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Sample records for estimated genetic barrier

  1. Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape.

    PubMed

    Theys, Kristof; Deforche, Koen; Beheydt, Gertjan; Moreau, Yves; van Laethem, Kristel; Lemey, Philippe; Camacho, Ricardo J; Rhee, Soo-Yon; Shafer, Robert W; Van Wijngaerden, Eric; Vandamme, Anne-Mieke

    2010-08-03

    Failure on Highly Active Anti-Retroviral Treatment is often accompanied with development of antiviral resistance to one or more drugs included in the treatment. In general, the virus is more likely to develop resistance to drugs with a lower genetic barrier. Previously, we developed a method to reverse engineer, from clinical sequence data, a fitness landscape experienced by HIV-1 under nelfinavir (NFV) treatment. By simulation of evolution over this landscape, the individualized genetic barrier to NFV resistance may be estimated for an isolate. We investigated the association of estimated genetic barrier with risk of development of NFV resistance at virological failure, in 201 patients that were predicted fully susceptible to NFV at baseline, and found that a higher estimated genetic barrier was indeed associated with lower odds for development of resistance at failure (OR 0.62 (0.45 - 0.94), per additional mutation needed, p = .02). Thus, variation in individualized genetic barrier to NFV resistance may impact effective treatment options available after treatment failure. If similar results apply for other drugs, then estimated genetic barrier may be a new clinical tool for choice of treatment regimen, which allows consideration of available treatment options after virological failure.

  2. Psoriasis genetics: breaking the barrier

    PubMed Central

    Roberson, Elisha D.O.; Bowcock, Anne M.

    2010-01-01

    Psoriasis is a common incurable inflammatory skin disease affecting 2–3% of the European population. Psoriatic skin contains large numbers of immune cells which produce many cytokines, chemokines and inflammatory molecules. The epidermis divides much faster than normal and has a defective outer layer or barrier which under normal circumstances protects from infection and dehydration. Psoriatic skin is characterized by a distinct set of inflammation and epidermal proliferation and differentiation markers, and it has not been clear if the genetic basis of psoriasis is due to defects of the immune system or the skin. One genetic determinant lies within the major histocompatibility complex class 1 region. Genome-wide association studies have revealed genetic susceptibility factors that play a role in the formation of immune cells found in psoriasis lesions. Others affect epidermal proliferation and the formation of the skin’s barrier. Hence, genetic components of both the immune system and the epidermis predispose to disease. PMID:20692714

  3. Quantifying the lag time to detect barriers in landscape genetics

    Treesearch

    E. L. Landguth; S. A Cushman; M. K. Schwartz; K. S. McKelvey; M. Murphy; G. Luikart

    2010-01-01

    Understanding how spatial genetic patterns respond to landscape change is crucial for advancing the emerging field of landscape genetics. We quantified the number of generations for new landscape barrier signatures to become detectable and for old signatures to disappear after barrier removal. We used spatially explicit, individualbased simulations to examine the...

  4. [Resistance profile and genetic barrier of dolutegravir].

    PubMed

    Llibre, Josep M; Clotet, Bonaventura

    2015-03-01

    The resistance profile of dolutegravir differs significantly from those of earlier integrase inhibitors (INI). Dolutegravir displays in vitro activity against mutant HIV-1 harboring any isolated resistance mutations selected during failures to raltegravir or elvitegravir (Y143C/H/, N155H, Q148H/K/R, E92G/Q, T66A/I/K, T97A, E138A/K, G140A/S). Its activity is only compromised by Q148X mutations combined with other mutations, particularly > 1 mutation. The drug has pharmacokinetic/pharmacodynamic properties (plasmatic t1/2 15.3 h, inhibitory quotient 19, dissociative t1/2 from the IN-DNA complex 71 h) that favor a high genetic barrier to resistance. In vitro the selection of HIV-1 resistance to dolutegravir is extremely difficult to achieve. The mutations eventually selected (R263K, H51Y and E138K) do not confer significant resistance, and induce a fitness cost that prevents HIV-1 from evading drug pressure. Suprisingly, HIV-1 is not able to compensate, leading the virus to a previously unnoticed evolutionary pathway with very low chances of developing resistance to INI or the backbone. No treatment-naïve patients starting dolutegravir therapy (+TDF/FTC o ABC/3TC) have selected resistance in IN or against the backbone. No INI- naïve patients with prior virologic failure selected phenotypic dolutegravir resistance. Only 4 out of 354 patients selected resistance mutations in IN, and rates of selection of mutations in IN or against the backbone were significantly lower than with raltegravir. In multitreated patients with widespread resistance including IN resistance, the high efficacy of dolutegravir was confirmed, irrespective of the previous pattern of IN mutations, provided that Q148X associated with other mutations was absent. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  5. Assessing a landscape barrier using genetic simulation modelling: implications for raccoon rabies management.

    PubMed

    Rees, Erin E; Pond, Bruce A; Cullingham, Catherine I; Tinline, Rowland; Ball, David; Kyle, Christopher J; White, Bradley N

    2008-08-15

    Landscape barriers influence movement patterns of animals, which in turn, affect spatio-temporal spread of infectious wildlife disease. We compare genetic data from computer simulations to those acquired from field samples to measure the effect of a landscape barrier on raccoon (Procyon lotor) movement, enabling risk assessment of raccoon rabies disease spread across the Niagara River from New York State into Ontario, an area currently uninfected by rabies. An individual-based spatially explicit model is used to simulate the expansion of a raccoon population to cross the Niagara River, for different permeabilities of the river to raccoon crossings. Since the model records individual raccoon genetics, the genetic population structure of neutral mitochondrial DNA haplotypes are characterised in the expanding population, every 25 years, using a genetic distance measure, phi ST, Mantel tests and a gene diversity measure. The river barrier effect is assessed by comparing genetic measures computed from model outputs to those calculated from 166 raccoons recently sampled from the same landscape. The "best fit" between modelled scenarios and field data indicate the river prevents 50% of attempts to cross the river. Founder effects dominated the colonizing genetic population structure, and, as the river barrier effect increased, its genetic diversity decreased. Using gene flow to calibrate the effect of the river as a barrier to movement provides an estimate of the effect of a river in reducing the likelihood of cross-river infection. Including individual genetic markers in simulation modelling benefits investigations of disease spread and control.

  6. The estimation of genetic divergence

    NASA Technical Reports Server (NTRS)

    Holmquist, R.; Conroy, T.

    1981-01-01

    Consideration is given to the criticism of Nei and Tateno (1978) of the REH (random evolutionary hits) theory of genetic divergence in nucleic acids and proteins, and to their proposed alternative estimator of total fixed mutations designated X2. It is argued that the assumption of nonuniform amino acid or nucleotide substitution will necessarily increase REH estimates relative to those made for a model where each locus has an equal likelihood of fixing mutations, thus the resulting value will not be an overestimation. The relative values of X2 and measures calculated on the basis of the PAM and REH theories for the number of nucleotide substitutions necessary to explain a given number of observed amino acid differences between two homologous proteins are compared, and the smaller values of X2 are attributed to (1) a mathematical model based on the incorrect assumption that an entire structural gene is free to fix mutations and (2) the assumptions of different numbers of variable codons for the X2 and REH calculations. Results of a repeat of the computer simulations of Nei and Tateno are presented which, in contrast to the original results, confirm the REH theory. It is pointed out that while a negative correlation is observed between estimations of the fixation intensity per varion and the number of varions for a given pair of sequences, the correlation between the two fixation intensities and varion numbers of two different pairs of sequences need not be negative. Finally, REH theory is used to resolve a paradox concerning the high rate of covarion turnover and the nature of general function sites as permanent covarions.

  7. The estimation of genetic divergence

    NASA Technical Reports Server (NTRS)

    Holmquist, R.; Conroy, T.

    1981-01-01

    Consideration is given to the criticism of Nei and Tateno (1978) of the REH (random evolutionary hits) theory of genetic divergence in nucleic acids and proteins, and to their proposed alternative estimator of total fixed mutations designated X2. It is argued that the assumption of nonuniform amino acid or nucleotide substitution will necessarily increase REH estimates relative to those made for a model where each locus has an equal likelihood of fixing mutations, thus the resulting value will not be an overestimation. The relative values of X2 and measures calculated on the basis of the PAM and REH theories for the number of nucleotide substitutions necessary to explain a given number of observed amino acid differences between two homologous proteins are compared, and the smaller values of X2 are attributed to (1) a mathematical model based on the incorrect assumption that an entire structural gene is free to fix mutations and (2) the assumptions of different numbers of variable codons for the X2 and REH calculations. Results of a repeat of the computer simulations of Nei and Tateno are presented which, in contrast to the original results, confirm the REH theory. It is pointed out that while a negative correlation is observed between estimations of the fixation intensity per varion and the number of varions for a given pair of sequences, the correlation between the two fixation intensities and varion numbers of two different pairs of sequences need not be negative. Finally, REH theory is used to resolve a paradox concerning the high rate of covarion turnover and the nature of general function sites as permanent covarions.

  8. Genetic manipulation of Staphylococci—breaking through the barrier

    PubMed Central

    Monk, Ian R.; Foster, Timothy J.

    2012-01-01

    Most strains of Staphylococcus aureus and Staphylococcus epidermidis possess a strong restriction barrier that hinders exchange of DNA. Recently, major advances have been made in identifying and characterizing the restriction-modification (RM) systems involved. In particular a novel type IV restriction enzyme that recognizes cytosine methylated DNA has been shown to be the major barrier to transfer of plasmid DNA from Escherichia coli into S. aureus and S. epidermidis. While the conserved type I RM system provides a further barrier. Here we review the recent advances in understanding of restriction systems in staphylococci and highlight how this has been exploited to improve our ability to manipulate genetically previously untransformable strains. PMID:22919640

  9. Ecological and genetic barriers differentiate natural populations of Saccharomyces cerevisiae

    DOE PAGES

    Clowers, Katie J.; Heilberger, Justin; Piotrowski, Jeff S.; ...

    2015-05-06

    How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causalmore » genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Lastly, our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations.« less

  10. Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae.

    PubMed

    Clowers, Katie J; Heilberger, Justin; Piotrowski, Jeff S; Will, Jessica L; Gasch, Audrey P

    2015-09-01

    How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. Hybridization at an ecotone: ecological and genetic barriers between three Iberian vipers.

    PubMed

    Tarroso, Pedro; Pereira, Ricardo J; Martínez-Freiría, Fernando; Godinho, Raquel; Brito, José C

    2014-03-01

    The formation of stable genetic boundaries between emerging species is often diagnosed by reduced hybrid fitness relative to parental taxa. This reduced fitness can arise from endogenous and/or exogenous barriers to gene flow. Although detecting exogenous barriers in nature is difficult, we can estimate the role of ecological divergence in driving species boundaries by integrating molecular and ecological niche modelling tools. Here, we focus on a three-way secondary contact zone between three viper species (Vipera aspis, V. latastei and V. seoanei) to test for the contribution of ecological divergence to the development of reproductive barriers at several species traits (morphology, nuclear DNA and mitochondrial DNA). Both the nuclear and mitochondrial data show that all taxa are genetically distinct and that the sister species V. aspis and V. latastei hybridize frequently and backcross over several generations. We find that the three taxa have diverged ecologically and meet at a hybrid zone coincident with a steep ecotone between the Atlantic and Mediterranean biogeographical provinces. Integrating landscape and genetic approaches, we show that hybridization is spatially restricted to habitats that are suboptimal for parental taxa. Together, these results suggest that niche separation and adaptation to an ecological gradient confer an important barrier to gene flow among taxa that have not achieved complete reproductive isolation. © 2014 John Wiley & Sons Ltd.

  12. Disentangle the Causes of the Road Barrier Effect in Small Mammals through Genetic Patterns.

    PubMed

    Ascensão, Fernando; Mata, Cristina; Malo, Juan E; Ruiz-Capillas, Pablo; Silva, Catarina; Silva, André P; Santos-Reis, Margarida; Fernandes, Carlos

    2016-01-01

    Road barrier effect is among the foremost negative impacts of roads on wildlife. Knowledge of the factors responsible for the road barrier effect is crucial to understand and predict species' responses to roads, and to improve mitigation measures in the context of management and conservation. We built a set of hypothesis aiming to infer the most probable cause of road barrier effect (traffic effect or road surface avoidance), while controlling for the potentially confounding effects road width, traffic volume and road age. The wood mouse Apodemus sylvaticus was used as a model species of small and forest-dwelling mammals, which are more likely to be affected by gaps in cover such as those resulting from road construction. We confront genetic patterns from opposite and same roadsides from samples of three highways and used computer simulations to infer migration rates between opposite roadsides. Genetic patterns from 302 samples (ca. 100 per highway) suggest that the highway barrier effect for wood mouse is due to road surface avoidance. However, from the simulations we estimated a migration rate of about 5% between opposite roadsides, indicating that some limited gene flow across highways does occur. To reduce highway impact on population genetic diversity and structure, possible mitigation measures could include retrofitting of culverts and underpasses to increase their attractiveness and facilitate their use by wood mice and other species, and setting aside roadside strips without vegetation removal to facilitate establishment and dispersal of small mammals.

  13. Disentangle the Causes of the Road Barrier Effect in Small Mammals through Genetic Patterns

    PubMed Central

    Ascensão, Fernando; Mata, Cristina; Malo, Juan E.; Ruiz-Capillas, Pablo; Silva, Catarina; Silva, André P.; Santos-Reis, Margarida; Fernandes, Carlos

    2016-01-01

    Road barrier effect is among the foremost negative impacts of roads on wildlife. Knowledge of the factors responsible for the road barrier effect is crucial to understand and predict species’ responses to roads, and to improve mitigation measures in the context of management and conservation. We built a set of hypothesis aiming to infer the most probable cause of road barrier effect (traffic effect or road surface avoidance), while controlling for the potentially confounding effects road width, traffic volume and road age. The wood mouse Apodemus sylvaticus was used as a model species of small and forest-dwelling mammals, which are more likely to be affected by gaps in cover such as those resulting from road construction. We confront genetic patterns from opposite and same roadsides from samples of three highways and used computer simulations to infer migration rates between opposite roadsides. Genetic patterns from 302 samples (ca. 100 per highway) suggest that the highway barrier effect for wood mouse is due to road surface avoidance. However, from the simulations we estimated a migration rate of about 5% between opposite roadsides, indicating that some limited gene flow across highways does occur. To reduce highway impact on population genetic diversity and structure, possible mitigation measures could include retrofitting of culverts and underpasses to increase their attractiveness and facilitate their use by wood mice and other species, and setting aside roadside strips without vegetation removal to facilitate establishment and dispersal of small mammals. PMID:26978779

  14. Debris flow impact estimation on a rigid barrier

    NASA Astrophysics Data System (ADS)

    Vagnon, Federico; Segalini, Andrea

    2016-07-01

    The aim of this paper is to analyse debris flow impact against rigid and undrained barrier in order to propose a new formulation for the estimation of acting force after the flow impact to safe design protection structures. For this reason, this work concentrates on the flow impact, by performing a series of small scale tests in a specifically created flume. Flow characteristics (flow height and velocity) and applied loads (dynamic and static) on barrier were measured using four ultrasonic devices, four load cells and a contact surface pressure gauge. The results obtained were compared with main existing models and a new equation is proposed. Furthermore, a brief review of the small scale theory was provided to analyse the scale effects that can affect the results.

  15. Barriers and paths to market for genetically engineered crops.

    PubMed

    Rommens, Caius M

    2010-02-01

    Each year, billions of dollars are invested in efforts to improve crops through genetic engineering (GE). These activities have resulted in a surge of publications and patents on technologies and genes: a momentum in basic research that, unfortunately, is not sustained throughout the subsequent phases of product development. After more than two decades of intensive research, the market for transgenic crops is still dominated by applications of just a handful of methods and genes. This discrepancy between research and development reflects difficulties in understanding and overcoming seven main barriers-to-entry: (1) trait efficacy in the field, (2) critical product concepts, (3) freedom-to-operate, (4) industry support, (5) identity preservation and stewardship, (6) regulatory approval and (7) retail and consumer acceptance. In this review, I describe the various roadblocks to market for transgenic crops and also discuss methods and approaches on how to overcome these, especially in the United States.

  16. Barriers to translating emerging genetic research on smoking into clinical practice. Perspectives of primary care physicians.

    PubMed

    Shields, Alexandra E; Blumenthal, David; Weiss, Kevin B; Comstock, Catherine B; Currivan, Douglas; Lerman, Caryn

    2005-02-01

    Smoking remains the leading cause of preventable death nationally. Emerging research may lead to improved smoking cessation treatment options, including tailoring treatment by genotype. Our objective was to assess primary care physicians' attitudes toward new genetic-based approaches to smoking treatment. A 2002 national survey of primary care physicians. Respondents were randomly assigned a survey including 1 of 2 scenarios: a scenario in which a new test to tailor smoking treatment was described as a "genetic" test or one in which the new test was described as a "serum protein" test. The study sample was randomly drawn from all U.S. primary care physicians in the American Medical Association Masterfile (e.g., those with a primary specialty of internal medicine, family practice, or general practice). Of 2,000 sampled physicians, 1,120 responded, yielding a response rate of 62.3%. Controlling for physician and practice characteristics, describing a new test as "genetic" resulted in a regression-adjusted mean adoption score of 73.5, compared to a score of 82.5 for a nongenetic test, reflecting an 11% reduction in physicians' likelihood of offering such a test to their patients. Merely describing a new test to tailor smoking treatment as "genetic" poses a significant barrier to physician adoption. Considering national estimates of those who smoke on a daily basis, this 11% reduction in adoption scores would translate into 3.9 million smokers who would not be offered a new genetic-based treatment for smoking. While emerging genetic research may lead to improved smoking treatment, the potential of novel interventions will likely go unrealized unless barriers to clinical integration are addressed.

  17. Crossing the impassable: genetic connections in 20 reef fishes across the eastern Pacific barrier

    PubMed Central

    Lessios, H.A; Robertson, D.R

    2006-01-01

    The ‘impassable’ Eastern Pacific Barrier (EPB), ca 5000 km of deep water separating the eastern from the central Pacific, is the World's widest marine biogeographic barrier. Sequencing of mitochondrial DNA in 20 reef fish morphospecies encountered on both sides of the barrier revealed cryptic speciation in two. Among the other 18 species only two showed significant differentiation (as revealed by haplotype networks and FST statistics) between the eastern and the central Pacific. Coalescence analyses indicated that genetic similarity in the 18 truly transpacific species resulted from different combinations of ages of most recent invasion and of levels of recurrent gene flow, with estimated times of initial separation ranging from approximately 30 000 to 1 Myr (ago). There is no suggestion of simultaneous interruptions of gene flow among the species. Migration across the EPB was previously thought to be exclusively eastward, but our evidence showed two invasions from east to west and eight cases in which subsequent gene flow possibly proceeded in the same direction. Thus, the EPB is sporadically permeable to propagules originating on either side. PMID:16901840

  18. Crossing the impassable: genetic connections in 20 reef fishes across the eastern Pacific barrier.

    PubMed

    Lessios, H A; Robertson, D R

    2006-09-07

    The 'impassable' Eastern Pacific Barrier (EPB), ca 5000 km of deep water separating the eastern from the central Pacific, is the World's widest marine biogeographic barrier. Sequencing of mitochondrial DNA in 20 reef fish morphospecies encountered on both sides of the barrier revealed cryptic speciation in two. Among the other 18 species only two showed significant differentiation (as revealed by haplotype networks and FST statistics) between the eastern and the central Pacific. Coalescence analyses indicated that genetic similarity in the 18 truly transpacific species resulted from different combinations of ages of most recent invasion and of levels of recurrent gene flow, with estimated times of initial separation ranging from approximately 30000 to 1 Myr (ago). There is no suggestion of simultaneous interruptions of gene flow among the species. Migration across the EPB was previously thought to be exclusively eastward, but our evidence showed two invasions from east to west and eight cases in which subsequent gene flow possibly proceeded in the same direction. Thus, the EPB is sporadically permeable to propagules originating on either side.

  19. Mechanisms and genetic control of interspecific crossing barriers in Lycopersicon

    SciTech Connect

    Mutschler, M.A. ); McCormick, S. . Plant Gene Expression Center)

    1993-03-27

    This study employs Lycopersicon esculentum and L. pennellii as model systems to study the interspecific reproductive barriers unilateral incongruity (UI), hybrid breakdown and interspecific aberrant ratio syndrome (IARS).

  20. Genetic background of skin barrier dysfunction in the pathogenesis of psoriasis vulgaris.

    PubMed

    Stawczyk-Macieja, Marta; Szczerkowska-Dobosz, Aneta; Rębała, Krzysztof; Purzycka-Bohdan, Dorota

    2015-04-01

    Psoriasis is a common inflammatory skin disease. It is known to be a complex condition with multifactorial mode of inheritance, however the associations between particular pathogenic pathways remain unclear. A novel report on the pathogenesis of psoriasis has recently included the genetic determination of the skin barrier dysfunction. In this paper, we focus on specific genetic variants associated with formation of the epidermal barrier and their role in the complex pathogenesis of the disease.

  1. Fragmentation reduces regional-scale spatial genetic structure in a wind-pollinated tree because genetic barriers are removed

    PubMed Central

    Wang, Rong; Compton, Stephen G; Shi, Yi-Su; Chen, Xiao-Yong

    2012-01-01

    Gene flow strongly influences the regional genetic structuring of plant populations. Seed and pollen dispersal patterns can respond differently to the increased isolation resulting from habitat fragmentation, with unpredictable consequences for gene flow and population structuring. In a recently fragmented landscape we compared the pre- and post-fragmentation genetic structure of populations of a tree species where pollen and seed dispersal respond differentially to forest fragmentation generated by flooding. Castanopsis sclerophylla is wind-pollinated, with seeds that are dispersed by gravity and rodents. Using microsatellites, we found no significant difference in genetic diversity between pre- and post-fragmentation cohorts. Significant genetic structure was observed in pre-fragmentation cohorts, due to an unknown genetic barrier that had isolated one small population. Among post-fragmentation cohorts this genetic barrier had disappeared and genetic structure was significantly weakened. The strengths of genetic structuring were at a similar level in both cohorts, suggesting that overall gene flow of C. sclerophylla has been unchanged by fragmentation at the regional scale. Fragmentation has blocked seed dispersal among habitats, but this appears to have been compensated for by enhanced pollen dispersal, as indicated by the disappearance of a genetic barrier, probably as a result of increased wind speeds and easier pollen movement over water. Extensive pollen flow can counteract some negative effects of fragmentation and assist the long-term persistence of small remnant populations. PMID:23139883

  2. Fragmentation reduces regional-scale spatial genetic structure in a wind-pollinated tree because genetic barriers are removed.

