expansion for using other hatcheries smolts and other off

  19. Immune response to Mycobacterium bovis-AN5 infection in genetically selected mice (selection IV-A

    Directory of Open Access Journals (Sweden)

    J. S. Cavaleiro

    2007-01-01

    Full Text Available Mice genetically selected for high (H and low (L antibody production (Selection IV-A were used as murine experimental model. The aim of the present work was to evaluate the macrophagic activity and to characterize the immune response in Mycobacterium bovis-AN5 infected mice (3X10(7 bacteria. The response profile previously observed in such strains was not similar to that obtained during M. bovis infection; however, it corroborated works carried out using Selection I, which is very similar to Selection IV-A regarding infection by M. tuberculosis and Bacillus Calmette-Guérin (BCG. Considering bacterial recovery, L IV-A mice showed higher control of the infectious process in the lungs than in the spleen, whereas H IV-A mice presented more resistance in the spleen. With respect to macrophagic activity, hydrogen peroxide (H2O2 was probably not involved in the infection control since there was an inhibition in the production of this metabolite. Nitric oxide (NO and TNF-alpha production seemed to be important in the control of bacterial replication and varied according to the strain, period and organ. Evaluation of the antibody production indicated that the multi-specific effect commonly observed in these strains was not the same in the response to M. bovis. Antibody concentrations were higher in L IV-A than in H IV-A mice at the beginning of the infection, being similar afterwards. Such data were compared with delayed-type hypersensitivity (DTH, which was more intense in H IV-A than in L IV-A mice, indicating that antibody production is independent of the capability to trigger DTH reactions and that cellular and humoral responses to M. bovis antigens show a polygenic control and an independent quantitative genetic regulation. Differences were observed among organs and metabolites, suggesting that different mechanisms play an important role in this infection in natural heterogeneous populations, indicating that NO, TNF-alpha and Th1 cytokines are

  20. The effect of selective solvent absorption on coal conversion. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, J.W.

    1993-11-01

    Using a pair of different recycle oils from Wilsonville and {sup 1}H NMR, {sup 13}C NMR, gel permeation (GPC) chromatography, high pressure liquid chromatography (HPLC), and elemental analysis, no significant differences were observed between the composition of the recycle oil and that portion of the oil not absorbed by the coal. For these complex mixtures, coals are not selective absorbants. Since most of the heteroatoms responsible for most of the specific interactions have been removed by hydrogenolyses, this is perhaps not surprising. To address the issue of the role of hydrogen bond donors in the reused as hydrogen donor coal, tetralin and 2-t-butyltetralin were used as hydrogen donor solvents. This work is reported in detail in Section 2. The basic idea is that the presence of the t-butyl group on the aromatic ring will hinder or block diffusion of the hydrogen donor into the coal resulting in lower conversions and less hydrogen transferred with 2-t-butyltetralin than with tetralin. Observed was identical amounts of hydrogen transfer and nearly identical conversions to pyridine solubles for both hydrogen donors. Diffusion of hydrogen donors into the coal does not seem to play a significant role in coal conversion. Finally, in Section 3 is discussed the unfavorable impact on conversion of the structural rearrangements which occur when Illinois No. 6 coal is swollen with a solvent. We believe this rearrangement results in a more strongly associated solid leading to the diminution of coal reactions. Hydrogen donor diffusion does not seem to be a major factor in coal conversion while the structural rearrangement does. Both areas warrant further exploration.

  1. A genetic algorithm for multiple relay selection in two-way relaying cognitive radio networks

    KAUST Repository

    Alsharoa, Ahmad M.

    2013-09-01

    In this paper, we investigate a multiple relay selection scheme for two-way relaying cognitive radio networks where primary users and secondary users operate on the same frequency band. More specifically, cooperative relays using Amplifyand- Forward (AF) protocol are optimally selected to maximize the sum rate of the secondary users without degrading the Quality of Service (QoS) of the primary users by respecting a tolerated interference threshold. A strong optimization tool based on genetic algorithm is employed to solve our formulated optimization problem where discrete relay power levels are considered. Our simulation results show that the practical heuristic approach achieves almost the same performance of the optimal multiple relay selection scheme either with discrete or continuous power distributions. Copyright © 2013 by the Institute of Electrical and Electronic Engineers, Inc.

  2. SOME USES OF MODELS OF QUANTITATIVE GENETIC SELECTION IN SOCIAL SCIENCE.

    Science.gov (United States)

    Weight, Michael D; Harpending, Henry

    2017-01-01

    The theory of selection of quantitative traits is widely used in evolutionary biology, agriculture and other related fields. The fundamental model known as the breeder's equation is simple, robust over short time scales, and it is often possible to estimate plausible parameters. In this paper it is suggested that the results of this model provide useful yardsticks for the description of social traits and the evaluation of transmission models. The differences on a standard personality test between samples of Old Order Amish and Indiana rural young men from the same county and the decline of homicide in Medieval Europe are used as illustrative examples of the overall approach. It is shown that the decline of homicide is unremarkable under a threshold model while the differences between rural Amish and non-Amish young men are too large to be a plausible outcome of simple genetic selection in which assortative mating by affiliation is equivalent to truncation selection.

  3. Supplier selection based on a neural network model using genetic algorithm.

    Science.gov (United States)

    Golmohammadi, Davood; Creese, Robert C; Valian, Haleh; Kolassa, John

    2009-09-01

    In this paper, a decision-making model was developed to select suppliers using neural networks (NNs). This model used historical supplier performance data for selection of vendor suppliers. Input and output were designed in a unique manner for training purposes. The managers' judgments about suppliers were simulated by using a pairwise comparisons matrix for output estimation in the NN. To obtain the benefit of a search technique for model structure and training, genetic algorithm (GA) was applied for the initial weights and architecture of the network. The suppliers' database information (input) can be updated over time to change the suppliers' score estimation based on their performance. The case study illustrated shows how the model can be applied for suppliers' selection.

  4. Sequential and Mixed Genetic Algorithm and Learning Automata (SGALA, MGALA) for Feature Selection in QSAR.

    Science.gov (United States)

    MotieGhader, Habib; Gharaghani, Sajjad; Masoudi-Sobhanzadeh, Yosef; Masoudi-Nejad, Ali

    2017-01-01

    Feature selection is of great importance in Quantitative Structure-Activity Relationship (QSAR) analysis. This problem has been solved using some meta-heuristic algorithms such as GA, PSO, ACO and so on. In this work two novel hybrid meta-heuristic algorithms i.e. Sequential GA and LA (SGALA) and Mixed GA and LA (MGALA), which are based on Genetic algorithm and learning automata for QSAR feature selection are proposed. SGALA algorithm uses advantages of Genetic algorithm and Learning Automata sequentially and the MGALA algorithm uses advantages of Genetic Algorithm and Learning Automata simultaneously. We applied our proposed algorithms to select the minimum possible number of features from three different datasets and also we observed that the MGALA and SGALA algorithms had the best outcome independently and in average compared to other feature selection algorithms. Through comparison of our proposed algorithms, we deduced that the rate of convergence to optimal result in MGALA and SGALA algorithms were better than the rate of GA, ACO, PSO and LA algorithms. In the end, the results of GA, ACO, PSO, LA, SGALA, and MGALA algorithms were applied as the input of LS-SVR model and the results from LS-SVR models showed that the LS-SVR model had more predictive ability with the input from SGALA and MGALA algorithms than the input from all other mentioned algorithms. Therefore, the results have corroborated that not only is the predictive efficiency of proposed algorithms better, but their rate of convergence is also superior to the all other mentioned algorithms.

  5. Transcriptome profile and unique genetic evolution of positively selected genes in yak lungs.

    Science.gov (United States)

    Lan, DaoLiang; Xiong, XianRong; Ji, WenHui; Li, Jian; Mipam, Tserang-Donko; Ai, Yi; Chai, ZhiXin

    2018-04-01

    The yak (Bos grunniens), which is a unique bovine breed that is distributed mainly in the Qinghai-Tibetan Plateau, is considered a good model for studying plateau adaptability in mammals. The lungs are important functional organs that enable animals to adapt to their external environment. However, the genetic mechanism underlying the adaptability of yak lungs to harsh plateau environments remains unknown. To explore the unique evolutionary process and genetic mechanism of yak adaptation to plateau environments, we performed transcriptome sequencing of yak and cattle (Bos taurus) lungs using RNA-Seq technology and a subsequent comparison analysis to identify the positively selected genes in the yak. After deep sequencing, a normal transcriptome profile of yak lung that containing a total of 16,815 expressed genes was obtained, and the characteristics of yak lungs transcriptome was described by functional analysis. Furthermore, Ka/Ks comparison statistics result showed that 39 strong positively selected genes are identified from yak lungs. Further GO and KEGG analysis was conducted for the functional annotation of these genes. The results of this study provide valuable data for further explorations of the unique evolutionary process of high-altitude hypoxia adaptation in yaks in the Tibetan Plateau and the genetic mechanism at the molecular level.

  6. Genetic diversity of selected genes that are potentially economically important in feral sheep of New Zealand

    Directory of Open Access Journals (Sweden)

    Sedcole J Richard

    2010-12-01

    Full Text Available Abstract Background Feral sheep are considered to be a source of genetic variation that has been lost from their domestic counterparts through selection. Methods This study investigates variation in the genes KRTAP1-1, KRT33, ADRB3 and DQA2 in Merino-like feral sheep populations from New Zealand and its offshore islands. These genes have previously been shown to influence wool, lamb survival and animal health. Results All the genes were polymorphic, but no new allele was identified in the feral populations. In some of these populations, allele frequencies differed from those observed in commercial Merino sheep and other breeds found in New Zealand. Heterozygosity levels were comparable to those observed in other studies on feral sheep. Our results suggest that some of the feral populations may have been either inbred or outbred over the duration of their apparent isolation. Conclusion The variation described here allows us to draw some conclusions about the likely genetic origin of the populations and selective pressures that may have acted upon them, but they do not appear to be a source of new genetic material, at least for these four genes.

  7. Genetic parameters and simultaneous selection for root yield, adaptability and stability of cassava genotypes

    Directory of Open Access Journals (Sweden)

    João Tomé de Farias Neto

    2013-12-01

    Full Text Available The objective of this work was to estimate genetic parameters and to evaluate simultaneous selection for root yield and for adaptability and stability of cassava genotypes. The effects of genotypes were assumed as fixed and random, and the mixed model methodology (REML/Blup was used to estimate genetic parameters and the harmonic mean of the relative performance of genotypic values (HMRPGV, for simultaneous selection purposes. Ten genotypes were analyzed in a complete randomized block design, with four replicates. The experiment was carried out in the municipalities of Altamira, Santarém, and Santa Luzia do Pará in the state of Pará, Brazil, in the growing seasons of 2009/2010, 2010/2011, and 2011/2012. Roots were harvested 12 months after planting, in all tested locations. Root yield had low coefficients of genotypic variation (4.25% and broad-sense heritability of individual plots (0.0424, which resulted in low genetic gain. Due to the low genotypic correlation (0.15, genotype classification as to root yield varied according to the environment. Genotypes CPATU 060, CPATU 229, and CPATU 404 stood out as to their yield, adaptability, and stability.

  8. The maintenance of genetic variation for oviposition rate in two-spotted spider mites: inferences from artificial selection

    NARCIS (Netherlands)

    Tien, N.S.H.; Sabelis, M.W.; Egas, M.

    2010-01-01

    Despite the directional selection acting on life-history traits, substantial amounts of standing variation for these traits have frequently been found. This variation may result from balancing selection (e.g., through genetic trade-offs) or from mutation-selection balance. These mechanisms affect

  9. Genetic Augmentation of Syringyl Lignin in Low-lignin Aspen Trees, Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Chung-Jui Tsai; Mark F. Davis; Vincent L. Chiang

    2004-11-10

    As a polysaccharide-encrusting component, lignin is critical to cell wall integrity and plant growth but also hinders recovery of cellulose fibers during the wood pulping process. To improve pulping efficiency, it is highly desirable to genetically modify lignin content and/or structure in pulpwood species to maximize pulp yields with minimal energy consumption and environmental impact. This project aimed to genetically augment the syringyl-to-guaiacyl lignin ratio in low-lignin transgenic aspen in order to produce trees with reduced lignin content, more reactive lignin structures and increased cellulose content. Transgenic aspen trees with reduced lignin content have already been achieved, prior to the start of this project, by antisense downregulation of a 4-coumarate:coenzyme A ligase gene (Hu et al., 1999 Nature Biotechnol 17: 808- 812). The primary objective of this study was to genetically augment syringyl lignin biosynthesis in these low-lignin trees in order to enhance lignin reactivity during chemical pulping. To accomplish this, both aspen and sweetgum genes encoding coniferaldehyde 5-hydroxylase (Osakabe et al., 1999 PNAS 96: 8955-8960) were targeted for over-expression in wildtype or low-lignin aspen under control of either a constitutive or a xylem-specific promoter. A second objective for this project was to develop reliable and cost-effective methods, such as pyrolysis Molecular Beam Mass Spectrometry and NMR, for rapid evaluation of cell wall chemical components of transgenic wood samples. With these high-throughput techniques, we observed increased syringyl-to-guaiacyl lignin ratios in the transgenic wood samples, regardless of the promoter used or gene origin. Our results confirmed that the coniferaldehyde 5-hydroxylase gene is key to syringyl lignin biosynthesis. The outcomes of this research should be readily applicable to other pulpwood species, and promise to bring direct economic and environmental benefits to the pulp and paper industry.

  10. Final Progress Report: Developing Ethical Practices for Genetics Testing in the Workplace

    Energy Technology Data Exchange (ETDEWEB)

    Laura Roberts, MD; Teddy Warner, PhD

    2008-05-14

    Our multidisciplinary research team for this project involved collaboration between the Department of Psychiatry and Behavioral Medicine at the Medical College of Wisconsin (MCW) and the Department of Family and Community Medicine at the University of New Mexico Health Sciences Center (UNM HSC). Our research team in Wisconsin was led by Laura Roberts, M.D., Principal Investigator, and included Scott Helberg, MLS (Project Coordinator), Kate Green Hammond, Ph.D. (Consultant), Krisy Edenharder (Research Coordinator), and Mark Talatzko (Research Assistant). Our New Mexico-based team was led by Teddy Warner, Ph.D., Co-Principal Investigator and UNM Site Principal Investigator, and included Suzanne Roybal (Project Assistant), Darlyn Mabon (Project Assistant), Kate Green Hammond, PhD (Senior Research Scientist on the UNM team from 2004 until January, 2007), and Paulette Christopher (Research Assistant). In addition, computer technical and web support for the web-based survey conducted on a secure server at the University of New Mexico was provided by Kevin Wiley and Kim Hagen of the Systems and Programming Team of the Health Sciences Center Library and Information Center. We stated 3 aims in the grant proposal: (1) To collect web survey reports of the ethical perspectives, concerns, preferences and decision-making related to genetic testing using surveys from employees at: (a) Los Alamos National Laboratory (LANL); (b) Sandia National Laboratories (SNL); and (c) the University of New Mexico Health Sciences Center (UNMHSC); (2) To perform an extensive literature search and the extant survey data to develop evidence-based policy recommendations for ethically sound genetic testing associated with research and occupational health activities in the workplace; and, (3) To host a conference at the Medical College of Wisconsin to provide employers, workers, health professionals, researchers, the public, and the media an opportunity to consider ethical issues involved in genetic

  11. Prediction of genetic gain from selection indices for disease resistance in papaya hybrids

    Directory of Open Access Journals (Sweden)

    Marcelo Vivas

    2012-12-01

    Full Text Available In order to select superior hybrids for the concentration of favorable alleles for resistance to papaya black spot, powdery mildew and phoma spot, 67 hybrids were evaluated in two seasons, in 2007, in a randomized block design with two replications. Genetic gains were estimated from the selection indices of Smith & Hazel, Pesek & Baker, Williams, Mulamba & Mock, with selection intensity of 22.39%, corresponding to 15 hybrids. The index of Mulamba & Mock showed gains more suitable for the five traits assessed when it was used the criterion of economic weight tentatively assigned. Together, severity of black spot on leaves and on fruits, characteristics considered most relevant to the selection of resistant materials, expressed percentage gain of -44.15%. In addition, there were gains for other characteristics, with negative predicted selective percentage gain. The results showed that the index of Mulamba & Mock is the most efficient procedure for simultaneous selection of papaya hybrid resistant to black spot, powdery mildew and phoma spot.

  12. Genetic diversity and natural selection of Plasmodium knowlesi merozoite surface protein 1 paralog gene in Malaysia.

    Science.gov (United States)

    Ahmed, Md Atique; Fauzi, Muh; Han, Eun-Taek

    2018-03-14

    Human infections due to the monkey malaria parasite Plasmodium knowlesi is on the rise in most Southeast Asian countries specifically Malaysia. The C-terminal 19 kDa domain of PvMSP1P is a potential vaccine candidate, however, no study has been conducted in the orthologous gene of P. knowlesi. This study investigates level of polymorphisms, haplotypes and natural selection of full-length pkmsp1p in clinical samples from Malaysia. A total of 36 full-length pkmsp1p sequences along with the reference H-strain and 40 C-terminal pkmsp1p sequences from clinical isolates of Malaysia were downloaded from published genomes. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 and MEGA 5.0 software. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (F ST ) and population structure of parasite was determined using Arlequin v3.5 and STRUCTURE v2.3.4 software. Comparison of 36 full-length pkmsp1p sequences along with the H-strain identified 339 SNPs (175 non-synonymous and 164 synonymous substitutions). The nucleotide diversity across the full-length gene was low compared to its ortholog pvmsp1p. The nucleotide diversity was higher toward the N-terminal domains (pkmsp1p-83 and 30) compared to the C-terminal domains (pkmsp1p-38, 33 and 19). Phylogenetic analysis of full-length genes identified 2 distinct clusters of P. knowlesi from Malaysian Borneo. The 40 pkmsp1p-19 sequences showed low polymorphisms with 16 polymorphisms leading to 18 haplotypes. In total there were 10 synonymous and 6 non-synonymous substitutions and 12 cysteine residues were intact within the two EGF domains. Evidence of strong purifying selection was observed within the full-length sequences as well in all the domains. Shared haplotypes of 40 pkmsp1p-19 were identified within Malaysian Borneo haplotypes. This study is the first to report on the genetic diversity and natural

  13. Juglans regia L., phenotypic selection and assessment of genetic variation within a simulated seed orchard

    Directory of Open Access Journals (Sweden)

    Fulvio Ducci

    2010-12-01

    Full Text Available Normal 0 14 false false false MicrosoftInternetExplorer4 Noble hardwoods are very important for the Italian furniture industry. Since 1985, approximately 170,000 ha have been planted in Italy with noble hardwoods. Among them, about 50% of species are represented by walnuts. Walnut (Juglans regia L., not native in Italy, has been the focus of a substantial research effort for breeding and improvement programmes. The priority has been to preserve the in situ genetic resource still existing after intensive felling. Phenotypes suitable for timber production showing important traits such as straight stem, nice branch architecture, dominance and adaptation (phenology have needed to be developed and selected. In order to reach this goals, selection of valuable progenies and the evaluation of the interaction genotype x environment, methods based essentially on a multi-trait Selection Index, were developed. Studies have been undertaken also to measure the variation of phenological traits, more correlated to traits valuable for architecture; in addition, neutral markers were used to assess genetic variation among different intensities of the adopted selections. The individual genetic component was found to be higher than at the inter-population level. Results showed that a hypothetical seed orchard made with progenies selected by morphology, phenology and genetic traits could provide material with a good performance and supply a variability similar to larger populations as the total plantation or the pseudo-natural system chosen for comparison. st1\\:*{behavior:url(#ieooui } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabella normale"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso

  14. Population genetic structure and natural selection of Plasmodium falciparum apical membrane antigen-1 in Myanmar isolates.

    Science.gov (United States)

    Kang, Jung-Mi; Lee, Jinyoung; Moe, Mya; Jun, Hojong; Lê, Hương Giang; Kim, Tae Im; Thái, Thị Lam; Sohn, Woon-Mok; Myint, Moe Kyaw; Lin, Khin; Shin, Ho-Joon; Kim, Tong-Soo; Na, Byoung-Kuk

    2018-02-07

    Plasmodium falciparum apical membrane antigen-1 (PfAMA-1) is one of leading blood stage malaria vaccine candidates. However, genetic variation and antigenic diversity identified in global PfAMA-1 are major hurdles in the development of an effective vaccine based on this antigen. In this study, genetic structure and the effect of natural selection of PfAMA-1 among Myanmar P. falciparum isolates were analysed. Blood samples were collected from 58 Myanmar patients with falciparum malaria. Full-length PfAMA-1 gene was amplified by polymerase chain reaction and cloned into a TA cloning vector. PfAMA-1 sequence of each isolate was sequenced. Polymorphic characteristics and effect of natural selection were analysed with using DNASTAR, MEGA4, and DnaSP programs. Polymorphic nature and natural selection in 459 global PfAMA-1 were also analysed. Thirty-seven different haplotypes of PfAMA-1 were identified in 58 Myanmar P. falciparum isolates. Most amino acid changes identified in Myanmar PfAMA-1 were found in domains I and III. Overall patterns of amino acid changes in Myanmar PfAMA-1 were similar to those in global PfAMA-1. However, frequencies of amino acid changes differed by country. Novel amino acid changes in Myanmar PfAMA-1 were also identified. Evidences for natural selection and recombination event were observed in global PfAMA-1. Among 51 commonly identified amino acid changes in global PfAMA-1 sequences, 43 were found in predicted RBC-binding sites, B-cell epitopes, or IUR regions. Myanmar PfAMA-1 showed similar patterns of nucleotide diversity and amino acid polymorphisms compared to those of global PfAMA-1. Balancing natural selection and intragenic recombination across PfAMA-1 are likely to play major roles in generating genetic diversity in global PfAMA-1. Most common amino acid changes in global PfAMA-1 were located in predicted B-cell epitopes where high levels of nucleotide diversity and balancing natural selection were found. These results highlight the

  15. Comparison between different selection criteria in the genetic evaluation of Valle del Belice sheep

    Directory of Open Access Journals (Sweden)

    F. Firpo

    2011-03-01

    Full Text Available Lactation length in dairy sheep affects milk yield like other genetic and environmental factors. The length of the production period is affected by management decisions such as culling, mating and particularly ranking of animals with different parity and lambing in different months or seasons. Moreover the low heritability of lactation length (Barillet and Boichard, 1987; Dahlin et al., 1998 does not allow its use as a selection criterion. For this reason to achieve a good reliability in phenotypic and genetic evaluation of dairy species, production variability caused by systematic environmental effects must be removed. This is of particular interest for dairy sheep and goats reared in Sicily, where the typical production system is based on pasture, and related food availability is strongly affected by seasonal and annual climatic variations, which results in considerable variations in daily yields........

  16. A modified genetic algorithm with fuzzy roulette wheel selection for job-shop scheduling problems

    Science.gov (United States)

    Thammano, Arit; Teekeng, Wannaporn

    2015-05-01

    The job-shop scheduling problem is one of the most difficult production planning problems. Since it is in the NP-hard class, a recent trend in solving the job-shop scheduling problem is shifting towards the use of heuristic and metaheuristic algorithms. This paper proposes a novel metaheuristic algorithm, which is a modification of the genetic algorithm. This proposed algorithm introduces two new concepts to the standard genetic algorithm: (1) fuzzy roulette wheel selection and (2) the mutation operation with tabu list. The proposed algorithm has been evaluated and compared with several state-of-the-art algorithms in the literature. The experimental results on 53 JSSPs show that the proposed algorithm is very effective in solving the combinatorial optimization problems. It outperforms all state-of-the-art algorithms on all benchmark problems in terms of the ability to achieve the optimal solution and the computational time.

  17. Systematic differences in the response of genetic variation to pedigree and genome-based selection methods.

    Science.gov (United States)

    Heidaritabar, M; Vereijken, A; Muir, W M; Meuwissen, T; Cheng, H; Megens, H-J; Groenen, M A M; Bastiaansen, J W M

    2014-12-01

    Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60 K SNP chip with markers spaced throughout the entire chicken genome, we compared the impact of GS and traditional BLUP (best linear unbiased prediction) selection methods applied side-by-side in three different lines of egg-laying chickens. Differences were demonstrated between methods, both at the level and genomic distribution of allele frequency changes. In all three lines, the average allele frequency changes were larger with GS, 0.056 0.064 and 0.066, compared with BLUP, 0.044, 0.045 and 0.036 for lines B1, B2 and W1, respectively. With BLUP, 35 selected regions (empirical P selected regions were identified. Empirical thresholds for local allele frequency changes were determined from gene dropping, and differed considerably between GS (0.167-0.198) and BLUP (0.105-0.126). Between lines, the genomic regions with large changes in allele frequencies showed limited overlap. Our results show that GS applies selection pressure much more locally than BLUP, resulting in larger allele frequency changes. With these results, novel insights into the nature of selection on quantitative traits have been gained and important questions regarding the long-term impact of GS are raised. The rapid changes to a part of the genetic architecture, while another part may not be selected, at least in the short term, require careful consideration, especially when selection occurs before phenotypes are observed.

  18. Sexual selection on spontaneous mutations strengthens the between-sex genetic correlation for fitness.

    Science.gov (United States)

    Allen, Scott L; McGuigan, Katrina; Connallon, Tim; Blows, Mark W; Chenoweth, Stephen F

    2017-10-01

    A proposed benefit to sexual selection is that it promotes purging of deleterious mutations from populations. For this benefit to be realized, sexual selection, which is usually stronger on males, must purge mutations deleterious to both sexes. Here, we experimentally test the hypothesis that sexual selection on males purges deleterious mutations that affect both male and female fitness. We measured male and female fitness in two panels of spontaneous mutation-accumulation lines of the fly, Drosophila serrata, each established from a common ancestor. One panel of mutation accumulation lines limited both natural and sexual selection (LS lines), whereas the other panel limited natural selection, but allowed sexual selection to operate (SS lines). Although mutation accumulation caused a significant reduction in male and female fitness in both the LS and SS lines, sexual selection had no detectable effect on the extent of the fitness reduction. Similarly, despite evidence of mutational variance for fitness in males and females of both treatments, sexual selection had no significant impact on the amount of mutational genetic variance for fitness. However, sexual selection did reshape the between-sex correlation for fitness: significantly strengthening it in the SS lines. After 25 generations, the between-sex correlation for fitness was positive but considerably less than one in the LS lines, suggesting that, although most mutations had sexually concordant fitness effects, sex-limited, and/or sex-biased mutations contributed substantially to the mutational variance. In the SS lines this correlation was strong and could not be distinguished from unity. Individual-based simulations that mimick the experimental setup reveal two conditions that may drive our results: (1) a modest-to-large fraction of mutations have sex-limited (or highly sex-biased) fitness effects, and (2) the average fitness effect of sex-limited mutations is larger than the average fitness effect of

  19. Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity.

    Directory of Open Access Journals (Sweden)

    Nicolas Heslot

    Full Text Available Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L. genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis.

  20. Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

    Science.gov (United States)

    Heslot, Nicolas; Rutkoski, Jessica; Poland, Jesse; Jannink, Jean-Luc; Sorrells, Mark E.

    2013-01-01

    Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS) is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology) and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS) accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis. PMID:24040295

  1. Effects of trawl selectivity and genetic parameters on fish body length under long-term trawling

    Science.gov (United States)

    Yu, Yang; Sun, Peng; Cui, He; Sheng, Huaxiang; Zhao, Fenfang; Tang, Yanli; Chen, Zelin

    2015-10-01

    Long-term fishing pressure affects the biological characteristics of exploited fish stocks. The biological characteristics of hairtail ( Trichiurus lepturus) in the East China Sea are unable to recover because of long-term trawling. Fishing induces evolutionary effects on the fish's biological characteristics. Evidence of these changes includes small size at age, a shift to earlier age structure, and early maturation. Natural and artificial selection usually affect the fish's life history. Selection can induce different chances of reproduction, and individual fish can give a different genetic contribution to the next generation. In this study, analysis of time-dependent probability of significance and test of sensitivity were used to explore the effects of fish exploitation rate, mesh size, and heritability with long-term trawling. Results showed that fishing parameters were important drivers to exploited fish population. However, genetic traits altered by fishing were slow, and the changes in biological characteristics were weaker than those caused by fishing selection. Exploitation rate and mesh size exhibited similar evolutionary trend tendency under long-term fishing. The time-dependent probability of significance trend showed a gradual growth and tended to be stable. Therefore, the direction of fishing-induced evolution and successful management of fish species require considerable attention to contribute to sustainable fisheries in China.

  2. The Genetic Theory of Infectious Diseases: A Brief History and Selected Illustrations

    Science.gov (United States)

    Casanova, Jean-Laurent; Abel, Laurent

    2016-01-01

    Until the mid-nineteenth century, life expectancy at birth averaged 20 years worldwide, owing mostly to childhood fevers. The germ theory of diseases then gradually overcame the belief that diseases were intrinsic. However, around the turn of the twentieth century, asymptomatic infection was discovered to be much more common than clinical disease. Paradoxically, this observation barely challenged the newly developed notion that infectious diseases were fundamentally extrinsic. Moreover, interindividual variability in the course of infection was typically explained by the emerging immunological (or somatic) theory of infectious diseases, best illustrated by the impact of vaccination. This powerful explanation is, however, best applicable to reactivation and secondary infections, particularly in adults; it can less easily account for interindividual variability in the course of primary infection during childhood. Population and clinical geneticists soon proposed a complementary hypothesis, a germline genetic theory of infectious diseases. Over the past century, this idea has gained some support, particularly among clinicians and geneticists, but has also encountered resistance, particularly among microbiologists and immunologists. We present here the genetic theory of infectious diseases and briefly discuss its history and the challenges encountered during its emergence in the context of the apparently competing but actually complementary microbiological and immunological theories. We also illustrate its recent achievements by highlighting inborn errors of immunity underlying eight life-threatening infectious diseases of children and young adults. Finally, we consider the far-reaching biological and clinical implications of the ongoing human genetic dissection of severe infectious diseases. PMID:23724903

  3. The genetic theory of infectious diseases: a brief history and selected illustrations.

    Science.gov (United States)

    Casanova, Jean-Laurent; Abel, Laurent

    2013-01-01

    Until the mid-nineteenth century, life expectancy at birth averaged 20 years worldwide, owing mostly to childhood fevers. The germ theory of diseases then gradually overcame the belief that diseases were intrinsic. However, around the turn of the twentieth century, asymptomatic infection was discovered to be much more common than clinical disease. Paradoxically, this observation barely challenged the newly developed notion that infectious diseases were fundamentally extrinsic. Moreover, interindividual variability in the course of infection was typically explained by the emerging immunological (or somatic) theory of infectious diseases, best illustrated by the impact of vaccination. This powerful explanation is, however, best applicable to reactivation and secondary infections, particularly in adults; it can less easily account for interindividual variability in the course of primary infection during childhood. Population and clinical geneticists soon proposed a complementary hypothesis, a germline genetic theory of infectious diseases. Over the past century, this idea has gained some support, particularly among clinicians and geneticists, but has also encountered resistance, particularly among microbiologists and immunologists. We present here the genetic theory of infectious diseases and briefly discuss its history and the challenges encountered during its emergence in the context of the apparently competing but actually complementary microbiological and immunological theories. We also illustrate its recent achievements by highlighting inborn errors of immunity underlying eight life-threatening infectious diseases of children and young adults. Finally, we consider the far-reaching biological and clinical implications of the ongoing human genetic dissection of severe infectious diseases.

  4. Indicator 1.08. Population levels of selected representative forest-associated species to describe genetic diversity

    Science.gov (United States)

    C. H. Sieg; S. M. Owen; C. H. Flather

    2011-01-01

    This indicator uses population trends of selected bird and tree species as a surrogate measure of genetic diversity. Population decreases, especially associated with small populations, can lead to decreases in genetic diversity, and contribute to increased risk of extinction. Many forest-associated species rely on some particular forest structure, vegetation...

  5. Estimating host genetic effects on susceptibility and infectivity to infectious diseases and their contribution to response to selection

    NARCIS (Netherlands)

    Anche, M.T.

    2016-01-01

    Mahlet Teka Anche. (2016). Estimating host genetic effects on susceptibility and infectivity to infectious diseases and their contribution to response to selection. PhD thesis, Wageningen University, the Netherlands

    Genetic approaches aiming to reduce the prevalence of an infection in a

  6. Recurrent selection of cocoa populations in Cote d'Ivoire: comparative genetic diversity between the first and second cycles

    Science.gov (United States)

    In Cote d'Ivore, the cocoa breeding programme has been based on the creation of hybrids between different genetic groups. From 1990 onward, a reciprocal recurrent selection programme has been set up with the purpose of improving simultaneously the characteristics of the two main genetic groups: Uppe...