    PubMed

    Wang, Rong; Compton, Stephen G; Shi, Yi-Su; Chen, Xiao-Yong

    2012-09-01

    Gene flow strongly influences the regional genetic structuring of plant populations. Seed and pollen dispersal patterns can respond differently to the increased isolation resulting from habitat fragmentation, with unpredictable consequences for gene flow and population structuring. In a recently fragmented landscape we compared the pre- and post-fragmentation genetic structure of populations of a tree species where pollen and seed dispersal respond differentially to forest fragmentation generated by flooding. Castanopsis sclerophylla is wind-pollinated, with seeds that are dispersed by gravity and rodents. Using microsatellites, we found no significant difference in genetic diversity between pre- and post-fragmentation cohorts. Significant genetic structure was observed in pre-fragmentation cohorts, due to an unknown genetic barrier that had isolated one small population. Among post-fragmentation cohorts this genetic barrier had disappeared and genetic structure was significantly weakened. The strengths of genetic structuring were at a similar level in both cohorts, suggesting that overall gene flow of C. sclerophylla has been unchanged by fragmentation at the regional scale. Fragmentation has blocked seed dispersal among habitats, but this appears to have been compensated for by enhanced pollen dispersal, as indicated by the disappearance of a genetic barrier, probably as a result of increased wind speeds and easier pollen movement over water. Extensive pollen flow can counteract some negative effects of fragmentation and assist the long-term persistence of small remnant populations.

  3. Genetic structure of juvenile cohorts of bicolor damselfish ( Stegastes partitus) along the Mesoamerican barrier reef: chaos through time

    NASA Astrophysics Data System (ADS)

    Hepburn, R. I.; Sale, P. F.; Dixon, B.; Heath, Daniel D.

    2009-03-01

    Dispersal in marine systems is a critical component of the ecology, evolution, and conservation of such systems; however, estimating dispersal is logistically difficult, especially in coral reef fish. Juvenile bicolor damselfish ( Stegastes partitus) were sampled at 13 sites along the Mesoamerican Barrier Reef System (MBRS), the barrier reefs on the east coast of Central America extending from the Yucatan, Mexico to Honduras, to evaluate genetic structure among recently settled cohorts. Using genotype data at eight microsatellite loci genetic structure was estimated at large and small spatial scales using exact tests for allele frequency differences and hierarchical analysis of molecular variance (AMOVA). Isolation-by-distance models of divergence were assessed at both spatial scales. Results showed genetic homogeneity of recently settled S. partitus at large geographic scales with subtle, but significant, genetic structure at smaller geographic scales. Genetic temporal stability was tested for using archived juvenile S. partitus collected earlier in the same year (nine sites), and in the previous year (six sites). The temporal analyses indicated that allele frequency differences among sites were not generally conserved over time, nor were pairwise genetic distances correlated through time, indicative of temporal instability. These results indicate that S. partitus larvae undergo high levels of dispersal along the MBRS, and that the structure detected at smaller spatial scales is likely driven by stochastic effects on dispersal coupled with microgeographic effects. Temporal variation in juvenile cohort genetic signature may be a fundamental characteristic of connectivity patterns in coral reef fishes, with various species and populations differing only in the magnitude of that instability. Such a scenario provides a basis for the reconciliation of conflicting views regarding levels of genetic structuring in S. partitus and possibly other coral reef fish species.

  4. Identification of a barrier height threshold where brook trout population genetic diversity, differentiation, and relatedness are affected

    Treesearch

    Anne Timm; Eric Hallerman; Andy Dolloff; Mark Hudy; Randall Kolka

    2016-01-01

    The overall goal of the study was to evaluate effects of landscape features, barriers, on Brook Trout Salvelinus fontinalis population genetics and to identify a potential barrier height threshold where genetic diversity was reduced upstream of the barrier and differentiation and relatedness increase. We screened variation at eight...

  5. Influence of barriers to movement on within-watershed genetic variation of coastal cutthroat trout

    USGS Publications Warehouse

    Wofford, John E.B.; Gresswell, Robert E.; Banks, Michael A.

    2005-01-01

    Because human land use activities often result in increased fragmentation of aquatic and terrestrial habitats, a better understanding of the effects of fragmentation on the genetic heterogeneity of animal populations may be useful for effective management. We used eight microsatellites to examine the genetic structure of coastal cutthroat trout (Oncorhynchus clarki clarki) in Camp Creek, an isolated headwater stream in western Oregon. Our objectives were to determine if coastal cutthroat trout were genetically structured within streams and to assess the effects of natural and anthropogenic barriers on coastal cutthroat trout genetic variation. Fish sampling occurred at 10 locations, and allele frequencies differed significantly among all sampling sections. Dispersal barriers strongly influenced coastal cutthroat trout genetic structure and were associated with reduced genetic diversity and increased genetic differentiation. Results indicate that Camp Creek coastal cutthroat trout exist as many small, partially independent populations that are strongly affected by genetic drift. In headwater streams, barriers to movement can result in genetic and demographic isolation leading to reduced coastal cutthroat trout genetic diversity, and potentially compromising long-term population persistence. When habitat fragmentation eliminates gene flow among small populations, similar results may occur in other species.

  6. Barriers and Facilitators to BRCA Genetic Counseling Among At-Risk Latinas in New York City

    PubMed Central

    Sussner, Katarina M.; Jandorf, Lina; Thompson, Hayley S.; Valdimarsdottir, Heiddis B.

    2012-01-01

    Objective Despite underuse of genetic services for hereditary breast and/or ovarian cancer risk among Latinas (including counseling and testing for BRCA mutations), there is little known about the barriers and facilitators to BRCA genetic counseling among this group. It is imperative to first understand factors that may impede Latinas seeking BRCA genetic counseling, as it is considered a prerequisite to testing. Methods Quantitative telephone interviews (N=120) were conducted with at-risk Latinas in New York City to investigate interest, barriers and beliefs about BRCA genetic counseling. Statistical analyses examined predictors of intention to undergo BRCA genetic counseling. Results Despite moderate levels of awareness, Latinas held largely positive beliefs, attitudes and knowledge about BRCA genetic counseling. Perceived barriers included logistic concerns (e.g., where to go, cost/health insurance coverage), emotional concerns (e.g., fear, distress) and competing life concerns (e.g, too many other things to worry about, too busy taking care of children or family members). Multivariate results showed that the strongest predictor of intention to undergo BRCA genetic counseling was competing life concerns; Latinas with more competing life concerns were less likely to intend to undergo BRCA genetic counseling (p=0.0002). Other significant predictors of intention included perceived risk of carrying a BRCA mutation (p=0.01) and referral by their physician (p=0.02). Conclusion Educational efforts to promote BRCA genetic counseling among at-risk Latinas and increase referrals by their physicians should incorporate discussion of perceived barriers to counseling, such as competing life concerns that Latinas may need to overcome in order to seek genetic counseling. PMID:22987526

  7. Comparing estimates of genetic variance across different relationship models.

    PubMed

    Legarra, Andres

    2016-02-01

    Use of relationships between individuals to estimate genetic variances and heritabilities via mixed models is standard practice in human, plant and livestock genetics. Different models or information for relationships may give different estimates of genetic variances. However, comparing these estimates across different relationship models is not straightforward as the implied base populations differ between relationship models. In this work, I present a method to compare estimates of variance components across different relationship models. I suggest referring genetic variances obtained using different relationship models to the same reference population, usually a set of individuals in the population. Expected genetic variance of this population is the estimated variance component from the mixed model times a statistic, Dk, which is the average self-relationship minus the average (self- and across-) relationship. For most typical models of relationships, Dk is close to 1. However, this is not true for very deep pedigrees, for identity-by-state relationships, or for non-parametric kernels, which tend to overestimate the genetic variance and the heritability. Using mice data, I show that heritabilities from identity-by-state and kernel-based relationships are overestimated. Weighting these estimates by Dk scales them to a base comparable to genomic or pedigree relationships, avoiding wrong comparisons, for instance, "missing heritabilities".

  8. Vicariance and dispersal across an intermittent barrier: population genetic structure of marine animals across the Torres Strait land bridge

    NASA Astrophysics Data System (ADS)

    Mirams, A. G. K.; Treml, E. A.; Shields, J. L.; Liggins, L.; Riginos, C.

    2011-12-01

    Biogeographic barriers, some transitory in duration, are likely to have been important contributing factors to modern marine biodiversity in the Indo-Pacific region. One such barrier was the Torres Strait land bridge between continental Australia and New Guinea that persisted through much of the late Pleistocene and separated Indian and Pacific Ocean taxa. Here, we examine the patterns of mitochondrial DNA diversity for marine animals with present-day distributions spanning the Torres Strait. Specifically, we investigate whether there are concordant signatures across species, consistent with either vicariance or recent colonization from either ocean basin. We survey four species of reef fishes ( Apogon doederleini, Pomacentrus coelestis, Dascyllus trimaculatus, and Acanthurus triostegus) for mtDNA cytochrome oxidase 1 and control region variation and contrast these results to previous mtDNA studies in diverse marine animals with similar distributions. We find substantial genetic partitioning (estimated from F-statistics and coalescent approaches) between Indian and Pacific Ocean populations for many species, consistent with regional persistence through the late Pleistocene in both ocean basins. The species-specific estimates of genetic divergence, however, vary greatly and for reef fishes we estimate substantially different divergence times among species. It is likely that Indian and Pacific Ocean populations have been isolated for multiple glacial cycles for some species, whereas for other species genetic connections have been more recent. Regional estimates of genetic diversity and directionality of gene flow also vary among species. Thus, there is no apparent consistency among historical patterns across the Torres Strait for these co-distributed marine animals.

  9. How to perform meaningful estimates of genetic effects.

    PubMed

    Alvarez-Castro, José M; Le Rouzic, Arnaud; Carlborg, Orjan

    2008-05-02

    Although the genotype-phenotype map plays a central role both in Quantitative and Evolutionary Genetics, the formalization of a completely general and satisfactory model of genetic effects, particularly accounting for epistasis, remains a theoretical challenge. Here, we use a two-locus genetic system in simulated populations with epistasis to show the convenience of using a recently developed model, NOIA, to perform estimates of genetic effects and the decomposition of the genetic variance that are orthogonal even under deviations from the Hardy-Weinberg proportions. We develop the theory for how to use this model in interval mapping of quantitative trait loci using Halley-Knott regressions, and we analyze a real data set to illustrate the advantage of using this approach in practice. In this example, we show that departures from the Hardy-Weinberg proportions that are expected by sampling alone substantially alter the orthogonal estimates of genetic effects when other statistical models, like F2 or G2A, are used instead of NOIA. Finally, for the first time from real data, we provide estimates of functional genetic effects as sets of effects of natural allele substitutions in a particular genotype, which enriches the debate on the interpretation of genetic effects as implemented both in functional and in statistical models. We also discuss further implementations leading to a completely general genotype-phenotype map.

  10. In vitro models to estimate drug penetration through the compromised stratum corneum barrier.

    PubMed

    Engesland, André; Škalko-Basnet, Nataša; Flaten, Gøril Eide

    2016-11-01

    The phospholipid vesicle-based permeation assay (PVPA) is a recently established in vitro stratum corneum model to estimate the permeability of intact and healthy skin. The aim here was to further evolve this model to mimic the stratum corneum in a compromised skin barrier by reducing the barrier functions in a controlled manner. To mimic compromised skin barriers, PVPA barriers were prepared with explicitly defined reduced barrier function and compared with literature data from both human and animal skin with compromised barrier properties. Caffeine, diclofenac sodium, chloramphenicol and the hydrophilic marker calcein were tested to compare the PVPA models with established models. The established PVPA models mimicking the stratum corneum in healthy skin showed good correlation with biological barriers by ranking drugs similar to those ranked by the pig ear skin model and were comparable to literature data on permeation through healthy human skin. The PVPA models provided reproducible and consistent results with a distinction between the barriers mimicking compromised and healthy skin. The trends in increasing drug permeation with an increasing degree of compromised barriers for the model drugs were similar to the literature data from other in vivo and in vitro models. The PVPA models have the potential to provide permeation predictions when investigating drugs or cosmeceuticals intended for various compromised skin conditions and can thus possibly reduce the time and cost of testing as well as the use of animal testing in the early development of drug candidates, drugs and cosmeceuticals.

  11. Estimation of Genetic Effects and Genotype-Phenotype Maps

    PubMed Central

    Le Rouzic, Arnaud; Álvarez-Castro, José M.

    2008-01-01

    Determining the genetic architecture of complex traits is a necessary step to understand phenotypic changes in natural, experimental and domestic populations. However, this is still a major challenge for modern genetics, since the estimation of genetic effects tends to be complicated by genetic interactions, which lead to changes in the effect of allelic substitutions depending on the genetic background. Recent progress in statistical tools aiming to describe and quantify genetic effects meaningfully improves the efficiency and the availability of genotype-to-phenotype mapping methods. In this contribution, we facilitate the practical use of the recently published ‘NOIA’ quantitative framework by providing an implementation of linear and multilinear regressions, change of reference operation and genotype-to-phenotype mapping in a package (‘noia’) for the software R, and we discuss theoretical and practical benefits evolutionary and quantitative geneticists may find in using proper modeling strategies to quantify the effects of genes. PMID:19204820

  12. Use of a portable electric barrier to estimate Chinook salmon escapement in a turbid Alaskan river

    USGS Publications Warehouse

    Palmisano, A.; Burger, C.V.

    1988-01-01

    We developed a portable electric barrier to aid in the capture of adult chinook salmon Oncorhynchus tshawytscha undergoing spawning migrations up a turbid stream in south-central Alaska. In 1981, we tagged and released 157 chinook salmon after diverting them from the main-stem Killey River into a conventional trap with the aid of the electric barrier. On the basis of returns of tagged salmon to Benjamin Creek, a clear-water tributary of the upper Killey River, we estimated spawners in the drainage to number 8,000 fish. Two different statistical approaches to the mark–recapture data yielded similar estimates. Through several modifications of the electric barrier, we were able to reduce mortality associated with the barrier's use.

  13. Maximum-likelihood estimation of admixture proportions from genetic data.

    PubMed Central

    Wang, Jinliang

    2003-01-01

    For an admixed population, an important question is how much genetic contribution comes from each parental population. Several methods have been developed to estimate such admixture proportions, using data on genetic markers sampled from parental and admixed populations. In this study, I propose a likelihood method to estimate jointly the admixture proportions, the genetic drift that occurred to the admixed population and each parental population during the period between the hybridization and sampling events, and the genetic drift in each ancestral population within the interval between their split and hybridization. The results from extensive simulations using various combinations of relevant parameter values show that in general much more accurate and precise estimates of admixture proportions are obtained from the likelihood method than from previous methods. The likelihood method also yields reasonable estimates of genetic drift that occurred to each population, which translate into relative effective sizes (N(e)) or absolute average N(e)'s if the times when the relevant events (such as population split, admixture, and sampling) occurred are known. The proposed likelihood method also has features such as relatively low computational requirement compared with previous ones, flexibility for admixture models, and marker types. In particular, it allows for missing data from a contributing parental population. The method is applied to a human data set and a wolflike canids data set, and the results obtained are discussed in comparison with those from other estimators and from previous studies. PMID:12807794

  14. Concordant genetic structure in two species of woodpecker distributed across the primary West African biogeographic barriers.

    PubMed

    Fuchs, Jérôme; Bowie, Rauri C K

    2015-07-01

    The lowland forests of western and central tropical Africa are separated by several potential biogeographic barriers to dispersal for forest adapted vertebrates. The two primary barriers are (1) the Dahomey Gap, a savanna corridor that reaches the coast of southern Ghana, Togo and Benin, and separates the West African rainforest into the Upper (Ghana west to Guinea) and Lower Guinea (Nigeria to Uganda and Angola) forest blocks, and (2) the Lower Niger River, a large delta that separates Western and Eastern Nigeria. Previous studies on terrestrial vertebrates (lizards, mammals and birds) have highlighted a genetic break in the Dahomey Gap/Lower Niger River area although the relative importance of each barrier has not been assessed due to limitations in geographic sampling. We compared the phylogeographic history of two co-distributed sister-species of woodpeckers (Campethera caroli and C. nivosa) using data from three loci representing all inheritance modes. Our analyses revealed that both the Dahomey Gap and possibly the Lower Niger River acted as strong biogeographic barriers for the two woodpecker species, with the Lower Niger River being the first barrier to have formed, leading to three distinct populations of C. nivosa. Our divergence time analyses revealed that both these biogeographic barriers formed during the Pleistocene, supporting the Pleistocene refuge hypothesis, with the Dahomey Gap likely appearing about 0.5 myr BP. No genetic structure was recovered among sampled populations in either the Upper or the Lower Guinea Forest Block for both species, despite the considerable geographic area covered.

  15. Estimation of recombination frequency in genetic linkage studies.

    PubMed

    Nordheim, E V; O'Malley, D M; Guries, R P

    1983-09-01

    A binomial-like model is developed that may be used in genetic linkage studies when data are generated by a testcross with parental phase unknown. Four methods of estimation for the recombination frequency are compared for data from a single group and also from several groups; these methods are maximum likelihood, two Bayesian procedures, and an ad hoc technique. The Bayes estimator using a noninformative prior usually has a lower mean squared error than the other estimators and because of this it is the recommended estimator. This estimator appears particularly useful for estimation of recombination frequencies indicative of weak linkage from samples of moderate size. Interval estimates corresponding to this estimator can be obtained numerically by discretizing the posterior distribution, thereby providing researchers with a range of plausible recombination values. Data from a linkage study on pitch pine are used as an example.

  16. Genetics of Crohn disease, an archetypal inflammatory barrier disease.

    PubMed

    Schreiber, Stefan; Rosenstiel, Philip; Albrecht, Mario; Hampe, Jochen; Krawczak, Michael

    2005-05-01

    Chronic inflammatory disorders such as Crohn disease, atopic eczema, asthma and psoriasis are triggered by hitherto unknown environmental factors that function on the background of some polygenic susceptibility. Recent technological advances have allowed us to unravel the genetic aetiology of these and other complex diseases. Using Crohn disease as an example, we show how the discovery of susceptibility genes furthers our understanding of the underlying disease mechanisms and how it will, ultimately, give rise to new therapeutic developments. The long-term goal of such endeavours is to develop targeted prophylactic strategies. These will probably target the molecular interaction on the mucosal surface between the products of the genome and the microbial metagenome of a patient.

  17. Commercializing genetically modified crops under EU regulations: objectives and barriers.

    PubMed

    Raybould, Alan; Poppy, Guy M

    2012-01-01

    Agriculture faces serious problems in feeding 9 billion people by 2050: production must be increased and ecosystem services maintained under conditions for growing crops that are predicted to worsen in many parts of the world. A proposed solution is sustainable intensification of agriculture, whereby yields are increased on land that is currently cultivated, so sparing land to deliver other ecosystem services. Genetically modified (GM) crops are already contributing to sustainable intensification through higher yields and lower environmental impacts, and have potential to deliver further significant improvements. Despite their widespread successful use elsewhere, the European Union (EU) has been slow to introduce GM crops: decisions on applications to import GM commodities are lengthy, and decision-making on applications to cultivate GM crops has virtually ceased. Delayed import approvals result in economic losses, particularly in the EU itself as a result of higher commodity prices. Failure to grant cultivation approvals costs EU farmers opportunities to reduce inputs, and results in loss of agricultural research and development from the EU to countries such as the United States and China. Delayed decision-making in the EU ostensibly results from scientific uncertainty about the effects of using GM crops; however, scientific uncertainty may be a means to justify a political decision to restrict cultivation of GM crops in the EU. The problems associated with delayed decision-making will not improve until there is clarity about the EU's agricultural policy objectives, and whether the use of GM crops will be permitted to contribute to achieving those objectives.

  18. Practical Barriers and Ethical Challenges in Genetic Data Sharing

    PubMed Central

    Simpson, Claire L.; Goldenberg, Aaron J.; Culverhouse, Rob; Daley, Denise; Igo, Robert P.; Jarvik, Gail P.; Mandal, Diptasri M.; Mascalzoni, Deborah; Montgomery, Courtney Gray; Pierce, Brandon L.; Plaetke, Rosemarie; Shete, Sanjay; Goddard, Katrina A. B.; Stein, Catherine M.

    2014-01-01

    The underlying ethos of dbGaP is that access to these data by secondary data analysts facilitates advancement of science. NIH has required that genome-wide association study data be deposited in the Database of Genotypes and Phenotypes (dbGaP) since 2003. In 2013, a proposed updated policy extended this requirement to next-generation sequencing data. However, recent literature and anecdotal reports suggest lingering logistical and ethical concerns about subject identifiability, informed consent, publication embargo enforcement, and difficulty in accessing dbGaP data. We surveyed the International Genetic Epidemiology Society (IGES) membership about their experiences. One hundred and seventy five (175) individuals completed the survey, a response rate of 27%. Of respondents who received data from dbGaP (43%), only 32% perceived the application process as easy but most (75%) received data within five months. Remaining challenges include difficulty in identifying an institutional signing official and an overlong application process. Only 24% of respondents had contributed data to dbGaP. Of these, 31% reported local IRB restrictions on data release; an additional 15% had to reconsent study participants before depositing data. The majority of respondents (56%) disagreed that the publication embargo period was sufficient. In response, we recommend longer embargo periods and use of varied data-sharing models rather than a one-size-fits-all approach. PMID:25153467

  19. The Presence of Hydraulic Barriers in Layered Snowpacks: Simulations using TOUGH2 and Diversion Length Estimates

    NASA Astrophysics Data System (ADS)

    Webb, R.; Fassnacht, S. R.; Gooseff, M. N.; Webb, S.

    2016-12-01

    Snow dominated hydrographs will vary in timing and volume of flow depending on when the snow melts and the lag time for the meltwater to reach the stream. Variable layers in a porous media such as snow have different hydraulic properties that can form hydraulic barriers at the interfaces between layers. Data from three snow pits located in the Spring Creek Intensive Study Area (part of the NASA CLPX dataset) of Colorado were used for simulations. Data for north, south, and relatively flat aspect slopes were chosen to represent the variable metamorphism that occurs under different conditions. The north and south aspect slopes each have a 20 degree slope whereas the flat location has a five degree slope. The data provided a maximum of 27 layers within a single snow pit for which hydraulic properties were estimated. Simulations were conducted at steady state infiltration rates of 0.1, 1.0, and 5.0 mm/hr using the EOS9 module of TOUGH2. Results demonstrate that conditions are present within a layered snowpack to produce multiple permeability barriers and capillary barriers, though capillary barriers were only identified on the north aspect snowpack. Diversion lengths of capillary barriers ranged from 1.0 m to greater than 25 m and permeability barriers ranged from 2.5 m to 9.5 m. Capillary barriers are likely less persistent temporally due to the increased rate of metamorphism in the presence of liquid water causing them to deteriorate completely or become permeability barriers, that are important at a longer time scale. Computational analysis shows the potential for capillary barriers in snow to cause large diversion lengths with increasing diversion capacity as the density of the top layer of a barrier decreases and as the density of the bottom layer increases. Furthermore, a grain radius of 0.6 mm or less in the top layer is necessary to produce a capillary barrier. Simulation results show the differences in diversion estimates using expressions for isolated

  20. The genetics of the skin barrier in eczema and other allergic disorders.

    PubMed

    Marenholz, Ingo; Esparza-Gordillo, Jorge; Lee, Young-Ae

    2015-10-01

    We summarize current knowledge on the genetic determinants of skin barrier deficiency in relation to eczema and disease progression to other allergic manifestations. There is increasing evidence that impairment of epidermal barrier function is not only a risk factor for the development of eczema but also for disease progression to allergic airway disease and food allergy. Support comes from recent association studies linking genetic variants in epidermal genes with eczema and food allergy, from monogenic diseases with severe skin barrier defects which display multiple allergic manifestations, and from mouse models providing a mechanism from skin inflammation to allergic reactions in the lung and intestine. The key role of the skin barrier defect in the development of eczema and eczema-associated allergic diseases may have important implications for prevention and treatment strategies. Initial clinical trials with moisturizing creams revealed promising results for the prevention of eczema in early infancy. Their long-term effects will be critical to demonstrate the potential benefit of barrier repair therapy in allergic disease prevention.

  1. Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout.

    PubMed

    Ardren, William R; Kapuscinski, Anne R

    2003-01-01

    Estimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.

  2. Horizontal hydraulic conductivity estimates for intact coal barriers between closed underground mines

    SciTech Connect

    Mccoy, K.J.; Donovan, J.J.; Leavitt, B.R.

    2006-08-15

    Unmined blocks of coal, called barriers, separate and restrict horizontal leakage between adjacent bituminous coal mines. Understanding the leakage rate across such barriers is important in planning mine closure and strongly affects recharge calculations for postmining flooding. This study presents upper-limit estimates for hydraulic conductivity (K) of intact barriers in two closed mines at moderate depth (75-300 m) in the Pittsburgh coal basin. The estimates are based on pumping rates from these mines for the years ranging from 1992 to 2000. The two mines do not approach the outcrop and are sufficiently deep that vertical infiltration is thought to be negligible. Similarly, there are no saturated zones on the pumped mines' side of shared barriers with other mines, and therefore pumping is the only outflow. Virtually all of the pumping is attributed to leakage across or over the top of barriers shared with upgradient flooded mines. The length of shared barriers totals 24 km for the two mines, and the barriers range in thickness from 15 to 50 m. K values calculated independently for each of the 9 years of the pumping record ranged from 0.037 m/d to 0.18 m/d using an isotropic model of barrier flow. Using an anisotropic model for differential K in the face cleat (K{sub f}) and butt cleat (K{sub b}) directions, results range from 0.074 to 0.34 m/d for K{sub f} and from 0.022 to 0.099 m/d for K{sub b}.

  3. Model-free Estimation of Recent Genetic Relatedness

    PubMed Central

    Conomos, Matthew P.; Reiner, Alexander P.; Weir, Bruce S.; Thornton, Timothy A.

    2016-01-01

    Genealogical inference from genetic data is essential for a variety of applications in human genetics. In genome-wide and sequencing association studies, for example, accurate inference on both recent genetic relatedness, such as family structure, and more distant genetic relatedness, such as population structure, is necessary for protection against spurious associations. Distinguishing familial relatedness from population structure with genotype data, however, is difficult because both manifest as genetic similarity through the sharing of alleles. Existing approaches for inference on recent genetic relatedness have limitations in the presence of population structure, where they either (1) make strong and simplifying assumptions about population structure, which are often untenable, or (2) require correct specification of and appropriate reference population panels for the ancestries in the sample, which might be unknown or not well defined. Here, we propose PC-Relate, a model-free approach for estimating commonly used measures of recent genetic relatedness, such as kinship coefficients and IBD sharing probabilities, in the presence of unspecified structure. PC-Relate uses principal components calculated from genome-screen data to partition genetic correlations among sampled individuals due to the sharing of recent ancestors and more distant common ancestry into two separate components, without requiring specification of the ancestral populations or reference population panels. In simulation studies with population structure, including admixture, we demonstrate that PC-Relate provides accurate estimates of genetic relatedness and improved relationship classification over widely used approaches. We further demonstrate the utility of PC-Relate in applications to three ancestrally diverse samples that vary in both size and genealogical complexity. PMID:26748516

  4. Can Genetic Estimators Provide Robust Estimates of the Effective Number of Breeders in Small Populations?

    PubMed Central

    Hoehn, Marion; Gruber, Bernd; Sarre, Stephen D.; Lange, Rebecca; Henle, Klaus

    2012-01-01

    The effective population size (Ne) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of Ne. Because geckos have overlapping generations, our goal was to demographically estimate NbI, the inbreeding effective number of breeders and to calculate the NbI/Na ratio (Na = number of adults) for four populations. Demographically estimated NbI ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (NbI/Na) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders NbI(gen) and the variance effective populations size NeV(gen) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14–55 and 24–48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate NbI for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes. PMID:23139784

  5. Barriers to participating in genetic counseling and BRCA testing during primary treatment for breast cancer.

    PubMed

    Schlich-Bakker, Kathryn J; ten Kroode, Herman F J; Wárlám-Rodenhuis, Carla C; van den Bout, Jan; Ausems, Margreet G E M

    2007-11-01

    Little is known about reasons why eligible breast cancer patients decline BRCA mutation testing. They may withdraw at different stages during genetic counseling for different reasons. We prospectively studied perceived benefits and barriers to genetic counseling and BRCA testing in 102 newly diagnosed breast cancer patients approached for genetic counseling at the start of radiotherapy. Patients completed questionnaires and participated in interviews at different stages of the counseling protocol. Participation was not influenced by distress, knowledge about hereditary breast cancer, previous genetic testing in relatives, or perceived risks and barriers. Immediate decliners (n = 23) do not believe genetic testing is relevant for them. Patients who decline after pedigree compilation (n = 14) are more hesitant and anxious about the influence of the test result on their future often wishing to postpone further testing. Late decliners (n = 7) withdraw afraid of the test result and/or after a relative's objection. These decliners are not easily identified upon approach because they are similar to patients who receive a DNA test result (n = 58). Notwithstanding their decline, 81% agreed to the timing or would have preferred an earlier approach for genetic counseling. Decliners may make more informed decisions after tailored health education, including adequate risk information.

  6. Estimates of genetic correlations among growth traits including competition effects

    USDA-ARS?s Scientific Manuscript database

    The objective was to estimate genetic parameters of direct and competition effects for traits measured at the end of a growth test utilizing multi-trait analyses. A total of 9,720 boars were tested with 15 boars per pen from about 71 to 161 d of age and weight from 31 to 120 kg. Traits analyzed wi...

  7. Estimation of genetic parameters for wool fiber diameter measures.

    PubMed

    Iman, N Y; Johnson, C L; Russell, W C; Stobart, R H

    1992-04-01

    Genetic and phenotypic correlations and heritability estimates of side, britch, and core diameters; side and britch CV; side and britch diameter difference; and clean fleece weight were investigated using 385 western white-faced ewes produced by 50 sires and maintained at two locations on a selection study. Data were analyzed using analysis of variance procedures, and effects in the final model included breed of sire-selection line combination, sire within breed-selection line, and location. Heritabilities were estimated by paternal half-sib analysis. Sires within breed-selection line represented a significant source of variation for all traits studied. Location had a significant effect on side diameter, side and britch diameter difference, and clean fleece weight. Age of ewe only affected clean fleece weight. Phenotypic and genetic correlations among side, britch, and core diameter measures were high and positive. Phenotypic correlations ranged from .68 to .75 and genetic correlations ranged from .74 to .89. The genetic correlations between side and britch diameter difference and side diameter or core diameter were small (-.16 and .28, respectively). However, there was a stronger genetic correlation between side and britch diameter difference and britch diameter (.55). Heritability of the difference between side and britch diameter was high (.46 +/- .16) and similar to heritability estimates reported for other wool traits. Results of this study indicate that relatively rapid genetic progress through selection for fiber diameter should be possible. In addition, increased uniformity in fiber diameter should be possible through selection for either side and britch diameter difference or side or britch CV.

  8. Genetic variability of Wagyu cattle estimated by statistical approaches.

    PubMed

    Oyama, Kenji

    2011-06-01

    The genetic evaluation of economically important traits utilizes estimates of genetic variability, which are represented by heritability. This review summarizes the published heritabilities of traits estimated in Wagyu cattle. Two different mean heritabilities, unweighted and weighted by standard errors, were calculated. In Japanese Black cattle, the average unweighted and weighted direct heritabilities of birth weight were 0.35 and 0.28, respectively, whereas the respective maternal heritabilities were 0.17 and 0.07. The mean unweighted heritability of calf market weight was estimated to be 0.30 in Japanese Black cattle. The mean unweighted heritability of daily gain during performance testing was 0.29 in Japanese Black and 0.40 in Japanese Shorthorn cattle. In Japanese Black cattle, the unweighted mean heritability was 0.48 for carcass weight, 0.46 for rib-eye area, 0.38 for rib thickness, 0.39 for subcutaneous fat thickness, and 0.55 for marbling. The mean weighted heritability of the calving interval was low, and estimated to be 0.05. In general, the heritabilities estimated in Wagyu cattle were similar to those estimated in other beef breeds. © 2011 The Author; Animal Science Journal © 2011 Japanese Society of Animal Science.

  9. Genetic Dissection of a Key Reproductive Barrier Between Nascent Species of House Mice

    PubMed Central

    White, Michael A.; Steffy, Brian; Wiltshire, Tim; Payseur, Bret A.

    2011-01-01

    Reproductive isolation between species is often caused by deleterious interactions among loci in hybrids. Finding the genes involved in these incompatibilities provides insight into the mechanisms of speciation. With recently diverged subspecies, house mice provide a powerful system for understanding the genetics of reproductive isolation early in the speciation process. Although previous studies have yielded important clues about the genetics of hybrid male sterility in house mice, they have been restricted to F1 sterility or incompatibilities involving the X chromosome. To provide a more complete characterization of this key reproductive barrier, we conducted an F2 intercross between wild-derived inbred strains from two subspecies of house mice, Mus musculus musculus and Mus musculus domesticus. We identified a suite of autosomal and X-linked QTL that underlie measures of hybrid male sterility, including testis weight, sperm density, and sperm morphology. In many cases, the autosomal loci were unique to a specific sterility trait and exhibited an effect only when homozygous, underscoring the importance of examining reproductive barriers beyond the F1 generation. We also found novel two-locus incompatibilities between the M. m. musculus X chromosome and M. m. domesticus autosomal alleles. Our results reveal a complex genetic architecture for hybrid male sterility and suggest a prominent role for reproductive barriers in advanced generations in maintaining subspecies integrity in house mice. PMID:21750261

  10. Estimation of genetic parameters for reproductive traits in Shall sheep.

    PubMed

    Amou Posht-e-Masari, Hesam; Shadparvar, Abdol Ahad; Ghavi Hossein-Zadeh, Navid; Hadi Tavatori, Mohammad Hossein

    2013-06-01

    The objective of this study was to estimate genetic parameters for reproductive traits in Shall sheep. Data included 1,316 records on reproductive performances of 395 Shall ewes from 41 sires and 136 dams which were collected from 2001 to 2007 in Shall breeding station in Qazvin province at the Northwest of Iran. Studied traits were litter size at birth (LSB), litter size at weaning (LSW), litter mean weight per lamb born (LMWLB), litter mean weight per lamb weaned (LMWLW), total litter weight at birth (TLWB), and total litter weight at weaning (TLWW). Test of significance to include fixed effects in the statistical model was performed using the general linear model procedure of SAS. The effects of lambing year and ewe age at lambing were significant (P<0.05). Genetic parameters were estimated using restricted maximum likelihood procedure, under repeatability animal models. Direct heritability estimates were 0.02, 0.01, 0.47, 0.40, 0.15, and 0.03 for LSB, LSW, LMWLB, LMWLW, TLWB, and TLWW, respectively, and corresponding repeatabilities were 0.02, 0.01, 0.73, 0.41, 0.27, and 0.03. Genetic correlation estimates between traits ranged from -0.99 for LSW-LMWLW to 0.99 for LSB-TLWB, LSW-TLWB, and LSW-TLWW. Phenotypic correlations ranged from -0.71 for LSB-LMWLW to 0.98 for LSB-TLWW and environmental correlations ranged from -0.89 for LSB-LMWLW to 0.99 for LSB-TLWW. Results showed that the highest heritability estimates were for LMWLB and LMWLW suggesting that direct selection based on these traits could be effective. Also, strong positive genetic correlations of LMWLB and LMWLW with other traits may improve meat production efficiency in Shall sheep.

  11. Quantitative genetic tools for insecticide resistance risk assessment: estimating the heritability of resistance

    Treesearch

    Michael J. Firko; Jane Leslie Hayes

    1990-01-01

    Quantitative genetic studies of resistance can provide estimates of genetic parameters not available with other types of genetic analyses. Three methods are discussed for estimating the amount of additive genetic variation in resistance to individual insecticides and subsequent estimation of heritability (h2) of resistance. Sibling analysis and...

  12. Estimation of genetic parameters and genetic changes for growth characteristics of Santa Ines sheep.

    PubMed

    Aguirre, E L; Mattos, E C; Eler, J P; Barreto Neto, A D; Ferraz, J B

    2016-08-19

    Studying genetic parameters and genetic changes in Santa Ines sheep is important, because it is the commonest breed in Brazil. This study obtained genetic data from 37,735 pedigree records of lambs over 12 years (2003-2014) from 33 flocks in 10 Brazilian States; 11,851 records of performance were available. (Co)variance components, genetic parameters and breeding values estimates were obtained by derivative-free restricted maximum likelihood in a univariate analysis that included maternal additive genetic and maternal permanent environmental effects. Birth weight, weaning weight, weight at 180 days of age, weight at 270 days of age, average daily weight gain in the following states: from birth to weaning, from weaning to 6 months, from 6 months to 9 months, and from weaning to 9 months; presence of hair in fur and leg muscularity were assessed. (Co)variance component values increased in the weight traits with age. A significant maternal effect was found in the pre-weaned stage that decreased in the post-weaned stage. High values were estimated for the maternal permanent environmental effect, possibly because of the extensive grassland that was available. High total heritability values were estimated for all of the traits evaluated. Significant, positive correlations were found between direct and maternal additive genetic traits with a gradual decrease as the lambs gained independence from their mothers. The genetic trends observed were irregular and incremental. Significant genetic variance suggests that direct selection for pre-weaning traits results in indirect selection of maternal abilities, and individual selection of any post-weaning trait results in rapid genetic improvement.

  13. High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

    NASA Astrophysics Data System (ADS)

    Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.

    2009-03-01

    The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise ΦST = 0.01-0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns.

  14. Estimating meiotic gene conversion rates from population genetic data.

    PubMed

    Gay, J; Myers, S; McVean, G

    2007-10-01

    Gene conversion plays an important part in shaping genetic diversity in populations, yet estimating the rate at which it occurs is difficult because of the short lengths of DNA involved. We have developed a new statistical approach to estimating gene conversion rates from genetic variation, by extending an existing model for haplotype data in the presence of crossover events. We show, by simulation, that when the rate of gene conversion events is at least comparable to the rate of crossover events, the method provides a powerful approach to the detection of gene conversion and estimation of its rate. Application of the method to data from the telomeric X chromosome of Drosophila melanogaster, in which crossover activity is suppressed, indicates that gene conversion occurs approximately 400 times more often than crossover events. We also extend the method to estimating variable crossover and gene conversion rates and estimate the rate of gene conversion to be approximately 1.5 times higher than the crossover rate in a region of human chromosome 1 with known recombination hotspots.

  15. Bayesian adaptive Markov chain Monte Carlo estimation of genetic parameters.

    PubMed

    Mathew, B; Bauer, A M; Koistinen, P; Reetz, T C; Léon, J; Sillanpää, M J

    2012-10-01

    Accurate and fast estimation of genetic parameters that underlie quantitative traits using mixed linear models with additive and dominance effects is of great importance in both natural and breeding populations. Here, we propose a new fast adaptive Markov chain Monte Carlo (MCMC) sampling algorithm for the estimation of genetic parameters in the linear mixed model with several random effects. In the learning phase of our algorithm, we use the hybrid Gibbs sampler to learn the covariance structure of the variance components. In the second phase of the algorithm, we use this covariance structure to formulate an effective proposal distribution for a Metropolis-Hastings algorithm, which uses a likelihood function in which the random effects have been integrated out. Compared with the hybrid Gibbs sampler, the new algorithm had better mixing properties and was approximately twice as fast to run. Our new algorithm was able to detect different modes in the posterior distribution. In addition, the posterior mode estimates from the adaptive MCMC method were close to the REML (residual maximum likelihood) estimates. Moreover, our exponential prior for inverse variance components was vague and enabled the estimated mode of the posterior variance to be practically zero, which was in agreement with the support from the likelihood (in the case of no dominance). The method performance is illustrated using simulated data sets with replicates and field data in barley.

  16. Genetic sampling for estimating density of common species.

    PubMed

    Cheng, Ellen; Hodges, Karen E; Sollmann, Rahel; Mills, L Scott

    2017-08-01

    Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult-to-capture species, genetic surveys from noninvasive collection of hair or scat has proved cost-efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping. We optimized a protocol for single-session NGS sampling of hares. We compared spatial capture-recapture population estimates from live trapping to estimates derived from NGS, and assessed NGS costs. NGS provided population estimates similar to those derived from live trapping, but a higher density of sampling plots was required for NGS. The optimal NGS protocol for our study entailed deploying 160 sampling plots for 4 days and genotyping one pellet per plot. NGS laboratory costs ranged from approximately $670 to $3000 USD per field site. While live trapping does not incur laboratory costs, its field costs can be considerably higher than for NGS, especially when study sites are difficult to access. We conclude that NGS can work for common species, but that it will require field and laboratory pilot testing to develop cost-effective sampling protocols.

  17. Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance.

    PubMed

    Mumma, Matthew A; Zieminski, Chris; Fuller, Todd K; Mahoney, Shane P; Waits, Lisette P

    2015-09-01

    Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical capture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calculated abundance estimates using program capwire, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of <10%. Scat sampling was effective for both coyotes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sampling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/individual. Our simulations suggested that ~3.4 captures/individual will result in a < 10% CV for abundance estimates when populations are small (23-39), but fewer captures/individual may be sufficient for larger populations. We found scat sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances.

  18. Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species.

    PubMed Central

    Rieseberg, L H; Whitton, J; Gardner, K

    1999-01-01

    Genetic analyses of reproductive barriers represent one of the few methods by which theories of speciation can be tested. However, genetic study is often restricted to model organisms that have short generation times and are easily propagated in the laboratory. Replicate hybrid zones with a diversity of recombinant genotypes of varying age offer increased resolution for genetic mapping experiments and expand the pool of organisms amenable to genetic study. Using 88 markers distributed across 17 chromosomes, we analyze the introgression of chromosomal segments of Helianthus petiolaris into H. annuus in three natural hybrid zones. Introgression was significantly reduced relative to neutral expectations for 26 chromosomal segments, suggesting that each segment contains one or more factors that contribute to isolation. Pollen sterility is significantly associated with 16 of these 26 segments, providing a straightforward explanation of why this subset of blocks is disadvantageous in hybrids. In addition, comparison of rates of introgression across colinear vs. rearranged chromosomes indicates that close to 50% of the barrier to introgression is due to chromosomal rearrangements. These results demonstrate the utility of hybrid zones for identifying factors contributing to isolation and verify the prediction of increased resolution relative to controlled crosses. PMID:10353912

  19. Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity.

    PubMed

    Eidesen, Pernille Bronken; Ehrich, Dorothee; Bakkestuen, Vegar; Alsos, Inger Greve; Gilg, Oliver; Taberlet, Pierre; Brochmann, Christian

    2013-11-01

    We provide the first comparative multispecies analysis of spatial genetic structure and diversity in the circumpolar Arctic using a common strategy for sampling and genetic analyses. We aimed to identify and explain potential general patterns of genetic discontinuity/connectivity and diversity, and to compare our findings with previously published hypotheses. We collected and analyzed 7707 samples of 17 widespread arctic-alpine plant species for amplified fragment length polymorphisms (AFLPs). Genetic structure, diversity and distinctiveness were analyzed for each species, and extrapolated to cover the geographic range of each species. The resulting maps were overlaid to produce metamaps. The Arctic and Atlantic Oceans, the Greenlandic ice cap, the Urals, and lowland areas between southern mountain ranges and the Arctic were the strongest barriers against gene flow. Diversity was highest in Beringia and gradually decreased into formerly glaciated areas. The highest degrees of distinctiveness were observed in Siberia. We conclude that large-scale general patterns exist in the Arctic, shaped by the Pleistocene glaciations combined with long-standing physical barriers against gene flow. Beringia served as both refugium and source for interglacial (re)colonization, whereas areas further west in Siberia served as refugia, but less as sources for (re)colonization. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  20. Performance of default risk model with barrier option framework and maximum likelihood estimation: Evidence from Taiwan

    NASA Astrophysics Data System (ADS)

    Chou, Heng-Chih; Wang, David

    2007-11-01

    We investigate the performance of a default risk model based on the barrier option framework with maximum likelihood estimation. We provide empirical validation of the model by showing that implied default barriers are statistically significant for a sample of construction firms in Taiwan over the period 1994-2004. We find that our model dominates the commonly adopted models, Merton model, Z-score model and ZETA model. Moreover, we test the n-year-ahead prediction performance of the model and find evidence that the prediction accuracy of the model improves as the forecast horizon decreases. Finally, we assess the effect of estimated default risk on equity returns and find that default risk is able to explain equity returns and that default risk is a variable worth considering in asset-pricing tests, above and beyond size and book-to-market.

  1. Genetic differentiation among populations of the brooding soft coral Clavularia koellikeri on the Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Bastidas, C.; Benzie, J.; Fabricius, K.

    2002-09-01

    The contribution of sexual and asexual reproduction, the spatial patterns of genetic structure, and the potential gene flow among populations were determined for the soft coral Clavularia koellikeri (Octocorallia: Alcyonacea, Clavulariidae) at ten sites among six reefs from two well-separated regions of the Great Barrier Reef (GBR), Australia. Eight allozyme loci indicated that colonies of C. koellikeri separated ≥3 m were produced sexually. Genetic diversity was lower in the southern (18°S) compared with the northern (10°S) populations, suggesting that reefs closer to the southernmost limit of the distribution of C. koellikeri within the GBR (19°S) may represent a more marginal habitat for this species. High levels of genetic differentiation were significant at all spatial scales (sites within reefs, reefs, and regions) from <4 km up to 1,000 km, indicating that C. koellikeri has restricted dispersal, consistent with having brooded larvae.

  2. Estimates of genetic parameters and genetic change for reproduction, weight, and wool characteristics of Targhee sheep.