  7. Behavioral stress response of genetically selected aggressive and nonaggressive wild house mice in the shock-probe/defensive burying test

    NARCIS (Netherlands)

    Sluyter, F; Korte, SM; Bohus, B; VanOortmerssen, GA

    Genetically selected aggressive and nonaggressive male wild house mice were tested in the shock-probe/defensive burying test. Five distinct behaviors (burying, immobility, rearing, grooming, and exploration) were recorded in two environmental situations: fresh and home cage sawdust. Nonaggressive

  8. Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity.

    Directory of Open Access Journals (Sweden)

    Stephen R Doyle

    2017-07-01

    Full Text Available Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana-exposed to more than a decade of regular ivermectin treatment-have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread.Pooled next generation sequencing (Pool-seq was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR and sub-optimal responder (SOR parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs, with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure had a significantly greater role in shaping genetic diversity than the evolution of SOR.This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic

  9. Genetic subdivision and candidate genes under selection in North American grey wolves.

    Science.gov (United States)

    Schweizer, Rena M; vonHoldt, Bridgett M; Harrigan, Ryan; Knowles, James C; Musiani, Marco; Coltman, David; Novembre, John; Wayne, Robert K

    2016-01-01

    Previous genetic studies of the highly mobile grey wolf (Canis lupus) found population structure that coincides with habitat and phenotype differences. We hypothesized that these ecologically distinct populations (ecotypes) should exhibit signatures of selection in genes related to morphology, coat colour and metabolism. To test these predictions, we quantified population structure related to habitat using a genotyping array to assess variation in 42 036 single-nucleotide polymorphisms (SNPs) in 111 North American grey wolves. Using these SNP data and individual-level measurements of 12 environmental variables, we identified six ecotypes: West Forest, Boreal Forest, Arctic, High Arctic, British Columbia and Atlantic Forest. Next, we explored signals of selection across these wolf ecotypes through the use of three complementary methods to detect selection: FST /haplotype homozygosity bivariate percentilae, bayescan, and environmentally correlated directional selection with bayenv. Across all methods, we found consistent signals of selection on genes related to morphology, coat coloration, metabolism, as predicted, as well as vision and hearing. In several high-ranking candidate genes, including LEPR, TYR and SLC14A2, we found variation in allele frequencies that follow environmental changes in temperature and precipitation, a result that is consistent with local adaptation rather than genetic drift. Our findings show that local adaptation can occur despite gene flow in a highly mobile species and can be detected through a moderately dense genomic scan. These patterns of local adaptation revealed by SNP genotyping likely reflect high fidelity to natal habitats of dispersing wolves, strong ecological divergence among habitats, and moderate levels of linkage in the wolf genome. © 2015 John Wiley & Sons Ltd.

  10. Genetic Bee Colony (GBC) algorithm: A new gene selection method for microarray cancer classification.

    Science.gov (United States)

    Alshamlan, Hala M; Badr, Ghada H; Alohali, Yousef A

    2015-06-01

    Naturally inspired evolutionary algorithms prove effectiveness when used for solving feature selection and classification problems. Artificial Bee Colony (ABC) is a relatively new swarm intelligence method. In this paper, we propose a new hybrid gene selection method, namely Genetic Bee Colony (GBC) algorithm. The proposed algorithm combines the used of a Genetic Algorithm (GA) along with Artificial Bee Colony (ABC) algorithm. The goal is to integrate the advantages of both algorithms. The proposed algorithm is applied to a microarray gene expression profile in order to select the most predictive and informative genes for cancer classification. In order to test the accuracy performance of the proposed algorithm, extensive experiments were conducted. Three binary microarray datasets are use, which include: colon, leukemia, and lung. In addition, another three multi-class microarray datasets are used, which are: SRBCT, lymphoma, and leukemia. Results of the GBC algorithm are compared with our recently proposed technique: mRMR when combined with the Artificial Bee Colony algorithm (mRMR-ABC). We also compared the combination of mRMR with GA (mRMR-GA) and Particle Swarm Optimization (mRMR-PSO) algorithms. In addition, we compared the GBC algorithm with other related algorithms that have been recently published in the literature, using all benchmark datasets. The GBC algorithm shows superior performance as it achieved the highest classification accuracy along with the lowest average number of selected genes. This proves that the GBC algorithm is a promising approach for solving the gene selection problem in both binary and multi-class cancer classification. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. On theoretical models of gene expression evolution with random genetic drift and natural selection.

    Science.gov (United States)

    Ogasawara, Osamu; Okubo, Kousaku

    2009-11-20

    The relative contributions of natural selection and random genetic drift are a major source of debate in the study of gene expression evolution, which is hypothesized to serve as a bridge from molecular to phenotypic evolution. It has been suggested that the conflict between views is caused by the lack of a definite model of the neutral hypothesis, which can describe the long-run behavior of evolutionary change in mRNA abundance. Therefore previous studies have used inadequate analogies with the neutral prediction of other phenomena, such as amino acid or nucleotide sequence evolution, as the null hypothesis of their statistical inference. In this study, we introduced two novel theoretical models, one based on neutral drift and the other assuming natural selection, by focusing on a common property of the distribution of mRNA abundance among a variety of eukaryotic cells, which reflects the result of long-term evolution. Our results demonstrated that (1) our models can reproduce two independently found phenomena simultaneously: the time development of gene expression divergence and Zipf's law of the transcriptome; (2) cytological constraints can be explicitly formulated to describe long-term evolution; (3) the model assuming that natural selection optimized relative mRNA abundance was more consistent with previously published observations than the model of optimized absolute mRNA abundances. The models introduced in this study give a formulation of evolutionary change in the mRNA abundance of each gene as a stochastic process, on the basis of previously published observations. This model provides a foundation for interpreting observed data in studies of gene expression evolution, including identifying an adequate time scale for discriminating the effect of natural selection from that of random genetic drift of selectively neutral variations.

  12. Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass

    Directory of Open Access Journals (Sweden)

    Zibei Lin

    2016-03-01

    Full Text Available Genomic selection (GS provides an attractive option for accelerating genetic gain in perennial ryegrass ( improvement given the long cycle times of most current breeding programs. The present study used simulation to investigate the level of genetic gain and inbreeding obtained from GS breeding strategies compared with traditional breeding strategies for key traits (persistency, yield, and flowering time. Base population genomes were simulated through random mating for 60,000 generations at an effective population size of 10,000. The degree of linkage disequilibrium (LD in the resulting population was compared with that obtained from empirical studies. Initial parental varieties were simulated to match diversity of current commercial cultivars. Genomic selection was designed to fit into a company breeding program at two selection points in the breeding cycle (spaced plants and miniplot. Genomic estimated breeding values (GEBVs for productivity traits were trained with phenotypes and genotypes from plots. Accuracy of GEBVs was 0.24 for persistency and 0.36 for yield for single plants, while for plots it was lower (0.17 and 0.19, respectively. Higher accuracy of GEBVs was obtained for flowering time (up to 0.7, partially as a result of the larger reference population size that was available from the clonal row stage. The availability of GEBVs permit a 4-yr reduction in cycle time, which led to at least a doubling and trebling genetic gain for persistency and yield, respectively, than the traditional program. However, a higher rate of inbreeding per cycle among varieties was also observed for the GS strategy.

  13. Model selection emphasises the importance of non-chromosomal information in genetic studies.

    Directory of Open Access Journals (Sweden)

    Reda Rawi

    Full Text Available Ever since the case of the missing heritability was highlighted some years ago, scientists have been investigating various possible explanations for the issue. However, none of these explanations include non-chromosomal genetic information. Here we describe explicitly how chromosomal and non-chromosomal modifiers collectively influence the heritability of a trait, in this case, the growth rate of yeast. Our results show that the non-chromosomal contribution can be large, adding another dimension to the estimation of heritability. We also discovered, combining the strength of LASSO with model selection, that the interaction of chromosomal and non-chromosomal information is essential in describing phenotypes.

  14. A Genetic Algorithm-based Antenna Selection Approach for Large-but-Finite MIMO Networks

    KAUST Repository

    Makki, Behrooz

    2016-12-29

    We study the performance of antenna selectionbased multiple-input-multiple-output (MIMO) networks with large but finite number of transmit antennas and receivers. Considering the continuous and bursty communication scenarios with different users’ data request probabilities, we develop an efficient antenna selection scheme using genetic algorithms (GA). As demonstrated, the proposed algorithm is generic in the sense that it can be used in the cases with different objective functions, precoding methods, levels of available channel state information and channel models. Our results show that the proposed GAbased algorithm reaches (almost) the same throughput as the exhaustive search-based optimal approach, with substantially less implementation complexity.

  15. Genetic differentiation and selection against migrants in evolutionarily replicated extreme environments.

    Science.gov (United States)

    Plath, Martin; Pfenninger, Markus; Lerp, Hannes; Riesch, Rüdiger; Eschenbrenner, Christoph; Slattery, Patrick A; Bierbach, David; Herrmann, Nina; Schulte, Matthias; Arias-Rodriguez, Lenin; Rimber Indy, Jeane; Passow, Courtney; Tobler, Michael

    2013-09-01

    We investigated mechanisms of reproductive isolation in livebearing fishes (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three replicate river drainages. Although sulfide spring fish convergently evolved divergent phenotypes, it was unclear if mechanisms of reproductive isolation also evolved convergently. Using microsatellites, we found strongly reduced gene flow between adjacent populations from different habitat types, suggesting that local adaptation to sulfidic habitats repeatedly caused the emergence of reproductive isolation. Reciprocal translocation experiments indicate strong selection against immigrants into sulfidic waters, but also variation among drainages in the strength of selection against immigrants into nonsulfidic waters. Mate choice experiments revealed the evolution of assortative mating preferences in females from nonsulfidic but not from sulfidic habitats. The inferred strength of sexual selection against immigrants (RI(s)) was negatively correlated with the strength of natural selection (RI(m)), a pattern that could be attributed to reinforcement, whereby natural selection strengthens behavioral isolation due to reduced hybrid fitness. Overall, reproductive isolation and genetic differentiation appear to be replicated and direct consequences of local adaptation to sulfide spring environments, but the relative contributions of different mechanisms of reproductive isolation vary across these evolutionarily independent replicates, highlighting both convergent and nonconvergent evolutionary trajectories of populations in each drainage. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  16. Examining applying high performance genetic data feature selection and classification algorithms for colon cancer diagnosis.

    Science.gov (United States)

    Al-Rajab, Murad; Lu, Joan; Xu, Qiang

    2017-07-01

    This paper examines the accuracy and efficiency (time complexity) of high performance genetic data feature selection and classification algorithms for colon cancer diagnosis. The need for this research derives from the urgent and increasing need for accurate and efficient algorithms. Colon cancer is a leading cause of death worldwide, hence it is vitally important for the cancer tissues to be expertly identified and classified in a rapid and timely manner, to assure both a fast detection of the disease and to expedite the drug discovery process. In this research, a three-phase approach was proposed and implemented: Phases One and Two examined the feature selection algorithms and classification algorithms employed separately, and Phase Three examined the performance of the combination of these. It was found from Phase One that the Particle Swarm Optimization (PSO) algorithm performed best with the colon dataset as a feature selection (29 genes selected) and from Phase Two that the Support Vector Machine (SVM) algorithm outperformed other classifications, with an accuracy of almost 86%. It was also found from Phase Three that the combined use of PSO and SVM surpassed other algorithms in accuracy and performance, and was faster in terms of time analysis (94%). It is concluded that applying feature selection algorithms prior to classification algorithms results in better accuracy than when the latter are applied alone. This conclusion is important and significant to industry and society. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Final Technical Report: Genetic Control of Nitrogen Assimilation in Klebsiella oxytoca.

    Energy Technology Data Exchange (ETDEWEB)

    Valley Stewart

    2007-03-07

    Klebsiella oxytoca, an enterobacterium closely related to Escherichia coli and amenable to molecular genetic analysis, is a long-established model organism for studies of bacterial nitrogen assimilation. Our work concerned utilization of purines, nitrogen-rich compounds that are widespread in the biosphere. This project began with our observation that molybdenum cofactor (chlorate-resistant) mutants can use (hypo)xanthine as sole nitrogen source (Garzón et al., J. Bacteriol. 174:6298, 1992). Since xanthine dehydrogenase is a molybdoenzyme, Klebsiella must use an alternate route for (hypo)xanthine catabolsim. We identified and characterized a cluster of 22 genes that encode the enzymes, permeases and regulators for utilizing hypoxanthine and xanthine as sole nitrogen source. (Hypoxanthine and xanthine arise from deamination of adenine and guanine, respectively.) Growth and complementation tests with insertion mutants, combined with protein sequence comparisons, allow us to assign probable functions for the products of these genes and to deduce the overall pathway. We present genetic evidence that the first two enzymes for the Klebsiella purine utilization pathway have been recruited from pathways involved in catabolism of aromatic compounds. The first, HxaAB enzyme catalyzing (hypo)xanthine oxidation, is related to well-studied aromatic ring hydroxylating oxygenases such as phthalate dioxygenase. The second, HxbA enzyme catalyzing urate hydroxylation, is related to single-component monooxygenases. Thus, the Klebsiella purine utilization pathway has likely experienced non-orthologous gene displacement, substituting these oxygenases for the conventional enzymes, xanthine dehydrogenase and uricase. We also present evidence that transcription of the hxaAB operon is subject to dual regulation: global general nitrogen regulation (Ntr) through an unknown mechanism, and (hypo)xanthine induction mediated by a LysR-type activator.

  18. Genetic analysis of a red tilapia (Oreochromis spp.) population undergoing three generations of selection for increased body weight at harvest.

    Science.gov (United States)

    Hamzah, Azhar; Thoa, Ngo Phu; Nguyen, Nguyen Hong

    2017-11-01

    Quantitative genetic analysis was performed on 10,919 data records collected over three generations from the selection programme for increased body weight at harvest in red tilapia (Oreochromis spp.). They were offspring of 224 sires and 226 dams (50 sires and 60 dams per generation, on average). Linear mixed models were used to analyse body traits (weight, length, width and depth), whereas threshold generalised models assuming probit distribution were employed to examine genetic inheritance of survival rate, sexual maturity and body colour. The estimates of heritability for traits studied (body weight, standard length, body width, body depth, body colour, early sexual maturation and survival) across statistical models were moderate to high (0.13-0.45). Genetic correlations among body traits and survival were high and positive (0.68-0.96). Body length and width exhibited negative genetic correlations with body colour (- 0.47 to - 0.25). Sexual maturity was genetically correlated positively with measurements of body traits (weight and length). Direct and correlated genetic responses to selection were measured as estimated breeding values in each generation and expressed in genetic standard deviation units (σ G ). The cumulative improvement achieved for harvest body weight was 1.72 σ G after three generations or 12.5% per generation when the gain was expressed as a percentage of the base population. Selection for improved body weight also resulted in correlated increase in other body traits (length, width and depth) and survival rate (ranging from 0.25 to 0.81 genetic standard deviation units). Avoidance of black spot parent matings also improved the overall red colour of the selected population. It is concluded that the selective breeding programme for red tilapia has succeeded in achieving significant genetic improvement for a range of commercially important traits in this species, and the large genetic variation in body colour and survival also shows that

  19. A biological/chemical process for reduced waste and energy consumption, Caprolactam production: Phase 1, Select microorganisms and demonstrate feasibility. Final report

    Energy Technology Data Exchange (ETDEWEB)

    St.Martin, E.J.

    1995-08-01

    A novel biological/chemical process for converting cyclohexane into caprolactam was investigated. Microorganisms in a bioreactor would be used to convert cyclohexane into caprolactone followed by chemical synthesis of caprolactam using ammonia. The proposed bioprocess would be more energy efficient and reduce byproducts and wastes that are generated by the current chemical process. We have been successful in isolating from natural soil and water samples two microorganisms that can utilize cyclohexane as a sole source of carbon and energy for growth. These microorganisms were shown to have the correct metabolic intermediates and enzymes to convert cyclohexane into cyclohexanol, cyclohexanone and caprolactone. Genetic techniques to create and select for caprolactone hydrolase negative-mutants are being developed. These blocked-mutants will be used to convert cyclohexane into caprolactone but, because of the block, be unable to metabolize the caprolactone further and excrete it as a final end product.

  20. An intelligent system for lung cancer diagnosis using a new genetic algorithm based feature selection method.

    Science.gov (United States)

    Lu, Chunhong; Zhu, Zhaomin; Gu, Xiaofeng

    2014-09-01

    In this paper, we develop a novel feature selection algorithm based on the genetic algorithm (GA) using a specifically devised trace-based separability criterion. According to the scores of class separability and variable separability, this criterion measures the significance of feature subset, independent of any specific classification. In addition, a mutual information matrix between variables is used as features for classification, and no prior knowledge about the cardinality of feature subset is required. Experiments are performed by using a standard lung cancer dataset. The obtained solutions are verified with three different classifiers, including the support vector machine (SVM), the back-propagation neural network (BPNN), and the K-nearest neighbor (KNN), and compared with those obtained by the whole feature set, the F-score and the correlation-based feature selection methods. The comparison results show that the proposed intelligent system has a good diagnosis performance and can be used as a promising tool for lung cancer diagnosis.

  1. Green supplier selection: a new genetic/immune strategy with industrial application

    Science.gov (United States)

    Kumar, Amit; Jain, Vipul; Kumar, Sameer; Chandra, Charu

    2016-10-01

    With the onset of the 'climate change movement', organisations are striving to include environmental criteria into the supplier selection process. This article hybridises a Green Data Envelopment Analysis (GDEA)-based approach with a new Genetic/Immune Strategy for Data Envelopment Analysis (GIS-DEA). A GIS-DEA approach provides a different view to solving multi-criteria decision making problems using data envelopment analysis (DEA) by considering DEA as a multi-objective optimisation problem with efficiency as one objective and proximity of solution to decision makers' preferences as the other objective. The hybrid approach called GIS-GDEA is applied here to a well-known automobile spare parts manufacturer in India and the results presented. User validation developed based on specific set of criteria suggests that the supplier selection process with GIS-GDEA is more practical than other approaches in a current industrial scenario with multiple decision makers.

  2. Genome-wide prediction of traits with different genetic architecture through efficient variable selection.

    Science.gov (United States)

    Wimmer, Valentin; Lehermeier, Christina; Albrecht, Theresa; Auinger, Hans-Jürgen; Wang, Yu; Schön, Chris-Carolin

    2013-10-01

    In genome-based prediction there is considerable uncertainty about the statistical model and method required to maximize prediction accuracy. For traits influenced by a small number of quantitative trait loci (QTL), predictions are expected to benefit from methods performing variable selection [e.g., BayesB or the least absolute shrinkage and selection operator (LASSO)] compared to methods distributing effects across the genome [ridge regression best linear unbiased prediction (RR-BLUP)]. We investigate the assumptions underlying successful variable selection by combining computer simulations with large-scale experimental data sets from rice (Oryza sativa L.), wheat (Triticum aestivum L.), and Arabidopsis thaliana (L.). We demonstrate that variable selection can be successful when the number of phenotyped individuals is much larger than the number of causal mutations contributing to the trait. We show that the sample size required for efficient variable selection increases dramatically with decreasing trait heritabilities and increasing extent of linkage disequilibrium (LD). We contrast and discuss contradictory results from simulation and experimental studies with respect to superiority of variable selection methods over RR-BLUP. Our results demonstrate that due to long-range LD, medium heritabilities, and small sample sizes, superiority of variable selection methods cannot be expected in plant breeding populations even for traits like FRIGIDA gene expression in Arabidopsis and flowering time in rice, assumed to be influenced by a few major QTL. We extend our conclusions to the analysis of whole-genome sequence data and infer upper bounds for the number of causal mutations which can be identified by LASSO. Our results have major impact on the choice of statistical method needed to make credible inferences about genetic architecture and prediction accuracy of complex traits.

  3. Trait variation and genetic diversity in a banana genomic selection training population.

    Directory of Open Access Journals (Sweden)

    Moses Nyine

    Full Text Available Banana (Musa spp. is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB. These include genomic selection (GS, which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31-35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R of hybrids. Genotyping using simple sequence repeat (SSR markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents.

  4. Trait variation and genetic diversity in a banana genomic selection training population.

    Science.gov (United States)

    Nyine, Moses; Uwimana, Brigitte; Swennen, Rony; Batte, Michael; Brown, Allan; Christelová, Pavla; Hřibová, Eva; Lorenzen, Jim; Doležel, Jaroslav

    2017-01-01

    Banana (Musa spp.) is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB). These include genomic selection (GS), which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31-35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R) of hybrids. Genotyping using simple sequence repeat (SSR) markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents.

  5. Trait variation and genetic diversity in a banana genomic selection training population

    Science.gov (United States)

    Nyine, Moses; Uwimana, Brigitte; Swennen, Rony; Batte, Michael; Brown, Allan; Christelová, Pavla; Hřibová, Eva; Lorenzen, Jim

    2017-01-01

    Banana (Musa spp.) is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB). These include genomic selection (GS), which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31–35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R) of hybrids. Genotyping using simple sequence repeat (SSR) markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents. PMID:28586365

  6. An intein with genetically selectable markers provides a new approach to internally label proteins with GFP

    Directory of Open Access Journals (Sweden)

    Davis Trisha N

    2011-06-01

    Full Text Available Abstract Background Inteins are proteins that catalyze their own removal from within larger precursor proteins. In the process they splice the flanking protein sequences, termed the N-and C-terminal exteins. Large inteins frequently have a homing endonuclease that is involved in maintaining the intein in the host. Splicing and nuclease activity are independent and distinct domains in the folded structure. We show here that other biochemical activities can be incorporated into an intein in place of the endonuclease without affecting splicing and that these activities can provide genetic selection for the intein. We have coupled such a genetically marked intein with GFP as the N-terminal extein to create a cassette to introduce GFP within the interior of a targeted protein. Results The Pch PRP8 mini-intein of Penicillium chrysogenum was modified to include: 1 aminoglycoside phosphotransferase; 2 imidazoleglycerol-phosphate dehydratase, His5 from S. pombe ; 3 hygromycin B phosphotransferase; and 4 the transcriptional activator LexA-VP16. The proteins were inserted at the site of the lost endonuclease. When expressed in E. coli, all of the modified inteins spliced at high efficiency. Splicing efficiency was also greater than 96% when expressed from a plasmid in S. cerevisiae. In addition the inteins conferred either G418 or hygromycin resistance, or histidine or leucine prototropy, depending on the inserted marker and the yeast genetic background. DNA encoding the marked inteins coupled to GFP as the N-terminal extein was PCR amplified with ends homologous to an internal site in the yeast calmodulin gene CMD1. The DNA was transformed into yeast and integrants obtained by direct selection for the intein's marker. The His5-marked intein yielded a fully functional calmodulin that was tagged with GFP within its central linker. Conclusions Inteins continue to show their flexibility as tools in molecular biology. The Pch PRP8 intein can successfully

  7. Genetic Parameters And Selection Response For Yield Traits In Bread Wheat Under Irrigated And Rainfed Environments

    Science.gov (United States)

    Khalil, Iftikhar Hussain; at-ur-Rahman, Hiday; Khan, Imran

    2008-01-01

    A set of 22 F5:7 experimental wheat lines along with four check cultivars (Dera-98, Fakhr-e-Sarhad, Ghaznavi-98 and Tatara) were evaluated as independent experiments under irrigated and rainfed environments using a randomized complete block design at NWFP Agricultural University, Peshawar during 2004-05. The two environments were statistically different for days to heading and spike length only. Highly significant genetic variability existed among the wheat lines (P<0.01) in the combined analysis across environments for all traits. Genotype×environment interactions were non-significant for all traits except 1000-grain weight indicating consistent performance of wheat genotypes across the two environments. Wheat lines and check cultivars were 2 to 5 days early in heading under rainfed environment compared to the irrigated. Plant height, spike length, 1000-grain weight, biological and grain yields were generally reduced under rainfed environment. Genetic variances were of greater magnitude than environmental variances for most of the traits in both environments. The heritability estimates were of higher magnitude (0.74 to 0.96) for days to heading, plant height, spike length, biological and grain yield, while medium (0.31 to 0.51) for 1000-grain weight. Selection differentials were negative for heading (-7.3 days in irrigated vs -9.4 days in rainfed) and plant height (-9.0 cm in irrigated vs -8.7 cm in rainfed) indicating possibility of selecting wheat genotypes with early heading and short plant stature. Positive selection differentials of 1.3 vs 1.6 cm for spike length, 3.8 vs 3.4 g for 1000-grain weight, 2488.2 vs 3139.7 kg ha-1 for biological yield and 691.6 vs 565.4 kg ha-1 for grain yield at 20% selection intensity were observed under irrigated and rainfed environments, respectively. Expected selection responses were 7.98 vs 8.91 days for heading, 8.20 vs 9.52 cm for plant height, 1.01 vs 1.61 cm for spike length, 2.12 vs 1.15 g for 1000-grain weight, 1655

  8. Crop yield, genetic parameter estimation and selection of sacha inchi in central Amazon

    Directory of Open Access Journals (Sweden)

    Mágno Sávio Ferreira Valente

    2017-06-01

    Full Text Available In Brazil, sacha inchi oil is produced by hand from plant materials with no breeding or detailed information about the chemical composition of seeds. In addition, most of the current information on the agronomic traits of this species originates from research carried out in the Peruvian Amazon. In order to promote the research and cultivation of sacha inchi in the Brazilian territory, this study aimed to analyze, in the central Amazon region, different accessions of this oilseed for characteristics of production and quality of fruits and seeds, as well as to estimate genetic parameters, through mixed models, with identification of superior accessions, for breeding purposes. A total of 37 non-domesticated accessions were evaluated in a randomized block design, with five replications and two plants per plot. The average oil content in seeds was 29.07 % and unsaturated fatty acids amounted to 91.5 % of the total fat content. For the yield traits, the estimates of individual broad-sense heritability were moderate (~0.33, while the heritability based on the average of progenies resulted in a selective accuracy of approximately 0.85. The use of the selection index provided simultaneous gains for yield traits (> 40 % and oil yield. A high genetic variability was observed for the main traits of commercial interest for the species, as well as promising perspectives for the development of superior varieties for agro-industrial use.

  9. Genetic gains in the UENF-14 popcorn population with recurrent selection.

    Science.gov (United States)

    Freitas, I L J; do Amaral Júnior, A T; Freitas, S P; Cabral, P D S; Ribeiro, R M; Gonçalves, L S A

    2014-01-21

    The popcorn breeding program of Universidade Estadual do Norte Fluminense Darcy Ribeiro aims to provide farmers a cultivar with desirable agronomic traits, particularly with respect to grain yield (GY) and popping expansion (PE). We evaluated full-sib families from the seventh cycle of recurrent selection and estimated the genetic progress with respect to GY and PE. Eight traits were evaluated in 200 full-sib families that were randomized into blocks with two replicates per set in two contrasting environments, Campos dos Goytacazes and Itaocara, located in north and northwest Rio de Janeiro State, respectively. There were significant differences between sets in families with respect to all traits evaluated, which indicates genetic variability that may be explored in future cycles. Using random economic weights in the selection of superior progenies, the Mulamba and Mock index showed gains for PE and GY of 5.11 and 7.78%, respectively. Significant PE and GY increases were found when comparing the evolution of mean values of these two parameters that were assessed at cycles C₀-C₆ and predicted for C₇. Thus, an advanced-cycle popcorn cultivar with genotypic superiority for the main traits of economic interest can be made available to farmers in Rio de Janeiro State.

  10. Inference of selection based on temporal genetic differentiation in the study of highly polymorphic multigene families.

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    Mark McMullan

    Full Text Available The co-evolutionary arms race between host immune genes and parasite virulence genes is known as Red Queen dynamics. Temporal fluctuations in allele frequencies, or the 'turnover' of alleles at immune genes, are concordant with predictions of the Red Queen hypothesis. Such observations are often taken as evidence of host-parasite co-evolution. Here, we use computer simulations of the Major Histocompatibility Complex (MHC of guppies (Poecilia reticulata to study the turnover rate of alleles (temporal genetic differentiation, G'(ST. Temporal fluctuations in MHC allele frequencies can be ≥≤order of magnitude larger than changes observed at neutral loci. Although such large fluctuations in the MHC are consistent with Red Queen dynamics, simulations show that other demographic and population genetic processes can account for this observation, these include: (1 overdominant selection, (2 fluctuating population size within a metapopulation, and (3 the number of novel MHC alleles introduced by immigrants when there are multiple duplicated genes. Synergy between these forces combined with migration rate and the effective population size can drive the rapid turnover in MHC alleles. We posit that rapid allelic turnover is an inherent property of highly polymorphic multigene families and that it cannot be taken as evidence of Red Queen dynamics. Furthermore, combining temporal samples in spatial F(ST outlier analysis may obscure the signal of selection.

  11. Genetic differentiation of the malaria vector Anopheles gambiae across Nigeria suggests that selection limits gene flow.

    Science.gov (United States)

    Onyabe, D Y; Conn, J E

    2001-12-01

    Gene flow was investigated in Anopheles gambiae from eight localities that span the ecological zones of Nigeria (arid savanna zones in the north gradually turn into humid forest zones in the south). Genetic differentiation was measured over 10 microsatellite loci and, to determine any effects of selection, five loci were located within chromosome inversions and the other five were outside inversions. Over all loci, the largest estimates of differentiation were in comparisons between localities in the savanna vs. forest zones (range FST 0.024-0.087, Nm 2.6-10.1; RST 0.014-0.100, Nm 2.2-16.4). However, three loci located within inversions on chromosome II, whose frequencies varied clinically from north to south, were responsible for virtually all of the differentiation. When the three loci were removed, genetic distances across the remaining seven loci were markedly reduced even between localities in the forest and savanna zones (range FST 0.001-0.019, Nm 12.7-226.1) or no longer significant (P > 0.05) in the case of RST. Although tests of isolation by distance gave seemingly equivocal results, geographical distance does not appear to limit gene flow. These observations suggest that gene flow is extensive across the country but that selection on genes located within some inversions on chromosome II counters the homogenizing effects of gene flow.

  12. Adaptation through genetic time travel? Fluctuating selection can drive the evolution of bacterial transformation.

    Science.gov (United States)

    Engelstädter, Jan; Moradigaravand, Danesh

    2014-01-22

    Natural transformation is a process whereby bacteria actively take up DNA from the surrounding environment and incorporate it into their genome. Natural transformation is widespread in bacteria, but its evolutionary significance is still debated. Here, we hypothesize that transformation may confer a fitness advantage in changing environments through a process we term 'genetic time travel': by taking up old genes that were retained in the environment, the bacteria may revert to a past genotypic state that proves advantageous in the present or a future environment. We scrutinize our hypothesis by means of a mathematical model involving two bacterial types (transforming and non-transforming), a single locus under natural selection and a free DNA pool. The two bacterial types were competed in environments with changing selection regimes. We demonstrate that for a wide range of parameter values for the DNA turnover rate, the transformation rate and the frequency of environmental change, the transforming type outcompetes the non-transforming type. We discuss the empirical plausibility of our hypothesis, as well as its relationship to other hypotheses for the evolution of transformation in bacteria and sex more generally, speculating that 'genetic time travel' may also be relevant in eukaryotes that undergo horizontal gene transfer.

  13. Antifungal activity and genetic diversity of selected Pseudomonas spp. from maize rhizosphere in Vojvodina

    Directory of Open Access Journals (Sweden)

    Jošić Dragana

    2012-01-01

    Full Text Available Antibiotic production by plant-associated microorganisms represents an environmentally compatible method of disease control in agriculture. However, a vide application of bacterial strains needs careful selection and genetic characterization. In this investigation, selected Pseudomonas strains were characterized by rep-PCR methods using ERIC and (GTG5 primers, and partial 16S rDNA sequence analysis. None of strains produced homoserine lactones (C4, C6, C8 as quorum sensing signal molecules. Very poor production of phenazines and no significant fungal inhibition was observed for PS4 and PS6 strains. High amount of phenazines were produced by Pseudomonas sp. strain PS2, which inhibited mycelial growth of 10 phytopatogenic fungi in percent of 25 (Verticillium sp. to 65 (Fusarium equiseti. Genetic characterization of the Pseudomonas sp. PS2 and evaluation of phenazines production, as the main trait for growth inhibition of phytopathogenic fungi, will allow its application as a biosafe PGPR for field experiments of plant disease control. [Projekat Ministarstva nauke Republike Srbije, br. III 46007: New indigenous bacterial isolates Lysobacter and Pseudomonas as an important sources of metabolites useful for biotechnology, plant growth stimulation and disease control: From isolates to inoculants

  14. Genetic variation in resistance to ionizing radiation. Final report, January 1, 1990--December 31, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Ayala, F.J.