    PubMed

    Hanford, K J; Van Vleck, L D; Snowder, G D

    2003-03-01

    Genetic parameters from both single-trait and bivariate analyses for prolificacy, weight, and wool traits were estimated using REML with animal models for Targhee sheep from data collected from 1950 to 1998 at the U.S. Sheep Experiment Station, Dubois, ID. Breeding values from both single-trait and seven-trait analyses calculated with the parameters estimated from the single-trait and bivariate analyses were compared across years of birth with respect to genetic trends. The numbers of observations were 38,625 for litter size at birth and litter size at weaning, 33,994 for birth weight, 32,715 for weaning weight, 36,807 for fleece weight and fleece grade, and 3,341 for staple length. Direct heritability estimates from single-trait analyses were 0.10 for litter size at birth, 0.07 for litter size at weaning, 0.25 for birth weight, 0.22 for weaning weight, 0.54 for fleece weight, 0.41 for fleece grade, and 0.65 for staple length. Estimate of direct genetic correlation between litter size at birth and weaning was 0.77 and between birth and weaning weights was 0.52. The estimate of genetic correlation between fleece weight and staple length was positive (0.54), but was negative between fleece weight and fleece grade (-0.47) and between staple length and fleece grade (-0.69). Estimates of genetic correlations were near zero between birth weight and litter size traits and small and positive between weaning weight and litter size traits. Fleece weight was slightly and negatively correlated with both litter size traits. Fleece grade was slightly and positively correlated with both litter size traits. Estimates of correlations between staple length and litter size at birth (-0.14) and litter size at weaning (0.05) were small. Estimates of correlations between weight traits and fleece weight were positive and low to moderate. Estimates of correlations between weight traits and fleece grade were negative and small, whereas estimates between weight traits and staple length were

  3. Estimation of genetic parameters for reproductive traits in alpacas.

    PubMed

    Cruz, A; Cervantes, I; Burgos, A; Morante, R; Gutiérrez, J P

    2015-12-01

    One of the main deficiencies affecting animal breeding programs in Peruvian alpacas is the low reproductive performance leading to low number of animals available to select from, decreasing strongly the selection intensity. Some reproductive traits could be improved by artificial selection, but very few information about genetic parameters exists for these traits in this specie. The aim of this study was to estimate genetic parameters for six reproductive traits in alpacas both in Suri (SU) and Huacaya (HU) ecotypes, as well as their genetic relationship with fiber and morphological traits. Dataset belonging to Pacomarca experimental farm collected between 2000 and 2014 was used. Number of records for age at first service (AFS), age at first calving (AFC), copulation time (CT), pregnancy diagnosis (PD), gestation length (GL), and calving interval (CI) were, respectively, 1704, 854, 19,770, 5874, 4290 and 934. Pedigree consisted of 7742 animals. Regarding reproductive traits, model of analysis included additive and residual random effects for all traits, and also permanent environmental effect for CT, PD, GL and CI traits, with color and year of recording as fixed effects for all the reproductive traits and also age at mating and sex of calf for GL trait. Estimated heritabilities, respectively for HU and SU were 0.19 and 0.09 for AFS, 0.45 and 0.59 for AFC, 0.04 and 0.05 for CT, 0.07 and 0.05 for PD, 0.12 and 0.20 for GL, and 0.14 and 0.09 for CI. Genetic correlations between them ranged from -0.96 to 0.70. No important genetic correlations were found between reproductive traits and fiber or morphological traits in HU. However, some moderate favorable genetic correlations were found between reproductive and either fiber and morphological traits in SU. According to estimated genetic correlations, some reproductive traits might be included as additional selection criteria in HU. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Genetic parameter estimation of reproductive traits of Litopenaeus vannamei

    NASA Astrophysics Data System (ADS)

    Tan, Jian; Kong, Jie; Cao, Baoxiang; Luo, Kun; Liu, Ning; Meng, Xianhong; Xu, Shengyu; Guo, Zhaojia; Chen, Guoliang; Luan, Sheng

    2017-02-01

    In this study, the heritability, repeatability, phenotypic correlation, and genetic correlation of the reproductive and growth traits of L. vannamei were investigated and estimated. Eight traits of 385 shrimps from forty-two families, including the number of eggs (EN), number of nauplii (NN), egg diameter (ED), spawning frequency (SF), spawning success (SS), female body weight (BW) and body length (BL) at insemination, and condition factor (K), were measured,. A total of 519 spawning records including multiple spawning and 91 no spawning records were collected. The genetic parameters were estimated using an animal model, a multinomial logit model (for SF), and a sire-dam and probit model (for SS). Because there were repeated records, permanent environmental effects were included in the models. The heritability estimates for BW, BL, EN, NN, ED, SF, SS, and K were 0.49 ± 0.14, 0.51 ± 0.14, 0.12 ± 0.08, 0, 0.01 ± 0.04, 0.06 ± 0.06, 0.18 ± 0.07, and 0.10 ± 0.06, respectively. The genetic correlation was 0.99 ± 0.01 between BW and BL, 0.90 ± 0.19 between BW and EN, 0.22 ± 0.97 between BW and ED, -0.77 ± 1.14 between EN and ED, and -0.27 ± 0.36 between BW and K. The heritability of EN estimated without a covariate was 0.12 ± 0.08, and the genetic correlation was 0.90 ± 0.19 between BW and EN, indicating that improving BW may be used in selection programs to genetically improve the reproductive output of L. vannamei during the breeding. For EN, the data were also analyzed using body weight as a covariate (EN-2). The heritability of EN-2 was 0.03 ± 0.05, indicating that it is difficult to improve the reproductive output by genetic improvement. Furthermore, excessive pursuit of this selection is often at the expense of growth speed. Therefore, the selection of high-performance spawners using BW and SS may be an important strategy to improve nauplii production.

  5. Ecological and genetic barriers differentiate natural populations of Saccharomyces cerevisiae

    SciTech Connect

    Clowers, Katie J.; Heilberger, Justin; Piotrowski, Jeff S.; Will, Jessica L.; Gasch, Audrey P.

    2015-05-06

    How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Lastly, our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations.

  6. Genetic analysis of post-mating reproductive barriers in hybridizing European Populus species

    PubMed Central

    Macaya-Sanz, D; Suter, L; Joseph, J; Barbará, T; Alba, N; González-Martínez, S C; Widmer, A; Lexer, C

    2011-01-01

    Molecular genetic analyses of experimental crosses provide important information on the strength and nature of post-mating barriers to gene exchange between divergent populations, which are topics of great interest to evolutionary geneticists and breeders. Although not a trivial task in long-lived organisms such as trees, experimental interspecific recombinants can sometimes be created through controlled crosses involving natural F1's. Here, we used this approach to understand the genetics of post-mating isolation and barriers to introgression in Populus alba and Populus tremula, two ecologically divergent, hybridizing forest trees. We studied 86 interspecific backcross (BC1) progeny and >350 individuals from natural populations of these species for up to 98 nuclear genetic markers, including microsatellites, indels and single nucleotide polymorphisms, and inferred the origin of the cytoplasm of the cross with plastid DNA. Genetic analysis of the BC1 revealed extensive segregation distortions on six chromosomes, and >90% of these (12 out of 13) favored P. tremula donor alleles in the heterospecific genomic background. Since selection was documented during early diploid stages of the progeny, this surprising result was attributed to epistasis, cyto-nuclear coadaptation, heterozygote advantage at nuclear loci experiencing introgression or a combination of these. Our results indicate that gene flow across ‘porous' species barriers affects these poplars and aspens beyond neutral, Mendelian expectations and suggests the mechanisms responsible. Contrary to expectations, the Populus sex determination region is not protected from introgression. Understanding the population dynamics of the Populus sex determination region will require tests based on natural interspecific hybrid zones. PMID:21587301

  7. Inclusion of African Americans in Genetic Studies: What Is the Barrier?

    PubMed Central

    Hartz, Sarah M.; Johnson, Eric O.; Saccone, Nancy L.; Hatsukami, Dorothy; Breslau, Naomi; Bierut, Laura J.

    2011-01-01

    To facilitate an increase in the amount of data on minority subjects collected for genetic databases, the authors attempted to clarify barriers to African-American participation in genetic studies. They randomly sampled 78,072 subjects from the community (Missouri Family Registry, 2002–2007). Of these, 28,658 participated in a telephone screening interview, 3,179 were eligible to participate in the genetic study, and 1,919 participated in the genetic study. Response rates were examined in relation to the proportion of subjects in the area who were African-American according to US Census 2000 zip code demographic data. Compared with zip codes with fewer than 5% African Americans (average = 2% African-American), zip codes with at least 60% African Americans (average = 87% African-American) had higher proportions of subjects with an incorrect address or telephone number but lower proportions of subjects who did not answer the telephone and subjects who refused the telephone interview (P < 0.0001). Based on reported race from the telephone screening, 71% of eligible African Americans and 57% of eligible European Americans participated in the genetic study (P < 0.0001). The results of this study suggest that increasing the number of African Americans in genetic databases may be achieved by increasing efforts to locate and contact them. PMID:21633120

  8. Using genetic data to estimate diffusion rates in heterogeneous landscapes.

    PubMed

    Roques, L; Walker, E; Franck, P; Soubeyrand, S; Klein, E K

    2016-08-01

    Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic-statistical method to estimate space-dependent diffusion parameters of spatially-explicit models based on stochastic differential equations, using genetic data. Dividing the total population into subpopulations corresponding to different habitat patches with known allele frequencies, the expected proportions of individuals from each subpopulation at each position is computed by solving a system of reaction-diffusion equations. Modelling the capture and genotyping of the individuals with a statistical approach, we derive a numerically tractable formula for the likelihood function associated with the diffusion parameters. In a simulated environment made of three types of regions, each associated with a different diffusion coefficient, we successfully estimate the diffusion parameters with a maximum-likelihood approach. Although higher genetic differentiation among subpopulations leads to more accurate estimations, once a certain level of differentiation has been reached, the finite size of the genotyped population becomes the limiting factor for accurate estimation.

  9. Estimates of genetic parameters and genetic change for reproduction, weight, and wool characteristics of Columbia sheep.

    PubMed

    Hanford, K J; Van Vleck, L D; Snowder, G D

    2002-12-01

    Genetic parameters from both single-trait and bivariate analyses for prolificacy, weight and wool traits were estimated using REML with animal models for Columbia sheep from data collected from 1950 to 1998 at the U.S. Sheep Experiment Station (USSES), Dubois, ID. Breeding values from both single-trait and seven-trait analyses calculated using the parameters estimated from the single-trait and bivariate analyses were compared with respect to genetic trends. Number of observations were 31,401 for litter size at birth and litter size at weaning, 24,741 for birth weight, 23,903 for weaning weight, 29,572 for fleece weight and fleece grade, and 2,449 for staple length. Direct heritability estimates from single-trait analyses were 0.09 for litter size at birth, 0.06 for litter size at weaning, 0.27 for birth weight, 0.16 for weaning weight, 0.53 for fleece weight, 0.41 for fleece grade, and 0.55 for staple length. Estimate of direct genetic correlation between littersize at birth and weaning was 0.84 and between birth and weaning weights was 0.56. Estimate of genetic correlation between fleece weight and staple length was positive (0.55) but negative between fleece weight and fleece grade (-0.47) and between staple length and fleece grade (-0.70). Estimates of genetic correlations were positive but small between birth weight and litter size traits and moderate and positive between weaning weight and litter size traits. Fleece weight was lowly and negatively correlated with both litter size traits. Fleece grade was lowly and positively correlated with both litter size traits, while staple length was lowly and negatively correlated with the litter size traits. Estimates of correlations between weight traits and fleece weight were positive and low to moderate. Estimates of correlations between weight traits and fleece grade were negative and small. Estimates of correlations between staple length and birth weight (0.05) and weaning weight were small (-0.04). Estimated

  10. Estimates of genetic parameters for growth traits in Kermani sheep.

    PubMed

    Bahreini Behzadi, M R; Shahroudi, F E; Van Vleck, L D

    2007-10-01

    Birth weight (BW), weaning weight (WW), 6-month weight (W6), 9-month weight (W9) and yearling weight (YW) of Kermani lambs were used to estimate genetic parameters. The data were collected from Shahrbabak Sheep Breeding Research Station in Iran during the period of 1993-1998. The fixed effects in the model were lambing year, sex, type of birth and age of dam. Number of days between birth date and the date of obtaining measurement of each record was used as a covariate. Estimates of (co)variance components and genetic parameters were obtained by restricted maximum likelihood, using single and two-trait animal models. Based on the most appropriate fitted model, direct and maternal heritabilities of BW, WW, W6, W9 and YW were estimated to be 0.10 +/- 0.06 and 0.27 +/- 0.04, 0.22 +/- 0.09 and 0.19 +/- 0.05, 0.09 +/- 0.06 and 0.25 +/- 0.04, 0.13 +/- 0.08 and 0.18 +/- 0.05, and 0.14 +/- 0.08 and 0.14 +/- 0.06 respectively. Direct and maternal genetic correlations between the lamb weights varied between 0.66 and 0.99, and 0.11 and 0.99. The results showed that the maternal influence on lamb weights decreased with age at measurement. Ignoring maternal effects in the model caused overestimation of direct heritability. Maternal effects are significant sources of variation for growth traits and ignoring maternal effects in the model would cause inaccurate genetic evaluation of lambs.

  11. Primary-care providers' perceived barriers to integration of genetics services: a systematic review of the literature.

    PubMed

    Mikat-Stevens, Natalie A; Larson, Ingrid A; Tarini, Beth A

    2015-03-01

    We aimed to systematically review the literature to identify primary-care providers' perceived barriers against provision of genetics services. We systematically searched PubMed and ERIC using key and Boolean term combinations for articles published from 2001 to 2012 that met inclusion/exclusion criteria. Specific barriers were identified and aggregated into categories based on topic similarity. These categories were then grouped into themes. Of the 4,174 citations identified by the search, 38 publications met inclusion criteria. There were 311 unique barriers that were classified into 38 categories across 4 themes: knowledge and skills; ethical, legal, and social implications; health-care systems; and scientific evidence. Barriers most frequently mentioned by primary-care providers included a lack of knowledge about genetics and genetic risk assessment, concern for patient anxiety, a lack of access to genetics, and a lack of time. Although studies reported that primary-care providers perceive genetics as being important, barriers to the integration of genetics medicine into routine patient care were identified. The promotion of practical guidelines, point-of-care risk assessment tools, tailored educational tools, and other systems-level strategies will assist primary-care providers in providing genetics services for their patients.

  12. Estimation of genetic diversity in Siri cattle from India.

    PubMed

    Sharma, Rekha; Pandey, A K; Singh, Y; Mishra, B P; Singh, P K; Singh, G

    2008-11-01

    Siri cattle, a dual purpose breed of India is currently showing declining population trend. Siri animals have been developing through natural selection and show high adaptation to wide range of hilly terrain (altitudes 150-2500 m). The present work evaluated the genetic diversity of 23 FAO recommended microsatellite loci in a sample of 50 animals. The allele and genotype frequencies, heterozygosities and gene diversity were estimated. A total of 141 alleles were detected by the 23 microsatellite markers investigated. Microsatellites were highly polymorphic with mean allelic number 6.13 +/- 1.63 (ranging from 3-10 per locus). The observed heterozygosity in the population varied from 0.26-0.80 with the mean of 0.53 +/- 0.16, indicating substantial genetic variation in this population. Heterozygote deficiency and mutation-drift equilibrium hypothesis were also examined. Population exhibited heterozygote deficit to the tune of 22.1%. Population was found to be in mutation-drift equilibrium. Substantial genetic variability verified in Siri cattle despite its reducing population size suggests that this breed has a rich reservoir of genetic diversity. This fact and its marked environmental adaptation reinforce the importance of its preservation as a pure breed, and/or its use in agricultural exploitation.

  13. Genetics of psoriasis: evidence for epistatic interaction between skin barrier abnormalities and immune deviation.

    PubMed

    Bergboer, Judith G M; Zeeuwen, Patrick L J M; Schalkwijk, Joost

    2012-10-01

    Psoriasis was until recently regarded as a T-cell-driven disease with presumed (auto)immune mechanisms as its primary cause. This view was supported by clinical data and genetic studies that identified risk factors functioning in adaptive and innate immunity, such as HLA-C*06, ERAP1, the IL-23 pathway, and NF-k B signaling. Candidate gene approaches and genome-wide association studies, however, have identified copy number polymorphisms of the b-defensin cluster and deletion of late cornified envelope (LCE) 3B and 3C genes (LCE3C_LCE3B-del) as psoriasis risk factors.As these genes are expressed in epithelial cells and not by the immune system, these findings may cause a change of paradigm for psoriasis, not unlike the reported filaggrin association that has profoundly changed the views on atopic dermatitis. In addition to genetic polymorphisms of the immune system, genetic variations affecting the skin barrier are likely to contribute to psoriasis. Recent studies have shown epistatic interactions involving HLA-C*06, ERAP1, and LCE3C_LCE3B-del, which makes psoriasis a unique model to investigate genetic and biological interactions of associated genes in a complex disease. We present a model for disease initiation and perpetuation, which integrates the available genetic, immunobiological, and clinical data.

  14. Relieving the Bottleneck: An Investigation of Barriers to Expansion of Supervision Networks at Genetic Counseling Training Programs.

    PubMed

    Berg, Jordan; Hoskovec, Jennifer; Hashmi, S Shahrukh; McCarthy Veach, Patricia; Ownby, Allison; Singletary, Claire N

    2017-09-06

    Rapid growth in the demand for genetic counselors has led to a workforce shortage. There is a prevailing assumption that the number of training slots for genetic counseling students is linked to the availability of clinical supervisors. This study aimed to determine and compare barriers to expansion of supervision networks at genetic counseling training programs as perceived by supervisors, non-supervisors, and Program Directors. Genetic counselors were recruited via National Society of Genetic Counselors e-blast; Program Directors received personal emails. Online surveys were completed by 216 supervisors, 98 non-supervisors, and 23 Program Directors. Respondents rated impact of 35 barriers; comparisons were made using Kruskal-Wallis and Wilcoxon ranked sum tests. Half of supervisors (51%) indicated willingness to increase supervision. All non-supervisors were willing to supervise. However, all agreed that being too busy impacted ability to supervise, highlighted by supervisors' most impactful barriers: lack of time, other responsibilities, intensive nature of supervision, desire for breaks, and unfilled positions. Non-supervisors noted unique barriers: distance, institutional barriers, and non-clinical roles. Program Directors' perceptions were congruent with those of genetic counselors with three exceptions they rated as impactful: lack of money, prefer not to supervise, and never been asked. In order to expand supervision networks and provide comprehensive student experiences, the profession must examine service delivery models to increase workplace efficiency, reconsider the supervision paradigm, and redefine what constitutes a countable case or place value on non-direct patient care experiences.

  15. [Transfer of genetic constructions through the transplacental barrier into mice embryos].

    PubMed

    Efremov, A M; Buglaeva, A O; Orlov, S V; Burov, S V; Ignatovich, I A; Dizhe, E B; Shavva, V S; Perevozchikov, A P

    2010-01-01

    Genetic modification of mammalian embryos is an important way to model various changes in human development; also, it is an instrument for studying the functions of certain genes in mammals. Using our own experience in developing modes of delivery of genetic constructions to mammals in a nonviral way, we present here data on the delivery of a eukaryotic expression vector to mice embryos through the transplacental barrier with the use of hydrodynamic intravenous injections of DNA-hybrid peptide complexes to pregnant females. The peptide has a cationic part for interaction with DNA and includes a ligand structure towards receptors of the releasing factor of luteinizing hormone (RFLH, luliberin). Advantages of the suggested method are simplicity, economy, nonimmunogenicity for females, and the ability to multiply repeat the procedure. On the basis of the method, systemic gene delivery into tissues of mammalian embryos may be developed.

  16. Eczema in early life: Genetics, the skin barrier, and lessons learned from birth cohort studies

    PubMed Central

    Biagini Myers, Jocelyn M.; Khurana Hershey, Gurjit K.

    2010-01-01

    Eczema is a chronic inflammatory disorder of the skin that affects up to 30% of children. It often afflicts infants in the first few months of life and can be the first indicator of the atopic march. Recent results from birth cohort studies have uncovered novel information regarding genetic and environmental factors that promote the development of eczema. Birth cohort studies provide an optimal study design to elucidate these associations and prospectively track longitudinal data including exposure assessment and health outcomes from birth into early life and childhood. This is especially relevant for eczema given the age specific emergence of this disease. In this review, we will provide a general overview of pediatric eczema and discuss the important findings in the literature with respect to genetics and environmental exposures, highlighting those derived from birth cohort studies. Additionally, we will review how these relate to the atopic march, the hygiene hypothesis and the integrity of the skin barrier. PMID:20739029

  17. Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier.

    PubMed

    Mökkönen, Harri; Ala-Nissila, Tapio; Jónsson, Hannes

    2016-09-07

    The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch between the initial and final state energy wells while the polymer beads undergo diffusive motion back and forth over the barrier. We present an efficient method for evaluating the correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product. This is analogous to what is done in forward flux sampling except that there the hyperplane sequence starts at the initial state. The method is applied to the escape of polymers with up to 64 beads from a potential well. For high temperature, the results are compared with direct Langevin dynamics simulations as well as forward flux sampling and excellent agreement between the three rate estimates is found. The use of a sequence of hyperplanes in the evaluation of the recrossing correction speeds up the calculation by an order of magnitude as compared with the traditional approach. As the temperature is lowered, the direct Langevin dynamics simulations as well as the forward flux simulations become computationally too demanding, while the harmonic transition state theory estimate corrected for recrossings can be calculated without significant increase in the computational effort.

  18. Estimation of recombination frequency in bi-parental genetic populations.

    PubMed

    Sun, Ziqi; Li, Huihui; Zhang, Luyan; Wang, Jiankang

    2012-06-01

    Summary Linkage analysis plays an important role in genetic studies. In linkage analysis, accurate estimation of recombination frequency is essential. Many bi-parental populations have been used, and determining an appropriate population is of great importance in precise recombination frequency. In this study, we investigated the estimation efficiency of recombination frequency in 12 bi-parental populations. The criteria that we used for comparison were LOD score in testing linkage relationship, deviation between estimated and real recombination frequency, standard error (SE) of estimates and the least theoretical population size (PS) required to observe at least one recombinant and to declare the statistically significant linkage relationship. Theoretical and simulation results indicated that larger PS and smaller recombination frequency resulted in higher LOD score and smaller deviation. Lower LOD score, higher deviation and higher SE for estimating the recombination frequency in the advanced backcrossing and selfing populations are larger than those in backcross and F2 populations, respectively. For advanced backcrossing and selfing populations, larger populations were needed in order to observe at least one recombinant and to declare significant linkage. In comparison, in F2 and F3 populations higher LOD score, lower deviation and SE were observed for co-dominant markers. A much larger population was needed to observe at least one recombinant and to detect loose linkage for dominant and recessive markers. Therefore, advanced backcrossing and selfing populations had lower precision in estimating the recombination frequency. F2 and F3 populations together with co-dominant markers represent the ideal situation for linkage analysis and linkage map construction.

  19. HIV integrase variability and genetic barrier in antiretroviral naïve and experienced patients

    PubMed Central

    2011-01-01

    Background HIV-1 integrase (IN) variability in treatment naïve patients with different HIV-1 subtypes is a major issue. In fact, the effect of previous exposure to antiretrovirals other than IN inhibitors (INI) on IN variability has not been satisfactorily defined. In addition, the genetic barrier for specific INI resistance mutations remains to be calculated. Methods IN variability was analyzed and compared with reverse transcriptase (RT) and protease (PR) variability in 41 treatment naïve and 54 RT inhibitor (RTI) and protease inhibitor (PRI) experienced patients from subjects infected with subtype B and non-B strains. In addition, four HIV-2 strains were analyzed in parallel. Frequency and distribution of IN mutations were compared between HAART-naïve and RTI/PI-experienced patients; the genetic barrier for 27 amino acid positions related to INI susceptibility was calculated as well. Results Primary mutations associated with resistance to INI were not detected in patients not previously treated with this class of drug. However, some secondary mutations which have been shown to contribute to INI resistance were found. Only limited differences in codon usage distribution between patient groups were found. HIV-2 strains from INI naïve patients showed the presence of both primary and secondary resistance mutations. Conclusion Exposure to antivirals other than INI does not seem to significantly influence the emergence of mutations implicated in INI resistance. HIV-2 strain might have reduced susceptibility to INI. PMID:21453487

  20. Genetic and Anatomical Basis of the Barrier Separating Wakefulness and Anesthetic-Induced Unresponsiveness

    PubMed Central

    Hung, Hsiao-Tung; Koh, Kyunghee; Sowcik, Mallory; Sehgal, Amita; Kelz, Max B.

    2013-01-01

    A robust, bistable switch regulates the fluctuations between wakefulness and natural sleep as well as those between wakefulness and anesthetic-induced unresponsiveness. We previously provided experimental evidence for the existence of a behavioral barrier to transitions between these states of arousal, which we call neural inertia. Here we show that neural inertia is controlled by processes that contribute to sleep homeostasis and requires four genes involved in electrical excitability: Sh, sss, na and unc79. Although loss of function mutations in these genes can increase or decrease sensitivity to anesthesia induction, surprisingly, they all collapse neural inertia. These effects are genetically selective: neural inertia is not perturbed by loss-of-function mutations in all genes required for the sleep/wake cycle. These effects are also anatomically selective: sss acts in different neurons to influence arousal-promoting and arousal-suppressing processes underlying neural inertia. Supporting the idea that anesthesia and sleep share some, but not all, genetic and anatomical arousal-regulating pathways, we demonstrate that increasing homeostatic sleep drive widens the neural inertial barrier. We propose that processes selectively contributing to sleep homeostasis and neural inertia may be impaired in pathophysiological conditions such as coma and persistent vegetative states. PMID:24039590

  1. A Genetic Algorithm Based Support Vector Machine Model for Blood-Brain Barrier Penetration Prediction

    PubMed Central

    Zhang, Daqing; Xiao, Jianfeng; Zhou, Nannan; Zheng, Mingyue; Luo, Xiaomin; Jiang, Hualiang; Chen, Kaixian

    2015-01-01

    Blood-brain barrier (BBB) is a highly complex physical barrier determining what substances are allowed to enter the brain. Support vector machine (SVM) is a kernel-based machine learning method that is widely used in QSAR study. For a successful SVM model, the kernel parameters for SVM and feature subset selection are the most important factors affecting prediction accuracy. In most studies, they are treated as two independent problems, but it has been proven that they could affect each other. We designed and implemented genetic algorithm (GA) to optimize kernel parameters and feature subset selection for SVM regression and applied it to the BBB penetration prediction. The results show that our GA/SVM model is more accurate than other currently available log BB models. Therefore, to optimize both SVM parameters and feature subset simultaneously with genetic algorithm is a better approach than other methods that treat the two problems separately. Analysis of our log BB model suggests that carboxylic acid group, polar surface area (PSA)/hydrogen-bonding ability, lipophilicity, and molecular charge play important role in BBB penetration. Among those properties relevant to BBB penetration, lipophilicity could enhance the BBB penetration while all the others are negatively correlated with BBB penetration. PMID:26504797

  2. Models for estimation of service life of concrete barriers in low-level radioactive waste disposal

    SciTech Connect

    Walton, J.C.; Plansky, L.E.; Smith, R.W. )

    1990-09-01

    Concrete barriers will be used as intimate parts of systems for isolation of low level radioactive wastes subsequent to disposal. This work reviews mathematical models for estimating the degradation rate of concrete in typical service environments. The models considered cover sulfate attack, reinforcement corrosion, calcium hydroxide leaching, carbonation, freeze/thaw, and cracking. Additionally, fluid flow, mass transport, and geochemical properties of concrete are briefly reviewed. Example calculations included illustrate the types of predictions expected of the models. 79 refs., 24 figs., 6 tabs.

  3. Estimation of the Barrier Layer Thickness in the Indian Ocean Using Aquarius Salinity

    DTIC Science & Technology

    2014-07-08

    108(C1), 3009 , doi:10.1029/2001JC000907. Reynolds, R. W., N. A. Rayner, T. M. Smith, D. C . Stokes, and W. Wang (2002), An improved in situ and satellite...SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: a. REPORT b. ABSTRACT c . THIS PAGE 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 19a. NAME OF...geol.sc.edu Citation: Felton, C . S., B. Subrahmanyam, V. S. N. Murty, and J. F. Shriver (2014), Estimation of the barrier layer thickness in the Indian Ocean

  4. Marker-Based Estimation of Genetic Parameters in Genomics

    PubMed Central

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing ‘big’ genomic data sets. PMID:25025305

  5. Application of genetic algorithm to hexagon-based motion estimation.

    PubMed

    Kung, Chih-Ming; Cheng, Wan-Shu; Jeng, Jyh-Horng

    2014-01-01

    With the improvement of science and technology, the development of the network, and the exploitation of the HDTV, the demands of audio and video become more and more important. Depending on the video coding technology would be the solution for achieving these requirements. Motion estimation, which removes the redundancy in video frames, plays an important role in the video coding. Therefore, many experts devote themselves to the issues. The existing fast algorithms rely on the assumption that the matching error decreases monotonically as the searched point moves closer to the global optimum. However, genetic algorithm is not fundamentally limited to this restriction. The character would help the proposed scheme to search the mean square error closer to the algorithm of full search than those fast algorithms. The aim of this paper is to propose a new technique which focuses on combing the hexagon-based search algorithm, which is faster than diamond search, and genetic algorithm. Experiments are performed to demonstrate the encoding speed and accuracy of hexagon-based search pattern method and proposed method.

  6. Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach.

    PubMed

    Risso, Davide; Taglioli, Luca; De Iasio, Sergio; Gueresi, Paola; Alfani, Guido; Nelli, Sergio; Rossi, Paolo; Paoli, Giorgio; Tofanelli, Sergio

    2015-01-01

    This research is the first empirical attempt to calculate the various components of the hidden bias associated with the sampling strategies routinely-used in human genetics, with special reference to surname-based strategies. We reconstructed surname distributions of 26 Italian communities with different demographic features across the last six centuries (years 1447-2001). The degree of overlapping between "reference founding core" distributions and the distributions obtained from sampling the present day communities by probabilistic and selective methods was quantified under different conditions and models. When taking into account only one individual per surname (low kinship model), the average discrepancy was 59.5%, with a peak of 84% by random sampling. When multiple individuals per surname were considered (high kinship model), the discrepancy decreased by 8-30% at the cost of a larger variance. Criteria aimed at maximizing locally-spread patrilineages and long-term residency appeared to be affected by recent gene flows much more than expected. Selection of the more frequent family names following low kinship criteria proved to be a suitable approach only for historically stable communities. In any other case true random sampling, despite its high variance, did not return more biased estimates than other selective methods. Our results indicate that the sampling of individuals bearing historically documented surnames (founders' method) should be applied, especially when studying the male-specific genome, to prevent an over-stratification of ancient and recent genetic components that heavily biases inferences and statistics.

  7. Application of Genetic Algorithm to Hexagon-Based Motion Estimation

    PubMed Central

    Cheng, Wan-Shu

    2014-01-01

    With the improvement of science and technology, the development of the network, and the exploitation of the HDTV, the demands of audio and video become more and more important. Depending on the video coding technology would be the solution for achieving these requirements. Motion estimation, which removes the redundancy in video frames, plays an important role in the video coding. Therefore, many experts devote themselves to the issues. The existing fast algorithms rely on the assumption that the matching error decreases monotonically as the searched point moves closer to the global optimum. However, genetic algorithm is not fundamentally limited to this restriction. The character would help the proposed scheme to search the mean square error closer to the algorithm of full search than those fast algorithms. The aim of this paper is to propose a new technique which focuses on combing the hexagon-based search algorithm, which is faster than diamond search, and genetic algorithm. Experiments are performed to demonstrate the encoding speed and accuracy of hexagon-based search pattern method and proposed method. PMID:24592178

  8. Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach

    PubMed Central

    Risso, Davide; Taglioli, Luca; De Iasio, Sergio; Gueresi, Paola; Alfani, Guido; Nelli, Sergio; Rossi, Paolo; Paoli, Giorgio; Tofanelli, Sergio

    2015-01-01

    This research is the first empirical attempt to calculate the various components of the hidden bias associated with the sampling strategies routinely-used in human genetics, with special reference to surname-based strategies. We reconstructed surname distributions of 26 Italian communities with different demographic features across the last six centuries (years 1447–2001). The degree of overlapping between "reference founding core" distributions and the distributions obtained from sampling the present day communities by probabilistic and selective methods was quantified under different conditions and models. When taking into account only one individual per surname (low kinship model), the average discrepancy was 59.5%, with a peak of 84% by random sampling. When multiple individuals per surname were considered (high kinship model), the discrepancy decreased by 8–30% at the cost of a larger variance. Criteria aimed at maximizing locally-spread patrilineages and long-term residency appeared to be affected by recent gene flows much more than expected. Selection of the more frequent family names following low kinship criteria proved to be a suitable approach only for historically stable communities. In any other case true random sampling, despite its high variance, did not return more biased estimates than other selective methods. Our results indicate that the sampling of individuals bearing historically documented surnames (founders' method) should be applied, especially when studying the male-specific genome, to prevent an over-stratification of ancient and recent genetic components that heavily biases inferences and statistics. PMID:26452043

  9. Joint estimation of crown of thorns (Acanthaster planci) densities on the Great Barrier Reef

    PubMed Central

    Mellin, Camille; Pratchett, Morgan S.; Hoey, Jessica; Anthony, Kenneth R.N.; Cheal, Alistair J.; Miller, Ian; Sweatman, Hugh; Cowan, Zara L.; Taylor, Sascha; Moon, Steven; Fonnesbeck, Chris J.

    2016-01-01

    Crown-of-thorns starfish (CoTS; Acanthaster spp.) are an outbreaking pest among many Indo-Pacific coral reefs that cause substantial ecological and economic damage. Despite ongoing CoTS research, there remain critical gaps in observing CoTS populations and accurately estimating their numbers, greatly limiting understanding of the causes and sources of CoTS outbreaks. Here we address two of these gaps by (1) estimating the detectability of adult CoTS on typical underwater visual count (UVC) surveys using covariates and (2) inter-calibrating multiple data sources to estimate CoTS densities within the Cairns sector of the Great Barrier Reef (GBR). We find that, on average, CoTS detectability is high at 0.82 [0.77, 0.87] (median highest posterior density (HPD) and [95% uncertainty intervals]), with CoTS disc width having the greatest influence on detection. Integrating this information with coincident surveys from alternative sampling programs, we estimate CoTS densities in the Cairns sector of the GBR averaged 44 [41, 48] adults per hectare in 2014. PMID:27635314

  10. Joint estimation of crown of thorns (Acanthaster planci) densities on the Great Barrier Reef.

    PubMed

    MacNeil, M Aaron; Mellin, Camille; Pratchett, Morgan S; Hoey, Jessica; Anthony, Kenneth R N; Cheal, Alistair J; Miller, Ian; Sweatman, Hugh; Cowan, Zara L; Taylor, Sascha; Moon, Steven; Fonnesbeck, Chris J

    2016-01-01

    Crown-of-thorns starfish (CoTS; Acanthaster spp.) are an outbreaking pest among many Indo-Pacific coral reefs that cause substantial ecological and economic damage. Despite ongoing CoTS research, there remain critical gaps in observing CoTS populations and accurately estimating their numbers, greatly limiting understanding of the causes and sources of CoTS outbreaks. Here we address two of these gaps by (1) estimating the detectability of adult CoTS on typical underwater visual count (UVC) surveys using covariates and (2) inter-calibrating multiple data sources to estimate CoTS densities within the Cairns sector of the Great Barrier Reef (GBR). We find that, on average, CoTS detectability is high at 0.82 [0.77, 0.87] (median highest posterior density (HPD) and [95% uncertainty intervals]), with CoTS disc width having the greatest influence on detection. Integrating this information with coincident surveys from alternative sampling programs, we estimate CoTS densities in the Cairns sector of the GBR averaged 44 [41, 48] adults per hectare in 2014.

  11. Microgeographic Population Genetic Structure of Baylisascaris procyonis (Nematoda: Ascaroidae) in Western Michigan Indicates the Grand River Is a Barrier to Gene Flow.

    PubMed

    Sarkissian, Christina A; Campbell, Sara K; Dharmarajan, Guha; Jacquot, Joseph; Page, L Kristen; Graham, Douglas H

    2015-12-01

    Baylisascaris procyonis , the raccoon roundworm, is increasingly being recognized for its zoonotic and public health importance. Fine-scale analyses of the population genetics of this species have been hampered due to a lack of appropriate genetic markers. To this end, we developed 8 novel polymorphic microsatellites for B. procyonis and used these markers to elucidate microgeographic structuring of this parasite in a 500-km(2) study area in western Michigan. Our analyses revealed significant levels of genetic differentiation amongst the 74 worms collected from 10 different raccoons. Critically, Bayesian clustering indicated 2 genetically distinct groups, one on either side of the Grand River which bisects our study area. Estimates of F(ST), and results from AMOVA and isolation by distance, further corroborated a scenario whereby the river is acting as a barrier to gene flow, a rather unexpected finding given the high vagility of raccoons and microgeographic scale of the analysis. It is possible that the Grand River is a major dispersal barrier for B. procyonis because raccoons are most likely to disperse across the river when it is frozen, and worm burden in raccoons approaches zero during the winter.

  12. Blood-testis barrier and spermatogenesis: lessons from genetically-modified mice

    PubMed Central

    Jiang, Xiao-Hua; Bukhari, Ihtisham; Zheng, Wei; Yin, Shi; Wang, Zheng; Cooke, Howard J; Shi, Qing-Hua

    2014-01-01

    The blood-testis barrier (BTB) is found between adjacent Sertoli cells in the testis where it creates a unique microenvironment for the development and maturation of meiotic and postmeiotic germ cells in seminiferous tubes. It is a compound proteinous structure, composed of several types of cell junctions including tight junctions (TJs), adhesion junctions and gap junctions (GJs). Some of the junctional proteins function as structural proteins of BTB and some have regulatory roles. The deletion or functional silencing of genes encoding these proteins may disrupt the BTB, which may cause immunological or other damages to meiotic and postmeiotic cells and ultimately lead to spermatogenic arrest and infertility. In this review, we will summarize the findings on the BTB structure and function from genetically-modified mouse models and discuss the future perspectives. PMID:24713828

  13. Genetic barrier and variant fitness in hepatitis C as critical parameters for drug resistance development.

    PubMed

    Welsch, Christoph

    2014-03-01

    The approval of direct-acting antiviral agents (DAAs) has marked a pivotal change in the treatment landscape of chronic hepatitis C. As for DAAs targeting other viral diseases, there are concerns regarding the development of resistant viral variants. Their selection allows the virus to escape from drug pressure with subsequent treatment failure. The emergence of resistant variants depends on multiple factors that range from genetic barriers to mutations to the fitness of viral variants. This article illustrates the basic mechanisms underlying development of resistance to specific antiviral agents with a special emphasis on NS3 protease inhibitors. The role of fitness deficits and compensation for variant selection and persistence is discussed together with technical issues in sequencing as well as clinical implications in the use of DAAs now and in the future.

  14. Landscape genetics of fishers (Martes pennanti) in the Northeast: dispersal barriers and historical influences.

    PubMed

    Hapeman, Paul; Latch, Emily K; Fike, Jennifer A; Rhodes, Olin E; Kilpatrick, C William

    2011-01-01

    Habitat fragmentation and overtrapping are thought to have resulted in severe population declines for fisher (Martes pennanti) across the northeastern United States, and by the end of the 1930s only 3 remnant populations remained. Subsequent trapping cessation, extensive reintroduction programs, and natural recolonization have helped fishers to reclaim much of their historical range. The degree to which these processes have impacted genetic structure in this species, however, remains unknown. We used 11 microsatellites from tissue samples (n = 432) of fishers to characterize contemporary population structure in light of historical population structure and thus to determine the relative influence of anthropogenic disturbances and natural landscape features in shaping genetic structure of the contemporary population. Our results indicated that 3 well-differentiated contemporary populations are present that correspond well with what would be expected based on their reported history. A course barrier to dispersal appears in the western portion of the study area associated with several lakes including Lake George and Great Sacandaga Lake. Large-scale reintroduction efforts and natural recolonizations have largely had predictable impacts on population structure. An important exception is the substantial impact of the reintroduction of fishers to Vermont.

  15. Bathymetric barriers promoting genetic structure in the deepwater demersal fish tusk (Brosme brosme).

    PubMed

    Knutsen, Halvor; Jorde, Per Erik; Sannaes, Hanne; Rus Hoelzel, A; Bergstad, Odd Aksel; Stefanni, Sergio; Johansen, Torild; Stenseth, Nils Chr

    2009-08-01

    Population structuring in the North Atlantic deepwater demersal fish tusk (Brosme brosme) was studied with microsatellite DNA analyses. Screening eight samples from across the range of the species for seven loci revealed low but significant genetic heterogeneity (F(ST) = 0.0014). Spatial genetic variability was only weakly related to geographical (Euclidean) distance between study sites or separation of study sites along the path of major ocean currents. Instead, we found a significant effect of habitat, indicated by significant differentiation between relatively closely spaced sites: Rockall, which is surrounded by very deep water (>1000 m), and the Mid-Atlantic Ridge, which is separated from the European slope by a deep ocean basin, were differentiated from relatively homogeneous sites across the Nordic Seas. Limited adult migration across bathymetric barriers in combination with limited intersite exchange of pelagic eggs and larvae due to site-specific circulatory retention or poor survival during drift phases across deep basins may be reducing gene flow. We regard these limitations to gene flow as the most likely mechanisms for the observed population structure in this demersal species. The results underscore the importance of habitat boundaries in marine species.

  16. Estimation of Rubber Material Property by Successive Zooming Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Kwon, Young-Doo; Kwon, Hyun-Wook; Kim, Wha-Jung; Yeo, Sim-Dong

    The industrial use of various kinds of rubber-like (hyper-elastic) material is rapidly increasing and growing in importance, especially in automobiles, trains, and machinery(1). In the past, rubber engineers and designers have predicted the behavior of rubber-like materials using analytic methods for limited problems or approximate methods for general problems. Yet, with the progress of digital computers, finite element methods(2), represented by the Mooney-Rivlin model, are now widely used to analyze hyper-elastic as well as isotropic materials. The conventional method used to evaluate the properties of rubber-like materials is the least square method (LSM), however, this method has a low precision and involves a tedious pre-solving process. Accordingly, this study proposes a simple yet powerful method for estimating the properties of rubber-like materials using a successive zooming genetic algorithm (SZGA). The proposed method results in dependable and precise rubber-like properties for various Mooney-Rivlin models based on simply changing the objective function. To demonstrate the effectiveness of the proposed method, it is compared with Haines & Wilson's method (LSM) and other commercial packages.

  17. Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters

    PubMed Central

    Fontaine, Michaël C; Baird, Stuart JE; Piry, Sylvain; Ray, Nicolas; Tolley, Krystal A; Duke, Sarah; Birkun, Alexei; Ferreira, Marisa; Jauniaux, Thierry; Llavona, Ángela; Öztürk, Bayram; A Öztürk, Ayaka; Ridoux, Vincent; Rogan, Emer; Sequeira, Marina; Siebert, Ursula; Vikingsson, Gísli A; Bouquegneau, Jean-Marie; Michaux, Johan R

    2007-01-01

    Background Understanding the role of seascape in shaping genetic and demographic population structure is highly challenging for marine pelagic species such as cetaceans for which there is generally little evidence of what could effectively restrict their dispersal. In the present work, we applied a combination of recent individual-based landscape genetic approaches to investigate the population genetic structure of a highly mobile extensive range cetacean, the harbour porpoise in the eastern North Atlantic, with regards to oceanographic characteristics that could constrain its dispersal. Results Analyses of 10 microsatellite loci for 752 individuals revealed that most of the sampled range in the eastern North Atlantic behaves as a 'continuous' population that widely extends over thousands of kilometres with significant isolation by distance (IBD). However, strong barriers to gene flow were detected in the south-eastern part of the range. These barriers coincided with profound changes in environmental characteristics and isolated, on a relatively small scale, porpoises from Iberian waters and on a larger scale porpoises from the Black Sea. Conclusion The presence of these barriers to gene flow that coincide with profound changes in oceanographic features, together with the spatial variation in IBD strength, provide for the first time strong evidence that physical processes have a major impact on the demographic and genetic structure of a cetacean. This genetic pattern further suggests habitat-related fragmentation of the porpoise range that is likely to intensify with predicted surface ocean warming. PMID:17651495

  18. Historical habitat barriers prevent ring-like genetic continuity throughout the distribution of threatened Alameda Striped Racers (Coluber lateralis euryxanthus)

    USGS Publications Warehouse

    Richmond, Jonathan Q.; Wood, Dustin A.; Swaim, Karen; Fisher, Robert N.; Vandergast, Amy

    2016-01-01

    We used microsatellites and mtDNA sequences to examine the mixed effects of geophysical, habitat, and contemporary urban barriers on the genetics of threatened Alameda Striped Racers (Coluber lateralis euryxanthus), a species with close ties to declining coastal scrub and chaparral habitat in the eastern San Francisco Bay area of California. We used cluster assignments to characterize population genetic structuring with respect to land management units and approximate Bayesian analysis to rank the ability of five alternative evolutionary hypotheses to explain the inferred structure. Then, we estimated rates of contemporary and historical migration among the major clusters and measured the fit of different historical migration models to better understand the formation of the current population structure. Our results reveal a ring-like pattern of historical connectivity around the Tri-Valley area of the East Bay (i.e., San Ramon, Amador, and Livermore valleys), with clusters largely corresponding to different management units. We found no evidence of continuous gene flow throughout the ring, however, and that the main gap in continuity is centered across the Livermore Valley. Historical migration models support higher rates of gene flow away from the terminal ends of the ring on the north and south sides of the Valley, compared with rates into those areas from western sites that border the interior San Francisco Bay. We attribute the break in ring-like connectivity to the presence of unsuitable habitat within the Livermore Valley that has been reinforced by 20th century urbanization, and the asymmetry in gene flow rates to spatial constraints on movement and east–west environmental gradients influenced by the proximity of the San Francisco Bay.