    1992-12-31

    Results of an investigation of the gene coding for Cu, Zn superoxide dismutase (Sod) in Drosophila melanogaster seeking to understand the enzyme`s role in cell protection against ionizing radiation are reported. Components of the investigation include molecular characterization of the gene; measuring the response of different genotypes to increasing levels of radiation; and investigation of the processes that maintain the Sod polymorphism in populations. While two alleles, S and F, are commonly found at the Sod locus in natural populations of D. melanogaster we have isolated from a natural population a null (CA1) mutant that yields only 3.5% of normal SOD activity. The S, F, and CA1 alleles provide a model system to investigate SOD-dependent radioresistance, because each allele yields different levels of SOD, so that S > F >> CAl. The radioprotective effects of SOD can be established by showing protective effects for the various genotypes that correspond to those inequalities. Because the allele variants studied are derived from natural populations, the proposed investigation avoids problems that arise when mutants obtained my mutagenesis are used. Moreover, each allele is studied in multiple genetic backgrounds, so that we correct for effects attributable to other loci by randomizing these effects.

  15. Genetic signatures of natural selection in response to air pollution in red spruce (Picea rubens, Pinaceae).

    Science.gov (United States)

    Bashalkhanov, Stanislav; Eckert, Andrew J; Rajora, Om P

    2013-12-01

    One of the most important drivers of local adaptation for forest trees is climate. Coupled to these patterns, however, are human-induced disturbances through habitat modification and pollution. The confounded effects of climate and disturbance have rarely been investigated with regard to selective pressure on forest trees. Here, we have developed and used a population genetic approach to search for signals of selection within a set of 36 candidate genes chosen for their putative effects on adaptation to climate and human-induced air pollution within five populations of red spruce (Picea rubens Sarg.), distributed across its natural range and air pollution gradient in eastern North America. Specifically, we used FST outlier and environmental correlation analyses to highlight a set of seven single nucleotide polymorphisms (SNPs) that were overly correlated with climate and levels of sulphate pollution after correcting for the confounding effects of population history. Use of three age cohorts within each population allowed the effects of climate and pollution to be separated temporally, as climate-related SNPs (n = 7) showed the strongest signals in the oldest cohort, while pollution-related SNPs (n = 3) showed the strongest signals in the youngest cohorts. These results highlight the usefulness of population genetic scans for the identification of putatively nonneutral evolution within genomes of nonmodel forest tree species, but also highlight the need for the development and application of robust methodologies to deal with the inherent multivariate nature of the genetic and ecological data used in these types of analyses. © 2013 John Wiley & Sons Ltd.

  16. Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian.

    Science.gov (United States)

    Cortázar-Chinarro, Maria; Lattenkamp, Ella Z; Meyer-Lucht, Yvonne; Luquet, Emilien; Laurila, Anssi; Höglund, Jacob

    2017-08-14

    Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.

  17. Estimation of genetic parameters and selection of high-yielding, upright common bean lines with slow seed-coat darkening.

    Science.gov (United States)

    Alvares, R C; Silva, F C; Melo, L C; Melo, P G S; Pereira, H S

    2016-11-21

    Slow seed coat darkening is desirable in common bean cultivars and genetic parameters are important to define breeding strategies. The aims of this study were to estimate genetic parameters for plant architecture, grain yield, grain size, and seed-coat darkening in common bean; identify any genetic association among these traits; and select lines that associate desirable phenotypes for these traits. Three experiments were set up in the winter 2012 growing season, in Santo Antônio de Goiás and Brasília, Brazil, including 220 lines obtained from four segregating populations and five parents. A triple lattice 15 x 15 experimental design was used. The traits evaluated were plant architecture, grain yield, grain size, and seed-coat darkening. Analyses of variance were carried out and genetic parameters such as heritability, gain expected from selection, and correlations, were estimated. For selection of superior lines, a "weight-free and parameter-free" index was used. The estimates of genetic variance, heritability, and gain expected from selection were high, indicating good possibility for success in selection of the four traits. The genotype x environment interaction was proportionally more important for yield than for the other traits. There was no strong genetic correlation observed among the four traits, which indicates the possibility of selection of superior lines with many traits. Considering simultaneous selection, it was not possible to join high genetic gains for the four traits. Forty-four lines that combined high yield, more upright plant architecture, slow darkening grains, and commercial grade size were selected.

  18. [Employees in high-reliability organizations: systematic selection of personnel as a final criterion].

    Science.gov (United States)

    Oubaid, V; Anheuser, P

    2014-05-01

    Employees represent an important safety factor in high-reliability organizations. The combination of clear organizational structures, a nonpunitive safety culture, and psychological personnel selection guarantee a high level of safety. The cockpit personnel selection process of a major German airline is presented in order to demonstrate a possible transferability into medicine and urology.

  19. Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies.

    Science.gov (United States)

    Chen, Jun; Källman, Thomas; Ma, Xiao-Fei; Zaina, Giusi; Morgante, Michele; Lascoux, Martin

    2016-07-07

    The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI. Copyright © 2016 Chen et al.

  20. A New Spectral Shape-Based Record Selection Approach Using Np and Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Edén Bojórquez

    2013-01-01

    Full Text Available With the aim to improve code-based real records selection criteria, an approach inspired in a parameter proxy of spectral shape, named Np, is analyzed. The procedure is based on several objectives aimed to minimize the record-to-record variability of the ground motions selected for seismic structural assessment. In order to select the best ground motion set of records to be used as an input for nonlinear dynamic analysis, an optimization approach is applied using genetic algorithms focuse on finding the set of records more compatible with a target spectrum and target Np values. The results of the new Np-based approach suggest that the real accelerograms obtained with this procedure, reduce the scatter of the response spectra as compared with the traditional approach; furthermore, the mean spectrum of the set of records is very similar to the target seismic design spectrum in the range of interest periods, and at the same time, similar Np values are obtained for the selected records and the target spectrum.

  1. Genetic variation assessed with microsatellites in mass selection lines of the Pacific oyster ( Crassostrea gigas) in China

    Science.gov (United States)

    Wang, Xubo; Li, Qi; Yu, Hong; Kong, Lingfeng

    2016-12-01

    Four successive mass selection lines of the Pacific oyster, Crassostrea gigas, selected for faster growth in breeding programs in China were examined at ten polymorphic microsatellite loci to assess the level of allelic diversity and estimate the effective population size. These data were compared with those of their base population. The results showed that the genetic variation of the four generations were maintained at high levels with an average allelic richness of 18.8-20.6, and a mean expected heterozygosity of 0.902-0.921. They were not reduced compared with those of their base population. Estimated effective population sizes based on temporal variances in microsatellite frequencies were smaller to that of sex ratio-corrected broodstock count estimates. Using a relatively large number of broodstock and keeping an equal sex ratio in the broodstock each generation may have contributed to retaining the original genetic diversity and maintaining relatively large effective population size. The results obtained in this study showed that the genetic variation was not affected greatly by mass selection progress and high genetic variation still existed in the mass selection lines, suggesting that there is still potential for increasing the gains in future generations of C. gigas. The present study provided important information for future genetic improvement by selective breeding, and for the design of suitable management guidelines for genetic breeding of C. gigas.

  2. Final Technical Report: Genetic and Molecular Analysis of a new control pathway in assimilate partitioning.

    Energy Technology Data Exchange (ETDEWEB)

    Bush, Daniel, R.

    2009-03-10

    Assimilate partitioning refers to the systemic distribution of photoassimilate from sites of primary assimilation (source tissue) to import-dependent tissues and organs (sinks). One of the defining questions in this area is how plants balance source productivity with sink demand. We discovered a sucrose-sensing signal transduction pathway that controls the activity of BvSUT1, a proton-sucrose symporter in sugar beet leaf tissue. Sucrose symporters are responsible for sucrose accumulation in the phloem of many plants and, therefore, they mediate the pivotal step in the long-distance transport of photoassimilate to non-photosynthetic tissues, such as roots and seed. We previously showed that sucrose transport activity is directly proportional to the transcription rate of BvSUT1 and that symporter mRNA and protein have high rates of turnover with half-lives on the order of 2 h. We further demonstrated that symporter transcription is regulated by sucrose levels in the leaf and that sucrose-dependent regulation of BvSUT1 transcription is mediated, at least in part, by a protein phosphorylation relay pathway. The goal of the experiments during this current grant were to use genetic and molecular approaches to identify essential components of this vital regulatory system. The initial objectives were to: (1) to characterize Arabidopsis mutants we've isolated that are resistant to growth inhibition by sucrose analogues that are recognized by the sucrose-sensor, (2) to screen for loss of function mutants in BvSUT1-promoter:luciferase transgenic plants that no longer respond to sucrose accumulation in the leaf using non-destructive visualization of luciferase activity, (3) to use gel mobility-shift assays and nuclease protection experiments to identify cis elements in the symporter promoter and DNA-binding proteins that are involved in sucrose regulation of symporter expression.

  3. The Effects of Both Recent and Long-Term Selection and Genetic Drift Are Readily Evident in North American Barley Breeding Populations

    Directory of Open Access Journals (Sweden)

    Ana M. Poets

    2016-03-01

    Full Text Available Barley was introduced to North America ∼400 yr ago but adaptation to modern production environments is more recent. Comparisons of allele frequencies among growth habits and spike (inflorescence types in North America indicate that significant genetic differentiation has accumulated in a relatively short evolutionary time span. Allele frequency differentiation is greatest among barley with two-row vs. six-row spikes, followed by spring vs. winter growth habit. Large changes in allele frequency among breeding programs suggest a major contribution of genetic drift and linked selection on genetic variation. Despite this, comparisons of 3613 modern North American cultivated barley breeding lines that differ for spike-type and growth habit permit the discovery of 142 single nucleotide polymorphism (SNP outliers putatively linked to targets of selection. For example, SNPs within the Cbf4, Ppd-H1, and Vrn-H1 loci, which have previously been associated with agronomically adaptive phenotypes, are identified as outliers. Analysis of extended haplotype sharing identifies genomic regions shared within and among breeding populations, suggestive of a number of genomic regions subject to recent selection. Finally, we are able to identify recent bouts of gene flow between breeding populations that could point to the sharing of agronomically adaptive variation. These results are supported by pedigrees and breeders’ understanding of germplasm sharing.

  4. Selectivity in Genetic Association with Sub-classified Migraine in Women

    Science.gov (United States)

    Chasman, Daniel I.; Anttila, Verneri; Buring, Julie E.; Ridker, Paul M.; Schürks, Markus; Kurth, Tobias

    2014-01-01

    Migraine can be sub-classified not only according to presence of migraine aura (MA) or absence of migraine aura (MO), but also by additional features accompanying migraine attacks, e.g. photophobia, phonophobia, nausea, etc. all of which are formally recognized by the International Classification of Headache Disorders. It remains unclear how aura status and the other migraine features may be related to underlying migraine pathophysiology. Recent genome-wide association studies (GWAS) have identified 12 independent loci at which single nucleotide polymorphisms (SNPs) are associated with migraine. Using a likelihood framework, we explored the selective association of these SNPs with migraine, sub-classified according to aura status and the other features in a large population-based cohort of women including 3,003 active migraineurs and 18,108 free of migraine. Five loci met stringent significance for association with migraine, among which four were selective for sub-classified migraine, including rs11172113 (LRP1) for MO. The number of loci associated with migraine increased to 11 at suggestive significance thresholds, including five additional selective associations for MO but none for MA. No two SNPs showed similar patterns of selective association with migraine characteristics. At one extreme, SNPs rs6790925 (near TGFBR2) and rs2274316 (MEF2D) were not associated with migraine overall, MA, or MO but were selective for migraine sub-classified by the presence of one or more of the additional migraine features. In contrast, SNP rs7577262 (TRPM8) was associated with migraine overall and showed little or no selectivity for any of the migraine characteristics. The results emphasize the multivalent nature of migraine pathophysiology and suggest that a complete understanding of the genetic influence on migraine may benefit from analyses that stratify migraine according to both aura status and the additional diagnostic features used for clinical characterization of

  5. Development and Validation of Marker-Aided Selection Methods for Wood Property Traits in Loblolly Pine and Hybrid Poplar; FINAL

    International Nuclear Information System (INIS)

    Tuskan, G.A.

    2001-01-01

    Wood properties influence pulp and paper quality. Certainly, overall pulp yields are directly related to the cellulose content, changes in hemicellulose content are associated with changes in pulp cohesiveness, and pulping efficiency is related to lignin content. Despite the importance of wood properties on product quality, little progress has been made in improving such traits because current methods of assessing wood and fiber characteristics are time-consuming, expensive, and often imprecise. Genetic improvement of wood and fiber properties has been further hampered by the large size of trees, delayed reproductive maturity and long harvest cycles. Recent developments in molecular genetics will help overcome the physical, economic and biological constraints in assessing and improving wood properties. Genetic maps consisting of numerous molecular markers are now available for loblolly pine and hybrid poplar. Such markers/maps may be used as part of a marker-aided selection and breeding effort or to expedite the isolation and characterization of genes and/or promoters that directly control wood properties. The objectives of this project are: (1) to apply new and rapid analytical techniques for assessing component wood properties to segregating F(sub 2) progeny populations of loblolly pine and hybrid poplar, (2) to map quantitative trait loci and identify molecular markers associated with wood properties in each of the above species and (3) to validate marker-aided selection methods for wood properties in loblolly pine and hybrid poplar

  6. Long-term response to genomic selection: effects of estimation method and reference population structure for different genetic architectures.

    Science.gov (United States)

    Bastiaansen, John W M; Coster, Albart; Calus, Mario P L; van Arendonk, Johan A M; Bovenhuis, Henk

    2012-01-24

    Genomic selection has become an important tool in the genetic improvement of animals and plants. The objective of this study was to investigate the impacts of breeding value estimation method, reference population structure, and trait genetic architecture, on long-term response to genomic selection without updating marker effects. Three methods were used to estimate genomic breeding values: a BLUP method with relationships estimated from genome-wide markers (GBLUP), a Bayesian method, and a partial least squares regression method (PLSR). A shallow (individuals from one generation) or deep reference population (individuals from five generations) was used with each method. The effects of the different selection approaches were compared under four different genetic architectures for the trait under selection. Selection was based on one of the three genomic breeding values, on pedigree BLUP breeding values, or performed at random. Selection continued for ten generations. Differences in long-term selection response were small. For a genetic architecture with a very small number of three to four quantitative trait loci (QTL), the Bayesian method achieved a response that was 0.05 to 0.1 genetic standard deviation higher than other methods in generation 10. For genetic architectures with approximately 30 to 300 QTL, PLSR (shallow reference) or GBLUP (deep reference) had an average advantage of 0.2 genetic standard deviation over the Bayesian method in generation 10. GBLUP resulted in 0.6% and 0.9% less inbreeding than PLSR and BM and on average a one third smaller reduction of genetic variance. Responses in early generations were greater with the shallow reference population while long-term response was not affected by reference population structure. The ranking of estimation methods was different with than without selection. Under selection, applying GBLUP led to lower inbreeding and a smaller reduction of genetic variance while a similar response to selection was

  7. Temporally isolated lineages of Pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation

    DEFF Research Database (Denmark)

    Limborg, Morten; Waples, R.K.; Seeb, J.E.

    2014-01-01

    A species’ genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbu...

  8. Selection for Cry3Bb1 resistance in a genetically diverse population of nondiapausing Western Corn Rootworm (Coleoptera: Chrysomelidae)

    Science.gov (United States)

    Five short-diapause laboratory lines of western corn rootworm (Diabrotica virgifera virgifera) were selected for resistance to MON863, a variety of corn genetically modified with the Bacillus thuringiensis (Bt) transgene that expresses the Cry3Bb1 endotoxin. Three of the selecte...

  9. Improved feature selection based on genetic algorithms for real time disruption prediction on JET

    Energy Technology Data Exchange (ETDEWEB)

    Ratta, G.A., E-mail: garatta@gateme.unsj.edu.ar [GATEME, Facultad de Ingenieria, Universidad Nacional de San Juan, Avda. San Martin 1109 (O), 5400 San Juan (Argentina); JET EFDA, Culham Science Centre, OX14 3DB Abingdon (United Kingdom); Vega, J. [Asociacion EURATOM/CIEMAT para Fusion, Avda. Complutense, 40, 28040 Madrid (Spain); JET EFDA, Culham Science Centre, OX14 3DB Abingdon (United Kingdom); Murari, A. [Associazione EURATOM-ENEA per la Fusione, Consorzio RFX, 4-35127 Padova (Italy); JET EFDA, Culham Science Centre, OX14 3DB Abingdon (United Kingdom)

    2012-09-15

    Highlights: Black-Right-Pointing-Pointer A new signal selection methodology to improve disruption prediction is reported. Black-Right-Pointing-Pointer The approach is based on Genetic Algorithms. Black-Right-Pointing-Pointer An advanced predictor has been created with the new set of signals. Black-Right-Pointing-Pointer The new system obtains considerably higher prediction rates. - Abstract: The early prediction of disruptions is an important aspect of the research in the field of Tokamak control. A very recent predictor, called 'Advanced Predictor Of Disruptions' (APODIS), developed for the 'Joint European Torus' (JET), implements the real time recognition of incoming disruptions with the best success rate achieved ever and an outstanding stability for long periods following training. In this article, a new methodology to select the set of the signals' parameters in order to maximize the performance of the predictor is reported. The approach is based on 'Genetic Algorithms' (GAs). With the feature selection derived from GAs, a new version of APODIS has been developed. The results are significantly better than the previous version not only in terms of success rates but also in extending the interval before the disruption in which reliable predictions are achieved. Correct disruption predictions with a success rate in excess of 90% have been achieved 200 ms before the time of the disruption. The predictor response is compared with that of JET's Protection System (JPS) and the ADODIS predictor is shown to be far superior. Both systems have been carefully tested with a wide number of discharges to understand their relative merits and the most profitable directions of further improvements.

  10. Improved feature selection based on genetic algorithms for real time disruption prediction on JET

    International Nuclear Information System (INIS)

    Rattá, G.A.; Vega, J.; Murari, A.

    2012-01-01

    Highlights: ► A new signal selection methodology to improve disruption prediction is reported. ► The approach is based on Genetic Algorithms. ► An advanced predictor has been created with the new set of signals. ► The new system obtains considerably higher prediction rates. - Abstract: The early prediction of disruptions is an important aspect of the research in the field of Tokamak control. A very recent predictor, called “Advanced Predictor Of Disruptions” (APODIS), developed for the “Joint European Torus” (JET), implements the real time recognition of incoming disruptions with the best success rate achieved ever and an outstanding stability for long periods following training. In this article, a new methodology to select the set of the signals’ parameters in order to maximize the performance of the predictor is reported. The approach is based on “Genetic Algorithms” (GAs). With the feature selection derived from GAs, a new version of APODIS has been developed. The results are significantly better than the previous version not only in terms of success rates but also in extending the interval before the disruption in which reliable predictions are achieved. Correct disruption predictions with a success rate in excess of 90% have been achieved 200 ms before the time of the disruption. The predictor response is compared with that of JET's Protection System (JPS) and the ADODIS predictor is shown to be far superior. Both systems have been carefully tested with a wide number of discharges to understand their relative merits and the most profitable directions of further improvements.

  11. Selecting representative microsatellite loci for genetic monitoring and analyzing genetic structure of an outbred population of orange tabby cats in China.

    Science.gov (United States)

    Du, X Y; Yi, S; Huo, X Y; Wang, C; Liu, D F; Ren, W Z; Chen, Z W

    2015-03-13

    We optimized a panel of microsatellite markers from cat and tiger genetic data for efficient genetic monitoring and used it to analyze the genetic structure of an outbred cat stock in China. We selected a set of rich polymorphic microsatellite loci from 131 cat microsatellite loci and 3 Sumatran tiger microsatellite loci using agarose gel electrophoresis. Next, the set of optimized genetic markers was used to analyze the genetic variation in an outbred population of orange tabby cats in China by simple-tandem repeat scanning. Thirty-one loci rich in polymorphisms were selected and the highest allele number in a single locus was 8. Analysis of the orange tabby cat population illustrated that the average observed number of alleles, mean effective allele number, mean Shannon's information index, mean expected heterozygosity, and observed heterozygosity were 3.8387, 2.4027, 0.9787, 0.5565, and 0.5528, respectively. The 31 microsatellite markers used were polymorphic and suitable for analyzing the genetic structure of cats. The population of orange tabby cats was confirmed to be a well-outbred stock.

  12. Geneletter: An Internet-based newsletter on the ethical, legal, and social implications of genetics. Final report to the Department of Energy [Final report

    Energy Technology Data Exchange (ETDEWEB)

    Reilly, Philip; Wertz, Dorothy C.

    2001-05-01

    The GeneLetter (http://www.geneletter.org) is an Internet newsletter on ethical, legal, and social issues in genetics, designed for a wide and varied audience, some of whom may not be familiar with genetic science. It appears every two months, with a variety of long and short feature articles on ethics and on genetic disorders, a section on new federal and state legislation, an international section, a student corner, book and video reviews, a summary of genetics in the news, and a list of upcoming conferences. Feature articles have ventured into an area of wide general concern, behavioral genetics. The newsletter also has an interactive chatbox and the opportunity of more private communications with the editors via email. The purpose of the GeneLetter is to help fill a communication and knowledge gap on ethical, legal and social issues surrounding genetics.

  13. Engineering evaluation of selective ion-exchange radioactive waste processing at Susquehanna Nuclear Power Plant: Final report

    International Nuclear Information System (INIS)

    Vance, J.N.

    1989-01-01

    This final report describes the work performed of an engineering feasibility evaluation of the use and benefits of a selective ion exchange treatment process in the Susquehanna radwaste system. The evaluation addressed operability and processing capability concerns, radiological impacts of operating in the radwaste discharge mode, required hardware modifications to the radwaste and plant make-up systems, impacts on plant water quality limits and impacts on higher waste classifications. An economic analysis is also reported showing the economic benefit of the use of selective ion exchange. 1 ref., 4 figs., 13 tabs

  14. Genetic algorithm based input selection for a neural network function approximator with applications to SSME health monitoring

    Science.gov (United States)

    Peck, Charles C.; Dhawan, Atam P.; Meyer, Claudia M.

    1991-01-01

    A genetic algorithm is used to select the inputs to a neural network function approximator. In the application considered, modeling critical parameters of the space shuttle main engine (SSME), the functional relationship between measured parameters is unknown and complex. Furthermore, the number of possible input parameters is quite large. Many approaches have been used for input selection, but they are either subjective or do not consider the complex multivariate relationships between parameters. Due to the optimization and space searching capabilities of genetic algorithms they were employed to systematize the input selection process. The results suggest that the genetic algorithm can generate parameter lists of high quality without the explicit use of problem domain knowledge. Suggestions for improving the performance of the input selection process are also provided.

  15. Population Bottlenecks Increase Additive Genetic Variance But Do Not Break a Selection Limit in Rainforest Drosophila

    DEFF Research Database (Denmark)

    van Heerwaarden, Belinda; Willi, Yvonne; Kristensen, Torsten N

    2008-01-01

    According to neutral quantitative genetic theory, population bottlenecks are expected to decrease standing levels of additive genetic variance of quantitative traits. However, some empirical and theoretical results suggest that, if nonadditive genetic effects influence the trait, bottlenecks may ...

  16. The Genetic Legacy of Zoroastrianism in Iran and India: Insights into Population Structure, Gene Flow, and Selection.

    Science.gov (United States)

    López, Saioa; Thomas, Mark G; van Dorp, Lucy; Ansari-Pour, Naser; Stewart, Sarah; Jones, Abigail L; Jelinek, Erik; Chikhi, Lounès; Parfitt, Tudor; Bradman, Neil; Weale, Michael E; Hellenthal, Garrett

    2017-09-07

    Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present genome-wide autosomal, Y chromosome, and mitochondrial DNA data from Iranian and Indian Zoroastrians and neighboring modern-day Indian and Iranian populations and conduct a comprehensive genome-wide genetic analysis in these groups. Using powerful haplotype-based techniques, we find that Zoroastrians in Iran and India have increased genetic homogeneity relative to other sampled groups in their respective countries, consistent with their current practices of endogamy. Despite this, we infer that Indian Zoroastrians (Parsis) intermixed with local groups sometime after their arrival in India, dating this mixture to 690-1390 CE and providing strong evidence that Iranian Zoroastrian ancestry was maintained primarily through the male line. By making use of the rich information in DNA from ancient human remains, we also highlight admixture in the ancestors of Iranian Zoroastrians dated to 570 BCE-746 CE, older than admixture seen in any other sampled Iranian group, consistent with a long-standing isolation of Zoroastrians from outside groups. Finally, we report results, and challenges, from a genome-wide scan to identify genomic regions showing signatures of positive selection in present-day Zoroastrians that might correlate to the prevalence of particular diseases among these communities. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  17. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution.

    Directory of Open Access Journals (Sweden)

    Matteo Fumagalli

    2011-11-01

    Full Text Available Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate. To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation. Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies. This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the

  18. Shared Selective Pressures on Fungal and Human Metabolic Pathways Lead to Divergent yet Analogous Genetic Responses.

    Science.gov (United States)

    Eidem, Haley R; McGary, Kriston L; Rokas, Antonis

    2015-06-01

    Reduced metabolic efficiency, toxic intermediate accumulation, and deficits of molecular building blocks, which all stem from disruptions of flux through metabolic pathways, reduce organismal fitness. Although these represent shared selection pressures across organisms, the genetic signatures of the responses to them may differ. In fungi, a frequently observed signature is the physical linkage of genes from the same metabolic pathway. In contrast, human metabolic genes are rarely tightly linked; rather, they tend to show tissue-specific coexpression. We hypothesized that the physical linkage of fungal metabolic genes and the tissue-specific coexpression of human metabolic genes are divergent yet analogous responses to the range of selective pressures imposed by disruptions of flux. To test this, we examined the degree to which the human homologs of physically linked metabolic genes in fungi (fungal linked homologs or FLOs) are coexpressed across six human tissues. We found that FLOs are significantly more correlated in their expression profiles across human tissues than other metabolic genes. We obtained similar results in analyses of the same six tissues from chimps, gorillas, orangutans, and macaques. We suggest that when selective pressures remain stable across large evolutionary distances, evidence of selection in a given evolutionary lineage can become a highly reliable predictor of the signature of selection in another, even though the specific adaptive response in each lineage is markedly different. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution.

    Science.gov (United States)

    Fumagalli, Matteo; Sironi, Manuela; Pozzoli, Uberto; Ferrer-Admetlla, Anna; Ferrer-Admettla, Anna; Pattini, Linda; Nielsen, Rasmus

    2011-11-01

    Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate. To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation. Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies. This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the hypothesis that some

  20. Engineered Dwarf Male-Sterile Rice: A Promising Genetic Tool for Facilitating Recurrent Selection in Rice.

    Science.gov (United States)

    Ansari, Afsana; Wang, Chunlian; Wang, Jian; Wang, Fujun; Liu, Piqing; Gao, Ying; Tang, Yongchao; Zhao, Kaijun

    2017-01-01

    Rice is a crop feeding half of the world's population. With the continuous raise of yield potential via genetic improvement, rice breeding has entered an era where multiple genes conferring complex traits must be efficiently manipulated to increase rice yield further. Recurrent selection is a sound strategy for manipulating multiple genes and it has been successfully performed in allogamous crops. However, the difficulties in emasculation and hand pollination had obstructed efficient use of recurrent selection in autogamous rice. Here, we report development of the dwarf male-sterile rice that can facilitate recurrent selection in rice breeding. We adopted RNAi technology to synergistically regulate rice plant height and male fertility to create the dwarf male-sterile rice. The RNAi construct pTCK-EGGE, targeting the OsGA20ox2 and OsEAT1 genes, was constructed and used to transform rice via Agrobacterium -mediated transformation. The transgenic T0 plants showing largely reduced plant height and complete male-sterile phenotypes were designated as the dwarf male-sterile plants. Progenies of the dwarf male-sterile plants were obtained by pollinating them with pollens from the wild-type. In the T1 and T2 populations, half of the plants were still dwarf male-sterile; the other half displayed normal plant height and male fertility which were designated as tall and male-fertile plants. The tall and male-fertile plants are transgene-free and can be self-pollinated to generate new varieties. Since emasculation and hand pollination for dwarf male-sterile rice plants is no longer needed, the dwarf male-sterile rice can be used to perform recurrent selection in rice. A dwarf male-sterile rice-based recurrent selection model has been proposed.

  1. Final state selection in the 4p photoemission of Rb by combining laser spectroscopy with soft-x-ray photoionization

    International Nuclear Information System (INIS)

    Schulz, J.; Tchaplyguine, M.; Rander, T.; Bergersen, H.; Lindblad, A.; Oehrwall, G.; Svensson, S.; Heinaesmaeki, S.; Sankari, R.; Osmekhin, S.; Aksela, S.; Aksela, H.

    2005-01-01

    Fine structure resolved 4p photoemission studies have been performed on free rubidium atoms in the ground state and after excitation into the [Kr]5p 2 P 1/2 and 2 P 3/2 states. The 4p 5 5p final states have been excited in the 4p 6 5s→4p 5 5p conjugate shakeup process from ground state atoms as well as by direct photoemission from laser excited atoms. The relative intensities differ considerably in these three excitation schemes. The differences in the laser excited spectra could be described well using calculations based on the pure jK-coupling scheme. Thereby it was possible to specify the character of the various final states. Furthermore it has been possible to resolve two of the final states whose energy separation is smaller than the experimental resolution by selectively exciting them in a two step scheme, where the laser selects the spin-orbit coupling in the intermediate state and determines the final state coupling after x-ray photoemission

  2. Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

    Directory of Open Access Journals (Sweden)

    Mallikarjuna Rao eKovi

    2015-11-01

    Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US] from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  3. Genetic selection system allowing monitoring of myofibrillogenesis in living cardiomyocytes derived from mouse embryonic stem cells

    Directory of Open Access Journals (Sweden)

    R Bugorsky

    2009-08-01

    Full Text Available Embryonic stem (ES cell-derived cardiomyocytes recapitulate cardiomyogenesis in vitro and are a potential source of cells for cardiac repair. However, this requires enrichment of mixed populations of differentiating ES cells into cardiomyocytes. Toward this goal, we have generated bicistronic vectors that express both the blasticidin S deaminase (bsd gene and a fusion protein consisting of either myosin light chain (MLC-3f or human a-actinin 2A and enhanced green fluorescent protein (EGFP under the transcriptional control of the a-cardiac myosin heavy chain (a-MHC promoter. Insertion of the DNase I-hypersensitive site (HS-2 element from the b-globin locus control region, which has been shown to reduce transgene silencing in other cell systems, upstream of the transgene promoter enhanced MLC3f-EGFP gene expression levels in mouse ES cell lines. The a-MHC-a- actinin-EGFP, but not the a-MHC-MLC3f-EGFP, construct resulted in the correct incorporation of the newly synthesized fusion protein at the Z-band of the sarcomeres in ES cellderived cardiomyocytes. Exposure of embryoid bodies to blasticidin S selected for a relatively pure population of cardiomyocytes within 3 days. Myofibrillogenesis could be monitored by fluorescence microscopy in living cells due to sarcomeric epitope tagging. Therefore, this genetic system permits the rapid selection of a relatively pure population of developing cardiomyocytes from a heterogeneous population of differentiating ES cells, simultaneously allowing monitoring of early myofibrillogenesis in the selected myocytes.

  4. Genetic architecture, inter-relationship and selection criteria for yield improvement in rice (Oryza sativa L.).

    Science.gov (United States)

    Yadav, S K; Pandey, P; Kumar, B; Suresh, B G

    2011-05-01

    This study has been conducted to determine the extent of genetic association between yield of Rice (Oryza sativa L.) and its components. The present experiment was carried out with 40 Rice (Oryza sativa L.) genotypes which were evaluated in a randomized block design with 3 replications during wet season of 2007 and 2008. Results showed that sufficient amount of variability was found in the entire gene pool for all traits studied. Higher magnitude of genotypic and phenotypic coefficients of variation was recorded for seed yield, harvest index, biological yield, number of spikelets per panicle, flag leaf length, plant height and number of tillers indicates that these characters are least influence by environment. High heritability coupled with high genetic advance as percent of mean was registered for seed yield, harvest index, number of spikelets per panicle, biological yield and flag leaf length, suggesting preponderance of additive gene action in the expression of these characters. Grain yield was significantly and positively associated with harvest index, number of tillers per hill, number of panicle per plant, panicle length, number of spikelet's per panicle and test weight at both genotypic and phenotypic levels. Path coefficient analysis revealed that harvest index, biological yield, number of tillers per hill, panicle length, number of spikelets per panicle, plant height and test weight had direct positive effect on seed yield, indicating these are the main contributors to yield. From this study it may be concluded that harvest index, number of tillers per hill, panicle length and number of spikelet per panicle and test weight are the most important characters that contributed directly to yield. Thus, these characters may serve selection criteria for improving genetic potential of rice.

  5. Genetic potential of common bean progenies selected for crude fiber content obtained through different breeding methods.