  19. Geographic barriers and Pleistocene climate change shaped patterns of genetic variation in the Eastern Afromontane biodiversity hotspot

    PubMed Central

    Mairal, Mario; Sanmartín, Isabel; Herrero, Alberto; Pokorny, Lisa; Vargas, Pablo; Aldasoro, Juan J.; Alarcón, Marisa

    2017-01-01

    The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii to explore causal explanations for this pattern. Phylogeographic analyses were undertaken using plastid regions and AFLP fragments. Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genetic diversity, genealogical relationships, structure, gene flow barriers, and the spatiotemporal evolution of populations. A strong phylogeographic structure was found, with two reciprocally monophyletic lineages on each side of the Great Rift System, high genetic exclusivity, and restricted gene flow among mountain ranges. We explain this pattern by topographic and ecological changes driven by geological rifting in Eastern Africa. Subsequent genetic structure is attributed to Pleistocene climatic changes, in which sky-islands acted as long-term refuges and cradles of genetic diversity. Our study highlights the importance of climate change and geographic barriers associated with the African Rift System in shaping population genetic patterns, as well as the need to preserve the high levels of exclusive and critically endangered biodiversity harboured by current patches of the Afromontane forest. PMID:28397796

  20. Geographic barriers and Pleistocene climate change shaped patterns of genetic variation in the Eastern Afromontane biodiversity hotspot.

    PubMed

    Mairal, Mario; Sanmartín, Isabel; Herrero, Alberto; Pokorny, Lisa; Vargas, Pablo; Aldasoro, Juan J; Alarcón, Marisa

    2017-04-11

    The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii to explore causal explanations for this pattern. Phylogeographic analyses were undertaken using plastid regions and AFLP fragments. Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genetic diversity, genealogical relationships, structure, gene flow barriers, and the spatiotemporal evolution of populations. A strong phylogeographic structure was found, with two reciprocally monophyletic lineages on each side of the Great Rift System, high genetic exclusivity, and restricted gene flow among mountain ranges. We explain this pattern by topographic and ecological changes driven by geological rifting in Eastern Africa. Subsequent genetic structure is attributed to Pleistocene climatic changes, in which sky-islands acted as long-term refuges and cradles of genetic diversity. Our study highlights the importance of climate change and geographic barriers associated with the African Rift System in shaping population genetic patterns, as well as the need to preserve the high levels of exclusive and critically endangered biodiversity harboured by current patches of the Afromontane forest.

  1. The Value of Systematic Reviews in Estimating the Cost and Barriers to Translation in Tissue Engineering.

    PubMed

    Cousin, Margot A; Greenberg, Alexandra J; Koep, Tyler H; Angius, Diana; Yaszemski, Michael J; Spinner, Robert J; Windebank, Anthony J

    2016-12-01

    Little quantitative data exist concerning barriers that impede translation from bench to bedside. We systematically reviewed synthetic or biosynthetic polymer nerve scaffolds for peripheral nerve repair to study a defined research area that is beyond the discovery phase and has potential for clinical application. Using electronic and manual search methods, we identified published English language articles, where scaffolds were tested in preclinical animal models. A systematic review of these 416 reports estimated all costs related to the use of animals, surgery, and evaluation methods. The research studied 17 different nerves in eight animal species, with use of 65 evaluation methods at an estimated cost of $61,264,910 for the preclinical studies. A total of 127 surveys were sent to authors, of whom 12 could not be accessed electronically and 45 (39%) responded. Major causes for failure to translate included lack of a commercial partner, insufficient financial resources, a research program not involved in translation, and lack of expertise in regulatory affairs. This review emphasizes the urgent need for standardization of preclinical models and the need to establish better collaboration between laboratory investigators, clinicians, and the companies involved in commercialization. It identifies important areas for education of future investigators in the process of translation from discovery to improved health such as those funded by the National Institutes of Health Clinical and Translational Science Awards.

  2. Nonstarter lactobacilli isolated from soft and semihard Argentinean cheeses: genetic characterization and resistance to biological barriers.

    PubMed

    Ugarte, Mariana Bude; Guglielmotti, Daniela; Giraffa, Giorgio; Reinheimer, Jorge; Hynes, Erica

    2006-12-01

    Nonstarter lactic acid bacteria isolated from Argentinean cheeses were identified and characterized by focusing on their resistance to biological barriers, along with other physiological features of potential interest, in the search for future probiotic organisms. Lactobacilli were enumerated and isolated from semihard and soft cheeses made with multistrain Streptococcus thermophilus starters. Lactobacilli counts in 1-week-old cheeses were between 10(5) and 10(7) CFU/g and then reached 10(7) CFU/ g in all 1-month samples, while streptococci were always above 10(9) CFU/g. A total number of 22 lactobacilli isolates were retained, identified, and characterized by in vitro tests. Species identity was determined by carbohydrate metabolism and species-specific PCR assays. Genetic diversity was explored by random amplified polymorphic DNA (RAPD) PCR analysis. The Lactobacillus strains were assigned to the species L. casei, L. plantarum, L. rhamnosus, L. curvatus, L. fermentum, and L. perolens. All the strains studied tolerated 25 ppm of lysozyme, and most of them showed resistance to 0.3% bile. After incubation in gastric solution (pH 2.0), counts decreased by several log units, ranging from 3.2 to 7.0. The strains were able to grow in the presence of bile salts, but only three isolates were capable of deconjugation. The nonstarter lactobacilli that were assayed fermented the prebiotic substrates (especially lactulose and inulin). Some strains showed high cell hydrophobicity and beta-galactosidase activity, as well as inhibitory activity against pathogenic bacteria. It was concluded that most of the lactobacilli isolated in this study demonstrated resistance to biological barriers and physiological characteristics compatible with probiotic properties, which make them suitable for further research in in vivo studies aimed at identifying new probiotic organisms.

  3. The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations

    PubMed Central

    Thomas, Stuart C

    2005-01-01

    Molecular marker data collected from natural populations allows information on genetic relationships to be established without referencing an exact pedigree. Numerous methods have been developed to exploit the marker data. These fall into two main categories: method of moment estimators and likelihood estimators. Method of moment estimators are essentially unbiased, but utilise weighting schemes that are only optimal if the analysed pair is unrelated. Thus, they differ in their efficiency at estimating parameters for different relationship categories. Likelihood estimators show smaller mean squared errors but are much more biased. Both types of estimator have been used in variance component analysis to estimate heritability. All marker-based heritability estimators require that adequate levels of the true relationship be present in the population of interest and that adequate amounts of informative marker data are available. I review the different approaches to relationship estimation, with particular attention to optimizing the use of this relationship information in subsequent variance component estimation. PMID:16048788

  4. Bridging the gaps between non-invasive genetic sampling and population parameter estimation

    Treesearch

    Francesca Marucco; Luigi Boitani; Daniel H. Pletscher; Michael K. Schwartz

    2011-01-01

    Reliable estimates of population parameters are necessary for effective management and conservation actions. The use of genetic data for capture­recapture (CR) analyses has become an important tool to estimate population parameters for elusive species. Strong emphasis has been placed on the genetic analysis of non-invasive samples, or on the CR analysis; however,...

  5. Landscape-scale evaluation of genetic structure among barrier-isolated populations of coastal cutthroat trout, Oncorhynchus clarkii clarkii

    USGS Publications Warehouse

    Guy, T.J.; Gresswell, R.E.; Banks, M.A.

    2008-01-01

    Relationships among landscape structure, stochastic disturbance, and genetic diversity were assessed by examining interactions between watershed-scale environmental factors and genetic diversity of coastal cutthroat trout (Oncorhynchus clarkii clarkii) in 27 barrier-isolated watersheds from western Oregon, USA. Headwater populations of coastal cutthroat trout were genetically differentiated (mean FST = 0.33) using data from seven microsatellite loci (2232 individuals), but intrapopulation microsatellite genetic diversity (mean number of alleles per locus = 5, mean He = 0.60) was only moderate. Genetic diversity of coastal cutthroat trout was greater (P = 0.02) in the Coast Range ecoregion (mean alleles = 47) than in the Cascades ecoregion (mean alleles = 30), and differences coincided with indices of regional within-watershed complexity and connectivity. Furthermore, regional patterns of diversity evident from isolation-by-distance plots suggested that retention of within-population genetic diversity in the Coast Range ecoregion is higher than that in the Cascades, where genetic drift is the dominant factor influencing genetic patterns. Thus, it appears that physical landscape features have influenced genetic patterns in these populations isolated from short-term immigration. ?? 2008 NRC.

  6. Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

    PubMed Central

    Bérénos, Camillo; Ellis, Philip A; Pilkington, Jill G; Pemberton, Josephine M

    2014-01-01

    The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (ii) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (iii) whole-genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics

  7. Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches.

    PubMed

    Bérénos, Camillo; Ellis, Philip A; Pilkington, Jill G; Pemberton, Josephine M

    2014-07-01

    The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (ii) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (iii) whole-genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics

  8. Temperature Estimation and Al Content Prediction Focusing on Microstructural Change in a Thermal Barrier Coating

    NASA Astrophysics Data System (ADS)

    Okada, Mitsutoshi; Hisamatsu, Tohru; Kitamura, Takayuki

    2009-03-01

    A superalloy with a thermal barrier coating (TBC) simulating a gas turbine blade is exposed to a high-temperature environment to develop a method for predicting the local temperature and Al content in a bond coat (BC). The Al content decreases with an increase in the test time due to the Al transport induced by the oxidation of the BC and the interdiffusion between the BC and the substrate. This brings about Al-decreased layer (ADL) at the boundary between the BC and the top coat. The thickness of the ADL increases in proportion to the square root of the test time, and the temperature dependence of the growth rate shows an Arrhenius-type behavior. Based on this relation, the local temperature of an in-service blade can be estimated by measuring the ADL thickness when the operation time is known. The Al content decreases in proportion to the ADL thickness. The prediction method of the Al content based on the relation is also presented.

  9. An approximate multitrait model for genetic evaluation in dairy cattle with a robust estimation of genetic trends.

    PubMed

    Lassen, Jan; Sørensen, Morten Kargo; Madsen, Per; Ducrocq, Vincent

    2007-01-01

    In a stochastic simulation study of a dairy cattle population three multitrait models for estimation of genetic parameters and prediction of breeding values were compared. The first model was an approximate multitrait model using a two-step procedure. The first step was a single trait model for all traits. The solutions for fixed effects from these analyses were subtracted from the phenotypes. A multitrait model only containing an overall mean, an additive genetic and a residual term was applied on these preadjusted data. The second model was similar to the first model, but the multitrait model also contained a year effect. The third model was a full multitrait model. Genetic trends for total merit and for the individual traits in the breeding goal were compared for the three scenarios to rank the models. The full multitrait model gave the highest genetic response, but was not significantly better than the approximate multitrait model including a year effect. The inclusion of a year effect into the second step of the approximate multitrait model significantly improved the genetic trend for total merit. In this study, estimation of genetic parameters for breeding value estimation using models corresponding to the ones used for prediction of breeding values increased the accuracy on the breeding values and thereby the genetic progress.

  10. Could refuge theory and rivers acting as barriers explain the genetic variability distribution in the Atlantic Forest?

    PubMed

    Cazé, Ana Luiza R; Mäder, Geraldo; Nunes, Teonildes S; Queiroz, Luciano P; de Oliveira, Guilherme; Diniz-Filho, José Alexandre F; Bonatto, Sandro L; Freitas, Loreta B

    2016-08-01

    The Atlantic Forest is one of the most species-rich ecoregions in the world. The historical origins of this richness and the evolutionary processes that produced diversification and promoted speciation in this ecosystem remain poorly understood. In this context, focusing on Passiflora contracta, an endemic species from the Atlantic Forest distributed exclusively at sea level along forest edges, this study aimed to characterize the patterns of genetic variability and explore two hypotheses that attempt to explain the possible causes of the genetic diversity in this region: the refuge and riverine barrier theories. We employed Bayesian methods combined with niche modeling to identify genetically homogeneous groups, to determine the diversification age, and identify long-term climate stability areas to species survival. The analyses were performed using molecular markers from nuclear and plastid genomes, with samples collected throughout the entire geographic distribution of the species, and comparisons with congeners species. The results indicated that populations were genetically structured and provided evidence of demographic stability. The molecular markers indicated the existence of a clear structure and the presence of five homogeneous groups. Interestingly, the separation of the groups coincides with the geographical locations of local rivers, corroborating the hypothesis of rivers acting as barriers to gene flow in this species. The highest levels of genetic diversity and the areas identified as having long-term climate stability were found in the same region reported for other species as a possible refuge area during the climatic changes of the Quaternary. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. A comparison of binary and continuous genetic algorithm in parameter estimation of a logistic growth model

    NASA Astrophysics Data System (ADS)

    Windarto, Indratno, S. W.; Nuraini, N.; Soewono, E.

    2014-02-01

    Genetic algorithm is an optimization method based on the principles of genetics and natural selection in life organisms. The algorithm begins by defining the optimization variables, defining the cost function (in a minimization problem) or the fitness function (in a maximization problem) and selecting genetic algorithm parameters. The main procedures in genetic algorithm are generating initial population, selecting some chromosomes (individual) as parent's individual, mating, and mutation. In this paper, binary and continuous genetic algorithms were implemented to estimate growth rate and carrying capacity parameter from poultry data cited from literature. For simplicity, all genetic algorithm parameters (selection rate and mutation rate) are set to be constant along implementation of the algorithm. It was found that by selecting suitable mutation rate, both algorithms can estimate these parameters well. Suitable range for mutation rate in continuous genetic algorithm is wider than the binary one.

  12. Genetics of postzygotic isolation in Eucalyptus: whole-genome analysis of barriers to introgression in a wide interspecific cross of Eucalyptus grandis and E. globulus.

    PubMed Central

    Myburg, Alexander A; Vogl, Claus; Griffin, A Rod; Sederoff, Ronald R; Whetten, Ross W

    2004-01-01

    The genetic architecture of hybrid fitness characters can provide valuable insights into the nature and evolution of postzygotic reproductive barriers in diverged species. We determined the genome-wide distribution of barriers to introgression in an F(1) hybrid of two Eucalyptus tree species, Eucalyptus grandis (W. Hill ex Maiden.) and E. globulus (Labill.). Two interspecific backcross families (N = 186) were used to construct comparative, single-tree, genetic linkage maps of an F(1) hybrid individual and two backcross parents. A total of 1354 testcross AFLP marker loci were evaluated in the three parental maps and a substantial proportion (27.7% average) exhibited transmission ratio distortion (alpha = 0.05). The distorted markers were located in distinct regions of the parental maps and marker alleles within each region were all biased toward either of the two parental species. We used a Bayesian approach to estimate the position and effect of transmission ratio distorting loci (TRDLs) in the distorted regions of each parental linkage map. The relative viability of TRDL alleles ranged from 0.20 to 0.72. Contrary to expectation, heterospecific (donor) alleles of TRDLs were favored as often as recurrent alleles in both backcrosses, suggesting that positive and negative heterospecific interactions affect introgression rates in this wide interspecific pedigree. PMID:15082559

  13. An implementation of continuous genetic algorithm in parameter estimation of predator-prey model

    NASA Astrophysics Data System (ADS)

    Windarto

    2016-03-01

    Genetic algorithm is an optimization method based on the principles of genetics and natural selection in life organisms. The main components of this algorithm are chromosomes population (individuals population), parent selection, crossover to produce new offspring, and random mutation. In this paper, continuous genetic algorithm was implemented to estimate parameters in a predator-prey model of Lotka-Volterra type. For simplicity, all genetic algorithm parameters (selection rate and mutation rate) are set to be constant along implementation of the algorithm. It was found that by selecting suitable mutation rate, the algorithms can estimate these parameters well.

  14. Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans

    PubMed Central

    Rogers, Rebekah L.

    2015-01-01

    Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes. I identify one case of new-gene creation through transposition from the Y chromosome to chromosome 10 that combines the 5′-end of the testis-specific gene Fank1 with previously untranscribed sequence. This new transcript experienced copy number expansion in archaic genomes, indicating rapid genomic change. Among rearrangements identified in Neanderthals, 13% are transposition of selfish genetic elements, whereas 32% appear to be ectopic exchange between repeats. In Denisovan, the pattern is similar but numbers are significantly higher with 18% of rearrangements reflecting transposition and 40% ectopic exchange between distantly related repeats. There is an excess of divergent rearrangements relative to polymorphism in Denisovan, which might result from nonuniform rates of mutation, possibly reflecting a burst of transposable element activity in the lineage that led to Denisovan. Finally, loci containing genome structure changes show diminished rates of introgression from Neanderthals into modern humans, consistent with the hypothesis that rearrangements serve as barriers to gene flow during hybridization. Together, these results suggest that this previously unidentified source of genomic variation has important biological consequences in human evolution. PMID:26399483

  15. The Influence of Natural Barriers in Shaping the Genetic Structure of Maharashtra Populations

    PubMed Central

    Crivellaro, Federica; Tamang, Rakesh; Upadhyay, Shashank; Sharma, Varun Kumar; Reddy, Alla G.; Walimbe, S. R.; Chaubey, Gyaneshwer; Kivisild, Toomas; Singh, Lalji

    2010-01-01

    Background The geographical position of Maharashtra state makes it rather essential to study the dispersal of modern humans in South Asia. Several hypotheses have been proposed to explain the cultural, linguistic and geographical affinity of the populations living in Maharashtra state with other South Asian populations. The genetic origin of populations living in this state is poorly understood and hitherto been described at low molecular resolution level. Methodology/Principal Findings To address this issue, we have analyzed the mitochondrial DNA (mtDNA) of 185 individuals and NRY (non-recombining region of Y chromosome) of 98 individuals belonging to two major tribal populations of Maharashtra, and compared their molecular variations with that of 54 South Asian contemporary populations of adjacent states. Inter and intra population comparisons reveal that the maternal gene pool of Maharashtra state populations is composed of mainly South Asian haplogroups with traces of east and west Eurasian haplogroups, while the paternal haplogroups comprise the South Asian as well as signature of near eastern specific haplogroup J2a. Conclusions/Significance Our analysis suggests that Indian populations, including Maharashtra state, are largely derived from Paleolithic ancient settlers; however, a more recent (∼10 Ky older) detectable paternal gene flow from west Asia is well reflected in the present study. These findings reveal movement of populations to Maharashtra through the western coast rather than mainland where Western Ghats-Vindhya Mountains and Narmada-Tapti rivers might have acted as a natural barrier. Comparing the Maharastrian populations with other South Asian populations reveals that they have a closer affinity with the South Indian than with the Central Indian populations. PMID:21187967

  16. Mechanisms and genetic control of interspecific crossing barriers in Lycopersicon. Second yearly progress report

    SciTech Connect

    Mutschler, M.A.; McCormick, S.

    1993-03-27

    This study employs Lycopersicon esculentum and L. pennellii as model systems to study the interspecific reproductive barriers unilateral incongruity (UI), hybrid breakdown and interspecific aberrant ratio syndrome (IARS).

  17. Genetic parameter estimation for pre- and post-weaning traits in Brahman cattle in Brazil.

    PubMed

    Vargas, Giovana; Buzanskas, Marcos Eli; Guidolin, Diego Gomes Freire; Grossi, Daniela do Amaral; Bonifácio, Alexandre da Silva; Lôbo, Raysildo Barbosa; da Fonseca, Ricardo; Oliveira, João Ademir de; Munari, Danísio Prado

    2014-10-01

    Beef cattle producers in Brazil use body weight traits as breeding program selection criteria due to their great economic importance. The objectives of this study were to evaluate different animal models, estimate genetic parameters, and define the most fitting model for Brahman cattle body weight standardized at 120 (BW120), 210 (BW210), 365 (BW365), 450 (BW450), and 550 (BW550) days of age. To estimate genetic parameters, single-, two-, and multi-trait analyses were performed using the animal model. The likelihood ratio test was verified between all models. For BW120 and BW210, additive direct genetic, maternal genetic, maternal permanent environment, and residual effects were considered, while for BW365 and BW450, additive direct genetic, maternal genetic, and residual effects were considered. Finally, for BW550, additive direct genetic and residual effects were considered. Estimates of direct heritability for BW120 were similar in all analyses; however, for the other traits, multi-trait analysis resulted in higher estimates. The maternal heritability and proportion of maternal permanent environmental variance to total variance were minimal in multi-trait analyses. Genetic, environmental, and phenotypic correlations were of high magnitude between all traits. Multi-trait analyses would aid in the parameter estimation for body weight at older ages because they are usually affected by a lower number of animals with phenotypic information due to culling and mortality.

  18. Role of recent and old riverine barriers in fine-scale population genetic structure of Geoffroy's tamarin (Saguinus geoffroyi) in the Panama Canal watershed

    PubMed Central

    Díaz-Muñoz, Samuel L

    2012-01-01

    The role of physical barriers in promoting population divergence and genetic structuring is well known. While it is well established that animals can show genetic structuring at small spatial scales, less well-resolved is how the timing of the appearance of barriers affects population structure. This study uses the Panama Canal watershed as a test of the effects of old and recent riverine barriers in creating population structure in Saguinus geoffroyi, a small cooperatively breeding Neotropical primate. Mitochondrial sequences and microsatellite genotypes from three sampling localities revealed genetic structure across the Chagres River and the Panama Canal, suggesting that both waterways act as barriers to gene flow. F-statistics and exact tests of population differentiation suggest population structure on either side of both riverine barriers. Genetic differentiation across the Canal, however, was less than observed across the Chagres. Accordingly, Bayesian clustering algorithms detected between two and three populations, with localities across the older Chagres River always assigned as distinct populations. While conclusions represent a preliminary assessment of genetic structure of S. geoffroyi, this study adds to the evidence indicating that riverine barriers create genetic structure across a wide variety of taxa in the Panama Canal watershed and highlights the potential of this study area for discerning modern from historical influences on observed patterns of population genetic structure. PMID:22423325

  19. Role of recent and old riverine barriers in fine-scale population genetic structure of Geoffroy's tamarin (Saguinus geoffroyi) in the Panama Canal watershed.

    PubMed

    Díaz-Muñoz, Samuel L

    2012-02-01

    The role of physical barriers in promoting population divergence and genetic structuring is well known. While it is well established that animals can show genetic structuring at small spatial scales, less well-resolved is how the timing of the appearance of barriers affects population structure. This study uses the Panama Canal watershed as a test of the effects of old and recent riverine barriers in creating population structure in Saguinus geoffroyi, a small cooperatively breeding Neotropical primate. Mitochondrial sequences and microsatellite genotypes from three sampling localities revealed genetic structure across the Chagres River and the Panama Canal, suggesting that both waterways act as barriers to gene flow. F-statistics and exact tests of population differentiation suggest population structure on either side of both riverine barriers. Genetic differentiation across the Canal, however, was less than observed across the Chagres. Accordingly, Bayesian clustering algorithms detected between two and three populations, with localities across the older Chagres River always assigned as distinct populations. While conclusions represent a preliminary assessment of genetic structure of S. geoffroyi, this study adds to the evidence indicating that riverine barriers create genetic structure across a wide variety of taxa in the Panama Canal watershed and highlights the potential of this study area for discerning modern from historical influences on observed patterns of population genetic structure.

  20. Genetic study of skin thickness and its association with postweaning growth in Nellore cattle: estimation of the genetic parameters.

    PubMed

    Maiorano, A M; Oliveira, M C S; Cyrillo, J N S G; Albuquerque, L G; Curi, R A; Silva, J A Iiv

    2016-02-19

    The objective of the present study was to estimate genetic parameters for skin thickness (ST) and postweaning weight gain (PWG550) in Nellore cattle. Records were obtained from 152,392 Nellore animals born between 2001 and 2011. ST was measured in the posterior region of the animal's scapula with a millimeter caliper. The animals were assigned to different contemporary groups, formed on the basis of farm, year, sex, feeding regimen at weaning, date of weaning, feeding regimen at 450 days of age, and date of weighing at 450 days of age. The genetic parameters were estimated by Bayesian analysis using the GIBBS1F90 program. The mean ST and PWG550 observed were 7.71 ± 2.04 mm and 115.95 ± 36.17 kg, respectively. The posterior mean estimates of heritability (h2) were 0.12 ± 0.02 and 0.29 ± 0.02 for ST and PWG550, respectively. The posterior mean estimates of the phenotypic, genetic, and environmental correlations between the traits were 0.16 ± 0.0, 0.17 ± 0.02, and 0.17 ± 0.09, respectively. The traits ST and PWG550 showed sufficient additive genetic variance to be used as selection criteria in breeding programs. The low genetic correlation obtained indicates that genes favoring the expression of one trait may not influence the other. Consequently, a selection favoring ST would be less efficient in increasing PWG550.

  1. Estimation of genetic diversity using SSR markers in sunflower

    USDA-ARS?s Scientific Manuscript database

    Sunflower is a major oilseed crop in central Asia, but little is known of the molecular diversity among collections of sunflower from Pakistan region. This paper described inherent genetic relationships among sunflower collections using Simple Sequence Repeat molecular markers. Results should help...

  2. Genetic structure and rabies spread potential in raccoons: the role of landscape barriers and sex-biased dispersal

    PubMed Central

    Côté, Héloïse; Garant, Dany; Robert, Karine; Mainguy, Julien; Pelletier, Fanie

    2012-01-01

    Identifying natural barriers to movements of hosts associated with infectious diseases is essential for developing effective control strategies. Raccoon rabies variant (RRV) is a zoonosis of concern for humans because its main vector, the raccoon (Procyon lotor), is found near residential areas. In Québec, Canada, all cases of RRV found in raccoons since 2006 were detected on the eastern side of the Richelieu River, suggesting that this river acts as a barrier to gene flow and thus the potential for RRV to spread. The objectives of this study were to characterize the genetic structure of raccoon populations and assess the effect of the Richelieu River on the population structure in southern Québec, Canada. We also evaluated whether RRV spread potential differed between sex and at a larger spatial scale. Our analyses revealed a weak signal of genetic differentiation among individuals located on each side of the Richelieu River. At a larger spatial scale, genetic structuring was weak. Our results suggest that rivers might not always efficiently restrain raccoon movements and spread of RRV. We suggest that the difference in genetic structure found between sexes can be partly explained by male movements during the breeding season in winter, when ice bridges allow passage over most rivers in Québec. PMID:25568059

  3. Estimates of genetic parameters and genetic trends for reproductive traits and weaning weight in Tabapuã cattle.

    PubMed

    Bernardes, P A; Grossi, D A; Savegnago, R P; Buzanskas, M E; Urbinati, I; Bezerra, L A F; Lôbo, R B; Munari, D P

    2015-11-01

    The Tabapuã breed is a beef cattle Brazilian breed known for its sexual precocity and desirable characteristics for tropical conditions. However, this is a newly formed breed and few studies have been conducted regarding genetic parameters and genetic trends for its reproductive traits. The objective of the present study was to estimate the genetic parameters, genetic trends, and relative selection efficiency for weaning weight adjusted to 210 d of age (W210), age at first calving (AFC), average calving interval (ACI), first calving interval (CI1), and accumulated productivity (ACP) among Tabapuã beef cattle. Pedigree data on 15,241 Tabapuã animals born between 1958 and 2011 and phenotype records from 7,340 cows born between 1970 and 2011 were supplied by the National Association of Breeders and Researchers (Associação Nacional de Criadores e Pesquisadores). Analysis through the least squares method assisted in defining the fixed effects that were considered within the models. The estimates for the genetic parameters were obtained through the REML, using a multitrait animal model. The likelihood ratio test applied for W210 was significant ( < 0.05) for the inclusion of maternal additive genetic and permanent environmental effects in the model. Genetic trends were calculated through linear regression of the EBV of the animals, according to the year of birth. The heritability estimates obtained ranged from 0.04 ± 0.03 for CI1 to 0.25 ± 0.05 for W210. The genetic correlations ranged from 0.004 ± 0.19 for W210-AFC and 0.93 ± 0.12 for ACI-CI1. The genetic trend was significant ( < 0.05) and favorable for CI1 and the maternal genetic effect of W210 and was significant ( < 0.05) and unfavorable for AFC, ACI, and ACP. The ACP could be used in the selection index to assist the breeding goal of improved productive and reproductive performance. The genetic trends indicated small and unfavorable genetic changes for AFC, ACI, and ACP in light of the recent

  4. Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurospora species indicates evolution via natural selection.

    PubMed

    Turner, Elizabeth; Jacobson, David J; Taylor, John W

    2011-08-01

    A role for natural selection in reinforcing premating barriers is recognized, but selection for reinforcement of postmating barriers remains controversial. Organisms lacking evolvable premating barriers can theoretically reinforce postmating isolation, but only under restrictive conditions: parental investment in hybrid progeny must inhibit subsequent reproduction, and selected postmating barriers must restore parents' capacity to reproduce successfully. We show that reinforced postmating isolation markedly increases maternal fitness in the fungus Neurospora crassa, and we detect the evolutionary genetic signature of natural selection by quantitative trait locus (QTL) analysis of the reinforced barrier. Hybrid progeny of N. crassa and N. intermedia are highly inviable. Fertilization by local N. intermedia results in early abortion of hybrid fruitbodies, and we show that abortion is adaptive because only aborted maternal colonies remain fully receptive to future reproduction. In the first QTL analysis of postmating reinforcement in microbial eukaryotes, we identify 11 loci for abortive hybrid fruitbody development, including three major QTLs that together explain 30% of trait variance. One of the major QTLs and six QTLs of lesser effect are found on the mating-type determining chromosome of Neurospora. Several reinforcement QTLs are flanked by genetic markers showing either segregation distortion or non-random associations with alleles at other loci in a cross between N. crassa of different clades, suggesting that the loci also are associated with local effects on same-species reproduction. Statistical analysis of the allelic effects distribution for abortive hybrid fruitbody development indicates its evolution occurred under positive selection. Our results strongly support a role for natural selection in the evolution of reinforced postmating isolation in N. crassa.

  5. Estimating the contribution of genetic variants to difference in incidence of disease between population groups.

    PubMed

    Moonesinghe, Ramal; Ioannidis, John P A; Flanders, W Dana; Yang, Quanhe; Truman, Benedict I; Khoury, Muin J

    2012-08-01

    Genome-wide association studies have identified multiple genetic susceptibility variants to several complex human diseases. However, risk-genotype frequency at loci showing robust associations might differ substantially among different populations. In this paper, we present methods to assess the contribution of genetic variants to the difference in the incidence of disease between different population groups for different scenarios. We derive expressions for the contribution of a single genetic variant, multiple genetic variants, and the contribution of the joint effect of a genetic variant and an environmental factor to the difference in the incidence of disease. The contribution of genetic variants to the difference in incidence increases with increasing difference in risk-genotype frequency, but declines with increasing difference in incidence between the two populations. The contribution of genetic variants also increases with increasing relative risk and the contribution of joint effect of genetic and environmental factors increases with increasing relative risk of the gene-environmental interaction. The contribution of genetic variants to the difference in incidence between two populations can be expressed as a function of the population attributable risks of the genetic variants in the two populations. The contribution of a group of genetic variants to the disparity in incidence of disease could change considerably by adding one more genetic variant to the group. Any estimate of genetic contribution to the disparity in incidence of disease between two populations at this stage seems to be an elusive goal.

  6. Estimating the contribution of genetic variants to difference in incidence of disease between population groups

    PubMed Central

    Moonesinghe, Ramal; Ioannidis, John PA; Flanders, W Dana; Yang, Quanhe; Truman, Benedict I; Khoury, Muin J

    2012-01-01

    Genome-wide association studies have identified multiple genetic susceptibility variants to several complex human diseases. However, risk-genotype frequency at loci showing robust associations might differ substantially among different populations. In this paper, we present methods to assess the contribution of genetic variants to the difference in the incidence of disease between different population groups for different scenarios. We derive expressions for the contribution of a single genetic variant, multiple genetic variants, and the contribution of the joint effect of a genetic variant and an environmental factor to the difference in the incidence of disease. The contribution of genetic variants to the difference in incidence increases with increasing difference in risk-genotype frequency, but declines with increasing difference in incidence between the two populations. The contribution of genetic variants also increases with increasing relative risk and the contribution of joint effect of genetic and environmental factors increases with increasing relative risk of the gene–environmental interaction. The contribution of genetic variants to the difference in incidence between two populations can be expressed as a function of the population attributable risks of the genetic variants in the two populations. The contribution of a group of genetic variants to the disparity in incidence of disease could change considerably by adding one more genetic variant to the group. Any estimate of genetic contribution to the disparity in incidence of disease between two populations at this stage seems to be an elusive goal. PMID:22333905

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

    SciTech Connect

    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.

  8. Genetic estimates of contemporary effective population size in an endangered butterfly indicate a possible role for genetic compensation.

    PubMed

    Saarinen, Emily V; Austin, James D; Daniels, Jaret C

    2010-01-01

    The effective population size (N e ) is a critical evolutionary and conservation parameter that can indicate the adaptive potential of populations. Robust estimates of N e of endangered taxa have been previously hampered by estimators that are sensitive to sample size. We estimated N e on two remaining populations of the endangered Miami blue butterfly, a formerly widespread taxon in Florida. Our goal was to determine the consistency of various temporal and point estimators on inferring N e and to determine the utility of this information for understanding the role of genetic stochasticity. We found that recently developed 'unbiased estimators' generally performed better than some older methods in that the former had more realistic N e estimates and were more consistent with what is known about adult population size. Overall, N e /N ratios based on census point counts were high. We suggest that this pattern may reflect genetic compensation caused by reduced reproductive variance due to breeding population size not being limited by resources. Assuming N e and N are not heavily biased, it appears that the lack of gene flow between distant populations may be a greater genetic threat in the short term than the loss of heterozygosity due to inbreeding.

  9. Data depth, data completeness, and their influence on quantitative genetic estimation in two contrasting bird populations.

    PubMed

    Quinn, J L; Charmantier, A; Garant, D; Sheldon, B C

    2006-05-01

    Evolutionary biologists increasingly use pedigree-based quantitative genetic methods to address questions about the evolutionary dynamics of traits in wild populations. In many cases, phenotypic data may have been collected only for recent parts of the study. How does this influence the performance of the models used to analyse these data? Here we explore how data depth (number of years) and completeness (number of observations) influence estimates of genetic variance and covariance within the context of an existing pedigree. Using long-term data from the great tit Parus major and the mute swan Cygnus olor, species with different life-histories, we examined the effect of manipulating the amount of data included on quantitative genetic parameter estimates. Manipulating data depth and completeness had little influence on estimated genetic variances, heritabilities, or genetic correlations, but (as expected) did influence confidence in these estimates. Estimated breeding values in the great tit were not influenced by data depth but were in the mute swan, probably because of differences in pedigree structure. Our analyses suggest the 'rule of thumb' that data from 3 years and a minimum of 100 individuals per year are needed to estimate genetic parameters with acceptable confidence, and that using pedigree data is worthwhile, even if phenotypes are only available toward the tips of the pedigree.

  10. Genetic diversity and population differentiation in the cockle Cerastoderma edule estimated by microsatellite markers

    NASA Astrophysics Data System (ADS)

    Martínez, L.; Méndez, J.; Insua, A.; Arias-Pérez, A.; Freire, R.

    2013-03-01

    The edible cockle Cerastoderma edule is a marine bivalve commercially fished in several European countries that have lately suffered a significant decrease in production. Despite its commercial importance, genetic studies in this species are scarce. In this work, genetic diversity and population differentiation of C. edule has been assessed using 11 microsatellite markers in eight locations from the European Atlantic coast. All localities showed similar observed and expected heterozygosity values, but displayed differences in allelic richness, with lowest values obtained for localities situated farther north. Global Fst value revealed the existence of significant genetic structure; all but one locality from the Iberian Peninsula were genetically homogeneous, while more remote localities from France, The Netherlands, and Scotland were significantly different from all other localities. A combined effect of isolation by distance and the existence of barriers that limit gene flow may explain the differentiation observed.

  11. A Genetic Algorithm Approach to Nonlinear Least Squares Estimation

    ERIC Educational Resources Information Center

    Olinsky, Alan D.; Quinn, John T.; Mangiameli, Paul M.; Chen, Shaw K.

    2004-01-01

    A common type of problem encountered in mathematics is optimizing nonlinear functions. Many popular algorithms that are currently available for finding nonlinear least squares estimators, a special class of nonlinear problems, are sometimes inadequate. They might not converge to an optimal value, or if they do, it could be to a local rather than…

  12. A Genetic Algorithm Approach to Nonlinear Least Squares Estimation

    ERIC Educational Resources Information Center

    Olinsky, Alan D.; Quinn, John T.; Mangiameli, Paul M.; Chen, Shaw K.

    2004-01-01

    A common type of problem encountered in mathematics is optimizing nonlinear functions. Many popular algorithms that are currently available for finding nonlinear least squares estimators, a special class of nonlinear problems, are sometimes inadequate. They might not converge to an optimal value, or if they do, it could be to a local rather than…

  13. An alternative covariance estimator to investigate genetic heterogeneity in populations

    USDA-ARS?s Scientific Manuscript database

    Genomic predictions and GWAS have used mixed models for identification of associations and trait predictions. In both cases, the covariance between individuals for performance is estimated using molecular markers. Mixed model properties indicate that the use of the data for prediction is optimal if ...

  14. Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers

    PubMed Central

    2010-01-01

    Genetic diversity of 60 Hevea genotypes, consisting of Asiatic, Amazonian, African and IAC clones, and pertaining to the genetic breeding program of the Agronomic Institute (IAC), Brazil, was estimated. Analyses were based on phenotypic multivariate parameters and microsatellites. Five agronomic descriptors were employed in multivariate procedures, such as Standard Euclidian Distance, Tocher clustering and principal component analysis. Genetic variability among the genotypes was estimated with 68 selected polymorphic SSRs, by way of Modified Rogers Genetic Distance and UPGMA clustering. Structure software in a Bayesian approach was used in discriminating among groups. Genetic diversity was estimated through Nei's statistics. The genotypes were clustered into 12 groups according to the Tocher method, while the molecular analysis identified six groups. In the phenotypic and microsatellite analyses, the Amazonian and IAC genotypes were distributed in several groups, whereas the Asiatic were in only a few. Observed heterozygosity ranged from 0.05 to 0.96. Both high total diversity (HT' = 0.58) and high gene differentiation (G st' = 0.61) were observed, and indicated high genetic variation among the 60 genotypes, which may be useful for breeding programs. The analyzed agronomic parameters and SSRs markers were effective in assessing genetic diversity among Hevea genotypes, besides proving to be useful for characterizing genetic variability. PMID:21637487

  15. Genetic estimates of contemporary effective population size in an endangered butterfly indicate a possible role for genetic compensation

    PubMed Central

    Saarinen, Emily V; Austin, James D; Daniels, Jaret C

    2010-01-01

    The effective population size (Ne) is a critical evolutionary and conservation parameter that can indicate the adaptive potential of populations. Robust estimates of Ne of endangered taxa have been previously hampered by estimators that are sensitive to sample size. We estimated Ne on two remaining populations of the endangered Miami blue butterfly, a formerly widespread taxon in Florida. Our goal was to determine the consistency of various temporal and point estimators on inferring Ne and to determine the utility of this information for understanding the role of genetic stochasticity. We found that recently developed ‘unbiased estimators’ generally performed better than some older methods in that the former had more realistic Ne estimates and were more consistent with what is known about adult population size. Overall, Ne/N ratios based on census point counts were high. We suggest that this pattern may reflect genetic compensation caused by reduced reproductive variance due to breeding population size not being limited by resources. Assuming Ne and N are not heavily biased, it appears that the lack of gene flow between distant populations may be a greater genetic threat in the short term than the loss of heterozygosity due to inbreeding. PMID:25567901

  16. Estimating black bear population density and genetic diversity at Tensas River, Louisiana using microsatellite DNA markers

    USGS Publications Warehouse

    Boersen, Mark R.; Clark, Joseph D.; King, Tim L.

    2003-01-01

    The Recovery Plan for the federally threatened Louisiana black bear (Ursus americanus luteolus) mandates that remnant populations be estimated and monitored. In 1999 we obtained genetic material with barbed-wire hair traps to estimate bear population size and genetic diversity at the 329-km2 Tensas River Tract, Louisiana. We constructed and monitored 122 hair traps, which produced 1,939 hair samples. Of those, we randomly selected 116 subsamples for genetic analysis and used up to 12 microsatellite DNA markers to obtain multilocus genotypes for 58 individuals. We used Program CAPTURE to compute estimates of population size using multiple mark-recapture models. The area of study was almost entirely circumscribed by agricultural land, thus the population was geographically closed. Also, study-area boundaries were biologically discreet, enabling us to accurately estimate population density. Using model Chao Mh to account for possible effects of individual heterogeneity in capture probabilities, we estimated the population size to be 119 (SE=29.4) bears, or 0.36 bears/km2. We were forced to examine a substantial number of loci to differentiate between some individuals because of low genetic variation. Despite the probable introduction of genes from Minnesota bears in the 1960s, the isolated population at Tensas exhibited characteristics consistent with inbreeding and genetic drift. Consequently, the effective population size at Tensas may be as few as 32, which warrants continued monitoring or possibly genetic augmentation.

  17. Computational approaches and software tools for genetic linkage map estimation in plants.

    PubMed

    Cheema, Jitender; Dicks, Jo

    2009-11-01

    Genetic maps are an important component within the plant biologist's toolkit, underpinning crop plant improvement programs. The estimation of plant genetic maps is a conceptually simple yet computationally complex problem, growing ever more so with the development of inexpensive, high-throughput DNA markers. The challenge for bioinformaticians is to develop analytical methods and accompanying software tools that can cope with datasets of differing sizes, from tens to thousands of markers, that can incorporate the expert knowledge that plant biologists typically use when developing their maps, and that facilitate user-friendly approaches to achieving these goals. Here, we aim to give a flavour of computational approaches for genetic map estimation, discussing briefly many of the key concepts involved, and describing a selection of software tools that employ them. This review is intended both for plant geneticists as an introduction to software tools with which to estimate genetic maps, and for bioinformaticians as an introduction to the underlying computational approaches.

  18. Effects of Genotype by Environment Interaction on Genetic Gain and Genetic Parameter Estimates in Red Tilapia (Oreochromis spp.).

    PubMed

    Nguyen, Nguyen H; Hamzah, Azhar; Thoa, Ngo P

    2017-01-01

    The extent to which genetic gain achieved from selection programs under strictly controlled environments in the nucleus that can be expressed in commercial production systems is not well-documented in aquaculture species. The main aim of this paper was to assess the effects of genotype by environment interaction on genetic response and genetic parameters for four body traits (harvest weight, standard length, body depth, body width) and survival in Red tilapia (Oreochromis spp.). The growth and survival data were recorded on 19,916 individual fish from a pedigreed population undergoing three generations of selection for increased harvest weight in earthen ponds from 2010 to 2012 at the Aquaculture Extension Center, Department of Fisheries, Jitra in Kedah, Malaysia. The pedigree comprised a total of 224 sires and 262 dams, tracing back to the base population in 2009. A multivariate animal model was used to measure genetic response and estimate variance and covariance components. When the homologous body traits in freshwater pond and cage were treated as genetically distinct traits, the genetic correlations between the two environments were high (0.85-0.90) for harvest weight and square root of harvest weight but the estimates were of lower magnitudes for length, width and depth (0.63-0.79). The heritabilities estimated for the five traits studied differed between pond (0.02 to 0.22) and cage (0.07 to 0.68). The common full-sib effects were large, ranging from 0.23 to 0.59 in pond and 0.11 to 0.31 in cage across all traits. The direct and correlated responses for four body traits were generally greater in pond than in cage environments (0.011-1.561 vs. -0.033-0.567 genetic standard deviation units, respectively). Selection for increased harvest body weight resulted in positive genetic changes in survival rate in both pond and cage culture. In conclusion, the reduced selection response and the magnitude of the genetic parameter estimates in the production environment

  19. 3D magnetic sources' framework estimation using Genetic Algorithm (GA)

    NASA Astrophysics Data System (ADS)

    Ponte-Neto, C. F.; Barbosa, V. C.

    2008-05-01

    We present a method for inverting total-field anomaly for determining simple 3D magnetic sources' framework such as: batholiths, dikes, sills, geological contacts, kimberlite and lamproite pipes. We use GA to obtain magnetic sources' frameworks and their magnetic features simultaneously. Specifically, we estimate the magnetization direction (inclination and declination) and the total dipole moment intensity, and the horizontal and vertical positions, in Cartesian coordinates , of a finite set of elementary magnetic dipoles. The spatial distribution of these magnetic dipoles composes the skeletal outlines of the geologic sources. We assume that the geologic sources have a homogeneous magnetization distribution and, thus all dipoles have the same magnetization direction and dipole moment intensity. To implement the GA, we use real-valued encoding with crossover, mutation, and elitism. To obtain a unique and stable solution, we set upper and lower bounds on declination and inclination of [0,360°] and [-90°, 90°], respectively. We also set the criterion of minimum scattering of the dipole-position coordinates, to guarantee that spatial distribution of the dipoles (defining the source skeleton) be as close as possible to continuous distribution. To this end, we fix the upper and lower bounds of the dipole moment intensity and we evaluate the dipole-position estimates. If the dipole scattering is greater than a value expected by the interpreter, the upper bound of the dipole moment intensity is reduced by 10 % of the latter. We repeat this procedure until the dipole scattering and the data fitting are acceptable. We apply our method to noise-corrupted magnetic data from simulated 3D magnetic sources with simple geometries and located at different depths. In tests simulating sources such as sphere and cube, all estimates of the dipole coordinates are agreeing with center of mass of these sources. To elongated-prismatic sources in an arbitrary direction, we estimate

  20. [Impact of maternal genetic effect on genetic parameter estimation of production traits for Qinghai fine-wool sheep].