    Science.gov (United States)

    Júnior, V A P; Melo, P G S; Pereira, H S; Bassinello, P Z; Melo, L C

    2015-05-29

    Gastrointestinal health is of great importance due to the increasing consumption of functional foods, especially those concern-ing diets rich in fiber content. The common bean has been valorized as a nutritious food due to its appreciable fiber content and the fact that it is consumed in many countries. The current study aimed to evaluate and compare the genetic potential of common bean progenies of the carioca group, developed through different breeding methods, for crude fiber content. The progenies originated through hybridization of two advanced strains, CNFC 7812 and CNFC 7829, up to the F7 generation using three breeding methods: bulk-population, bulk within F2 families, and single seed descent. Fifteen F8 progenies were evaluated in each method, as well as two check cultivars and both parents, us-ing a 7 x 7 simple lattice design, with experimental plots comprised of two 4-m long rows. Field trials were conducted in eleven environments encompassing four Brazilian states and three different sowing times during 2009 and 2010. Estimates of genetic parameters indicate differences among the breeding methods, which seem to be related to the different processes for sampling the advanced progenies inherent to each method, given that the trait in question is not subject to natural selection. Variability amongst progenies occurred within the three breeding methods and there was also a significant effect of environment on the progeny for all methods. Progenies developed by bulk-population attained the highest estimates of genetic parameters, had less interaction with the environment, and greater variability.

  6. Genetic analysis of the regulation of TCH gene expression, Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Braam, Janet

    2008-10-28

    multiple XTH::GUS genes suggesting that XTHs may contribute to morphogenesis at every developmental stage and in every plant organ. Different XTHs have remarkably diverse and distinct expression patterns indicating that paralogous genes have evolved differential expression regulation perhaps contributing to the maintenance of the large gene family. Extensive overlap in XTH expression patterns is evident; thus, XTHs may act combinatorially in determining wall properties of specific tissues or organs. Knowledge of gene-specific expression among family members yields evidence of where and when gene products may function and provides insights to guide rational approaches to investigate function through reverse genetics.

  7. Presence of Stenotrophomonas maltophilia exhibiting high genetic similarity to clinical isolates in final effluents of pig farm wastewater treatment plants.

    Science.gov (United States)

    Kim, Young-Ji; Park, Jin-Hyeong; Seo, Kun-Ho

    2018-03-01

    Although the prevalence of community-acquired Stenotrophomonas maltophilia infections is sharply increasing, the sources and likely transmission routes of this bacterium are poorly understood. We studied the significance of the presence of S. maltophilia in final effluents and receiving rivers of pig farm wastewater treatment plants (WWTPs). The loads and antibiotic resistance profiles of S. maltophilia in final effluents were assessed. Antibiotic resistance determinants and biofilm formation genes were detected by PCR, and genetic similarity to clinical isolates was investigated using multilocus sequence typing (MLST). S. maltophilia was recovered from final effluents at two of three farms and one corresponding receiving river. Tests of resistance to antibiotics recommended for S. maltophilia infection revealed that for each agent, at least one isolate was classified as resistant or intermediate, with the exception of minocycline. Furthermore, multidrug resistant S. maltophilia susceptible to antibiotics of only two categories was isolated and found to carry the sul2 gene, conferring trimethoprim/sulfamethoxazole resistance. All isolates carried spgM, encoding a major factor in biofilm formation. MLST revealed that isolates of the same sequence type (ST; ST189) were present in both effluent and receiving river samples, and phylogenetic analysis showed that all of the STs identified in this study clustered with clinical isolates. Moreover, one isolate (ST192) recovered in this investigation demonstrated 99.61% sequence identity with a clinical isolate (ST98) associated with a fatal infection in South Korea. Thus, the pathogenicity of the isolates reported here is likely similar to that of those from clinical environments, and WWTPs may play a role as a source of S. maltophilia from which this bacterium spreads to human communities. To the best of our knowledge, this represents the first report of S. maltophilia in pig farm WWTPs. Our results indicate that

  8. Genetic algorithm based feature selection combined with dual classification for the automated detection of proliferative diabetic retinopathy.

    Science.gov (United States)

    Welikala, R A; Fraz, M M; Dehmeshki, J; Hoppe, A; Tah, V; Mann, S; Williamson, T H; Barman, S A

    2015-07-01

    Proliferative diabetic retinopathy (PDR) is a condition that carries a high risk of severe visual impairment. The hallmark of PDR is the growth of abnormal new vessels. In this paper, an automated method for the detection of new vessels from retinal images is presented. This method is based on a dual classification approach. Two vessel segmentation approaches are applied to create two separate binary vessel map which each hold vital information. Local morphology features are measured from each binary vessel map to produce two separate 4-D feature vectors. Independent classification is performed for each feature vector using a support vector machine (SVM) classifier. The system then combines these individual outcomes to produce a final decision. This is followed by the creation of additional features to generate 21-D feature vectors, which feed into a genetic algorithm based feature selection approach with the objective of finding feature subsets that improve the performance of the classification. Sensitivity and specificity results using a dataset of 60 images are 0.9138 and 0.9600, respectively, on a per patch basis and 1.000 and 0.975, respectively, on a per image basis. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Construction and genetic selection of small transmembrane proteins that activate the human erythropoietin receptor.

    Science.gov (United States)

    Cammett, Tobin J; Jun, Susan J; Cohen, Emily B; Barrera, Francisco N; Engelman, Donald M; Dimaio, Daniel

    2010-02-23

    This work describes a genetic approach to isolate small, artificial transmembrane (TM) proteins with biological activity. The bovine papillomavirus E5 protein is a dimeric, 44-amino acid TM protein that transforms cells by specifically binding and activating the platelet-derived growth factor beta receptor (PDGFbetaR). We used the E5 protein as a scaffold to construct a retrovirus library expressing approximately 500,000 unique 44-amino acid proteins with randomized TM domains. We screened this library to select small, dimeric TM proteins that were structurally unrelated to erythropoietin (EPO), but specifically activated the human EPO receptor (hEPOR). These proteins did not activate the murine EPOR or the PDGFbetaR. Genetic studies with one of these activators suggested that it interacted with the TM domain of the hEPOR. Furthermore, this TM activator supported erythroid differentiation of primary human hematopoietic progenitor cells in vitro in the absence of EPO. Thus, we have changed the specificity of a protein so that it no longer recognizes its natural target but, instead, modulates an entirely different protein. This represents a novel strategy to isolate small artificial proteins that affect diverse membrane proteins. We suggest the word "traptamer" for these transmembrane aptamers.

  10. Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups.

    Science.gov (United States)

    Cesconeto, Robson Jose; Joost, Stéphane; McManus, Concepta Margaret; Paiva, Samuel Rezende; Cobuci, Jaime Araujo; Braccini, Jose

    2017-11-01

    Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as F ST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in both methods, with a Kappa value of 0.073 (95% CI: 0.011-0.134). The frequency of these markers indicated a clear north-south country division that reflects Brazilian environmental differences in temperature, solar radiation, and precipitation. Global spatial territory correlation for environmental variables corroborates this finding (average Moran's I = 0.89, range from 0.55 to 0.97). The distribution of alleles over the territory was not strongly correlated with the breed/genetic groups. These results are congruent with previous mtDNA studies and should be used to direct germplasm collection for the National gene bank.

  11. Genetic feature selection to optimally detect P300 in brain computer interfaces.

    Science.gov (United States)

    Atum, Yanina; Gareis, Iván; Gentiletti, Gerardo; Acevedo, Rubén; Rufiner, Leonardo

    2010-01-01

    A Brain Computer Interface is a system that provides an artificial communication between the human brain and the external world. The paradigm based on event related evoked potentials is used in this work. Our main goal was to efficiently solve a binary classification problem: presence or absence of P300 in the registers. Genetic Algorithms and Support Vector Machines were used in a wrapper configuration for feature selection and classification. The original input patterns were provided by two channels (Oz and Fz) of resampled EEG registers and wavelet coefficients. To evaluate the performance of the system, accuracy, sensibility and specificity were calculated. The wrapped wavelet patterns show a better performance than the temporal ones. The results were similar for patterns from channel Oz and Fz, together or separated.

  12. A Genetic Algorithm for Selection of Fixed-Size Subsets with Application to Design Problems

    Directory of Open Access Journals (Sweden)

    Mark A. Wolters

    2015-11-01

    Full Text Available The R function kofnGA conducts a genetic algorithm search for the best subset of k items from a set of n alternatives, given an objective function that measures the quality of a subset. The function fills a gap in the presently available subset selection software, which typically searches over a range of subset sizes, restricts the types of objective functions considered, or does not include freely available code. The new function is demonstrated on two types of problem where a fixed-size subset search is desirable: design of environmental monitoring networks, and D-optimal design of experiments. Additionally, the performance is evaluated on a class of constructed test problems with a novel design that is interesting in its own right.

  13. Genetic improvement and evaluation of black cottonwood for short- rotation biomass production. Final report, 1987--1992

    Energy Technology Data Exchange (ETDEWEB)

    Stettler, R.F.; Hinckley, T.M. [Washington Univ., Seattle, WA (United States). Coll. of Forest Resources; Heilman, P.E. [Washington State Univ., Puyallup, WA (United States). Research and Extension Center; Bradshaw, H.D. Jr. [Washington Univ., Seattle, WA (United States). Dept. of Biochemistry

    1993-04-30

    This project was initiated in 1978 to serve three objectives: (1) develop genetically improved poplar cultivars offering increased productivity under short-rotation culture; (2) identify the major components of productivity in poplar and determine ways in which they can be manipulated, genetically and culturally; and (3) engage in technology transfer to regional industry and agencies so as to make poplar culture in the Pacific Northwest economically feasible. The project is aimed at capturing natural variation in the native black cottonwood. Populus trichocarpa T & G, and enhancing it through selective breeding. Major emphasis has been placed on hybridization of black cottonwood with P deltoides and P maximowiczii, more recently with p nigra. First-generation (F{sub 1}) hybrids have consistently outperformed black cottonwood by a factor of 1.5.-2. The high yields of woody biomass obtained from these clonally propagated hybrids, in rotations of 4-7 years, have fostered the establishment of large-scale plantations by the pulp and paper industry in the region. Physiological studies have helped to elucidate hybrid superiority and several of the underlying mechanisms.

  14. Most of the Long-Term Genetic Gains from Optimum-Contribution Selection can be Realised with Restrictions Imposed

    DEFF Research Database (Denmark)

    Henryon, Mark; Ostersen, Tage; Ask, Birgitte

    Text: We reasoned that optimum-contribution selection (OCS) with restrictions imposed during optimisation will realise most of the long-term genetic gains realised by OCS without restrictions. We used stochastic simulation to estimate long-term rates of genetic gain realised by breeding schemes...... using OCS without and with restrictions imposed during optimisation. In all but a few exceptions, the long-term rates of genetic gain realised by OCS with restrictions was 95-100% of the rates realised by OCS without restrictions. It was only when the restrictions became overly strict that we began...... to lose gain. We also present evidence from the Danish pig-breeding scheme for Duroc that practical implementation of OCS with restrictions increases genetic gains and decreases rates of inbreeding. OCS has gone from a selection method that was difficult to apply in practice, to one that is readily...

  15. Available phosphorus in diets for 15 to 30 kg pigs genetically selected for meat deposition

    Directory of Open Access Journals (Sweden)

    Cláudio Luiz Corrêa Arouca

    2012-01-01

    Full Text Available With the objective to evaluate the effect of dietary available phosphorus levels (aP on the performance, blood and bone parameters of castrated male and female pigs, genetically selected for meat deposition, 60 commercial hybrids pigs with initial weight of 15.54±0.68 kg were allotted in a completely randomized block design, with six treatments (0.103, 0.210, 0.317, 0.424, 0.531, and 0.638% aP, five replicates, and two animals per experimental unit. Pigs were fed ad libitum and water was provided until the end of the experimental period (21 days, when animals reached 31.31±2.94 kg. Daily weight gain and daily feed intake increased, while the feed conversion improved quadratically up to 0.534, 0.487, and 0.574% aP maximum responses, respectively. The aP intake and the values of inorganic phosphorus in serum increased linearly with increasing the levels of aP in the diets. Alkaline phosphatase activity increased quadratically up to 0.558% maximum response. Bone breaking strength and calcium, phosphorus, and ash contents in the bones increased linearly with increasing aP concentration in the diets. The available phosphorus requirement of castrated male and female pigs genetically selected for meat deposition from 15 to 30 kg for best results of performance is 0.574%, corresponding to a daily intake of 8.26 g of available phosphorus.

  16. Gendered dimensions in ERC grant selection - gendERC : Final Report

    NARCIS (Netherlands)

    Schiffbaenker, Helene; van den Besselaar, P.A.A.

    2017-01-01

    To explain lower success rates of female applicants in ERC grants, we collected data about past performance of the applicants and interviewed panel members about how selection criteria are practiced in general and specifically for female vs. male applicants. Controlling for past performance, we

  17. Discourse, Paragraph, and Sentence Structure in Selected Philippine Languages. Final Report. Volume II, Sentence Structure.

    Science.gov (United States)

    Longacre, Robert E.

    Volume II of "Discourse, Paragraph, and Sentence Structure in Selected Philippine Languages" begins with an explanation of certain assumptions and postulates regarding sentence structure. A detailed treatment of systems of sentence structure and the parameters of such systems follows. Data in the various indigenous languages are…

  18. 76 FR 33740 - Final Priorities and Selection Criterion; National Institute on Disability and Rehabilitation...

    Science.gov (United States)

    2011-06-09

    ... selection criterion. Public Comment: In response to our invitation in the NPP, nine parties submitted... treating SCI and innovative approaches to assessing outcomes. This commenter stated that it would be more reasonable to require projects to test either innovative approaches to treating SCI or innovative approaches...

  19. 76 FR 21985 - Notice of Final Priorities, Requirements, Definitions, and Selection Criteria

    Science.gov (United States)

    2011-04-19

    ... take these actions to focus Federal financial assistance on the pressing need to improve the assessment... on the ELP assessment system and not on academic performance. The commenter noted that excluding..., Requirements, Definitions, and Selection Criteria Enhanced Assessment Instruments; Catalog of Federal Domestic...

  20. A Comparison of a Selected Dimension of Counselor and Non-Counselor Behavior. Final Report.

    Science.gov (United States)

    Gellen, Murray I.

    To determine whether or not counselors are demonstrably different from noncounselors in terms of empathy, the concept of empathy was translated into an operational variable consisting of an affective (tonal) component and a cognitive (perceptual) component. Some 11 items judged as affect-laden by two rater groups were selected from the Squires…

  1. Can Selective MHC Downregulation Explain the Specificity and Genetic Diversity of NK Cell Receptors?

    Science.gov (United States)

    Carrillo-Bustamante, Paola; Kesmir, Can; de Boer, Rob J.

    2015-01-01

    Natural killer (NK) cells express inhibiting receptors (iNKRs), which specifically bind MHC-I molecules on the surface of healthy cells. When the expression of MHC-I on the cell surface decreases, which might occur during certain viral infections and cancer, iNKRs lose inhibiting signals and the infected cells become target for NK cell activation (missing-self detection). Although the detection of MHC-I deficient cells can be achieved by conserved receptor-ligand interactions, several iNKRs are encoded by gene families with a remarkable genetic diversity, containing many haplotypes varying in gene content and allelic polymorphism. So far, the biological function of this expansion within the NKR cluster has remained poorly understood. Here, we investigate whether the evolution of diverse iNKRs genes can be driven by a specific viral immunoevasive mechanism: selective MHC downregulation. Several viruses, including EBV, CMV, and HIV, decrease the expression of MHC-I to escape from T cell responses. This downregulation does not always affect all MHC loci in the same way, as viruses target particular MHC molecules. To study the selection pressure of selective MHC downregulation on iNKRs, we have developed an agent-based model simulating an evolutionary scenario of hosts infected with herpes-like viruses, which are able to selectively downregulate the expression of MHC-I molecules on the cell surface. We show that iNKRs evolve specificity and, depending on the similarity of MHC alleles within each locus and the differences between the loci, they can specialize to a particular MHC-I locus. The easier it is to classify an MHC allele to its locus, the lower the required diversity of the NKRs. Thus, the diversification of the iNKR cluster depends on the locus specific MHC structure. PMID:26136746

  2. Balancing selection, random genetic drift, and genetic variation at the major histocompatibility complex in two wild populations of guppies (Poecilia reticulata).

    Science.gov (United States)

    Van Oosterhout, Cock; Joyce, Domino A; Cummings, Stephen M; Blais, Jonatan; Barson, Nicola J; Ramnarine, Indar W; Mohammed, Ryan S; Persad, Nadia; Cable, Joanne

    2006-12-01

    Our understanding of the evolution of genes of the major histocompatibility complex (MHC) is rapidly increasing, but there are still enigmatic questions remaining, particularly regarding the maintenance of high levels of MHC polymorphisms in small, isolated populations. Here, we analyze the genetic variation at eight microsatellite loci and sequence variation at exon 2 of the MHC class IIB (DAB) genes in two wild populations of the Trinidadian guppy, Poecilia reticulata. We compare the genetic variation of a small (Ne, 100) and relatively isolated upland population to that of its much larger (Ne approximately 2400) downstream counterpart. As predicted, microsatellite diversity in the upland population is significantly lower and highly differentiated from the population further downstream. Surprisingly, however, these guppy populations are not differentiated by MHC genetic variation and show very similar levels of allelic richness. Computer simulations indicate that the observed level of genetic variation can be maintained with overdominant selection acting at three DAB loci. The selection coefficients differ dramatically between the upland (s > or = 0.2) and lowland (s guppies in the upland habitat, which has resulted in high levels of MHC diversity being maintained in this population despite considerable genetic drift.

  3. Stochastic dynamic simulation modeling including multitrait genetics to estimate genetic, technical, and financial consequences of dairy farm reproduction and selection strategies.

    Science.gov (United States)

    Kaniyamattam, K; Elzo, M A; Cole, J B; De Vries, A

    2016-10-01

    The objective of this study was to develop a daily stochastic dynamic dairy simulation model that included multitrait genetics and to evaluate the effects of reduced genetic models and various reproduction and selection strategies on the genetic, technical, and financial performance of a dairy herd. The 12 correlated genetic traits included in the 2014 lifetime net merit (NM$) index were modeled for each animal. For each animal, a true breeding value (TBV) for each trait was calculated as the average of the sire's and dam's TBV, plus a fraction of the inbreeding and Mendelian sampling variability. Similarly, an environmental component for each trait was calculated and was partitioned into a permanent and a daily (temporary) effect. The combined TBV and environmental effects were converted into the phenotypic performance of each animal. Hence, genetics and phenotypic performances were associated. Estimated breeding values (EBV) were also simulated. Genetic trends for each trait for the service sire were based on expected trends in US Holsteins. Surplus heifers were culled based on various ranking criteria to maintain a herd size of 1,000 milking cows. In the first 8 scenarios, culling of surplus heifers was either random or based on the EBV of NM$. Four different genetic models, depending on the presence or absence of genetic trends or genetic and environmental correlations, or both, were evaluated to measure the effect of excluding multitrait genetics on animal performance. In the last 5 scenarios, the full genetic model was used and culling of surplus heifers was either random or based on the EBV of NM$ or the EBV of milk. Sexed semen use and reliability of the EBV were also varied. Each scenario was simulated for 15yr into the future. Results showed that genetic models without all 12 genetic trends and genetic and environmental correlations provided biased estimates of the genetic, technical, and financial performance of the dairy herd. Average TBV of NM$ of all

  4. Which Individuals To Choose To Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs.

    Science.gov (United States)

    Eynard, Sonia E; Croiseau, Pascal; Laloë, Denis; Fritz, Sebastien; Calus, Mario P L; Restoux, Gwendal

    2018-01-04

    Genomic selection (GS) is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC) strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations. Copyright © 2018 Eynard et al.

  5. Which Individuals To Choose To Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs

    Directory of Open Access Journals (Sweden)

    Sonia E. Eynard

    2018-01-01

    Full Text Available Genomic selection (GS is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations.

  6. Social and economical aspects in the selection of the site for the final Goiania waste repository

    International Nuclear Information System (INIS)

    Paschoa, A.S.; Tranjan Filho, A.; Rosenthal, J.J.

    2000-01-01

    Site selection criteria for low and intermediate level waste repositories are usually well established as far as the technological and scientific bases are concerned. However, social, cultural and economical aspects need to be examined on a case by case basis because there are many situations to be faced before succeeding to convince the public and authorities that a waste repository is to be built at any chosen site. In the specific case of Goiania there is an ongoing process that started several years ago, to make the repository accepted by local, state and national authorities, and to answer legitimate questions raised by significant segments of the population. This paper will summarise those more relevant aspects concerning the site selection process for the Goiania repository. (author)

  7. Comparing the effects of genetic drift and fluctuating selection on genotype frequency changes in the scarlet tiger moth.

    Science.gov (United States)

    O'Hara, R B

    2005-01-22

    One of the recurring arguments in evolutionary biology is whether evolution occurs principally through natural selection or through neutral processes such as genetic drift. A 60-year-long time series of changes in the genotype frequency of a colour polymorphism of the scarlet tiger moth, Callimorpha dominula, was used to compare the relative effects of genetic drift and variable natural selection. The analysis showed that most of the variation in frequency was the result of genetic drift. In addition, although selection was acting, mean fitness barely increased. This supports the 'Red Queen's hypothesis' that long-term improvements in fitness may not occur, because populations have to keep pace with changes in the environment.

  8. Improving the Selection, Classification, and Utilization of Army Enlisted Personnel: Final Report on Project A

    Science.gov (United States)

    1991-08-01

    Houston (1980), and Peterson, Houston, and Rosse (1984) to identify predictors for the cbs of firefighter, correctional officer , and entry-level occupations...for Industrial and Organiza- tional Psychology, Atlanta. Peterson, N. 6., & Houston, J. S. (1980). The prediction of correctional officer Job...M. J., & Dunnette, HI. D. (1977). A study of the correctional officer job at Marion Correctional Institu- tion, Ohio: Development of selection

  9. Analysis of factors affecting the final body weight in selected rabbit breeds

    Directory of Open Access Journals (Sweden)

    Jacek Zawiślak

    2015-06-01

    Full Text Available The objective of this research was to determine the effect of breed, feed type and sex, on the final body weight in New Zealand white and Blanc de Termonde rabbits. The experiment was conducted on a farm in the Małopolska Province in the south of Poland. Rabbits of both breeds were kept in identical conditions up to the age of 90 days. However, they were fed using two different methods – with commercial balanced (granulated feed (9.75 MJ, 155 g protein and farm-made feed (9.54 MJ, 157 g protein. Among New Zealand White rabbits, commercial balanced feed was given to 38 males and 42 females, whereas farm-made feed to 37 males and 38 females. Among Blanc de Termonde rabbits, commercial balanced feed was given to 65 males and 68 females, and farm-made feed to 54 males and 60 females. Daily gains were determined for both examined breeds divided into sexes. Then, we calculated interactions between breed and feed type, between breed and sex, as well as between feed type and sex. The mean body weights on the 90th day of fattening differed for both sexes and feed types. For both rabbit breeds, the higher mean final body weight was observed in case of feeding with the commercial balanced feed, whereas the highest body weight (2515.13 g was registered for the females of Blanc de Termonde rabbits.

  10. The cost of ethanol production from lignocellulosic biomass -- A comparison of selected alternative processes. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Grethlein, H.E.; Dill, T.

    1993-04-30

    The purpose of this report is to compare the cost of selected alternative processes for the conversion of lignocellulosic biomass to ethanol. In turn, this information will be used by the ARS/USDA to guide the management of research and development programs in biomass conversion. The report will identify where the cost leverages are for the selected alternatives and what performance parameters need to be achieved to improve the economics. The process alternatives considered here are not exhaustive, but are selected on the basis of having a reasonable potential in improving the economics of producing ethanol from biomass. When other alternatives come under consideration, they should be evaluated by the same methodology used in this report to give fair comparisons of opportunities. A generic plant design is developed for an annual production of 25 million gallons of anhydrous ethanol using corn stover as the model substrate at $30/dry ton. Standard chemical engineering techniques are used to give first order estimates of the capital and operating costs. Following the format of the corn to ethanol plant, there are nine sections to the plant; feed preparation, pretreatment, hydrolysis, fermentation, distillation and dehydration, stillage evaporation, storage and denaturation, utilities, and enzyme production. There are three pretreatment alternatives considered: the AFEX process, the modified AFEX process (which is abbreviated as MAFEX), and the STAKETECH process. These all use enzymatic hydrolysis and so an enzyme production section is included in the plant. The STAKETECH is the only commercially available process among the alternative processes.

  11. Among-year variation in selection during early life stages and the genetic basis of fitness in Arabidopsis thaliana.

    Science.gov (United States)

    Postma, Froukje M; Ågren, Jon

    2018-04-19

    Incomplete information regarding both selection regimes and the genetic basis of fitness limits our understanding of adaptive evolution. Among-year variation in the genetic basis of fitness is rarely quantified, and estimates of selection are typically based on single components of fitness, thus potentially missing conflicting selection acting during other life-history stages. Here, we examined among-year variation in selection on a key life-history trait and the genetic basis of fitness covering the whole life cycle in the annual plant Arabidopsis thaliana. We planted freshly-matured seeds of >200 recombinant inbred lines (RILs) derived from a cross between two locally-adapted populations (Italy and Sweden), and both parental genotypes at the native site of the Swedish population in three consecutive years. We quantified selection against the nonlocal Italian genotype, mapped quantitative trait loci (QTL) for fitness and its components, and quantified selection on timing of germination during different life stages. In all three years, the local Swedish genotype outperformed the non-local Italian genotype. However, both the contribution of early life stages to relative fitness, and the effects of fitness QTL varied among years. Timing of germination was under conflicting selection through seedling establishment vs. adult survival and fecundity, and both the direction and magnitude of net selection varied among years. Our results demonstrate that selection during early life stages and the genetic basis of fitness can vary markedly among years, emphasizing the need for multi-year studies considering the whole life cycle for a full understanding of natural selection and mechanisms maintaining local adaptation. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  12. The effects of selective breeding against scrapie susceptibility on the genetic variability of the Latxa Black-Faced sheep breed

    Directory of Open Access Journals (Sweden)

    Legarra Andrés

    2006-09-01

    Full Text Available Abstract Breeding sheep populations for scrapie resistance could result in a loss of genetic variability. In this study, the effect on genetic variability of selection for increasing the ARR allele frequency was estimated in the Latxa breed. Two sources of information were used, pedigree and genetic polymorphisms (fifteen microsatellites. The results based on the genealogical information were conditioned by a low pedigree completeness level that revealed the interest of also using the information provided by the molecular markers. The overall results suggest that no great negative effect on genetic variability can be expected in the short time in the population analysed by selection of only ARR/ARR males. The estimated average relationship of ARR/ARR males with reproductive females was similar to that of all available males whatever its genotype: 0.010 vs. 0.012 for a genealogical relationship and 0.257 vs. 0.296 for molecular coancestry, respectively. However, selection of only ARR/ARR males implied important losses in founder animals (87 percent and low frequency alleles (30 percent in the ram population. The evaluation of mild selection strategies against scrapie susceptibility based on the use of some ARR heterozygous males was difficult because the genetic relationships estimated among animals differed when pedigree or molecular information was used, and the use of more molecular markers should be evaluated.

  13. Genetic versus antigenic differences among highly pathogenic H5N1 avian influenza A viruses: Consequences for vaccine strain selection.

    Science.gov (United States)

    Peeters, Ben; Reemers, Sylvia; Dortmans, Jos; de Vries, Erik; de Jong, Mart; van de Zande, Saskia; Rottier, Peter J M; de Haan, Cornelis A M

    2017-03-01

    Highly pathogenic H5N1 avian influenza A viruses display a remarkable genetic and antigenic diversity. We examined to what extent genetic distances between several H5N1 viruses from different clades correlate with antigenic differences and vaccine performance. H5-specific antisera were generated, and cross-reactivity and antigenic distances between 12 different viruses were determined. In general, antigenic distances increased proportional to genetic distances although notable exceptions were observed. Antigenic distances correlated better with genetic variation in 27 selected, antigenically-relevant H5 residues, than in the complete HA1 domain. Variation in these selected residues could accurately predict the antigenic distances for a novel H5N8 virus. Protection provided by vaccines against heterologous H5N1 challenge viruses indicated that cross-protection also correlates better with genetic variation in the selected antigenically-relevant residues than in complete HA1. When time is limited, variation at these selected residues may be used to accurately predict antigenic distance and vaccine performance. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Feature selection for disruption prediction from scratch in JET by using genetic algorithms and probabilistic predictors

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Augusto, E-mail: augusto.pereira@ciemat.es [Laboratorio Nacional de Fusión, CIEMAT, Madrid (Spain); Vega, Jesús; Moreno, Raúl [Laboratorio Nacional de Fusión, CIEMAT, Madrid (Spain); Dormido-Canto, Sebastián [Dpto. Informática y Automática – UNED, Madrid (Spain); Rattá, Giuseppe A. [Laboratorio Nacional de Fusión, CIEMAT, Madrid (Spain); Pavón, Fernando [Dpto. Informática y Automática – UNED, Madrid (Spain)

    2015-10-15

    Recently, a probabilistic classifier has been developed at JET to be used as predictor from scratch. It has been applied to a database of 1237 JET ITER-like wall (ILW) discharges (of which 201 disrupted) with good results: success rate of 94% and false alarm rate of 4.21%. A combinatorial analysis between 14 features to ensure the selection of the best ones to achieve good enough results in terms of success rate and false alarm rate was performed. All possible combinations with a number of features between 2 and 7 were tested and 9893 different predictors were analyzed. An important drawback in this analysis was the time required to compute the results that can be estimated in 1731 h (∼2.4 months). Genetic algorithms (GA) are searching algorithms that simulate the process of natural selection. In this article, the GA and the Venn predictors are combined with the objective not only of finding good enough features within the 14 available ones but also of reducing the computational time requirements. Five different performance metrics as measures of the GA fitness function have been evaluated. The best metric was the measurement called Informedness, with just 6 generations (168 predictors at 29.4 h).

  15. Feature selection for outcome prediction in oesophageal cancer using genetic algorithm and random forest classifier.

    Science.gov (United States)

    Paul, Desbordes; Su, Ruan; Romain, Modzelewski; Sébastien, Vauclin; Pierre, Vera; Isabelle, Gardin

    2017-09-01

    The outcome prediction of patients can greatly help to personalize cancer treatment. A large amount of quantitative features (clinical exams, imaging, …) are potentially useful to assess the patient outcome. The challenge is to choose the most predictive subset of features. In this paper, we propose a new feature selection strategy called GARF (genetic algorithm based on random forest) extracted from positron emission tomography (PET) images and clinical data. The most relevant features, predictive of the therapeutic response or which are prognoses of the patient survival 3 years after the end of treatment, were selected using GARF on a cohort of 65 patients with a local advanced oesophageal cancer eligible for chemo-radiation therapy. The most relevant predictive results were obtained with a subset of 9 features leading to a random forest misclassification rate of 18±4% and an areas under the of receiver operating characteristic (ROC) curves (AUC) of 0.823±0.032. The most relevant prognostic results were obtained with 8 features leading to an error rate of 20±7% and an AUC of 0.750±0.108. Both predictive and prognostic results show better performances using GARF than using 4 other studied methods. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. DWFS: A Wrapper Feature Selection Tool Based on a Parallel Genetic Algorithm

    KAUST Repository

    Soufan, Othman

    2015-02-26

    Many scientific problems can be formulated as classification tasks. Data that harbor relevant information are usually described by a large number of features. Frequently, many of these features are irrelevant for the class prediction. The efficient implementation of classification models requires identification of suitable combinations of features. The smaller number of features reduces the problem\\'s dimensionality and may result in higher classification performance. We developed DWFS, a web-based tool that allows for efficient selection of features for a variety of problems. DWFS follows the wrapper paradigm and applies a search strategy based on Genetic Algorithms (GAs). A parallel GA implementation examines and evaluates simultaneously large number of candidate collections of features. DWFS also integrates various filteringmethods thatmay be applied as a pre-processing step in the feature selection process. Furthermore, weights and parameters in the fitness function of GA can be adjusted according to the application requirements. Experiments using heterogeneous datasets from different biomedical applications demonstrate that DWFS is fast and leads to a significant reduction of the number of features without sacrificing performance as compared to several widely used existing methods. DWFS can be accessed online at www.cbrc.kaust.edu.sa/dwfs.

  17. Selection of male-sterile and dwarfism genetically modified zoysia japonica through gamma irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Tae Woong; Song, In Ja; Kang, Hong Gyu; Jeong, Ok Cheol; Sun, Hyeon Jin; Ko, Suk Min; Lim, Pyung Ok; Song, Pill Soon; Song, Sung Jun; Lee, Hyo Yeon [Jeju National University, Jeju (Korea, Republic of)

    2010-09-15

    The aim of this study is selection of the male-sterile plant for inhibiting transgene flow through gamma-irradiation ({sup 60}Co) at the pollination and fertilization cycle of herbicide-tolerant genetically modified (GM) zoysiagrass (Zoysia japonica Steud.). High frequencies of plant mutations were obtained about 18% from M{sub 1} generation at the doses (10 to 50 Gy). We also found that some M{sub 1} plants showed male-sterile plants using de-husked seeds and comparison of stainable pollen using KI-I{sub 2} solution. Besides the effects of irradiation on pollination and fertilization cycle, various other mutation like dwarf, cold tolerance, increasing grains and mass were observed. Four of dwarfism plants were selected through comparison of morphological characteristic between control and mutants during 4 years. These results demonstrated that the gamma-irradiation on pollination and fertilization cycle is very effective to induce the various mutations, and the male-sterile mutants are useful for controlling transgene flow and developing of high quality turfgasses.

  18. Post-translocational adaptation drives evolution through genetic selection and transcriptional shift in Saccharomyces cerevisiae.

    Science.gov (United States)

    Tosato, Valentina; Sims, Jason; West, Nicole; Colombin, Martina; Bruschi, Carlo V

    2017-05-01

    Adaptation by natural selection might improve the fitness of an organism and its probability to survive in unfavorable environmental conditions. Decoding the genetic basis of adaptive evolution is one of the great challenges to deal with. To this purpose, Saccharomyces cerevisiae has been largely investigated because of its short division time, excellent aneuploidy tolerance and the availability of the complete sequence of its genome with a thorough genome database. In the past, we developed a system, named bridge-induced translocation, to trigger specific, non-reciprocal translocations, exploiting the endogenous recombination system of budding yeast. This technique allows users to generate a heterogeneous population of cells with different aneuploidies and increased phenotypic variation. In this work, we demonstrate that ad hoc chromosomal translocations might induce adaptation, fostering selection of thermo-tolerant yeast strains with improved phenotypic fitness. This "yeast eugenomics" correlates with a shift to enhanced expression of genes involved in stress response, heat shock as well as carbohydrate metabolism. We propose that the bridge-induced translocation is a suitable approach to generate adapted, physiologically boosted strains for biotechnological applications.

  19. Feature selection for disruption prediction from scratch in JET by using genetic algorithms and probabilistic predictors

    International Nuclear Information System (INIS)

    Pereira, Augusto; Vega, Jesús; Moreno, Raúl; Dormido-Canto, Sebastián; Rattá, Giuseppe A.; Pavón, Fernando

    2015-01-01

    Recently, a probabilistic classifier has been developed at JET to be used as predictor from scratch. It has been applied to a database of 1237 JET ITER-like wall (ILW) discharges (of which 201 disrupted) with good results: success rate of 94% and false alarm rate of 4.21%. A combinatorial analysis between 14 features to ensure the selection of the best ones to achieve good enough results in terms of success rate and false alarm rate was performed. All possible combinations with a number of features between 2 and 7 were tested and 9893 different predictors were analyzed. An important drawback in this analysis was the time required to compute the results that can be estimated in 1731 h (∼2.4 months). Genetic algorithms (GA) are searching algorithms that simulate the process of natural selection. In this article, the GA and the Venn predictors are combined with the objective not only of finding good enough features within the 14 available ones but also of reducing the computational time requirements. Five different performance metrics as measures of the GA fitness function have been evaluated. The best metric was the measurement called Informedness, with just 6 generations (168 predictors at 29.4 h).

  20. Novel genetic tools for diaminopimelic acid selection in virulence studies of Yersinia pestis.

    Science.gov (United States)

    Bland, David M; Eisele, Nicholas A; Keleher, Lauren L; Anderson, Paul E; Anderson, Deborah M

    2011-03-02

    Molecular studies of bacterial virulence are enhanced by expression of recombinant DNA during infection to allow complementation of mutants and expression of reporter proteins in vivo. For highly pathogenic bacteria, such as Yersinia pestis, these studies are currently limited because deliberate introduction of antibiotic resistance is restricted to those few which are not human treatment options. In this work, we report the development of alternatives to antibiotics as tools for host-pathogen research during Yersinia pestis infections focusing on the diaminopimelic acid (DAP) pathway, a requirement for cell wall synthesis in eubacteria. We generated a mutation in the dapA-nlpB(dapX) operon of Yersinia pestis KIM D27 and CO92 which eliminated the expression of both genes. The resulting strains were auxotrophic for diaminopimelic acid and this phenotype was complemented in trans by expressing dapA in single and multi-copy. In vivo, we found that plasmids derived from the p15a replicon were cured without selection, while selection for DAP enhanced stability without detectable loss of any of the three resident virulence plasmids. The dapAX mutation rendered Y. pestis avirulent in mouse models of bubonic and septicemic plague which could be complemented when dapAX was inserted in single or multi-copy, restoring development of disease that was indistinguishable from the wild type parent strain. We further identified a high level, constitutive promoter in Y. pestis that could be used to drive expression of fluorescent reporters in dapAX strains that had minimal impact to virulence in mouse models while enabling sensitive detection of bacteria during infection. Thus, diaminopimelic acid selection for single or multi-copy genetic systems in Yersinia pestis offers an improved alternative to antibiotics for in vivo studies that causes minimal disruption to virulence.

  1. Novel genetic tools for diaminopimelic acid selection in virulence studies of Yersinia pestis.

    Directory of Open Access Journals (Sweden)

    David M Bland

    2011-03-01

    Full Text Available Molecular studies of bacterial virulence are enhanced by expression of recombinant DNA during infection to allow complementation of mutants and expression of reporter proteins in vivo. For highly pathogenic bacteria, such as Yersinia pestis, these studies are currently limited because deliberate introduction of antibiotic resistance is restricted to those few which are not human treatment options. In this work, we report the development of alternatives to antibiotics as tools for host-pathogen research during Yersinia pestis infections focusing on the diaminopimelic acid (DAP pathway, a requirement for cell wall synthesis in eubacteria. We generated a mutation in the dapA-nlpB(dapX operon of Yersinia pestis KIM D27 and CO92 which eliminated the expression of both genes. The resulting strains were auxotrophic for diaminopimelic acid and this phenotype was complemented in trans by expressing dapA in single and multi-copy. In vivo, we found that plasmids derived from the p15a replicon were cured without selection, while selection for DAP enhanced stability without detectable loss of any of the three resident virulence plasmids. The dapAX mutation rendered Y. pestis avirulent in mouse models of bubonic and septicemic plague which could be complemented when dapAX was inserted in single or multi-copy, restoring development of disease that was indistinguishable from the wild type parent strain. We further identified a high level, constitutive promoter in Y. pestis that could be used to drive expression of fluorescent reporters in dapAX strains that had minimal impact to virulence in mouse models while enabling sensitive detection of bacteria during infection. Thus, diaminopimelic acid selection for single or multi-copy genetic systems in Yersinia pestis offers an improved alternative to antibiotics for in vivo studies that causes minimal disruption to virulence.

  2. Genetic diversity and selection of common bean lines based on technological quality and biofortification.

    Science.gov (United States)

    Steckling, S de M; Ribeiro, N D; Arns, F D; Mezzomo, H C; Possobom, M T D F

    2017-03-22

    The development of common bean cultivars with high technological quality that are biofortified with minerals, is required to meet the demand for food with health benefits. The objectives of this study were to evaluate whether common bean genotypes differ in terms of technological and mineral biofortification traits, to study the correlations between these characters, to analyze the genetic dissimilarity of common bean genotypes, and to select superior lines for these traits. For this, 14 common bean genotypes were evaluated in experiments conducted in three growing seasons in the Rio Grande do Sul State, Brazil. A significant genotype x environment interaction was observed for technological quality (mass of 100 grains and cooking time) and biofortification traits (concentration of potassium, phosphorus, calcium, iron, zinc, and copper). Positive correlation estimates were obtained between phosphorus and potassium (r = 0.575), iron and zinc (r = 0.641), copper and iron (r = 0.729), and copper and phosphorus (r = 0.533). In the main component cluster analysis, four groups of genotypes were formed. The following lines are recommended for selection: LP 11-363 for fast-cooking, CNFC 11 948 for high iron concentration, and LEC 03-14 for high potassium, phosphorus, and calcium concentrations in grains. Common bean lines with high phosphorus and iron concentrations in grains can be indirectly selected based on higher potassium, copper, and zinc concentrations. Controlled crossings between LP 11-363 x CNFC 11 948 and LP 11-363 x LEC 03-14 are recommended to obtain segregating lines that are fast-cooking and biofortified with minerals.

  3. Runaway sexual selection without genetic correlations: social environments and flexible mate choice initiate and enhance the Fisher process.

    Science.gov (United States)

    Bailey, Nathan W; Moore, Allen J

    2012-09-01

    Female mating preferences are often flexible, reflecting the social environment in which they are expressed. Associated indirect genetic effects (IGEs) can affect the rate and direction of evolutionary change, but sexual selection models do not capture these dynamics. We incorporate IGEs into quantitative genetic models to explore how variation in social environments and mate choice flexibility influence Fisherian sexual selection. The importance of IGEs is that runaway sexual selection can occur in the absence of a genetic correlation between male traits and female preferences. Social influences can facilitate the initiation of the runaway process and increase the rate of trait elaboration. Incorporating costs to choice do not alter the main findings. Our model provides testable predictions: (1) genetic covariances between male traits and female preferences may not exist, (2) social flexibility in female choice will be common in populations experiencing strong sexual selection, (3) variation in social environments should be associated with rapid sexual trait divergence, and (4) secondary sexual traits will be more elaborate than previously predicted. Allowing feedback from the social environment resolves discrepancies between theoretical predictions and empirical data, such as why indirect selection on female preferences, theoretically weak, might be sufficient for preferences to become elaborated. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  4. Accounting for the physical and mental health benefits of entry into marriage: a genetically informed study of selection and causation.

    Science.gov (United States)

    Horn, Erin E; Xu, Yishan; Beam, Christopher R; Turkheimer, Eric; Emery, Robert E

    2013-02-01

    Married adults show better psychological adjustment and physical health than their separated/divorced or never-married counterparts. However, this apparent "marriage benefit" may be due to social selection, social causation, or both processes. Genetically informed research designs offer critical advantages for helping to disentangle selection from causation by controlling for measured and unmeasured genetic and shared environmental selection. Using young-adult twin and sibling pairs from the National Longitudinal Study of Adolescent Health (Harris, 2009), we conducted genetically informed analyses of the association between entry into marriage, cohabitation, or singlehood and multiple indices of psychological and physical health. The relation between physical health and marriage was completely explained by nonrandom selection. For internalizing behaviors, selection did not fully explain the benefits of marriage or cohabitation relative to being single, whereas for externalizing symptoms, marriage predicted benefits over cohabitation. The genetically informed approach provides perhaps the strongest nonexperimental evidence that these observed effects are causal. PsycINFO Database Record (c) 2013 APA, all rights reserved.

  5. Histopathology Discrepancy of Preoperative Endometrial Sampling and Final Specimen: How Does This Influence Selective Lymph Node Dissection?

    Science.gov (United States)

    Corr, Bradley R; Carrubba, Aakriti; Sheeder, Jeanelle; Cheng, Georgina; Guntupalli, Saketh R

    2017-02-01

    Preoperative histology is a major component in the perioperative selective lymph node (LN) dissection decision process. Discrepancy between preoperative endometrial sampling and final specimen histopathology is generally accepted. The goals of this project are to determine if discrepancy of histopathology is associated with alteration of adjuvant treatment or outcome. We performed a retrospective cross-sectional analysis of all patients undergoing surgery for endometrial cancer at a single institution from 2010 to 2014. All patients had preoperative endometrial sampling. Histopathology discrepancy was evaluated for potential in variation of perioperative LN dissection. Criteria for not performing LN dissection was defined as preoperative endometrioid histology, grade 1 or 2 lesion, myometrial invasion of 50% or less, and primary tumor diameter 2 cm or less. A total of 352 patients were identified; 44 were excluded because of no preoperative pathology or no residual disease on final pathology. Discrepancy of histopathology was noted in 64/308 (20.8%; 95% confidence interval [CI], 16.2%-25.3%) patients. Preoperative endometrioid histology was noted in 272 patients, and 17/272 (6.3%; 95% CI, 3.4%-9.1%) had preoperative sampling reviewed as a grade 1 or 2 endometrioid lesion and final specimen was upgraded to grade 3. Downstaging occurred in 3/272 (1.1%; 95% CI, 0%-2.3%) patients with preoperative grade 3 lesion and final specimen demonstrated grade 1 or 2 disease. All 3 patients' primary tumor diameter was greater than 2 cm and therefore received LN dissection. Histopathological discrepancy that would alter perioperative LN dissection decision based on the aforementioned criteria occurred in 2/272 (0.7%; 95% CI, 0%-1.8%). Despite a 20% discrepancy of preoperative and postoperative histopathology, discrepancy that would alter a perioperative decision for LN dissection occurs in only 0.7% of cases in this retrospective single-institutional experience. Myometrial

  6. Influence of genetic architecture on contemporary local evolution in the soapberry bug, Jadera haematoloma: artificial selection on beak length.

    Science.gov (United States)

    Dingle, H; Carroll, S P; Famula, T R

    2009-10-01

    Little is known about the influence of genetic architecture on local adaptation. We investigated the genetic architecture of the rapid contemporary evolution of mouthparts, the flight polymorphism and life history traits in the soapberry bug Jadera haematoloma (Hemiptera) using laboratory selection. The mouthparts of these seed-feeding bugs have adapted in 40-50 years by decreasing in length following novel natural selection induced by a host switch to the seeds of an introduced tree with smaller fruits than those of the native host vine. Laboratory selection on beak length in both an ancestral population feeding on the native host and a derived population feeding on the introduced host reveals genetic variance allowing a rapid response (heritabilities of 0.51-0.87) to selection for either longer or shorter beaks. This selection resulted in reverse evolution by restoring long beaks in the derived population and forward evolution by re-creating short beaks in the ancestral bugs. There were strong genetic correlations (0.68-0.84) in both populations between beak lengths and the frequency of flight morphs, with short beaks associated with short wings. The results reveal a genetically interrelated set of adaptive multivariate traits including both beak length and flight morph. This suite of traits reflects host plant patchiness and seeding phenology. Weaker evidence suggests that egg mass and early egg production may be elements of the same suite. Reversible or forward evolution thus may occur in a broad set of genetically correlated multivariate traits undergoing rapid contemporary adaptation to altered local environments.

  7. [Cloning goat producing human lactoferrin with genetically modified donor cells selected by single or dual markers].

    Science.gov (United States)

    An, Liyou; Yuan, Yuguo; Yu, Baoli; Yang, Tingjia; Cheng, Yong

    2012-12-01

    We compared the efficiency of cloning goat using human lactoferrin (hLF) with genetically modified donor cells marked by single (Neo(r)) or double (Neo(r)/GFP) markers. Single marker expression vector (pBLC14) or dual markers expression vector (pAPLM) was delivered to goat fetal fibroblasts (GFF), and then the transgenic GFF was used as donor cells to produce transgenic goats. Respectively, 58.8% (20/34) and 86.7% (26/30) resistant cell lines confirmed the transgenic integration by PCR. Moreover, pAPLM cells lines were subcultured with several passages, only 20% (6/30) cell lines was observed fluorescence from each cell during the cell passage. Somatic cell nuclear transfer using the donor cells harbouring pBLC14 or pAPLM construct, resulting in a total of 806 reconstructed embryos, a pregnancy rate at 35 d (53.8%, 39.1%) and 60 d (26.9%, 21.7%), and an offspring birth rate (1.9%, 1.4%) with 5 and 7 newborn cloned goats, respectively. Transgene was confirmed by PCR and southern-blot in all cloned offspring. There were no significant differences at the reconstructed embryo fusion rates, pregnancy rates and the birth rate (P > 0.05) between single and double markers groups. The Neo(r)/GFP double markers could improve the reliability for accurately and efficiently selecting the genetically modified donor cells. No adverse effect was observed on the efficiency of transgenic goat production by SCNT using somatic cells transfected with double (Neo(r)/GFP) markers vector.

  8. Genetic selection for increased mean and reduced variance of twinning rate in Belclare ewes.

    Science.gov (United States)

    Cottle, D J; Gilmour, A R; Pabiou, T; Amer, P R; Fahey, A G

    2016-04-01

    It is sometimes possible to breed for more uniform individuals by selecting animals with a greater tendency to be less variable, that is, those with a smaller environmental variance. This approach has been applied to reproduction traits in various animal species. We have evaluated fecundity in the Irish Belclare sheep breed by analyses of flocks with differing average litter size (number of lambs per ewe per year, NLB) and have estimated the genetic variance in environmental variance of lambing traits using double hierarchical generalized linear models (DHGLM). The data set comprised of 9470 litter size records from 4407 ewes collected in 56 flocks. The percentage of pedigreed lambing ewes with singles, twins and triplets was 30, 54 and 14%, respectively, in 2013 and has been relatively constant for the last 15 years. The variance of NLB increases with the mean in this data; the correlation of mean and standard deviation across sires is 0.50. The breeding goal is to increase the mean NLB without unduly increasing the incidence of triplets and higher litter sizes. The heritability estimates for lambing traits were NLB, 0.09; triplet occurrence (TRI) 0.07; and twin occurrence (TWN), 0.02. The highest and lowest twinning flocks differed by 23% (75% versus 52%) in the proportion of ewes lambing twins. Fitting bivariate sire models to NLB and the residual from the NLB model using a double hierarchical generalized linear model (DHGLM) model found a strong genetic correlation (0.88 ± 0.07) between the sire effect for the magnitude of the residual (VE ) and sire effects for NLB, confirming the general observation that increased average litter size is associated with increased variability in litter size. We propose a threshold model that may help breeders with low litter size increase the percentage of twin bearers without unduly increasing the percentage of ewes bearing triplets in Belclare sheep. © 2015 Blackwell Verlag GmbH.

  9. Change in genetic correlation due to selection using animal model evaluation.

    Science.gov (United States)

    Strandén, I; Mäntysaari, E A; Mäki-Tanila, A

    1993-01-12

    Monte Carlo simulation and analytical calculations were used to study the effect of selection on genetic correlation between two traits. The simulated breeding program was based on a closed adult multiple ovulation and embryo transfer nucleus breeding scheme. Selection was on an index calculated using multi-trait animal model (AM). Analytical formulae applicable to any evaluation method were derived to predict change in genetic (co)variance due to selection under multi-trait selection using different evaluation methods. Two formulae were investigated, one assuming phenotypic selection and the other based on a recursive two-generation AM selection index. The recursive AM method approximated information due to relatives by a relationship matrix of two generations. Genetic correlation after selection was compared under different levels of initial genetic and environmental correlations with two different selection criteria. Changes in genetic correlation were similar in simulation and analytical predictions. After one round of selection the recursive AM method and the simulation gave similar predictions while the phenotypic selection predicted usually more change in genetic correlation. After several rounds of selection both analytical formulae predicted more change in genetic correlation than the simulation. ZUSAMMENFASSUNG: Änderung der genetischen Korrelation bei Selektion mit einem Tiermodell Der Selektionseffekt auf die genetische Korrelation zwischen zwei Merkmalen wurde mit Hilfe von Monte Carlo-Simulation und analytischen Berechnungen untersucht. Ein geschlossener Adulter - MOET (Multiple Ovulation and Embryo Transfer) Zuchtplan wurde simuliert. Die Selektion gründete sich auf einen Index, der die Zuchtwertschätzung des Mehrmerkmals-Tiermodells benutzte. Analytische Formeln für die Voraussage der Änderung der genetischen (Ko)varianz unter multivariate Selektion für verschiedene Zuchtwertschätzungsmethode wurden deduziert. Zwei Formeln wurden studiert

  10. Selective IR reflective coatings development. Final report, 24 July 1978-24 October 1979

    Energy Technology Data Exchange (ETDEWEB)

    Lefkow, A R; Lee, J C

    1979-10-01

    The objective of this program is to develop selective infrared (IR) reflective solar transparent coatings for use on plastic glazing materials. The coating systems studied for this application were indium-tin oxide, tin oxide, and antimony-doped tin oxide. These semiconductor thin films were deposited by two plasma-assisted deposition techniques, ion plating and chemical vapor plasma deposition (CVPD), in which electron kinetic energy from the plasma mitigates the high substate temperature usually required to achieve sufficient thin film crystallinity. The best coating performance obtained in the program by these approaches was 80 to 85% solar transmission and 35% (at 10 microns) to 50% (at 40 microns) IR reflectance for Sb:SnO/sub 2/ films plasma-deposited from Sn(CH/sub 3/)/sub 4/ and SbCl/sub 5/ vapor sources. This is not thought to be the ultimate performance achievable for CVPD-grown Sb:SnO/sub 2/ films.

  11. Selected problems in experimental intermediate energy physics. Final technical report, February 1, 1991--January 31, 1994

    International Nuclear Information System (INIS)

    Mayes, B.W.; Hungerford, E.V.; Pinsky, L.S.

    1997-01-01

    A complete description of the research program of the intermediate energy group at the University of Houston may be found in previous progress reports, renewal proposals, and proposals to various accelerator advisory committees. The summaries of activities are presented in the next section. The objectives of the research program are to: (1) investigate selected, forefront problems in experimental intermediate energy physics; (2) educate students in this field of research; and (3) develop the instrumentation necessary to undertake this experimental program. There were three major thrusts of the program: (1) strange particle physics, where a strange quark is embedded in the nuclear medium; (2) muon electro-weak decay, which involves a search for a violation of the standard model of the electro-weak interaction; and (3) measurement of the spin dependent structure function of the neutron and proton

  12. Genetic engineering technology for the improvement of the sterile insect technique. Proceedings of a final research co-ordination meeting

    International Nuclear Information System (INIS)

    1998-01-01

    Since the beginning of the joint FAO/IAEA programme on the research and development of insect pest control methodology, emphasis has been placed on the basic and applied aspects of implementing the sterile insect technique (SIT). Special emphasis has always been directed at the assembly of technological progress into workable systems that can be implemented in developing countries. The general intention is to solve problems associated with insect pests that have an adverse impact on production of food and fibre. For several insect species SIT has proven to be a powerful method for control. This includes the New World screwworm fly (Cochliomyia hominivorox), the Mediterranean fruit fly (Ceratitis capitata), the melon fly (Bactrocera cucurbitae), the Queensland fruit fly (Bactrocera tryoni) and one tsetse fly species (Glossina austeni). Improvements of the SIT are possible, especially through the use of molecular techniques. The final report of the Co-ordinated Research Programme on ''Genetic Engineering Technology for the Improvement of the Sterile Insect Technique'' highlights the progress made towards the development of transformation systems for non-drosophilid insects and the research aimed at the identification and engineering of potential target genes or traits

  13. Black germanium selective absorber surfaces. Final technical report, September 1, 1978-June 30, 1979

    Energy Technology Data Exchange (ETDEWEB)

    Messier, R.; Vedam, K.; Krishnaswamy, S.V.

    1979-12-01

    Semiconductor films with an appropriate band gap (approx. 0.5 to 1.25 ev) have a high absorption coefficient in the solar spectrum region and high transmission in the IR thermal-emission region and thus make nearly ideal selective absorbers. However, due to their high refractive index, semiconductor films have high reflectance above their absorption edge which limits their total absorption. A coating which would retain the advantages of the semiconductor's selectivity and also reduce the reflectance from the present values of 30 to 50% to a level of less than 2% would be a significant advancement in the state of the art. This study describes work on the preparation and characterization of structurally anisotropic black Ge films by rf-sputtering and postdeposition etching. It has been shown that by controlling the sputtering preparation conditions of noncrystalline Ge films the surface microstructure can be drastically altered by simply etching in 30% H/sub 2/O/sub 2/. The total reflectance of the resulting surface was reduced from about 45% to less than 1%. Furthermore, the films appear black over a wide range of angles of incidence ( up to 45% from the normal). This flat black appearance is shown to be due to a dense array of aligned, needle-like protrusions which have an extremely high aspect ratio and both a cross-sectional area and a separation between the needles on th order of the wavelength of solar radiation. Black Ge films were obtained with a solar absorptance, ..cap alpha../sub S/, of greater than 0.99 in the best cases. Variation of ..cap alpha../sub S/ and epsilon/sub IR/ (IR emittance) with the thickness of the film and other preparation conditions is described. Further, the various microstructures are classified and understood on the basis of a structure zone model.

  14. Genetic diversity of MHC class I loci in six non-model frogs is shaped by positive selection and gene duplication

    Science.gov (United States)

    Kiemnec-Tyburczy, K M; Richmond, J Q; Savage, A E; Lips, K R; Zamudio, K R

    2012-01-01

    Comparative studies of major histocompatibility complex (MHC) genes across vertebrate species can reveal the evolutionary processes that shape the structure and function of immune regulatory proteins. In this study, we characterized MHC class I sequences from six frog species representing three anuran families (Hylidae, Centrolenidae and Ranidae). Using cDNA from our focal species, we amplified a total of 79 unique sequences spanning exons 2–4 that encode the extracellular domains of the functional alpha chain protein. We compared intra- and interspecific nucleotide and amino-acid divergence, tested for recombination, and identified codon sites under selection by estimating the rate of non-synonymous to synonymous substitutions with multiple codon-based maximum likelihood methods. We determined that positive (diversifying) selection was acting on specific amino-acid sites located within the domains that bind pathogen-derived peptides. We also found significant signals of recombination across the physical distance of the genes. Finally, we determined that all the six species expressed two or three putative classical class I loci, in contrast to the single locus condition of Xenopus laevis. Our results suggest that MHC evolution in anurans is a dynamic process and that variation in numbers of loci and genetic diversity can exist among taxa. Thus, the accumulation of genetic data for more species will be useful in further characterizing the relative importance of processes such as selection, recombination and gene duplication in shaping MHC loci among amphibian lineages. PMID:22549517

  15. Estimates of genetic correlations and correlated responses to selection in cashew (Anacardium occidentale L.

    Directory of Open Access Journals (Sweden)

    Diógenes Manoel Pedroza de Azevedo

    1998-09-01

    Full Text Available The present study estimates variances and genetic and phenotypic correlations for five traits in 27 progenies of cashew trees (Anacardium occidentale L.. Data were obtained from a trial conducted in 1992 at Pacajus, Ceará, experimental station of Embrapa Agroindústria Tropical. The characters studied were plant height (PH, North-South and East-West canopy spreads (NSS, EWS, and primary and secondary branch numbers (PBN, SBN. All genetic and phenotypic correlations presented positive and significant values. Selection to increase or decrease the average of any one of the five characteristics of cashew plants in the progenies studied affected the average of the others. The 16-month-old canopy spread can be predicted from NSS or EWS since correlations between them were high. Correlations between PH and SBN were low, indicating that there is a good possibility of obtaining smaller plants without causing drastic reductions in SBN. PH and SBN showed, respectively, the lowest and highest genetic variance estimates relative to the corresponding population means.Neste trabalho são estimadas variâncias, correlações genéticas e fenotípicas e respostas correlacionadas, envolvendo cinco caracteres em 27 progênies de cajueiro (Anacardium occidentale L.. Os dados foram obtidos em Pacajus-CE, num ensaio conduzido no Campo Experimental da Embrapa Agroindústria Tropical, em l992. Os caracteres estudados foram altura de planta (PH, envergaduras norte-sul (NSS e leste-oeste (EWS e número de ramos primários (PBN e secundários (SBN. Todas as correlacões genéticas e fenotípicas obtidas foram positivas e significativas. A seleção para aumentar ou reduzir a média de qualquer um dos cinco caracteres estudados nas progênies de cajueiro afetou indiretamente a média dos outros quatro caracteres. A envergadura da copa aos 16 meses pode ser representada por NSS ou EWS, tendo em vista que a correlação entre elas foi elevada. As correlações envolvendo PH

  16. Genetic variation of Lymnaea stagnalis tolerance to copper: A test of selection hypotheses and its relevance for ecological risk assessment

    International Nuclear Information System (INIS)

    Côte, Jessica; Bouétard, Anthony; Pronost, Yannick; Besnard, Anne-Laure; Coke, Maïra; Piquet, Fabien; Caquet, Thierry; Coutellec, Marie-Agnès

    2015-01-01

    The use of standardized monospecific testing to assess the ecological risk of chemicals implicitly relies on the strong assumption that intraspecific variation in sensitivity is negligible or irrelevant in this context. In this study, we investigated genetic variation in copper sensitivity of the freshwater snail Lymnaea stagnalis, using lineages stemming from eight natural populations or strains found to be genetically differentiated at neutral markers. Copper-induced mortality varied widely among populations, as did the estimated daily death rate and time to 50% mortality (LT50). Population genetic divergence in copper sensitivity was compared to neutral differentiation using the Q ST -F ST approach. No evidence for homogenizing selection could be detected. This result demonstrates that species-level extrapolations from single population studies are highly unreliable. The study provides a simple example of how evolutionary principles could be incorporated into ecotoxicity testing in order to refine ecological risk assessment. - Highlights: • Genetic variation in copper tolerance occurs between Lymnaea stagnalis populations. • We used the Q ST -F ST approach to test evolutionary patterns in copper tolerance. • No evidence for uniform selection was found. • Results suggest that extrapolations to the species level are not safe. • A method is proposed to refine ecological risk assessment using genetic parameters. - Genetic variation in copper tolerance occurs in Lymnaea stagnalis. A method is proposed for considering evolutionary parameters in ecological risk assessment

  17. Insights into population ecology and sexual selection in snakes through the application of DNA-based genetic markers.

    Science.gov (United States)

    Gibbs, H L; Weatherhead, P J

    2001-01-01

    Hypervariable genetic markers have revolutionized studies of kinship, behavioral ecology, and population biology in vertebrate groups such as birds, but their use in snakes remains limited. To illustrate the value of such markers in snakes, we review studies that have used microsatellite DNA loci to analyze local population differentiation and parentage in snakes. Four ecologically distinct species of snakes all show evidence for differentiation at small spatial scales (2-15 km), but with substantial differences among species. This result highlights how genetic analysis can reveal hidden aspects of the natural history of difficult-to-observe taxa, and it raises important questions about the ecological factors that may contribute to restricted gene flow. A 3-year study of genetic parentage in marked populations of the northern water snake showed that (1) participation in mating aggregations was a poor predictor of genetic-based measures of reproductive success; (2) multiple paternity was high, yet there was no detectable fitness advantage to multiple mating by females; and (3) the opportunity for selection was far higher in males than in females due to a larger variance in male reproductive success, and yet this resulted in no detectable selection on morphological variation in males. Thus genetic markers have provided accurate measures of individual reproductive success in this species, an important step toward resolving the adaptive significance of key features including multiple paternity and reversed sexual size dimorphism. Overall these studies illustrate how genetic analyses of snakes provide previously unobtainable information of long-standing interest to behavioral ecologists.

  18. Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure.

    Science.gov (United States)

    Orsini, Luisa; Marshall, Hollie; Cuenca Cambronero, Maria; Chaturvedi, Anurag; Thomas, Kelley W; Pfrender, Michael E; Spanier, Katina I; De Meester, Luc

    2016-12-01

    Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species' evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank. © 2016 John Wiley & Sons Ltd.

  19. THE ROLES OF INDUSTRY AND SCIENCE, INCLUDING GENETIC SELECTION, IN IMPROVING ANIMAL WELFARE

    Directory of Open Access Journals (Sweden)

    D.M. BROOM

    2009-10-01

    Full Text Available Animal producers have to predict future situations and be aware of changing public views. At present, those in the animal industry are often trying to fight off change rather than preparing for and pre-empting it. As a consequence, many animal producers have bad public images. It is better to be proactive than reactive. Producer groups should be aware of new developments in knowledge and in public attitudes to animal-related activities. They should inform their members about how to manage animals in such a way that the welfare of the animals is good and the people involved in animal care are well-respected in society. This is especially important also for those who design and manufacture housing and equipment and those who breed animals for they can have substantial effects on animal welfare. It is important for animal welfare scientists to provide objective information about the welfare of animals, so that decisions can be taken about how animals should be bred, housed and treated. Animals use a wide range of coping mechanisms and these involve high-level brain function, with associated good and bad feelings. Where welfare is poor, the best overall assessment of welfare is a function of how bad is the effect on the individual and the duration of that effect. Conventional breeding, cloning and transgenesis can all have effects on the welfare of the animals produced. Selection for fast growth and high feed conversion efficiency in broiler chickens and other meat producing animals leads to too high an incidence of leg and other disorders. Selection for high milk yield in dairy cows leads to poor welfare associated with leg disorders, mastitis and reproductive disorders. These effects should be evaluated using a range of animal welfare measures and if there are adverse effects of genetic engineering, the usage of the animals should not be permitted except for research. In the case of genetically modified or cloned animals, any effects on function

  20. Mapping genetic research in non-communicable disease publications in selected Arab countries: first step towards a guided research agenda.