    PubMed

    Wang, Peng-Yu; Guanque, Zha-Xi; Qi, Quan-Qing; De, Mao; Zhang, Wen-Guang; Li, Jin-Quan

    2012-05-01

    The maternal genetic effects on estimating genetic parameters for growth traits and wool traits of Qinghai fine-wool sheep were investigated.The genetic parameters for production traits of Qinghai fine-wool sheep were estimated by average information restricted maximum likelihood (AIREML) with different animal models, and the differences between different animal models were tested by likelihood ratio test. Fixed effects, direct genetic effects, and residual effects were included all models; and random effects were individual permanence environmental effects, maternal genetic effects, and maternal permanence environmental effects. The six models differ in the way of considering random effects: in model 1 individual permanence environmental effects, maternal genetic effects, and maternal permanence environmental effects were not contained; in model 2 maternal permanence environmental effects were included; in model 3 maternal genetic effects were included; in model 4 both maternal genetic effects and maternal permanence environmental effects were include; in model 5 both individual permanence environmental effects and maternal genetic effects were contained;in model 6 all random effects were contained. The direct heritabilities were 0.1896~0.3781, 0.2537~0.2890, 0.2244~0.3225, 0.2205~0.3983, 0.1218~0.1490, 0.0983~0.4802, and 0.1170~0.1311 for birth weight, weaning weight, yearling weight, hogget weight,greasy fleece weight, fiber diameter, and staple length,respectively. Compared with model 1, model 3 was-significant(P<0.01) for birth weight and weaning weight, other models were not significant (P>0.05)for Yearling weight, Hogget weight; and paralleled with model 6, both model 4 and model 5 were significant(P<0.01) for fiber diameter,model 4 was significant(P<0.05) for staple length, and other models were not significant(P>0.05) for greasy fleece weight by likelihood ratio test.The maternal effects were important determinants of estimated the genetic parameters for

  1. Graphical approach to evaluate genetic estimates of calf survival.

    PubMed

    Schlesser, H N; Shanks, R D; Berger, P J; Healey, M H

    2009-05-01

    Genetic variation and resemblance among relatives are fundamentals of quantitative genetics. Our purpose was to identify bulls with a bimodal pattern of inheritance in the quest for new discoveries about the inheritance of calf survival. A bimodal pattern of inheritance for calf survival was identified in sons of Holstein bulls. A bimodal pattern of inheritance indicates 2 groups of sons resulting from an allele effect, a grandsire effect, or some other common factor. Different combinations (AA, Aa, aa) of 2 alleles at a locus cause varying phenotypes to be expressed. Bulls that are heterozygous for loci affecting reproductive performance may have a bimodal pattern of inheritance if the difference in effect of the 2 alleles is large. If the bimodal pattern is caused by an allele effect, then molecular markers can be identified for use in marker-assisted selection breeding programs. Data on predicted transmitting ability for perinatal survival for the first parity of 8,678 sons of 599 sires were collected from 1984 through 1997 from the National Association of Animal Breeders calving ease database, which included 7 Midwestern states. Sixteen bulls were identified with a potential bimodal pattern of inheritance because they had 2 distinct groups of sons. The 2 groups of sons were separated by calculating the coefficient of variation for each possible combination of sons; the combination that gave the smallest coefficient of variation difference between the 2 groups was considered the correct distribution of the sons into those groups. Bulls with a bimodal distribution were analyzed to determine the distribution of the grandsons among the maternal grandsires (MGS) of the 2 groups of the bimodal distribution. The bimodal distribution may be a result of heterozygous sires or MGS that are homozygous for low or high survival. If the bimodal distribution is caused by a MGS effect, then marker-assisted selection can still be used by evaluating the MGS instead of the sires.

  2. The flow of antimicrobial peptide genes through a genetic barrier between Mytilus edulis and M. galloprovincialis.

    PubMed

    Boon, Eva; Faure, Matthieu F; Bierne, Nicolas

    2009-05-01

    We studied the population genetics of two antimicrobial peptide (AMP) loci, called Mytilin B and Mytilus galloprovincialis defensin 2 (MGD2), in the secondary contact mosaic hybrid zone between Mytilus edulis and M. galloprovincialis. The isolation period between the two species was estimated to be approximately 1 million years (range, 0.5 million to 2 million years) long. During this period, coevolution between microbes and the immune system has likely occurred. The secondary contact, which would date back to approximately 25,000 (0-200,000) years, recently allowed these coadaptations to be rearranged through hybridization. Distinctive polymorphisms were uncovered in coding sequences of the two AMP loci such as insertion/deletion of codons or bisubstituted codons. Very low levels of differentiation were observed between populations of the two species at both loci, while other nuclear loci often showed marked structure among the same samples. The absence of population differentiation proved to be the consequence of secondary introgression of highly divergent alleles. While only a few recombinants were observed at the Mytilin B locus, the MGD2 locus showed a high intragenic recombination rate, which increased in the exon coding for the mature peptide. In addition, standard neutrality tests revealed significant deviations from the mutation-drift equilibrium at both loci. These results suggest that either balancing or directional selection is likely to play a role in the evolution of the two AMPs and introgression would be adaptive. However, evidence accumulated at the Mytilin B locus allows neither for identification of the direction of selection nor for any conclusions on whether selection acted directly on the antimicrobial peptide itself. At the MGD2 locus, a spatial variation of polymorphism patterns along the sequence suggests that selection was direct, although the precise nature of the selection (directional vs. balancing) remains unclear. This study concurs

  3. Genetic relatedness of foraminiferan ( Marginopora vertebralis) populations from reefs in the Western Coral Sea and Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Benzie, John A. H.

    1991-07-01

    Allozyme variation at four loci and phenetic variation for esterase were examined in M. vertebralis populations from 10 reefs from the Western Coral Sea and two from the Great Barrier Reef (GBR). Genetic distances (Nei's D) among populations on different reefs ranged from 0 0.932 and was neither related to geographical separation of reefs nor to depth of water separating reefs. These findings suggest long-distance dispersal by some means is sufficient to prevent genetic differentiation of M. vertebralis populations, and that M. vertebralis populations need not be connected by habitats suitable for the continued existence of the foraminiferan for genetic differentiation to be prevented. The Western Coral Sea reef populations did not form a related group that were genetically distinct from those on the GBR but were differentiated latitudinally. Reefs to the extreme north and south formed outliers while those on the northern half of the Queensland Plateau showed some differentiation from those on the southern half of the Plateau. This pattern of genetic variation appeared to reflect the distribution of populations north and south of the southern limit of the Southern Equatorial Current. Further work will be required to establish the soundness of this relationship, and to exclude other possible explanations related to historical events or the effects of selection. Relatively high dispersal was inferred between the Southern Queensland Plateau reefs and those sampled on the GBR (average Neis D=0.011). Holmes and Marion reefs formed discrete genetic outliers (average Neis D=0.69 and 0.20 respectively). In the case of Holmes reef other factors (e.g. history of recruitment) will need to be investigated to account for its marked genetic differentiation from the other reefs in the Queensland Plateau.

  4. Barriers against required nurse estimation models applying in Iran hospitals from health system experts’ point of view

    PubMed Central

    Tabatabaee, Seyed Saeed; Nekoie-Moghadam, Mahmood; Vafaee-Najar, Ali; Amiresmaili, Mohammad Reza

    2016-01-01

    Introduction One of the strategies for accessing effective nursing care is to design and implement a nursing estimation model. The purpose of this research was to determine barriers in applying models or norms for estimating the size of a hospital’s nursing team. Methods This study was conducted from November 2015 to March 2016 among three levels of managers at the Ministry of Health, medical universities, and hospitals in Iran. We carried out a qualitative study using a Colaizzi method. We used semistructured and in-depth interviews by purposive, quota, and snowball sampling of 32 participants (10 informed experts in the area of policymaking in human resources in the Ministry of Health, 10 decision makers in employment and distribution of human resources in treatment and administrative chancellors of Medical Universities, and 12 nursing managers in hospitals). The data were analyzed by Atlas.ti software version 6.0.15. Results The following 14 subthemes emerged from data analysis: Lack of specific steward, weakness in attracting stakeholder contributions, lack of authorities trust to the models, lack of mutual interests between stakeholders, shortage of nurses, financial deficit, non-native models, designing models by people unfamiliar with nursing process, lack of attention to the nature of work in each ward, lack of attention to hospital classification, lack of transparency in defining models, reduced nurses available time, increased indirect activity of nurses, and outdated norms. The main themes were inappropriate planning and policymaking in high levels, resource constraints, and poor design of models and lack of updating the model. Conclusion The results of present study indicate that many barriers exist in applying models for estimating the size of a hospital’s nursing team. Therefore, for designing an appropriate nursing staff estimation model and implementing it, in addition to considering the present barriers, identifying the norm required features

  5. Geographical distance and barriers explain population genetic patterns in an endangered island perennial

    PubMed Central

    Dias, Elisabete F.; Moura, M.; Schaefer, H.; Silva, Luís

    2016-01-01

    Island plants are frequently used as model systems in evolutionary biology to understand factors that might explain genetic diversity and population differentiation levels. Theory suggests that island plants should have lower levels of genetic diversity than their continental relatives, but this hypothesis has been rejected in several recent studies. In the Azores, the population level genetic diversity is generally low. However, like in most island systems, there are high levels of genetic differentiation between different islands. The Azores lettuce, Lactuca watsoniana, is an endangered Asteraceae with small population sizes. Therefore, we expect to find a lower level of genetic diversity than in the other more common endemic Asteraceae. The intra- and interpopulation genetic structure and diversity of L. watsoniana was assessed using eight newly developed microsatellite markers. We included 135 individuals, from all 13 known populations in the study. Because our microsatellite results suggested that the species is tetraploid, we analysed the microsatellite data (i) in codominant format using PolySat (Principal Coordinate Analysis, PCoA) and SPAgedi (genetic diversity indexes) and (ii) in dominant format using Arlequin (AMOVA) and STRUCTURE (Bayesian genetic cluster analysis). A total of 129 alleles were found for all L. watsoniana populations. In contrast to our expectations, we found a high level of intrapopulation genetic diversity (total heterozigosity = 0.85; total multilocus average proportion of private alleles per population = 26.5 %, Fis = −0.19). Our results show the existence of five well-defined genetic groups, one for each of the three islands São Miguel, Terceira and Faial, plus two groups for the East and West side of Pico Island (Fst = 0.45). The study revealed the existence of high levels of genetic diversity, which should be interpreted taking into consideration the ploidy level of this rare taxon. PMID:27742648

  6. Geographical distance and barriers explain population genetic patterns in an endangered island perennial.

    PubMed

    Dias, Elisabete F; Moura, M; Schaefer, H; Silva, Luís

    2016-01-01

    Island plants are frequently used as model systems in evolutionary biology to understand factors that might explain genetic diversity and population differentiation levels. Theory suggests that island plants should have lower levels of genetic diversity than their continental relatives, but this hypothesis has been rejected in several recent studies. In the Azores, the population level genetic diversity is generally low. However, like in most island systems, there are high levels of genetic differentiation between different islands. The Azores lettuce, Lactuca watsoniana, is an endangered Asteraceae with small population sizes. Therefore, we expect to find a lower level of genetic diversity than in the other more common endemic Asteraceae. The intra- and interpopulation genetic structure and diversity of L. watsoniana was assessed using eight newly developed microsatellite markers. We included 135 individuals, from all 13 known populations in the study. Because our microsatellite results suggested that the species is tetraploid, we analysed the microsatellite data (i) in codominant format using PolySat (Principal Coordinate Analysis, PCoA) and SPAgedi (genetic diversity indexes) and (ii) in dominant format using Arlequin (AMOVA) and STRUCTURE (Bayesian genetic cluster analysis). A total of 129 alleles were found for all L. watsoniana populations. In contrast to our expectations, we found a high level of intrapopulation genetic diversity (total heterozigosity = 0.85; total multilocus average proportion of private alleles per population = 26.5 %, Fis = -0.19). Our results show the existence of five well-defined genetic groups, one for each of the three islands São Miguel, Terceira and Faial, plus two groups for the East and West side of Pico Island (Fst = 0.45). The study revealed the existence of high levels of genetic diversity, which should be interpreted taking into consideration the ploidy level of this rare taxon.

  7. Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models.

    PubMed

    Genheden, Samuel; Eriksson, Leif A

    2016-09-13

    Liposomes are common carriers of drug molecules, providing enhanced delivery and accumulation of hydrophilic agents or larger biomolecules. Molecular simulations can be used to estimate key features of the drug molecules upon interaction with the liposomes, such as penetration barriers and localization. Herein, we investigate several aspects of the computational estimation of penetration barriers, viz. the potential of mean force (PMFs) along a vector spanning the membrane. First, we provide an evaluation of the all-atom (AA) and coarse-grained (CG) parametrization of 5-aminolevulinic acid (5-ALA) and two of its alkyl esters by computing n-octanol/water partition coefficients. We find that the CG parametrization of the esters performs significantly better than the CG model of 5-ALA, highlighting the difficulty to coarse-grain small, polar molecules. However, the expected trend in partition coefficients is reproduced also with the CG models. Second, we compare PMFs in a small membrane slab described with either the AA or CG models. Here, we are able to reproduce the all-atom PMF of 5-ALA with CG. However, for the alkyl esters it is unfortunately not possible to correctly reproduce both the depth and the penetration barrier of the PMF seen in the AA simulations with any of the tested CG models. We argue that it is more important to choose a CG parametrization that reproduces the depth of the PMF. Third, we compare, using the CG model, PMFs in the membrane slab with PMFs in a large, realistic liposome. We find similar depths but slightly different penetration barriers most likely due to differences in the lipid density along the membrane axis. Finally, we compute PMFs in liposomes with three different lipid compositions. Unfortunately, differences in the PMFs could not be quantified, and it remains to be investigated to what extent liposome simulations can fully reproduce experimental findings.

  8. Estimating cancer survival and clinical outcome based on genetic tumor progression scores.

    PubMed

    Rahnenführer, Jörg; Beerenwinkel, Niko; Schulz, Wolfgang A; Hartmann, Christian; von Deimling, Andreas; Wullich, Bernd; Lengauer, Thomas

    2005-05-15

    In cancer research, prediction of time to death or relapse is important for a meaningful tumor classification and selecting appropriate therapies. Survival prognosis is typically based on clinical and histological parameters. There is increasing interest in identifying genetic markers that better capture the status of a tumor in order to improve on existing predictions. The accumulation of genetic alterations during tumor progression can be used for the assessment of the genetic status of the tumor. For modeling dependences between the genetic events, evolutionary tree models have been applied. Mixture models of oncogenetic trees provide a probabilistic framework for the estimation of typical pathogenetic routes. From these models we derive a genetic progression score (GPS) that estimates the genetic status of a tumor. GPS is calculated for glioblastoma patients from loss of heterozygosity measurements and for prostate cancer patients from comparative genomic hybridization measurements. Cox proportional hazard models are then fitted to observed survival times of glioblastoma patients and to times until PSA relapse following radical prostatectomy of prostate cancer patients. It turns out that the genetically defined GPS is predictive even after adjustment for classical clinical markers and thus can be considered a medically relevant prognostic factor. Mtreemix, a software package for estimating tree mixture models, is freely available for non-commercial users at http://mtreemix.bioinf.mpi-sb.mpg.de. The raw cancer datasets and R code for the analysis with Cox models are available upon request from the corresponding author.

  9. Restricted maximum likelihood estimation of genetic principal components and smoothed covariance matrices

    PubMed Central

    Meyer, Karin; Kirkpatrick, Mark

    2005-01-01

    Principal component analysis is a widely used 'dimension reduction' technique, albeit generally at a phenotypic level. It is shown that we can estimate genetic principal components directly through a simple reparameterisation of the usual linear, mixed model. This is applicable to any analysis fitting multiple, correlated genetic effects, whether effects for individual traits or sets of random regression coefficients to model trajectories. Depending on the magnitude of genetic correlation, a subset of the principal component generally suffices to capture the bulk of genetic variation. Corresponding estimates of genetic covariance matrices are more parsimonious, have reduced rank and are smoothed, with the number of parameters required to model the dispersion structure reduced from k(k + 1)/2 to m(2k - m + 1)/2 for k effects and m principal components. Estimation of these parameters, the largest eigenvalues and pertaining eigenvectors of the genetic covariance matrix, via restricted maximum likelihood using derivatives of the likelihood, is described. It is shown that reduced rank estimation can reduce computational requirements of multivariate analyses substantially. An application to the analysis of eight traits recorded via live ultrasound scanning of beef cattle is given. PMID:15588566

  10. Genetic parameter estimates of growth curve and reproduction traits in Japanese quail.

    PubMed

    Narinc, Dogan; Karaman, Emre; Aksoy, Tulin; Firat, Mehmet Ziya

    2014-01-01

    The goal of selection studies in broilers is to obtain genetically superior chicks in terms of major economic traits, which are mainly growth rate, meat yield, and feed conversion ratio. Multiple selection schedules for growth and reproduction are used in selection programs within commercial broiler dam lines. Modern genetic improvement methods have not been applied in experimental quail lines. The current research was conducted to estimate heritabilities and genetic correlations for growth and reproduction traits in a Japanese quail flock. The Gompertz equation was used to determine growth curve parameters. The Gibbs sampling under a multi-trait animal model was applied to estimate the heritabilities and genetic correlations for these traits. A total of 948 quail were used with complete pedigree information to estimate the genetic parameters. Heritability estimates of BW, absolute and relative growth rates at 5 wk of age (AGR and RGR), β0 and β2 parameters, and age at point of inflection (IPT) of Gompertz growth curve, total egg number (EN) from the day of first lay to 24 wk of age were moderate to high, with values ranging from 0.25 to 0.40. A low heritability (0.07) for fertility (FR) and a strong genetic correlation (0.83) between FR and EN were estimated in our study. Body weight exhibited negative genetic correlation with EN, FR, RGR, and IPT. This genetic antagonism among the mentioned traits may be overcome using modern poultry breeding methods such as selection using multi-trait best linear unbiased prediction and crossbreeding.

  11. Paleoclimate effects and geographic barriers shape regional population genetic structure of blackbrush (Coleogyne ramosissima: Rosaceae)

    Treesearch

    Bryce A. Richardson; Susan E. Meyer

    2012-01-01

    Coleogyne ramosissima Torr. (blackbrush) is a dominant xerophytic shrub species in the ecotone between the warm and cold deserts of interior western North America. Amplified fragment length polymorphisms (AFLPs) were used to survey genetic diversity and population genetic structure at 14 collection sites across the species range. Analysis revealed significant...

  12. Why Is Cancer Genetic Counseling Underutilized by Women Identified as at Risk for Hereditary Breast Cancer? Patient Perceptions of Barriers Following a Referral Letter.

    PubMed

    Kne, Alyssa; Zierhut, Heather; Baldinger, Shari; Swenson, Karen K; Mink, Pamela; Veach, Patricia McCarthy; Tsai, Michaela L

    2017-08-01

    Family history information comprises an important tool in identifying and referring patients at risk for hereditary breast and ovarian cancer (HBOC) to cancer genetic counseling. Despite recommendations and support provided by numerous professional organizations, cancer genetic counseling services are underutilized by atrisk patients. This study aimed to: (1) determine the rate of genetic counseling utilization following a referral letter, (2) characterize factors (barriers and supports) which influenced uptake of services, and (3) identify potential strategies for increasing utilization. This study evaluated the uptake of cancer genetic counseling among 603 screening mammography patients identified as having an increased risk for HBOC based on National Comprehensive Cancer Network (NCCN) guidelines. At risk individuals and their primary care providers were mailed a referral letter recommending genetic counseling. Three focus groups (N = 24) were conducted to identify responses to receiving a letter recommending genetic counseling, barriers to seeking genetic counseling, and facilitating factors to utilizing these services. Participant responses were qualitatively analyzed using thematic and cross case analysis. Within one year, 50/603 (8 %) of the identified at-risk women completed a genetic counseling appointment. Participant-perceived barriers which influenced their decision not to seek genetic counseling included lack of relevance and utility, limited knowledge about genetic counseling, concerns about the genetic counseling process, and concerns about cost and insurance coverage. Participant-perceived facilitating factors which would support a decision to seek genetic counseling included greater awareness and education about genetic counseling services when receiving a referral, and improved follow up and guidance from their provider. Findings from this study support the need for patient and primary care provider education, and improved provider

  13. Spatial and temporal genetic structure of Symbiodinium populations within a common reef-building coral on the Great Barrier Reef.

    PubMed

    Howells, Emily J; Willis, Bette L; Bay, Line K; van Oppen, Madeleine J H

    2013-07-01

    The dinoflagellate photosymbiont Symbiodinium plays a fundamental role in defining the physiological tolerances of coral holobionts, but little is known about the dynamics of these endosymbiotic populations on coral reefs. Sparse data indicate that Symbiodinium populations show limited spatial connectivity; however, no studies have investigated temporal dynamics for in hospite Symbiodinium populations following significant mortality and recruitment events in coral populations. We investigated the combined influences of spatial isolation and disturbance on the population dynamics of the generalist Symbiodinium type C2 (ITS1 rDNA) hosted by the scleractinian coral Acropora millepora in the central Great Barrier Reef. Using eight microsatellite markers, we genotyped Symbiodinium in a total of 401 coral colonies, which were sampled from seven sites across a 12-year period including during flood plume-induced coral bleaching. Genetic differentiation of Symbiodinium was greatest within sites, explaining 70-86% of the total genetic variation. An additional 9-27% of variation was explained by significant differentiation of populations among sites separated by 0.4-13 km, which is consistent with low levels of dispersal via water movement and historical disturbance regimes. Sampling year accounted for 6-7% of total genetic variation and was related to significant coral mortality following severe bleaching in 1998 and a cyclone in 2006. Only 3% of the total genetic variation was related to coral bleaching status, reflecting generally small (8%) reductions in allelic diversity within bleached corals. This reduction probably reflected a loss of genotypes in hospite during bleaching, although no site-wide changes in genetic diversity were observed. Combined, our results indicate the importance of disturbance regimes acting together with limited oceanographic transport to determine the genetic composition of Symbiodinium types within reefs.

  14. Single-generation estimates of individual fitness as proxies for long-term genetic contribution.

    PubMed

    Brommer, Jon E; Gustafsson, Lars; Pietiäinen, Hannu; Merilä, Juha

    2004-04-01

    Individual fitness is a central evolutionary concept, but the question of how it should be defined in empirical studies of natural selection remains contentious. Using founding cohorts from long-term population studies of two species of individually marked birds (collared flycatcher Ficedula albicollis and Ural owl Strix uralensis), we compared a rate-sensitive (lambdaind) and a rate-insensitive (lifetime reproductive success [LRS]) estimate of individual fitness with an estimate of long-term genetic fitness. The latter was calculated as the number of gene copies present in the population after more than two generations, as estimated by tracing genetic lineages and accounting for the fact that populations were not completely closed. When counting fledglings, rate-insensitive estimates of individual fitness correlated better than rate-sensitive estimates with estimated long-term genetic contribution. When counting recruits, both classes of estimates performed equally well. The results support the contention that simple, rate-insensitive measures of fitness, such as LRS, provide a valid and good estimate of fitness in evolutionary studies of natural populations.

  15. Estimation of population growth or decline in genetically monitored populations.

    PubMed Central

    Beaumont, Mark A

    2003-01-01

    This article introduces a new general method for genealogical inference that samples independent genealogical histories using importance sampling (IS) and then samples other parameters with Markov chain Monte Carlo (MCMC). It is then possible to more easily utilize the advantages of importance sampling in a fully Bayesian framework. The method is applied to the problem of estimating recent changes in effective population size from temporally spaced gene frequency data. The method gives