    Science.gov (United States)

    Jamaluddine, Zeina; Sibai, Abla Mehio; Othman, Shahd; Yazbek, Soha

    2016-11-10

    In the Arab world, intervention and policy response to non-communicable diseases (NCD) has been weak despite extensive epidemiological evidence highlighting the alarmingly increased prevalence of chronic diseases. Generating genetic information is one key component to promote efficient disease management strategies. This study undertook a scoping review to generate the profile of the undertaken research on genetics of NCD publications in selected Arab countries. An analysis of the research produced examined the extent, range, nature, topic and methods of published research. The study aimed at identifying the gaps in genetic NCD research to inform policy action for NCD prevention and control. The scoping review was conducted based on the five-stage methodological framework and included countries in Arab region selected to represent various economies and epidemiological transitions. The search identified 555 articles that focus on genetics-NCD research in the selected Arab countries over the duration of this study (January 2000 to December 2013). The most commonly conducted research was descriptive and clinically focused, rather than etiologically focused. Country-specific carrier and risk screening studies were not among the top research designs. The genetic component of certain highly heritable diseases, as well as diabetes, obesity, hypertension, chronic lung dysfunction and metabolic syndrome were all under investigated. This scoping review identified gaps for further research in the context of bioinformatics and genome-wide association studies. Genetic research in the Arab region has to be redirected towards NCDs with the highest morbidity, heritability and health burden within each country. A focused research plan to include community genetics is required for its proper integration in the Arab community.

  1. Modelled in vivo HIV fitness under drug selective pressure and estimated genetic barrier towards resistance are predictive for virological response

    DEFF Research Database (Denmark)

    Deforche, Koen; Cozzi-Lepri, Alessandro; Theys, Kristof

    2008-01-01

    BACKGROUND: A method has been developed to estimate a fitness landscape experienced by HIV-1 under treatment selective pressure as a function of the genotypic sequence thereby also estimating the genetic barrier to resistance. METHODS: We evaluated the performance of two estimated fitness landsca...

  2. Which individuals to choose to update the reference population? Minimizing the loss of genetic diversity in animal genomic selection programs

    NARCIS (Netherlands)

    Eynard, Sonia E.; Croiseau, Pascal; Laloë, Denis; Fritz, Sebastien; Calus, Mario P.L.; Restoux, Gwendal

    2018-01-01

    Genomic selection (GS) is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a

  3. Genetics

    Science.gov (United States)

    ... Likelihood of getting certain diseases Mental abilities Natural talents An abnormal trait (anomaly) that is passed down ... one of them has a genetic disorder. Information Human beings have cells with 46 chromosomes . These consist ...

  4. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Directory of Open Access Journals (Sweden)

    Chiao-Ling Lo

    2016-08-01

    Full Text Available Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP. This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross resulted in small haplotype blocks (HB with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS, were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50% of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284 and intronic regions (169 with the least in exon's (4, suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a, excitatory receptors (Grin2a, Gria3, Grip1, neurotransmitters (Pomc, and synapses (Snap29. This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.

  5. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Science.gov (United States)

    Lo, Chiao-Ling; Lossie, Amy C; Liang, Tiebing; Liu, Yunlong; Xuei, Xiaoling; Lumeng, Lawrence; Zhou, Feng C; Muir, William M

    2016-08-01

    Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder) in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP). This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross) resulted in small haplotype blocks (HB) with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate) to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS), were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50%) of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284) and intronic regions (169) with the least in exon's (4), suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a), excitatory receptors (Grin2a, Gria3, Grip1), neurotransmitters (Pomc), and synapses (Snap29). This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.

  6. Random genetic drift, natural selection, and noise in human cranial evolution.

    Science.gov (United States)

    Roseman, Charles C

    2016-08-01

    This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Effects of selected thermophilic microorganisms on crude oils at elevated temperatures and pressures. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Premuzic, E.T.; Lin, M.S.

    1995-07-01

    During the past several years, a considerable amount of work has been carried out showing that microbially enhanced oil recovery (MEOR) is promising and the resulting biotechnology may be deliverable. At the Brookhaven National Laboratory (BNL), systematic studies have been conducted which dealt with the effects of thermophilic and thermoadapted bacteria on the chemical and physical properties of selected types of crude oils at elevated temperatures and pressures. Particular attention was paid to heavy crude oils from Venezuela, California, Alabama, Arkansas, Wyoming, Alaska, and other oil producing areas. Current studies indicate that during the biotreatment several chemical and physical properties of crude oils are affected. The oils are (1) emulsified; (2) acidified; (3) there is a qualitative and quantitative change in light and heavy fractions of the crudes; (4) there are chemical changes in fractions containing sulfur compounds; (5) there is an apparent reduction in the concentration of trace metals; (6) the qualitative and quantitative changes appear to be microbial species dependent; and (7) there is a distinction between {open_quotes}biodegraded{close_quotes} and {open_quotes}biotreated{close_quotes} oils. Preliminary results indicate the introduced microorganisms may become the dominant species in the bioconversion of oils. These studies also indicate the biochemical interactions between crude oils and microorganisms follow distinct trends, characterized by a group of chemical markers. Core-flooding experiments have shown significant additional crude oil recoveries are achievable with thermophilic microorganisms at elevated temperatures similar to those found in oil reservoirs. In addition, the biochemical treatment of crude oils has technological applications in downstream processing of crude oils such as in upgrading of low grade oils and the production of hydrocarbon based detergents.

  8. From First Principles Design to Realization of Bimetallic Catalysts for Ultrahigh Selectivity - Final Project Report

    Energy Technology Data Exchange (ETDEWEB)

    Richard M. Crooks

    2007-04-11

    (A) Synthesis, Characterization, and Fundamental Properties of Bimetallic DENs. AuAg alloy and core/shell bimetallic DENs were synthesized and characterized. Selective extraction was used as a structural characterization tool for these bimetallic nanoparticles. This is significant because there are few easily accessible methods for structure elucidation of bimetallic nanoparticles in this size regime. As a first step towards the synthesis of catalytically active, bimetallic heterogeneous materials we reported the incorporation of Au and Pd monometallic DENs and AuPd bimetallic DENs into amorphous titania networks. The compositional fidelity of the original DENs, and to some extent their size, is retained following dendrimer removal. Gas-phase catalytic activity for CO oxidation is higher for the bimetallic catalysts than for the corresponding Pd-only and Au-only monometallics. (B) Electrocatalysts based on dendrimer-encapsulated nanoparticles. Platinum dendrimer-encapsulated nanoparticles (DENs) were prepared within fourth-generation, hydroxyl-terminated, poly(amidoamine) dendrimers and immobilized on glassy carbon electrodes using an electrochemical immobilization strategy. X-ray photoelectron spectroscopy, electron microscopy, and electrochemical experiments confirm that the Pt DENs are about 1.4 nm in diameter and that they remain within the dendrimer following surface immobilization. The resulting Pt DEN films were electrocatalytically active for the oxygen reduction reaction (ORR). The films are also robust, surviving up to 50 consecutive cyclic voltammograms and sonication. Monometallic Pd DENs were also prepared and found to have little catalytic activity for the ORR. However, PtPd bimetallic DENs had catalytic activity nearly identical to that found for Pt-only DENs. This indicates an overall catalytic enhancement for the bimetallic electrocatalysts.

  9. The impact of selection on population genetic structure in the clam Meretrix petechialis revealed by microsatellite markers.

    Science.gov (United States)

    Lu, Xia; Wang, Hongxia; Li, Yan; Liu, Baozhong

    2016-02-01

    The aim of our work is to evaluate the impact of mass selection on genetic structure in artificially closed populations of the clam Meretrix petechialis. In the present study, we performed mass selection over four generations (from 2004 to 2010) on two clam populations [shell features of purple lines (SP) and black dots (SB)] and analyzed their temporal genetic variation and structure using microsatellite makers. The two closed populations originated from the natural Shandong population (SD); thus, a natural SD population (10SD) was used to detect the current genetic structure after 6 years of natural selection. The results showed that the genetic diversity of the four generations of SB and SP was gradually reduced but remained at relatively high levels (SB, A = 18.9.4-16.8, Ho = 0.7389-0.6971, and He = 0.8897-0.8591; SP, A = 20.0-17.8, Ho = 0.7512-0.7043, and He = 0.8938-0.8625), which has not been reduced compared with that of the 10SD population (A = 17.8, Ho = 0.6803, and He = 0.8302). The Ne estimates for the two populations were almost at the same levels as the actual numbers of parental individuals. In addition, a low inbreeding coefficient was detected in the two populations (SB, 0.00201-0.00639; SP, 0.00176-0.00541). Based on the results, the present mass selection has not made a large impact on the population genetic structure of the closed populations. The present investigation provides important information for the development of management strategies for genetic breeding of the clam.

  10. Selection of security system design via games of imperfect information and multi-objective genetic algorithm

    International Nuclear Information System (INIS)

    Lins, Isis Didier; Rêgo, Leandro Chaves; Moura, Márcio das Chagas

    2013-01-01

    This work analyzes the strategic interaction between a defender and an intelligent attacker by means of a game and reliability framework involving a multi-objective approach and imperfect information so as to support decision-makers in choosing efficiently designed security systems. A multi-objective genetic algorithm is used to determine the optimal security system's configurations representing the tradeoff between the probability of a successful defense and the acquisition and operational costs. Games with imperfect information are considered, in which the attacker has limited knowledge about the actual security system. The types of security alternatives are readily observable, but the number of redundancies actually implemented in each security subsystem is not known. The proposed methodology is applied to an illustrative example considering power transmission lines in the Northeast of Brazil, which are often targets for attackers who aims at selling the aluminum conductors. The empirical results show that the framework succeeds in handling this sort of strategic interaction. -- Highlights: ► Security components must have feasible costs and must be reliable. ► The optimal design of security systems considers a multi-objective approach. ► Games of imperfect information enable the choice of non-dominated configurations. ► MOGA, reliability and games support the entire defender's decision process. ► The selection of effective security systems may discourage attacker's actions

  11. Selection bias in genetic-epidemiological studies of cleft lip and palate

    Energy Technology Data Exchange (ETDEWEB)

    Christensen, K.; Holm, N.V.; Kock, K. (Odense Univ. (Denmark)); Olsen, J. (Aarhus Univ. (Denmark)); Fogh-Anderson, P.

    1992-09-01

    The possible impact of selection bias in genetic and epidemiological studies of cleft lip and palate was studied, using three nationwide ascertainment sources and an autopsy study in a 10% sample of the Danish population. A total of 670 cases were identified. Two national record systems, when used together, were found suitable for ascertaining facial cleft in live births. More than 95% ascertainment was obtained by means of surgical files for cleft lip (with or without cleft palate) without associated malformations/syndromes. However, surgical files could be a poor source for studying isolated cleft palate (CP) (only a 60% and biased ascertainment), and they cannot be used to study the prevalence of associated malformations or syndromes in facial cleft cases. The male:female ratio was 0.88 in surgically treated cases of CP and was 1.5 in nonoperated CP cases, making the overall sex ratio for CP 1.1 (95% confidence limits 0.86-1.4) The sex ratio for CP without associated malformation was 1.1 (95% confidence limits 0.84-1.6). One of the major test criteria in CP multifactorial threshold models (higher CP liability among male CP relatives) must be reconsidered, if other investigations confirm that a CP sex-ratio reversal to male predominance occurs when high ascertainment is achieved. 24 refs., 1 fig., 4 tabs.

  12. Procedure to select test organisms for environmental risk assessment of genetically modified crops in aquatic systems.

    Science.gov (United States)

    Hilbeck, Angelika; Bundschuh, Rebecca; Bundschuh, Mirco; Hofmann, Frieder; Oehen, Bernadette; Otto, Mathias; Schulz, Ralf; Trtikova, Miluse

    2017-11-01

    For a long time, the environmental risk assessment (ERA) of genetically modified (GM) crops focused mainly on terrestrial ecosystems. This changed when it was scientifically established that aquatic ecosystems are exposed to GM crop residues that may negatively affect aquatic species. To assist the risk assessment process, we present a tool to identify ecologically relevant species usable in tiered testing prior to authorization or for biological monitoring in the field. The tool is derived from a selection procedure for terrestrial ecosystems with substantial but necessary changes to adequately consider the differences in the type of ecosystems. By using available information from the Water Framework Directive (2000/60/EC), the procedure can draw upon existing biological data on aquatic systems. The proposed procedure for aquatic ecosystems was tested for the first time during an expert workshop in 2013, using the cultivation of Bacillus thuringiensis (Bt) maize as the GM crop and 1 stream type as the receiving environment in the model system. During this workshop, species executing important ecological functions in aquatic environments were identified in a stepwise procedure according to predefined ecological criteria. By doing so, we demonstrated that the procedure is practicable with regard to its goal: From the initial long list of 141 potentially exposed aquatic species, 7 species and 1 genus were identified as the most suitable candidates for nontarget testing programs. Integr Environ Assess Manag 2017;13:974-979. © 2017 SETAC. © 2017 SETAC.

  13. Adaptive Test Selection for Factorization-based Surrogate Fitness in Genetic Programming

    Directory of Open Access Journals (Sweden)

    Krawiec Krzysztof

    2017-12-01

    Full Text Available Genetic programming (GP is a variant of evolutionary algorithm where the entities undergoing simulated evolution are computer programs. A fitness function in GP is usually based on a set of tests, each of which defines the desired output a correct program should return for an exemplary input. The outcomes of interactions between programs and tests in GP can be represented as an interaction matrix, with rows corresponding to programs in the current population and columns corresponding to tests. In previous work, we proposed SFIMX, a method that performs only a fraction of interactions and employs non-negative matrix factorization to estimate the outcomes of remaining ones, shortening GP’s runtime. In this paper, we build upon that work and propose three extensions of SFIMX, in which the subset of tests drawn to perform interactions is selected with respect to test difficulty. The conducted experiment indicates that the proposed extensions surpass the original SFIMX on a suite of discrete GP benchmarks.

  14. Detecting Cyber-Attacks on Wireless Mobile Networks Using Multicriterion Fuzzy Classifier with Genetic Attribute Selection

    Directory of Open Access Journals (Sweden)

    El-Sayed M. El-Alfy

    2015-01-01

    Full Text Available With the proliferation of wireless and mobile network infrastructures and capabilities, a wide range of exploitable vulnerabilities emerges due to the use of multivendor and multidomain cross-network services for signaling and transport of Internet- and wireless-based data. Consequently, the rates and types of cyber-attacks have grown considerably and current security countermeasures for protecting information and communication may be no longer sufficient. In this paper, we investigate a novel methodology based on multicriterion decision making and fuzzy classification that can provide a viable second-line of defense for mitigating cyber-attacks. The proposed approach has the advantage of dealing with various types and sizes of attributes related to network traffic such as basic packet headers, content, and time. To increase the effectiveness and construct optimal models, we augmented the proposed approach with a genetic attribute selection strategy. This allows efficient and simpler models which can be replicated at various network components to cooperatively detect and report malicious behaviors. Using three datasets covering a variety of network attacks, the performance enhancements due to the proposed approach are manifested in terms of detection errors and model construction times.

  15. The Genetic Legacy of the Indian Ocean Slave Trade: Recent Admixture and Post-admixture Selection in the Makranis of Pakistan.

    Science.gov (United States)

    Laso-Jadart, Romuald; Harmant, Christine; Quach, Hélène; Zidane, Nora; Tyler-Smith, Chris; Mehdi, Qasim; Ayub, Qasim; Quintana-Murci, Lluis; Patin, Etienne

    2017-12-07

    From the eighth century onward, the Indian Ocean was the scene of extensive trade of sub-Saharan African slaves via sea routes controlled by Muslim Arab and Swahili traders. Several populations in present-day Pakistan and India are thought to be the descendants of such slaves, yet their history of admixture and natural selection remains largely undefined. Here, we studied the genome-wide diversity of the African-descent Makranis, who reside on the Arabian Sea coast of Pakistan, as well that of four neighboring Pakistani populations, to investigate the genetic legacy, population dynamics, and tempo of the Indian Ocean slave trade. We show that the Makranis are the result of an admixture event between local Baluch tribes and Bantu-speaking populations from eastern or southeastern Africa; we dated this event to ∼300 years ago during the Omani Empire domination. Levels of parental relatedness, measured through runs of homozygosity, were found to be similar across Pakistani populations, suggesting that the Makranis rapidly adopted the traditional practice of endogamous marriages. Finally, we searched for signatures of post-admixture selection at traits evolving under positive selection, including skin color, lactase persistence, and resistance to malaria. We demonstrate that the African-specific Duffy-null blood group-believed to confer resistance against Plasmodium vivax infection-was recently introduced to Pakistan through the slave trade and evolved adaptively in this P. vivax malaria-endemic region. Our study reconstructs the genetic and adaptive history of a neglected episode of the African Diaspora and illustrates the impact of recent admixture on the diffusion of adaptive traits across human populations. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  16. Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models

    NARCIS (Netherlands)

    Reed, Thomas E; Gienapp, Phillip; Visser, Marcel E

    2016-01-01

    ey life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document micro-evolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have

  17. Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models

    NARCIS (Netherlands)

    Reed, Thomas E; Gienapp, Phillip; Visser, Marcel E

    2016-01-01

    Key life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document micro-evolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have

  18. Genetic parameter estimates and response to selection for weight and testicular traits in Nelore cattle.

    Science.gov (United States)

    Araujo Neto, F R; Lôbo, R B; Mota, M D S; Oliveira, H N

    2011-12-19

    We estimated genetic parameters for various phases of body and testicular growth until 550 days of age in Nelore cattle, using Bayesian inference, including correlation values and error estimates. Weight and scrotal records of 54,182 Nelore animals originating from 18 farms participating in the Brazilian Nelore Breeding Program (PMGRN) were included. The following traits were measured: weight at standard ages of 120 (W120), 210 (W210), 365 (W365), 450 (W450), and 550 (W550) days; weight gain between 120/210 (WG1), 210/365 (WG2), 365/450 (WG3), 450/550 (WG4), 120/365 (WG5), 120/450 (WG6), 120/550 (WG7), 210/450 (WG8), 210/550 (WG9), and 365/550 (WG10) days of age; scrotal circumference at 365 (SC365), 450 (SC450) and 550 (SC550) days of age, and testicular growth between 365/450 (TG1), 450/550 (TG2) and 365/550 (TG3) days of age. The model included contemporary group (current farm, year and two-month period of birth, sex, and management group) and age of dam at calving, divided into classes as fixed effects. The model also included random effects for direct additive, maternal additive and maternal permanent environmental, and residual effects. The direct heritability estimates ranged from 0.23 to 0.39, 0.13 to 0.39 and 0.32 to 0.56 for weights at standard ages, weight gains and testicular measures, respectively. The genetic correlations between weights (0.69 to 0.94) and scrotal circumferences (0.91 to 0.97) measured at standard ages were higher than those between weight gain and testicular growth (0.18 to 0.97 and 0.36 to 0.77, respectively). The weights at standard ages responded more effectively to selection, and also gave strong correlations with the other traits.

  19. Further development of public participation in the site-selection and approval process of a final repository in Germany

    Energy Technology Data Exchange (ETDEWEB)

    Barth, Regine; Kallenbach-Herbert, Beate [OeEo-Institute e.V., Inst. for Applied Ecology, Darmstadt (Germany); Arens, Georg [Federal Office for Radiation Protection (BfS), Salzgitter (Germany)

    2006-09-15

    This paper reflects the first findings of a current research project funded by the German Federal Office for Radiation Protection and conducted by an interdisciplinary working group of the OEko-Institute. One focus of this project is the systematic analysis of past and existing participatory processes in different nuclear and non-nuclear projects. On the basis of this analysis and a literature review a specific concept for public participation in the site-selection and approval process of a repository for high radioactive waste (HAW repository) in Germany will be derived. The concept shall foster transparency and acceptance. The working group of the OEko-Institute combines long standing research experience and an intimate knowledge of radioactive waste management including political, technical, management and social problems of final disposal on the one hand. On the other hand members play an active role in stakeholder processes of different non-nuclear projects as well as experience with a wide range of participative measures and their impact. This allows an approach which integrates the specific features of radioactive waste disposal with a wider perspective on the demands and opportunities of stakeholder processes. The procedure of site selection for a HAW repository in Germany still has to be specified. The procedure introduced by the 'Committee on a Site Selection Procedure for Repository Sites' (Arbeitskreis Auswahlverfahren Endlagerstandorte - AkEnd) has not been adopted. The Committee had suggested installing a negotiation group to discuss the AkEnd proposals in the so called 'Phase II'. This suggestion could not be followed because not all relevant stakeholders were willing to participate. An internal draft for a federal law implementing main elements of the AkEnd findings was developed by the Ministry for Environment in 2005, but has never been brought to the cabinet. Due to the change of Government in Germany, the next steps still are

  20. Multi-Stage Feature Selection by Using Genetic Algorithms for Fault Diagnosis in Gearboxes Based on Vibration Signal.

    Science.gov (United States)

    Cerrada, Mariela; Vinicio Sánchez, René; Cabrera, Diego; Zurita, Grover; Li, Chuan

    2015-09-18

    There are growing demands for condition-based monitoring of gearboxes, and techniques to improve the reliability, effectiveness and accuracy for fault diagnosis are considered valuable contributions. Feature selection is still an important aspect in machine learning-based diagnosis in order to reach good performance in the diagnosis system. The main aim of this research is to propose a multi-stage feature selection mechanism for selecting the best set of condition parameters on the time, frequency and time-frequency domains, which are extracted from vibration signals for fault diagnosis purposes in gearboxes. The selection is based on genetic algorithms, proposing in each stage a new subset of the best features regarding the classifier performance in a supervised environment. The selected features are augmented at each stage and used as input for a neural network classifier in the next step, while a new subset of feature candidates is treated by the selection process. As a result, the inherent exploration and exploitation of the genetic algorithms for finding the best solutions of the selection problem are locally focused. The Sensors 2015, 15 23904 approach is tested on a dataset from a real test bed with several fault classes under different running conditions of load and velocity. The model performance for diagnosis is over 98%.

  1. Quantitative genetics theory for genomic selection and efficiency of breeding value prediction in open-pollinated populations

    Directory of Open Access Journals (Sweden)

    José Marcelo Soriano Viana

    2016-06-01

    Full Text Available ABSTRACT To date, the quantitative genetics theory for genomic selection has focused mainly on the relationship between marker and additive variances assuming one marker and one quantitative trait locus (QTL. This study extends the quantitative genetics theory to genomic selection in order to prove that prediction of breeding values based on thousands of single nucleotide polymorphisms (SNPs depends on linkage disequilibrium (LD between markers and QTLs, assuming dominance. We also assessed the efficiency of genomic selection in relation to phenotypic selection, assuming mass selection in an open-pollinated population, all QTLs of lower effect, and reduced sample size, based on simulated data. We show that the average effect of a SNP substitution is proportional to LD measure and to average effect of a gene substitution for each QTL that is in LD with the marker. Weighted (by SNP frequencies and unweighted breeding value predictors have the same accuracy. Efficiency of genomic selection in relation to phenotypic selection is inversely proportional to heritability. Accuracy of breeding value prediction is not affected by the dominance degree and the method of analysis, however, it is influenced by LD extent and magnitude of additive variance. The increase in the number of markers asymptotically improved accuracy of breeding value prediction. The decrease in the sample size from 500 to 200 did not reduce considerably accuracy of breeding value prediction.

  2. A link between altruism and sexual selection: genetic influence on altruistic behaviour and mate preference towards it.

    Science.gov (United States)

    Phillips, Tim; Ferguson, Eamonn; Rijsdijk, Fruhling

    2010-11-01

    Altruistic behaviour raises major questions for psychology and biology. One hypothesis proposes that human altruistic behaviour evolved as a result of sexual selection. Mechanisms that seek to explain how sexual selection works suggest genetic influence acting on both the mate preference for the trait and the preferred trait itself. We used a twin study to estimate whether genetic effects influenced responses to psychometric scales measuring mate preference towards altruistic traits (MPAT) and the preferred trait (i.e., 'altruistic personality'). As predicted, we found significant genetic effects influencing variation in both. We also predicted that individuals expressing stronger MPAT and 'altruistic personality' would have mated at a greater frequency in ancestral populations. We found evidence for this in that 67% of the covariance in the phenotypic correlation between the two scales was associated with significant genetic effects. Both sets of findings are thus consistent with the hypothesized link between sexual selection and human altruism towards non-kin. We discuss how this study contributes to our understanding of altruistic behaviour and how further work might extend this understanding.

  3. Genetic Diversity of Selected Mangifera Species Revealed by Inter Simple Sequence Repeats Markers

    OpenAIRE

    Ariffin, Zulhairil; Md Sah, Muhammad Shafie; Idris, Salma; Hashim, Nuradni

    2015-01-01

    ISSR markers were employed to reveal genetic diversity and genetic relatedness among 28 Mangifera accessions collected from Yan (Kedah), Bukit Gantang (Perak), Sibuti (Sarawak), and Papar (Sabah). A total of 198 markers were generated using nine anchored primers and one nonanchored primer. Genetic variation among the 28 accessions of Mangifera species including wild relatives, landraces, and clonal varieties is high, with an average degree of polymorphism of 98% and mean Shannon index, H0=7.5...

  4. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  5. G-STRATEGY: Optimal Selection of Individuals for Sequencing in Genetic Association Studies

    Science.gov (United States)

    Wang, Miaoyan; Jakobsdottir, Johanna; Smith, Albert V.; McPeek, Mary Sara

    2017-01-01

    In a large-scale genetic association study, the number of phenotyped individuals available for sequencing may, in some cases, be greater than the study’s sequencing budget will allow. In that case, it can be important to prioritize individuals for sequencing in a way that optimizes power for association with the trait. Suppose a cohort of phenotyped individuals is available, with some subset of them possibly already sequenced, and one wants to choose an additional fixed-size subset of individuals to sequence in such a way that the power to detect association is maximized. When the phenotyped sample includes related individuals, power for association can be gained by including partial information, such as phenotype data of ungenotyped relatives, in the analysis, and this should be taken into account when assessing whom to sequence. We propose G-STRATEGY, which uses simulated annealing to choose a subset of individuals for sequencing that maximizes the expected power for association. In simulations, G-STRATEGY performs extremely well for a range of complex disease models and outperforms other strategies with, in many cases, relative power increases of 20–40% over the next best strategy, while maintaining correct type 1 error. G-STRATEGY is computationally feasible even for large datasets and complex pedigrees. We apply G-STRATEGY to data on HDL and LDL from the AGES-Reykjavik and REFINE-Reykjavik studies, in which G-STRATEGY is able to closely-approximate the power of sequencing the full sample by selecting for sequencing a only small subset of the individuals. PMID:27256766

  6. Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World

    Directory of Open Access Journals (Sweden)

    Watkins W

    2012-05-01

    Full Text Available Abstract Background Populations of the Americas were founded by early migrants from Asia, and some have experienced recent genetic admixture. To better characterize the native and non-native ancestry components in populations from the Americas, we analyzed 815,377 autosomal SNPs, mitochondrial hypervariable segments I and II, and 36 Y-chromosome STRs from 24 Mesoamerican Totonacs and 23 South American Bolivians. Results and Conclusions We analyzed common genomic regions from native Bolivian and Totonac populations to identify 324 highly predictive Native American ancestry informative markers (AIMs. As few as 40–50 of these AIMs perform nearly as well as large panels of random genome-wide SNPs for predicting and estimating Native American ancestry and admixture levels. These AIMs have greater New World vs. Old World specificity than previous AIMs sets. We identify highly-divergent New World SNPs that coincide with high-frequency haplotypes found at similar frequencies in all populations examined, including the HGDP Pima, Maya, Colombian, Karitiana, and Surui American populations. Some of these regions are potential candidates for positive selection. European admixture in the Bolivian sample is approximately 12%, though individual estimates range from 0–48%. We estimate that the admixture occurred ~360–384 years ago. Little evidence of European or African admixture was found in Totonac individuals. Bolivians with pre-Columbian mtDNA and Y-chromosome haplogroups had 5–30% autosomal European ancestry, demonstrating the limitations of Y-chromosome and mtDNA haplogroups and the need for autosomal ancestry informative markers for assessing ancestry in admixed populations.

  7. Maternal Style Selectively Shapes Amygdalar Development and Social Behavior in Rats Genetically Prone to High Anxiety.

    Science.gov (United States)

    Cohen, Joshua L; Glover, Matthew E; Pugh, Phyllis C; Fant, Andrew D; Simmons, Rebecca K; Akil, Huda; Kerman, Ilan A; Clinton, Sarah M

    2015-01-01

    The early-life environment critically influences neurodevelopment and later psychological health. To elucidate neural and environmental elements that shape emotional behavior, we developed a rat model of individual differences in temperament and environmental reactivity. We selectively bred rats for high versus low behavioral response to novelty and found that high-reactive (bred high-responder, bHR) rats displayed greater risk-taking, impulsivity and aggression relative to low-reactive (bred low-responder, bLR) rats, which showed high levels of anxiety/depression-like behavior and certain stress vulnerability. The bHR/bLR traits are heritable, but prior work revealed bHR/bLR maternal style differences, with bLR dams showing more maternal attention than bHRs. The present study implemented a cross-fostering paradigm to examine the contribution of maternal behavior to the brain development and emotional behavior of bLR offspring. bLR offspring were reared by biological bLR mothers or fostered to a bLR or bHR mother and then evaluated to determine the effects on the following: (1) developmental gene expression in the hippocampus and amygdala and (2) adult anxiety/depression-like behavior. Genome-wide expression profiling showed that cross-fostering bLR rats to bHR mothers shifted developmental gene expression in the amygdala (but not hippocampus), reduced adult anxiety and enhanced social interaction. Our findings illustrate how an early-life manipulation such as cross-fostering changes the brain's developmental trajectory and ultimately impacts adult behavior. Moreover, while earlier studies highlighted hippocampal differences contributing to the bHR/bLR phenotypes, our results point to a role of the amygdala as well. Future work will pursue genetic and cellular mechanisms within the amygdala that contribute to bHR/bLR behavior either at baseline or following environmental manipulations. © 2015 S. Karger AG, Basel.

  8. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  9. The Potential of Aspen Clonal Forestry in Alberta: Breeding Regions and Estimates of Genetic Gain from Selection

    Science.gov (United States)

    Gylander, Tim; Hamann, Andreas; Brouard, Jean S.; Thomas, Barb R.

    2012-01-01

    Background Aspen naturally grows in large, single-species, even-aged stands that regenerate clonally after fire disturbance. This offers an opportunity for an intensive clonal forestry system that closely emulates the natural life history of the species. In this paper, we assess the potential of genetic tree improvement and clonal deployment to enhance the productivity of aspen forests in Alberta. We further investigate geographic patterns of genetic variation in aspen and infer forest management strategies under uncertain future climates. Methodology/Principal Findings Genetic variation among 242 clones from Alberta was evaluated in 13 common garden trials after 5–8 growing seasons in the field. Broad-sense heritabilities for height and diameter at breast height (DBH) ranged from 0.36 to 0.64, allowing 5–15% genetic gains in height and 9–34% genetic gains in DBH. Geographic partitioning of genetic variance revealed predominant latitudinal genetic differentiation. We further observed that northward movement of clones almost always resulted in increased growth relative to local planting material, while southward movement had a strong opposite effect. Conclusion/Significance Aspen forests are an important natural resource in western Canada that is used for pulp and oriented strandboard production, accounting for ∼40% of the total forest harvest. Moderate to high broad-sense heritabilities in growth traits suggest good potential for a genetic tree improvement program with aspen. Significant productivity gains appear possible through clonal selection from existing trials. We propose two breeding regions for Alberta, and suggest that well-tested southern clones may be used in the northern breeding region, accounting for a general warming trend observed over the last several decades in Alberta. PMID:22957006

  10. Dynamics of genetic differentiation in experimental Drosophila metapopulations : Unravelling the interplay of selection and migration

    NARCIS (Netherlands)

    Kleefsman, Maria

    2015-01-01

    As a result of the fragmentation of their habitats, many organisms live in small and relatively isolated populations. In my thesis, I investigate the interplay of migration and local adaptation. Migration promotes genetic exchange among populations, thus contributing to the maintenance of genetic

  11. Age trends in Douglas-fir genetic parameters and implications for optimum selection age.

    Science.gov (United States)

    G.R. Johnson; R.A. Sniezko; N.L. Mandel

    1997-01-01

    rends in genetic variation were examined over 51 progeny test sites throughout western Oregon. Narrow sense heritabilities for height and diameter showed an increasing trend to age 25, the oldest age examined. Before age 10, height heritabilities were relatively unstable. Type B site-site genetic correlations increased slowly with age for height and remained relatively...

  12. Cost-efficient selection of a marker panel in genetic studies

    Science.gov (United States)

    Jamie S. Sanderlin; Nicole Lazar; Michael J. Conroy; Jaxk Reeves

    2012-01-01

    Genetic techniques are frequently used to sample and monitor wildlife populations. The goal of these studies is to maximize the ability to distinguish individuals for various genetic inference applications, a process which is often complicated by genotyping error. However, wildlife studies usually have fixed budgets, which limit the number of geneticmarkers available...

  13. Prediction of breeding values and selection responses with genetic heterogeneity of environmental variance

    NARCIS (Netherlands)

    Mulder, H.A.; Bijma, P.; Hill, W.G.

    2007-01-01

    There is empirical evidence that genotypes differ not only in mean, but also in environmental variance of the traits they affect. Genetic heterogeneity of environmental variance may indicate genetic differences in environmental sensitivity. The aim of this study was to develop a general framework

  14. Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by microsatellite markers

    Science.gov (United States)

    Dinarti, Diny; Susilo, Agung W.; Meinhardt, Lyndel W.; Ji, Kun; Motilal, Lambert A.; Mischke, Sue; Zhang, Dapeng

    2015-01-01

    Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers’ fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. PMID:26719747

  15. Divergent selection on home pen locomotor activity in a chicken model: Selection program, genetic parameters and direct response on activity and body weight.

    Directory of Open Access Journals (Sweden)

    Joergen B Kjaer

    Full Text Available General locomotor activity (GLA in poultry has attracted attention, as it negatively influences production costs (energy expenditure and feed consumption and welfare parameters (bone strength, litter quality, feather pecking and cannibalism. Laying hen lines diverging in the average level of spontaneous locomotor activity in the home pen were developed by genetic selection using the founder New Hampshire line. Activity was recorded using RFID technology at around five weeks of age during four to five days in the home pen. After initial phenotyping, the least active birds were selected for the low activity line and the most active for the high activity line, with no gene transfer between lines. In each of six generations, approximately ten sires were mated to twenty dams producing 158 to 334 offspring per line per generation. The response to selection was rapid and of a considerable magnitude. In sixth generation, the level of GLA was approximately halved in the low and doubled in the high line compared to the control (7.2, 14.9 and 28.7 recordings/h. Estimated heritability of locomotor activity in the low and high line was 0.38 and 0.33, respectively. Males, in general, were more active than females. High line birds were significantly heavier than low line birds. In fourth, fifth, and sixth generation, low as well as high line birds were lighter than control line birds. This selection experiment demonstrates variation in heritability for GLA and, as a result, genetically diverged lines have been developed. These lines can be used as models for further studies of underlying physiological, neural and molecular genetic mechanisms of spontaneous locomotor activity.

  16. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers.

    Science.gov (United States)

    Brito, Luiz F; Kijas, James W; Ventura, Ricardo V; Sargolzaei, Mehdi; Porto-Neto, Laercio R; Cánovas, Angela; Feng, Zeny; Jafarikia, Mohsen; Schenkel, Flávio S

    2017-03-14

    The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean H O and H E was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures F EH , F VR , F LEUT , F ROH and F PED was 0.129, -0.012, -0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds' development history. The information reported here will be useful for

  17. Major histocompatibility complex variation in insular populations of the Egyptian vulture: inferences about the roles of genetic drift and selection.

    Science.gov (United States)

    Agudo, Rosa; Alcaide, Miguel; Rico, Ciro; Lemus, Jesus A; Blanco, Guillermo; Hiraldo, Fernando; Donázar, Jose A

    2011-06-01

    Insular populations have attracted the attention of evolutionary biologists because of their morphological and ecological peculiarities with respect to their mainland counterparts. Founder effects and genetic drift are known to distribute neutral genetic variability in these demes. However, elucidating whether these evolutionary forces have also shaped adaptive variation is crucial to evaluate the real impact of reduced genetic variation in small populations. Genes of the major histocompatibility complex (MHC) are classical examples of evolutionarily relevant loci because of their well-known role in pathogen confrontation and clearance. In this study, we aim to disentangle the partial roles of genetic drift and natural selection in the spatial distribution of MHC variation in insular populations. To this end, we integrate the study of neutral (22 microsatellites and one mtDNA locus) and MHC class II variation in one mainland (Iberia) and two insular populations (Fuerteventura and Menorca) of the endangered Egyptian vulture (Neophron percnopterus). Overall, the distribution of the frequencies of individual MHC alleles (n=17 alleles from two class II B loci) does not significantly depart from neutral expectations, which indicates a prominent role for genetic drift over selection. However, our results point towards an interesting co-evolution of gene duplicates that maintains different pairs of divergent alleles in strong linkage disequilibrium on islands. We hypothesize that the co-evolution of genes may counteract the loss of genetic diversity in insular demes, maximize antigen recognition capabilities when gene diversity is reduced, and promote the co-segregation of the most efficient allele combinations to cope with local pathogen communities. © 2011 Blackwell Publishing Ltd.

  18. Data compression can discriminate broilers by selection line, detect haplotypes, and estimate genetic potential for complex phenotypes.

    Science.gov (United States)

    Hudson, N J; Hawken, R J; Okimoto, R; Sapp, R L; Reverter, A

    2017-09-01

    Accurately establishing the relationships among individuals lays the foundation for genetic analyses such as genome-wide association studies and identification of selection signatures. Of particular interest to the poultry industry are estimates of genetic merit based on molecular data. These estimates can be commercially exploited in marker-assisted breeding programs to accelerate genetic improvement. Here, we test the utility of a new method we have recently developed to estimate animal relatedness and applied it to genetic parameter estimation in commercial broilers. Our approach is based on the concept of data compression from information theory. Using the real-world compressor gzip to estimate normalized compression distance (NCD) we have built compression-based relationship matrices (CRM) for 988 chickens from 4 commercial broiler lines-2 male and 2 female lines. For all pairs of individuals, we found a strong negative relationship between the commonly used genomic relationship matrix (GRM) and NCD. This reflects the fact that "similarity" is the inverse of "distance." The CRM explained more genetic variation than the corresponding GRM in 2 of 3 phenotypes, with corresponding improvements in accuracy of genomic-enabled predictions of breeding value. A sliding-window version of the analysis highlighted haplotype regions of the genome apparently under selection in a line-specific manner. In the male lines, we retrieved high population-specific scores for IGF-1 and a cognate receptor, INSR. For the female lines, we detected an extreme score for a region containing a reproductive hormone receptor (GNRHR). We conclude that our compression-based method is a valid approach to established relationships and identify regions under selective pressure in commercial lines of broiler chickens. © 2017 Poultry Science Association Inc.

  19. BAPJ69-4A: a yeast two-hybrid strain for both positive and negative genetic selection.

    Science.gov (United States)

    Shaffer, Hally Anne; Rood, Michael Kenneth; Kashlan, Badar; Chang, Eileen I-ling; Doyle, Donald Francis; Azizi, Bahareh

    2012-10-01

    Genetic selection systems, such as the yeast two-hybrid system, are efficient methods to detect protein-protein and protein-ligand interactions. These systems have been further developed to assess negative interactions, such as inhibition, using the URA3 genetic selection marker. Previously, chemical complementation was used to assess positive selection in Saccharomyces cerevisiae. In this work, a new S. cerevisiae strain, called BAPJ69-4A, containing three selective markers ADE2, HIS3, and URA3 as well as the lacZ gene controlled by Gal4 response elements, was developed and characterized using the retinoid X receptor (RXR) and its ligand 9-cis retinoic acid (9cRA). Further characterization was performed using RXR variants and the synthetic ligand LG335. To assess the functionality of the strain, RXR was compared to the parent strain PJ69-4A in adenine, histidine, and uracil selective media. In positive selection, associating partners that lead to cell growth were observed in all media in the presence of ligand, whereas partners that did not associate due to the absence of ligand displayed no growth. Conversely, in negative selection, partners that did not associate in 5-FOA medium did not display cell death due to the lack of expression of the URA3 gene. The creation of the BAPJ69-4A yeast strain provides a high-throughput selection system, called negative chemical complementation, which can be used for both positive and negative selection, providing a fast, powerful tool for discovering novel ligand receptor pairs for applications in drug discovery and protein engineering. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. Selection of genetic and phenotypic features associated with inflammatory status of patients on dialysis using relaxed linear separability method.

    Directory of Open Access Journals (Sweden)

    Leon Bobrowski

    Full Text Available Identification of risk factors in patients with a particular disease can be analyzed in clinical data sets by using feature selection procedures of pattern recognition and data mining methods. The applicability of the relaxed linear separability (RLS method of feature subset selection was checked for high-dimensional and mixed type (genetic and phenotypic clinical data of patients with end-stage renal disease. The RLS method allowed for substantial reduction of the dimensionality through omitting redundant features while maintaining the linear separability of data sets of patients with high and low levels of an inflammatory biomarker. The synergy between genetic and phenotypic features in differentiation between these two subgroups was demonstrated.

  1. ISSR marker-assisted genetic diversity analysis of Dioscorea hispida and selection of the best variety for sustainable production.

    Science.gov (United States)

    Nudin, Nur Fatihah Hasan; Ali, Abdul Manaf; Ngah, Norhayati; Mazlan, Nor Zuhailah; Mat, Nashriyah; Ghani, Mohd Noor Abd; Alias, Nadiawati; Zakaria, Abd Jamil; Jahan, Md Sarwar

    2017-08-01

    Plant breeding is a way of selection of a particular individual for the production of the progeny by separating or combining desired characteristics. The objective of this study was to justify different characteristics of Dioscorea hispida (Ubi gadong) varieties using molecular techniques to select the best variety for sustainable production at the farmer's level. A total of 160 germplasms of Ubi gadong were collected from different locations at the Terengganu and Kelantan states of Malaysia. Forty eight (48) out of 160 germplasms were selected as "primary" selection based on yield and other qualitative characters. Selected collections were then grown and maintained for ISSR marker-assisted genetic diversity analysis. Overall plant growth and yield of tubers were also determined. A total of 12 ISSR markers were tested to justify the characteristics of Ubi gadong varieties among which three markers showed polymorphic bands and on average 57.3% polymorphism were observed representing the highest variation among germplasms. The ISSR marker based on UPGMA cluster analysis grouped all 48 D. hispida into 10 vital groups that proved a vast genetic variation among germplasm collections. Therefore, hybridization should be made between two distant populations. The D. hispida is already proved as the highest starch content tuber crops and very rich in vitamins with both micro and macro minerals. Considering all these criteria and results from marker-assisted diversity analysis, accessions that are far apart based on their genetic coefficient (like DH27 and DH71; DH30 and DH70; DH43 and DH62; DH45 and DH61; DH77 and DH61; DH78 and DH57) could be selected as parents for further breeding programs. This will bring about greater diversity, which will lead to high productive index in terms of increase in yield and overall quality and for the ultimate target of sustainable Ubi gadong production. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights

  2. Nontraditional inheritance: Genetics and the nature of science, now titled, The puzzle of inheritance: Genetics and the methods of science. Final report

    Energy Technology Data Exchange (ETDEWEB)

    McInerney, J.D.

    1998-08-31

    This project led to the development of an instructional module designed for use in high school biology classes. The module contains two major components. The first is an overview for teachers, which introduces the module, describes the Human Genome Project, and addresses issues in the philosophy of science and some of the ethical, legal, and social implications of research in genetics. It provides a survey of fundamental genetics concepts and of new, nontraditional concepts of inheritance. The second component provides six instructional activities appropriate for high school or introductory college students.

  3. Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population.

    Science.gov (United States)

    Bolund, Elisabeth; Bouwhuis, Sandra; Pettay, Jenni E; Lummaa, Virpi

    2013-12-07

    The sexes often have different phenotypic optima for important life-history traits, and because of a largely shared genome this can lead to a conflict over trait expression. In mammals, the obligate costs of reproduction are higher for females, making reproductive timing and rate especially liable to conflict between the sexes. While studies from wild vertebrates support such sexual conflict, it remains unexplored in humans. We used a pedigreed human population from preindustrial Finland to estimate sexual conflict over age at first and last reproduction, reproductive lifespan and reproductive rate. We found that the phenotypic selection gradients differed between the sexes. We next established significant heritabilities in both sexes for all traits. All traits, except reproductive rate, showed strongly positive intersexual genetic correlations and were strongly genetically correlated with fitness in both sexes. Moreover, the genetic correlations with fitness were almost identical in men and women. For reproductive rate, the intersexual correlation and the correlation with fitness were weaker but again similar between the sexes. Thus, in this population, an apparent sexual conflict at the phenotypic level did not reflect an underlying genetic conflict over the studied reproductive traits. These findings emphasize the need for incorporating genetic perspectives into studies of human life-history evolution.

  4. Genetic structure and contrasting selection pattern at two major histocompatibility complex genes in wild house mouse populations

    Czech Academy of Sciences Publication Activity Database

    Čížková, Dagmar; Goüy de Bellocq, J.; Baird, S. J. E.; Piálek, Jaroslav; Bryja, Josef

    2011-01-01

    Roč. 106, č. 5 (2011), s. 727-740 ISSN 0018-067X R&D Projects: GA AV ČR IAA600930608; GA ČR GA206/08/0640 Institutional research plan: CEZ:AV0Z60930519 Keywords : MHC * house mouse * selection * population structure * trans-species polymorphism Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.597, year: 2011

  5. Selection by mating competitiveness improves the performance of Anastrepha ludens males of the genetic sexing strain Tapachula-7.

    Science.gov (United States)

    Quintero-Fong, L; Toledo, J; Ruiz, L; Rendón, P; Orozco-Dávila, D; Cruz, L; Liedo, P

    2016-10-01

    The sexual performance of Anastrepha ludens males of the Tapachula-7 genetic sexing strain, produced via selection based on mating success, was compared with that of males produced without selection in competition with wild males. Mating competition, development time, survival, mass-rearing quality parameters and pheromone production were compared. The results showed that selection based on mating competitiveness significantly improved the sexual performance of offspring. Development time, survival of larvae, pupae and adults, and weights of larvae and pupae increased with each selection cycle. Differences in the relative quantity of the pheromone compounds (Z)-3-nonenol and anastrephin were observed when comparing the parental males with the F4 and wild males. The implications of this colony management method on the sterile insect technique are discussed.

  6. Selection and Estimation the Genetic Parameters of Rootstock Characteristics on Cocoa Seedling of Half-sibs Families

    Directory of Open Access Journals (Sweden)

    Agung Wahyu Susilo

    2005-12-01

    Full Text Available For cocoa clonal propagation it need rootstock with good characteristics. Half sibs families is the most appropriate alternative for rootstock selection. This study was aimed to select and estimate genetic parameters of cocoa seedling on the half sibs families of DR 1, DR 2, ICS 60, DRC 15, BLC 4, DRC 16, KEE 2, ICS 13, KW 162, KW 163, PA 300, RCC 70, TSH 858, Sca 6 and Sca 12. Research was carried out in Kaliwining Experimental Station of Indonesian Coffee and Cocoa Research Institute. Genetic parameter were estimated based on variance and covariance component of the variables of the number of leaf, stem height, stem girth, leaf acreage, the volume of fresh root, the length of secondary root and the length of primary root which assessed along seed growth till 90 day after planting. The result showed that most of the recorded variables perform high category of narrow sense heritability (h 2>0.5. Stem girth, leaf acreage, volume of fresh root, length of secondary root and the length of primary root were assessed as the broad category of genetic variability (d2 A >2Sed 2 A . Therefore, length of primary root and length of secondary root would be the main criterion for rootstock selection as their performance on broad category of genetic variability and high category of narrow sense heritability. Length of secondary root can be estimated based on the performance of stem girth (r = 0.5 * and leaf acreage (r = 0.23* and the primary root can be stimated based on the performance of stem height (r = 0.81 * and leaf acreage (r = 0.72*. Based on positive selection of primary root lenght and negative selection of secondary root lenght it was identified that the families of KEE 2 and Sca 12 potentially would be good rootstock due to their long category of the primary root and short category of the secondary root that having characteristics of high water uptake and low vigor. Key words: selection, genetic parameter, half-sib familiy, rootstock, cocoa.

  7. The oncolytic poxvirus JX-594 selectively replicates in and destroys cancer cells driven by genetic pathways commonly activated in cancers.

    Science.gov (United States)

    Parato, Kelley A; Breitbach, Caroline J; Le Boeuf, Fabrice; Wang, Jiahu; Storbeck, Chris; Ilkow, Carolina; Diallo, Jean-Simon; Falls, Theresa; Burns, Joseph; Garcia, Vanessa; Kanji, Femina; Evgin, Laura; Hu, Kang; Paradis, Francois; Knowles, Shane; Hwang, Tae-Ho; Vanderhyden, Barbara C; Auer, Rebecca; Kirn, David H; Bell, John C

    2012-04-01

    Oncolytic viruses are generally designed to be cancer selective on the basis of a single genetic mutation. JX-594 is a thymidine kinase (TK) gene-inactivated oncolytic vaccinia virus expressing granulocyte-macrophage colony-stimulating factor (GM-CSF) and lac-Z transgenes that is designed to destroy cancer cells through replication-dependent cell lysis and stimulation of antitumoral immunity. JX-594 has demonstrated a favorable safety profile and reproducible tumor necrosis in a variety of solid cancer types in clinical trials. However, the mechanism(s) responsible for its cancer-selectivity have not yet been well described. We analyzed the replication of JX-594 in three model systems: primary normal and cancer cells, surgical explants, and murine tumor models. JX-594 replication, transgene expression, and cytopathic effects were highly cancer-selective, and broad spectrum activity was demonstrated. JX-594 cancer-selectivity was multi-mechanistic; replication was activated by epidermal growth factor receptor (EGFR)/Ras pathway signaling, cellular TK levels, and cancer cell resistance to type-I interferons (IFNs). These findings confirm a large therapeutic index for JX-594 that is driven by common genetic abnormalities in human solid tumors. This appears to be the first description of multiple selectivity mechanisms, both inherent and engineered, for an oncolytic virus. These findings have implications for oncolytic viruses in general, and suggest that their cancer targeting is a complex and multifactorial process.

  8. Aquaporins in the wild: natural genetic diversity and selective pressure in the PIP gene family in five Neotropical tree species.

    Science.gov (United States)

    Audigeos, Delphine; Buonamici, Anna; Belkadi, Laurent; Rymer, Paul; Boshier, David; Scotti-Saintagne, Caroline; Vendramin, Giovanni G; Scotti, Ivan

    2010-06-29

    Tropical trees undergo severe stress through seasonal drought and flooding, and the ability of these species to respond may be a major factor in their survival in tropical ecosystems, particularly in relation to global climate change. Aquaporins are involved in the regulation of water flow and have been shown to be involved in drought response; they may therefore play a major adaptive role in these species. We describe genetic diversity in the PIP sub-family of the widespread gene family of Aquaporins in five Neotropical tree species covering four botanical families. PIP Aquaporin subfamily genes were isolated, and their DNA sequence polymorphisms characterised in natural populations. Sequence data were analysed with statistical tests of standard neutral equilibrium and demographic scenarios simulated to compare with the observed results. Chloroplast SSRs were also used to test demographic transitions. Most gene fragments are highly polymorphic and display signatures of balancing selection or bottlenecks; chloroplast SSR markers have significant statistics that do not conform to expectations for population bottlenecks. Although not incompatible with a purely demographic scenario, the combination of all tests tends to favour a selective interpretation of extant gene diversity. Tropical tree PIP genes may generally undergo balancing selection, which may maintain high levels of genetic diversity at these loci. Genetic variation at PIP genes may represent a response to variable environmental conditions.

  9. Estimates for Genetic Variance Components in Reciprocal Recurrent Selection in Populations Derived from Maize Single-Cross Hybrids

    Directory of Open Access Journals (Sweden)

    Matheus Costa dos Reis

    2014-01-01

    Full Text Available This study was carried out to obtain the estimates of genetic variance and covariance components related to intra- and interpopulation in the original populations (C0 and in the third cycle (C3 of reciprocal recurrent selection (RRS which allows breeders to define the best breeding strategy. For that purpose, the half-sib progenies of intrapopulation (P11 and P22 and interpopulation (P12 and P21 from populations 1 and 2 derived from single-cross hybrids in the 0 and 3 cycles of the reciprocal recurrent selection program were used. The intra- and interpopulation progenies were evaluated in a 10×10 triple lattice design in two separate locations. The data for unhusked ear weight (ear weight without husk and plant height were collected. All genetic variance and covariance components were estimated from the expected mean squares. The breakdown of additive variance into intrapopulation and interpopulation additive deviations (στ2 and the covariance between these and their intrapopulation additive effects (CovAτ found predominance of the dominance effect for unhusked ear weight. Plant height for these components shows that the intrapopulation additive effect explains most of the variation. Estimates for intrapopulation and interpopulation additive genetic variances confirm that populations derived from single-cross hybrids have potential for recurrent selection programs.

  10. A unifying framework for robust association testing, estimation, and genetic model selection using the generalized linear model.

    Science.gov (United States)

    Loley, Christina; König, Inke R; Hothorn, Ludwig; Ziegler, Andreas

    2013-12-01

    The analysis of genome-wide genetic association studies generally starts with univariate statistical tests of each single-nucleotide polymorphism. The standard approach is the Cochran-Armitage trend test or its logistic regression equivalent although this approach can lose considerable power if the underlying genetic model is not additive. An alternative is the MAX test, which is robust against the three basic modes of inheritance. Here, the asymptotic distribution of the MAX test is derived using the generalized linear model together with the Delta method and multiple contrasts. The approach is applicable to binary, quantitative, and survival traits. It may be used for unrelated individuals, family-based studies, and matched pairs. The approach provides point and interval effect estimates and allows selecting the most plausible genetic model using the minimum P-value. R code is provided. A Monte-Carlo simulation study shows that the asymptotic MAX test framework meets type I error levels well, has good power, and good model selection properties for minor allele frequencies ≥0.3. Pearson's χ(2)-test is superior for lower minor allele frequencies with low frequencies for the rare homozygous genotype. In these cases, the model selection procedure should be used with caution. The use of the MAX test is illustrated by reanalyzing findings from seven genome-wide association studies including case-control, matched pairs, and quantitative trait data.

  11. Aquaporins in the wild: natural genetic diversity and selective pressure in the PIP gene family in five Neotropical tree species

    Directory of Open Access Journals (Sweden)

    Vendramin Giovanni G

    2010-06-01

    Full Text Available Abstract Background Tropical trees undergo severe stress through seasonal drought and flooding, and the ability of these species to respond may be a major factor in their survival in tropical ecosystems, particularly in relation to global climate change. Aquaporins are involved in the regulation of water flow and have been shown to be involved in drought response; they may therefore play a major adaptive role in these species. We describe genetic diversity in the PIP sub-family of the widespread gene family of Aquaporins in five Neotropical tree species covering four botanical families. Results PIP Aquaporin subfamily genes were isolated, and their DNA sequence polymorphisms characterised in natural populations. Sequence data were analysed with statistical tests of standard neutral equilibrium and demographic scenarios simulated to compare with the observed results. Chloroplast SSRs were also used to test demographic transitions. Most gene fragments are highly polymorphic and display signatures of balancing selection or bottlenecks; chloroplast SSR markers have significant statistics that do not conform to expectations for population bottlenecks. Although not incompatible with a purely demographic scenario, the combination of all tests tends to favour a selective interpretation of extant gene diversity. Conclusions Tropical tree PIP genes may generally undergo balancing selection, which may maintain high levels of genetic diversity at these loci. Genetic variation at PIP genes may represent a response to variable environmental conditions.

  12. Inverse European Latitudinal Cline at the timeless Locus of Drosophila melanogaster Reveals Selection on a Clock Gene: Population Genetics of ls-tim.

    Science.gov (United States)

    Zonato, Valeria; Vanin, Stefano; Costa, Rodolfo; Tauber, Eran; Kyriacou, Charalambos P

    2018-02-01

    The spread of adaptive genetic variants in populations is a cornerstone of evolutionary theory but with relatively few biologically well-understood examples. Previous work on the ls-tim variant of timeless, which encodes the light-sensitive circadian regulator in Drosophila melanogaster, suggests that it may have originated in southeastern Italy. Flies characterized by the new allele show photoperiod-related phenotypes likely to be adaptive in seasonal environments. ls-tim may be spreading from its point of origin in Italy by directional selection, but there are alternative explanations for its observed clinal geographical distribution, including balancing selection and demography. From population analyses of ls-tim frequencies collected on the eastern side of the Iberian Peninsula, we show that ls-tim frequencies are inverted compared with those in Italy. This pattern is consistent with a scenario of directional selection rather than latitude-associated balancing selection. Neutrality tests further reveal the signature of directional selection at the ls-tim site, which is reduced a few kb pairs either side of ls-tim. A reanalysis of allele frequencies from a large number of microsatellite loci do not demonstrate any frequent ls-tim-like spatial patterns, so a general demographic effect or population expansion from southeastern Italy cannot readily explain current ls-tim frequencies. Finally, a revised estimate of the age of ls-tim allele using linkage disequilibrium and coalescent-based approaches reveals that it may be only 300 to 3000 years old, perhaps explaining why it has not yet gone to fixation. ls-tim thus provides a rare temporal snapshot of a new allele that has come under selection before it reaches equilibrium.

  13. Use of novel DNA fingerprinting techniques for the detection and characterization of genetic variation in vegetatively propagated crops. Proceedings of a final research co-ordination meeting

    International Nuclear Information System (INIS)

    1998-10-01

    Vegetative propagated crops, such as banana and platain, sweet potato, yam, sugarcane and cassava, represent important sources of food in the developing countries. Although some of these crops may produce seeds, they must for practical purposes be propagated vegetatively. As normal plant breeding strategies based on genetic hybridization are of limited value or not applicable to such crops, it is necessary to assess the genetic diversity already existing in these crops and to design breeding strategies accordingly. If the existing genetic variation is shown to be too narrow for breeding purposes, one promising possibility for the introduction of genetic variability is the use of mutations induced by radiation or chemical mutagens. This CRP focused on: the detection of genetic diversity induced by mutagenic treatment or in vitro culture; the development of crop-specific markers; and increasing co-operation between molecular biologists in advanced laboratories and plant breeders and molecular biologists in the developing countries. The success of this CRP is evidenced by the introduction and application of new molecular methods by laboratories in developing countries, specially for the analysis of local crop genetic diversity. These exciting preliminary results show the potential for applications in crop improvement but much work remains to be done. Many of the vegetatively propagated species are ''orphan crops'', under-investigated on the international level. The development of new uses of transgenesis for the development of edible vaccines should not be overlooked. The challenge that remains is in the application of these new tools for practical end-user oriented improvements in vegetatively propagated crops. The present publication summarizes the third and final Research Co-ordination Meeting on the Use of Novel DNA Fingerprinting Techniques for the Detection and Characterization of Genetic Variation in Vegetatively Propagated Crops

  14. Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines.

    Science.gov (United States)

    Boschiero, Clarissa; Moreira, Gabriel Costa Monteiro; Gheyas, Almas Ara; Godoy, Thaís Fernanda; Gasparin, Gustavo; Mariani, Pilar Drummond Sampaio Corrêa; Paduan, Marcela; Cesar, Aline Silva Mello; Ledur, Mônica Corrêa; Coutinho, Luiz Lehmann

    2018-01-25

    Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection. A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development. In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common

  15. Genetic Improvement of Traits Affected by Interactions Among Individuals: Sib Selection Schemes

    NARCIS (Netherlands)

    Ellen, E.D.; Muir, W.M.; Teuscher, F.; Bijma, P.

    2007-01-01

    Livestock populations are usually kept in groups. As a consequence, social interactions among individuals affect productivity, health, and welfare. Current selection methods (individual selection), however, ignore those interactions and yield suboptimal or in some cases even negative responses. In

  16. Changes in competence of public authorities in connection with final storage pursuant to the omnibus law on site selection

    International Nuclear Information System (INIS)

    Keienburg, Bettina

    2012-01-01

    The omnibus law on site finding and selection for a repository for radioactive waste generating heat, and with amendments to other laws, of June 13, 2012 is to reshuffle fundamentally the competences of public authorities for final storage. The federal government is to assume more responsibilities from former federal state competences. Moreover, most of the existing competences of the Federal Office for Radiation Protection are to be transferred to a federal agency yet to be founded, which is called Federal Office for Nuclear Safety in the present draft legislation. The Federal Office for Radiation Protection will only retain its responsibility as project agent for repositories, and that only in the phases of site exploration and licensing. Afterwards, the duty of final storage in the draft legislation is transferred to a 3rd party. Again in the version of the draft legislation, and unlike present regulations, this 3rd party may only be a company whose sole owner is the federal government, which also is to strengthen the influence of the federal government under aspects of company law. Legislative efforts seeking to strengthen the federal government and its competences by assigning licensing duties for repositories to federal agencies are understandable under feasibility aspects and may even be in the emotional interest of the states and their competent representatives in public authorities who, merely because their work is connected with the disputed topic of final storage, often face attacks and accusations by the public. Nevertheless, the transfer to federal agencies of administrative duties is subject to constitutional limits which must be observed. These constitutional aspects are highlighted in the publication. It is left to the reader to assess the meaningfulness of establishing another independent high-level federal agency in the area of responsibility of the Federal Ministry of the Environment (BMU), i.e. a Federal Office for Nuclear Safety, alongside the

  17. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

    Directory of Open Access Journals (Sweden)

    Damien C Tully

    2016-05-01

    Full Text Available Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU, we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic "signatures" within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission.

  18. Determination of Genetic Diversity Using 15 Simple Sequence Repeats Markers in Long Term Selected Japanese Quail Lines.

    Science.gov (United States)

    Karabağ, Kemal; Balcıoğlu, Murat Soner; Karlı, Taki; Alkan, Sezai

    2016-12-01

    Japanese quail is still used as a model for poultry research because of their usefulness as laying, meat, and laboratory animals. Microsatellite markers are the most widely used molecular markers, due to their relative ease of scoring and high levels of polymorphism. The objective of the research was to determine genetic diversity and population genetic structures of selected Japanese quail lines (high body weight 1 [HBW1], HBW2, low body weight [LBW], and layer [L]) throughout 15th generations and an unselected control (C). A total of 69 individuals from five quail lines were genotyped by fifteen microsatellite markers. When analyzed profiles of the markers the observed (H o ) and expected (H e ) heterozygosity ranged from 0.04 (GUJ0027) to 0.64 (GUJ0087) and 0.21 (GUJ0027) to 0.84 (GUJ0037), respectively. Also, H o and H e were separated from 0.30 (L and LBW) to 0.33 (C and HBW2) and from 0.52 (HBW2) to 0.58 (L and LBW), respectively. The mean polymorphic information content (PIC) ranged from 0.46 (HBW2) to 0.52 (L). Approximately half of the markers were informative (PIC≥0.50). Genetic distances were calculated from 0.09 (HBW1 and HBW2) to 0.33 (C and L). Phylogenetic dendrogram showed that the quail lines were clearly defined by the microsatellite markers used here. Bayesian model-based clustering supported the results from the phylogenetic tree. These results reflect that the set of studied markers can be used effectively to capture the magnitude of genetic variability in selected Japanese quail lines. Also, to identify markers and alleles which are specific to the divergence lines, further generations of selection are required.

  19. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

    Science.gov (United States)

    Tully, Damien C; Ogilvie, Colin B; Batorsky, Rebecca E; Bean, David J; Power, Karen A; Ghebremichael, Musie; Bedard, Hunter E; Gladden, Adrianne D; Seese, Aaron M; Amero, Molly A; Lane, Kimberly; McGrath, Graham; Bazner, Suzane B; Tinsley, Jake; Lennon, Niall J; Henn, Matthew R; Brumme, Zabrina L; Norris, Philip J; Rosenberg, Eric S; Mayer, Kenneth H; Jessen, Heiko; Kosakovsky Pond, Sergei L; Walker, Bruce D; Altfeld, Marcus; Carlson, Jonathan M; Allen, Todd M

    2016-05-01

    Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM) exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX) transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU), we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic "signatures" within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission.

  20. Genetic analysis of nile tilapia (oreochromis niloticus) selection line reared in two input environments.

    NARCIS (Netherlands)

    Khaw, H.L.; Bovenhuis, H.; Ponzoni, R.W.; Rezk, M.A.; Charo, H.; Komen, J.

    2009-01-01

    Ascertaining the appropriate selection environment for Nile tilapia (Oreochromis niloticus) in Africa is a critical issue. Two data sets derived from two selection lines originating from a common base population were analysed in this study. The lines were selected in two different input

  1. Conference report: 2012 Repository Symposium. Final storage in Germany. New start - ways and consequences of the site selection procedure

    International Nuclear Information System (INIS)

    Kettler, John

    2012-01-01

    The Aachen Institute for Nuclear Training invited participants to the 3-day '2012 Repository Symposium - Final Storage in Germany' held in Bonn. The subtitle of the event, 'New Start - Ways and Consequences of the Site Selection Procedure,' expressed the organizers' summary that the Repository Finding Act currently under discussion did not give rise to any expectation of a repository for high-level radioactive waste before 2080. The symposium was attended by more than 120 persons from Germany and abroad. They discussed the basic elements of the site selection procedure and its consequences on the basis of the draft so far known to the public. While extensive public participation is envisaged for the stage of finding a repository, this does not apply to the draft legislation in the same way. The legal determinations are negotiated in a small circle by the political parties and the state governments. Michael Sailer (Oeko-Institut e.V.) holds that agreement on a repository finding act is urgent. Prof. Dr. Bruno Thomauske (RWTH Aachen) arrives at the conclusion mentioned above, that no repository for high-level radioactive waste can start operation before 2080 on the basis of the Repository Finding Act. Dr. Bettina Keienburg, attorney at law, in her paper drew attention to the points of dispute in the draft legislation with regard to changes in competency of public authorities. The draft law indicated a clear shift of competency for finding a repository from the Federal Office for Radiation Protection to a federal agency yet to be set up. Prof. Dr. Christoph Moench outlined the deficiencies of the draft legislation in matters of refinancing and the polluter-pays principle. Among the tentative solutions discussed it was above all the Swedish model which was acclaimed most widely. (orig.)

  2. The environmental factors to be considered in the site selection studies of the spent fuel final disposal

    International Nuclear Information System (INIS)

    Aeikaes, Timo

    1985-10-01

    The ojective of the work has been to elucidate environmental factors, which could have an influence on the selection of areas. The factors were identified and their significance evaluated by going through the present plan for the final disposal of spent fuel. Population density and transport conditions were the most important factors. Protected areas, groundwater reservoirs and restrictions presented in regional land-use plans were also noted. The potential areas have been identified by the Geological Survey of Finland. First 327 large bedrock blocks were identified. The extent of the block areas was between 100-200 km 2 . The environmental factors of these areas were mapped and the areas were classified. The study was based on maps, published regional plans and inventory of groundwater reservoirs. The Geological Survey of Finland selected 162 block areas for preliminary characterization and geological classification. 61 block areas were chosen for further geological studies. By interpretation of aerial photographs and field reconnaissance trip the Geological Survey identified 134 potential investigation areas. A large block area typically contained two possible investigation areas. The extent of these areas varied between 5-10 km 2 . The environmental factors of 134 possible investigation areas were studied in detail. Due to the classification made earlier, the areas were typically sparsely populated forest areas. In the detailed study the main emphasis was but on evaluation of population density, transport and inventory of land ownership. The land-ownership is important for practical reasons. Land-owner's permission is needed for the operations in the field. Areas were classified separately according to population density, transport and land-ownership. In classification the most suitable areas were uninhabited regions with few landowners and locating close (less than 10 km) to the railroad. Only a minority of the areas fell in this category with the requirement

  3. Genetic Particle Swarm Optimization-Based Feature Selection for Very-High-Resolution Remotely Sensed Imagery Object Change Detection.

    Science.gov (United States)

    Chen, Qiang; Chen, Yunhao; Jiang, Weiguo

    2016-07-30

    In the field of multiple features Object-Based Change Detection (OBCD) for very-high-resolution remotely sensed images, image objects have abundant features and feature selection affects the precision and efficiency of OBCD. Through object-based image analysis, this paper proposes a Genetic Particle Swarm Optimization (GPSO)-based feature selection algorithm to solve the optimization problem of feature selection in multiple features OBCD. We select the Ratio of Mean to Variance (RMV) as the fitness function of GPSO, and apply the proposed algorithm to the object-based hybrid multivariate alternative detection model. Two experiment cases on Worldview-2/3 images confirm that GPSO can significantly improve the speed of convergence, and effectively avoid the problem of premature convergence, relative to other feature selection algorithms. According to the accuracy evaluation of OBCD, GPSO is superior at overall accuracy (84.17% and 83.59%) and Kappa coefficient (0.6771 and 0.6314) than other algorithms. Moreover, the sensitivity analysis results show that the proposed algorithm is not easily influenced by the initial parameters, but the number of features to be selected and the size of the particle swarm would affect the algorithm. The comparison experiment results reveal that RMV is more suitable than other functions as the fitness function of GPSO-based feature selection algorithm.

  4. Genetic and biochemical analysis of a laboratory-selected spirodiclofen-resistant strain of Tetranychus urticae Koch (Acari: Tetranychidae).

    Science.gov (United States)

    Van Pottelberge, Steven; Van Leeuwen, Thomas; Khajehali, Jahangir; Tirry, Luc

    2009-04-01

    Spirodiclofen is a selective, non-systemic acaricide from the new chemical class of tetronic acid derivatives. In order to develop strategies to minimise resistance in the field, a laboratory-selected spirodiclofen-resistant strain of the two-spotted spider mite, Tetranychus urticae Koch, was used to determine genetic, toxicological, biochemical and cross-resistance data. Selecting for spirodiclofen resistance in the laboratory yielded a strain (SR-VP) with a resistance ratio of 274, determined on the larval stage. The egg stage remained far more susceptible. No cross-resistance was found against other established acaricides, except for spiromesifen. Based on synergist experiments and enzyme assays, it appeared that especially P450 monooxygenases, but also esterases and glutathione-S-transferases, could be involved in the metabolic detoxification of spirodiclofen. Genetic analysis showed that the resistance is inherited as an intermediate trait under control of more than one gene. Resistance to spirodiclofen exceeded by far the recommended field rate. A good acaricide resistance management programme is necessary to prevent fast resistance build-up in the field. Spirodiclofen can be used in alternation with most established acaricides, except for other tetronic acid derivatives. Without selection pressure, resistance tends to be unstable and can decrease in the presence of susceptible individuals owing to the intermediate, polygenic inheritance mode. Copyright (c) 2009 Society of Chemical Industry.

  5. Genetic progress in the UNB-2U population of popcorn under recurrent selection in Rio de Janeiro, Brazil.

    Science.gov (United States)

    Ribeiro, R M; do Amaral Júnior, A T; Gonçalves, L S A; Candido, L S; Silva, T R C; Pena, G F

    2012-05-15

    As part of the Universidade Estadual do Norte Fluminense recurrent selection program of popcorn, we evaluated full-sib families of the sixth cycle of recurrent selection and estimated genetic progress for grain yield and expansion capacity. We assessed 200 full-sib families for 10 agronomic traits, in a randomized block design, with two replications within sets in two environments: Campos dos Goytacazes and Itaocara, in the State of Rio de Janeiro, Brazil. There were significant differences for families/"sets" for all traits, indicating genetic variability that could be exploited in future cycles. In the selection of superior progenies, the Mulamba and Mock index gave the best gains for popping expansion (PE) and grain yield (GY), with values of 10.97 and 15.30%, respectively, using random economic weights. By comparing the evolution of the means obtained for PE and GY in the cycles C(0), C(1), C(2), C(3), C(4), C(5), and predicted for C(6), a steady increase was observed for both PE and GY, with the addition of 1.71 mL/g (R(2) = 0.93) and 192.87 kg/ha (R(2) = 0.88), respectively, in each cycle. Given the good performance of this popcorn population in successive cycles of intrapopulation recurrent selection, we expect that a productive variety with high expansion capacity will soon be available for producers in the north and northwest regions of Rio de Janeiro State, Brazil.

  6. Similar genetic basis of resistance to Bt toxin Cry1Ac in Boll-selected and diet-selected strains of pink bollworm.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Fabrick

    Full Text Available Genetically engineered cotton and corn plants producing insecticidal Bacillus thuringiensis (Bt toxins kill some key insect pests. Yet, evolution of resistance by pests threatens long-term insect control by these transgenic Bt crops. We compared the genetic basis of resistance to Bt toxin Cry1Ac in two independently derived, laboratory-selected strains of a major cotton pest, the pink bollworm (Pectinophora gossypiella [Saunders]. The Arizona pooled resistant strain (AZP-R was started with pink bollworm from 10 field populations and selected with Cry1Ac in diet. The Bt4R resistant strain was started with a long-term susceptible laboratory strain and selected first with Bt cotton bolls and later with Cry1Ac in diet. Previous work showed that AZP-R had three recessive mutations (r1, r2, and r3 in the pink bollworm cadherin gene (PgCad1 linked with resistance to Cry1Ac and Bt cotton producing Cry1Ac. Here we report that inheritance of resistance to a diagnostic concentration of Cry1Ac was recessive in Bt4R. In interstrain complementation tests for allelism, F(1 progeny from crosses between AZP-R and Bt4R were resistant to Cry1Ac, indicating a shared resistance locus in the two strains. Molecular analysis of the Bt4R cadherin gene identified a novel 15-bp deletion (r4 predicted to cause the loss of five amino acids upstream of the Cry1Ac-binding region of the cadherin protein. Four recessive mutations in PgCad1 are now implicated in resistance in five different strains, showing that mutations in cadherin are the primary mechanism of resistance to Cry1Ac in laboratory-selected strains of pink bollworm from Arizona.

  7. Population genetics and natural selection in the gene encoding the Duffy binding protein II in Iranian Plasmodium vivax wild isolates.

    Science.gov (United States)

    Valizadeh, Vahideh; Zakeri, Sedigheh; Mehrizi, Akram Abouie; Djadid, Navid Dinparast

    2014-01-01

    Region II of Duffy binding protein (PvDBP-II) is one of the most promising blood-stage vaccine candidate antigens against Plasmodium vivax and having knowledge of the nature and genetic polymorphism of PvDBP-II among global P. vivax isolates is important for developing a DBP-based vaccine. By using PCR and sequencing, the present molecular population genetic approach was carried out to investigate sequence diversity and natural selection of dbp-II gene in 63 P. vivax isolates collected from unstable and low transmission malaria-endemic areas of Iran during 2008-2012. Also, phylogenetic analysis, the diversifying natural selection, and recombination across the pvdbp-II gene, including regions containing B-cell epitopes were analyzed using the DnaSP and MEGA4 programs. Twenty two single nucleotide polymorphisms (SNPs, including 20 non-synonymous and 2 synonymous) were identified in PvDBP-II, resulting in 16 different PvDBP-II haplotypes among the Iranian P. vivax isolates. High binding inhibitory B-cell epitope (H3) overlapping with intrinsically unstructured/disordered region (aa: 384-392) appeared to be highly polymorphic (D384G/E385K/ K386N/Q/R390H), and positive selective pressure acted on this region. Most of the polymorphic amino acids, which are located on the surface of the protein, are under selective pressure that implies increased recombination events and exposure to the human immune system. In summary, PvDBP-II gene displays genetic polymorphism among Iranian P. vivax isolates and it is under selective pressure. Mutations, recombination, and positive selection seem to play a role in the resulting genetic diversity, and phylogenetic analysis of DNA sequences demonstrates that Iranian isolates represent a sample of the global population. These results are useful for understanding the nature of the P. vivax population in Iran and also for development of PvDBP-II-based malaria vaccine. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Selecting the Best Forecasting-Implied Volatility Model Using Genetic Programming

    Directory of Open Access Journals (Sweden)

    Wafa Abdelmalek

    2009-01-01

    Full Text Available The volatility is a crucial variable in option pricing and hedging strategies. The aim of this paper is to provide some initial evidence of the empirical relevance of genetic programming to volatility's forecasting. By using real data from S&P500 index options, the genetic programming's ability to forecast Black and Scholes-implied volatility is compared between time series samples and moneyness-time to maturity classes. Total and out-of-sample mean squared errors are used as forecasting's performance measures. Comparisons reveal that the time series model seems to be more accurate in forecasting-implied volatility than moneyness time to maturity models. Overall, results are strongly encouraging and suggest that the genetic programming approach works well in solving financial problems.

  9. Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill.

    Science.gov (United States)

    Budde, Katharina B; González-Martínez, Santiago C; Navascués, Miguel; Burgarella, Concetta; Mosca, Elena; Lorenzo, Zaida; Zabal-Aguirre, Mario; Vendramin, Giovanni G; Verdú, Miguel; Pausas, Juli G; Heuertz, Myriam

    2017-04-01

    The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits

  10. A Systems Genetic Approach to Identify Low Dose Radiation-Induced Lymphoma Susceptibility/DOE2013FinalReport

    Energy Technology Data Exchange (ETDEWEB)

    Balmain, Allan [University of California, San Francisco; Song, Ihn Young [University of California, San Francisco

    2013-05-15

    The ultimate goal of this project is to identify the combinations of genetic variants that confer an individual's susceptibility to the effects of low dose (0.1 Gy) gamma-radiation, in particular with regard to tumor development. In contrast to the known effects of high dose radiation in cancer induction, the responses to low dose radiation (defined as 0.1 Gy or less) are much less well understood, and have been proposed to involve a protective anti-tumor effect in some in vivo scientific models. These conflicting results confound attempts to develop predictive models of the risk of exposure to low dose radiation, particularly when combined with the strong effects of inherited genetic variants on both radiation effects and cancer susceptibility. We have used a Systems Genetics approach in mice that combines genetic background analysis with responses to low and high dose radiation, in order to develop insights that will allow us to reconcile these disparate observations. Using this comprehensive approach we have analyzed normal tissue gene expression (in this case the skin and thymus), together with the changes that take place in this gene expression architecture a) in response to low or high- dose radiation and b) during tumor development. Additionally, we have demonstrated that using our expression analysis approach in our genetically heterogeneous/defined radiation-induced tumor mouse models can uniquely identify genes and pathways relevant to human T-ALL, and uncover interactions between common genetic variants of genes which may lead to tumor susceptibility.

  11. Genetic variation in the odorant receptors family 13 and the mhc loci influence mate selection in a multiple sclerosis dataset

    Directory of Open Access Journals (Sweden)

    Hauser Stephen L

    2010-11-01

    Full Text Available Abstract Background When selecting mates, many vertebrate species seek partners with major histocompatibility complex (MHC genes different from their own, presumably in response to selective pressure against inbreeding and towards MHC diversity. Attempts at replication of these genetic results in human studies, however, have reached conflicting conclusions. Results Using a multi-analytical strategy, we report validated genome-wide relationships between genetic identity and human mate choice in 930 couples of European ancestry. We found significant similarity between spouses in the MHC at class I region in chromosome 6p21, and at the odorant receptor family 13 locus in chromosome 9. Conversely, there was significant dissimilarity in the MHC class II region, near the HLA-DQA1 and -DQB1 genes. We also found that genomic regions with significant similarity between spouses show excessive homozygosity in the general population (assessed in the HapMap CEU dataset. Conversely, loci that were significantly dissimilar among spouses were more likely to show excessive heterozygosity in the general population. Conclusions This study highlights complex patterns of genomic identity among partners in unrelated couples, consistent with a multi-faceted role for genetic factors in mate choice behavior in human populations.

  12. AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection.

    Science.gov (United States)

    Tollenaere, C; Duplantier, J-M; Rahalison, L; Ranjalahy, M; Brouat, C

    2011-03-01

    The black rat (Rattus rattus) is the main reservoir of plague (Yersinia pestis infection) in Madagascar's rural zones. Black rats are highly resistant to plague within the plague focus (central highland), whereas they are susceptible where the disease is absent (low altitude zone). To better understand plague wildlife circulation and host evolution in response to a highly virulent pathogen, we attempted to determine genetic markers associated with plague resistance in this species. To this purpose, we combined a population genomics approach and an association study, both performed on 249 AFLP markers, in Malagasy R. rattus. Simulated distributions of genetic differentiation were compared to observed data in four independent pairs, each consisting of one population from the plague focus and one from the plague-free zone. We found 22 loci (9% of 249) with higher differentiation in at least two independent population pairs or with combining P-values over the four pairs significant. Among the 22 outlier loci, 16 presented significant association with plague zone (plague focus vs. plague-free zone). Population genetic structure inferred from outlier loci was structured by plague zone, whereas the neutral loci dataset revealed structure by geography (eastern vs. western populations). A phenotype association study revealed that two of the 22 loci were significantly associated with differentiation between dying and surviving rats following experimental plague challenge. The 22 outlier loci identified in this study may undergo plague selective pressure either directly or more probably indirectly due to hitchhiking with selected loci. © 2010 Blackwell Publishing Ltd.

  13. Relaxation of herbivore-mediated selection drives the evolution of genetic covariances between plant competitive and defense traits.

    Science.gov (United States)

    Uesugi, Akane; Connallon, Tim; Kessler, André; Monro, Keyne

    2017-06-01

    Insect herbivores are important mediators of selection on traits that impact plant defense against herbivory and competitive ability. Although recent experiments demonstrate a central role for herbivory in driving rapid evolution of defense and competition-mediating traits, whether and how herbivory shapes heritable variation in these traits remains poorly understood. Here, we evaluate the structure and evolutionary stability of the G matrix for plant metabolites that are involved in defense and allelopathy in the tall goldenrod, Solidago altissima. We show that G has evolutionarily diverged between experimentally replicated populations that evolved in the presence versus the absence of ambient herbivory, providing direct evidence for the evolution of G by natural selection. Specifically, evolution in an herbivore-free habitat altered the orientation of G, revealing a negative genetic covariation between defense- and competition-related metabolites that is typically masked in herbivore-exposed populations. Our results may be explained by predictions of classical quantitative genetic theory, as well as the theory of acquisition-allocation trade-offs. The study provides compelling evidence that herbivory drives the evolution of plant genetic architecture. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  14. Natural resistance to experimental feline infectious peritonitis virus infection is decreased rather than increased by positive genetic selection.

    Science.gov (United States)

    Pedersen, Niels C; Liu, Hongwei; Durden, Monica; Lyons, Leslie A

    2016-03-01

    A previous study demonstrated the existence of a natural resistance to feline infectious peritonitis virus (FIPV) among 36% of randomly bred laboratory cats. A genome wide association study (GWAS) on this population suggested that resistance was polygenic but failed to identify any strong specific associations. In order to enhance the power of GWAS or whole genome sequencing to identify strong genetic associations, a decision was made to positively select for resistance over three generations. The inbreeding experiment began with a genetically related parental (P) population consisting of three toms and four queens identified from among the survivors of the earlier study and belonging to a closely related subgroup (B). The subsequent effects of inbreeding were measured using 42 genome-wide STR markers. P generation cats produced 57 first filial (F1) kittens, only five of which (9.0%) demonstrated a natural resistance to FIPV infection. One of these five F1 survivors was then used to produce six F1/P-backcrosses kittens, only one of which proved resistant to FIP. Six of eight of the F1 and F1/P survivors succumbed to a secondary exposure 4-12 months later. Therefore, survival after both primary and secondary infection was decreased rather than increased by positive selection for resistance. The common genetic factor associated with this diminished resistance was a loss of heterozygosity. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  15. Redd Site Selection and Spawning Habitat Use by Fall Chinook Salmon, Hanford Reach, Columbia River : Final Report 1995 - 1998.

    Energy Technology Data Exchange (ETDEWEB)

    Geist, David R.

    1999-05-01

    year to year. The tendency to spawn in clusters suggests fall chinook salmon's use of spawning habitat is highly selective. Hydraulic characteristics of the redd clusters were significantly different than the habitat surrounding them. Velocity and lateral slope of the river bottom were the most important habitat variables in predicting redd site selection. While these variables explained a large proportion of the variance in redd site selection (86 to 96%), some unmeasured factors still accounted for a small percentage of actual spawning site selection. Chapter three describes the results from an investigation into the hyporheic characteristics of the two spawning areas studied in chapter two. This investigation showed that the magnitude and chemical characteristics of hyporheic discharge were different between and within two spawning areas. Apparently, fall chinook salmon used chemical and physical cues from the discharge to locate spawning areas. Finally, chapter four describes a unique method that was developed to install piezometers into the cobble bed of the Columbia River.

  16. Trait variation and genetic diversity in a banana genomic selection training population

    Czech Academy of Sciences Publication Activity Database

    Nyine, Moses; Uwimana, B.; Swennen, R.; Batte, M.; Brown, A.; Christelová, Pavla; Hřibová, Eva; Lorenzen, J.; Doležel, Jaroslav

    2017-01-01

    Roč. 12, č. 6 (2017), č. článku e0178734. E-ISSN 1932-6203 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : PLANTAIN MUSA * AAB GROUP * IMPROVEMENT Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 2.806, year: 2016

  17. Balancing selection and genetic drift create unusual patterns of MHCII variation in Galapagos mockingbirds

    Czech Academy of Sciences Publication Activity Database

    Vlček, Jakub; Hoeck, P. E. A.; Keller, L. F.; Wayhart, J. P.; Dolinová, I.; Štefka, Jan

    2016-01-01

    Roč. 25, č. 19 (2016), s. 4757-4772 ISSN 0962-1083 R&D Projects: GA ČR GPP506/12/P529 Institutional support: RVO:60077344 Keywords : major histocompatibility complex * Mimus * genetic diversity * population size * trans-species polymorphism Subject RIV: EG - Zoology Impact factor: 6.086, year: 2016

  18. Natural Selection and Evolution: Using Multimedia Slide Shows to Emphasize the Role of Genetic Variation

    Science.gov (United States)

    Malone, Molly

    2012-01-01

    Most middle school students comprehend that organisms have adaptations that enable their survival and that successful adaptations prevail in a population over time. Yet they often miss that those bird beaks, moth-wing colors, or whatever traits are the result of random, normal genetic variations that just happen to confer a negative, neutral, or…

  19. Alternative Somatic Cell Count Traits as Mastitis Indicators for Genetic Selection

    NARCIS (Netherlands)

    Haas, de Y.; Ouweltjes, W.; Napel, ten J.; Windig, J.J.; Jong, de G.

    2008-01-01

    The aim of this study was to define alternative traits of somatic cell count (SCC) that can be used to decrease genetic susceptibility to clinical and subclinical mastitis (CM and SCM, respectively). Three kinds of SCC traits were evaluated: 1) lactation-averages of SCC, 2) traits derived from the

  20. Analysis of the genetic diversity of selected East African sweet potato

    African Journals Online (AJOL)

    Aghomotsegin

    Key words: Sweet potato, cluster analysis, genetic diversity, principal component analysis, Simple Sequence ... Author(s) agree that this article remains permanently open access under the terms of the Creative Commons Attribution License 4.0 ..... Karuri HW, Ateka EM, Amata R, Nyende AB, Muigai AWT, Mwasame E,.

  1. A test for the genetic basis of natural selection: an individual-based longitudinal study in a stream-dwelling fish.

    Science.gov (United States)

    Morrissey, Michael B; Ferguson, Moira M

    2011-04-01

    In addition to the well-studied evolutionary parameters of (1) phenotype-fitness covariance and (2) the genetic basis of phenotypic variation, adaptive evolution by natural selection requires that (3) fitness variation is effected by heritable genetic differences among individuals and (4) phenotype-fitness covariances must be, at least in part, underlain by genetic covariances. These latter two requirements for adaptive evolutionary change are relatively unstudied in natural populations. Absence of the latter requirements could explain stasis of apparently directionally selected heritable traits. We provide complementary analyses of selection and variation at phenotypic and genetic levels for juvenile growth rate in brook charr Salvelinus fontinalis in Freshwater River, Newfoundland, Canada. Contrary to the vast majority of reports in fish, we found very little viability selection of juvenile body size. Large body size appears nonetheless to be selectively advantageous via a relationship with early maturity. Genetic patterns in evolutionary parameters largely reflected phenotypic patterns. We have provided inference of selection based on longitudinal data, which are uncommon in high fecundity organisms. Furthermore we have provided a practicable framework for further studies of the genetic basis of natural selection. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

  2. Selection of a seed orchard of Eucalyptus dunnii based on genetic diversity criteria calculated using molecular markers.

    Science.gov (United States)

    Marcucci Poltri, S N; Zelener, N; Rodriguez Traverso, J; Gelid, P; Hopp, H E

    2003-06-01

    A Eucalyptus dunnii Maiden breeding population of 46 accessions originated in Australia and selected for fitness to subtropical and cold environments was screened by Amplified Fragment Length Polymorphism (AFLP) and microsatellite markers to obtain quantitative estimates of genetic diversity. A randomly chosen group of AFLP primers generated 205 AFLP bands that were used to fingerprint the genotypes and to evaluate genetic relationships among accessions. Sixty-eight percent (140) of the bands were polymorphic markers. The mean diversity index (DI) was 0.33 and about 52% of the loci had values greater than 0.4. Cluster analysis derived from similarity indices (SI) revealed no particular grouping among accessions suggesting the absence of closely related genotypes, except for five pairs of genotypes. Bootstrap analysis results confirmed the suitability of AFLP to describe genetic relationships in this breeding population. In addition, four highly informative microsatellites were used to construct an identification matrix that discriminated nearly all of the genotypes. Mean values for the number of alleles per locus, DI and SI among accessions were 13, 0.78 and 0.19, respectively, indicating that the breeding population has high genetic diversity. However, several genotypes showed the presence of single microsatellite bands suggesting a putatively important degree of homozygosity. Molecular data were used to design a clonal seed orchard. To achieve this aim, the nine most divergent pairs of genotypes were chosen, thereby retaining 95.2% of the total number of alleles from the 140 polymorphic AFLP loci and the four microsatellite loci analyzed. Mean DI and SI for AFLP and microsatellites showed no significant differences between the original breeding population and the selected seed orchard, confirming that a seed orchard can be designed with a limited number of individuals, which allows similar accessions to be discarded and avoids inbreeding.

  3. Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq.

    Science.gov (United States)

    Marra, Nicholas J; Romero, Andrea; DeWoody, J Andrew

    2014-06-01

    One adaptation of ecological and evolutionary interest is the extraordinary ability of desert rodents to retain water during waste production. Much is known regarding the unique kidney physiology of kangaroo rats (Dipodomys spp.) and their ability to retain water during waste production, yet the genetic basis of these physiological adaptations is relatively unknown. Herein, we utilized RNA-seq data to conduct a comparative study to identify osmoregulatory genes expressed in heteromyid rodents. We sequenced kidney tissue from two temperate desert species (Dipodomys spectabilis and Chaetodipus baileyi) from two separate subfamilies of the Heteromyidae and compared these transcriptomes to a tropical mesic species (Heteromys desmarestianus) from a third subfamily. The evolutionary history of these subfamilies provided a robust phylogenetic control that allowed us to separate shared evolutionary history from convergence. Using two methods to detect differential expression (DE), we identified 1890 genes that showed consistent patterns of DE between the arid and mesic species. A three-species reciprocal BLAST analysis revealed 3511 sets of putative orthologues that, upon comparison to known Mus musculus sequences, revealed 323 annotated and full-length genic regions. Selection tests displayed evidence of positive selection (dn/ds > 1) on six genes in the two desert species and remained significant for one of these genes after correction for multiple testing. Thus, our data suggest that both the coding sequence and expression of genes have been shaped by natural selection to provide the genetic architecture for efficient osmoregulation in desert-adapted heteromyid rodents. © 2014 John Wiley & Sons Ltd.

  4. Short communication: Genomic selection in a crossbred cattle population using data from the Dairy Genetics East Africa Project.

    Science.gov (United States)

    Brown, A; Ojango, J; Gibson, J; Coffey, M; Okeyo, M; Mrode, R

    2016-09-01

    Due to the absence of accurate pedigree information, it has not been possible to implement genetic evaluations for crossbred cattle in African small-holder systems. Genomic selection techniques that do not rely on pedigree information could, therefore, be a useful alternative. The objective of this study was to examine the feasibility of using genomic selection techniques in a crossbred cattle population using data from Kenya provided by the Dairy Genetics East Africa Project. Genomic estimated breeding values for milk yield were estimated using 2 prediction methods, GBLUP and BayesC, and accuracies were calculated as the correlation between yield deviations and genomic breeding values included in the estimation process, mimicking the situation for young bulls. The accuracy of evaluation ranged from 0.28 to 0.41, depending on the validation population and prediction method used. No significant differences were found in accuracy between the 2 prediction methods. The results suggest that there is potential for implementing genomic selection for young bulls in crossbred small-holder cattle populations, and targeted genotyping and phenotyping should be pursued to facilitate this. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  5. Genetic rules for the dermatoglyphics of human fingertips and their role in spouse selection: a preliminary study.

    Science.gov (United States)

    Yang, Xiao; Xiaojun, Jin; Yixuan, Zhou; Hui, Liu

    2016-01-01

    We assessed the genetic rules for the dermatoglyphics of human fingertips. We also evaluated the correlation between spouse selection with the number of whorls on fingertips. Data were collected for the number of whorls from 118 families (couples and their children). Distribution of whorls was analyzed further to investigate the relationship between heredity and spouse selection. Through multiple regression analysis, we found that the number of whorls on fingertips was affected considerably by genetic factors. In a married couple with a moderate number of whorls, the probability of their children having a high number of whorls was 26.5 %, and the probability of their children having a low number of whorls was 23.5. These values were close to the theoretical value (25 %). A significant correlation between whorl count between spouses was observed. These data suggest that whorls are inherited from a single gene or a group of closely linked genes. Our findings provide an initial insight on the potential contribution of biologic characteristics on spouse selection.

  6. Genetic trends of selection for pelt traits in Karakul sheep II ...

    African Journals Online (AJOL)

    Correlated responses of curl development, hair quality, hair thickness, hair stiffness, hair length, lustre and pattern to selection for an increase in pattern and hair quality and a decrease in hair length and curl development were deter- mined with mixed model methodology in a single trait selection experiment with Karakul ...

  7. Comparing artificial and natural selection in rate of adaptation to genetic stress in Aspergillus nidulans

    NARCIS (Netherlands)

    Schoustra, S.E.; Slakhorst-Wandel, S.M.; Debets, A.J.M.; Hoekstra, R.F.

    2005-01-01

    In an experimental study of adaptation to negative pleiotropic effects of a major fungicide resistance mutation in the filamentous fungus Aspergillus nidulans we have investigated the relative effectiveness of artificial selection vs. natural selection on the rate of compensatory evolution. Using

  8. Behavioral profiles of genetically selected aggressive and nonaggressive male wild house mice in two anxiety tests

    NARCIS (Netherlands)

    Hogg, S; Wurbel, H; Steimer, T; de Ruiter, A; Koolhaas, J; Sluyter, F; Driscoll, Peter

    2000-01-01

    Artificially selected aggressive (SAL) and non-aggressive (LAL) male house mice were tested in a hexagonal tunnel maze and light-dark preference (LD) box to determine if the bidirectional selection for aggressive behavior leads to a coselection for different levels of trait anxiety. The tunnel maze

  9. Systematic differences in the response of genetic variation to pedigree and genome-based selection methods

    NARCIS (Netherlands)

    Heidaritabar, M.; Vereijken, A.; Muir, W.M.; Meuwissen, T.H.E.; Cheng, H.; Megens, H.J.W.C.; Groenen, M.; Bastiaansen, J.W.M.

    2014-01-01

    Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60¿K SNP chip with markers spaced throughout the

  10. Feature selection using genetic algorithm for breast cancer diagnosis: experiment on three different datasets

    NARCIS (Netherlands)

    Aalaei, Shokoufeh; Shahraki, Hadi; Rowhanimanesh, Alireza; Eslami, Saeid

    2016-01-01

    This study addresses feature selection for breast cancer diagnosis. The present process uses a wrapper approach using GA-based on feature selection and PS-classifier. The results of experiment show that the proposed model is comparable to the other models on Wisconsin breast cancer datasets. To

  11. Selection of individuals for genetic testing for familial hypercholesterolaemia: development and external validation of a prediction model for the presence of a mutation causing familial hypercholesterolaemia

    NARCIS (Netherlands)

    Besseling, Joost; Reitsma, Johannes B.; Gaudet, Daniel; Brisson, Diane; Kastelein, John J. P.; Hovingh, G. Kees; Hutten, Barbara A.

    2017-01-01

    Familial hypercholesterolaemia (FH) is an autosomal dominant disease that warrants early diagnosis to prevent premature cardiovascular disease (CVD). However, genetic testing to make a definite diagnosis is costly, and careful selection of eligible subjects is important. Unfortunately, accuracy of

  12. Selection of individuals for genetic testing for familial hypercholesterolaemia : development and external validation of a prediction model for the presence of a mutation causing familial hypercholesterolaemia

    NARCIS (Netherlands)

    Besseling, Joost; Reitsma, Johannes B; Gaudet, Daniel; Brisson, Diane; Kastelein, John J P; Hovingh, G Kees; Hutten, Barbara A

    2017-01-01

    AIMS: Familial hypercholesterolaemia (FH) is an autosomal dominant disease that warrants early diagnosis to prevent premature cardiovascular disease (CVD). However, genetic testing to make a definite diagnosis is costly, and careful selection of eligible subjects is important. Unfortunately,

  13. Thinking too positive? Revisiting current methods of population genetic selection inference.

    Science.gov (United States)

    Bank, Claudia; Ewing, Gregory B; Ferrer-Admettla, Anna; Foll, Matthieu; Jensen, Jeffrey D

    2014-12-01

    In the age of next-generation sequencing, the availability of increasing amounts and improved quality of data at decreasing cost ought to allow for a better understanding of how natural selection is shaping the genome than ever before. However, alternative forces, such as demography and background selection (BGS), obscure the footprints of positive selection that we would like to identify. In this review, we illustrate recent developments in this area, and outline a roadmap for improved selection inference. We argue (i) that the development and obligatory use of advanced simulation tools is necessary for improved identification of selected loci, (ii) that genomic information from multiple time points will enhance the power of inference, and (iii) that results from experimental evolution should be utilized to better inform population genomic studies. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish.

    Science.gov (United States)

    Pavlova, A; Gan, H M; Lee, Y P; Austin, C M; Gilligan, D M; Lintermans, M; Sunnucks, P

    2017-05-01

    Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection</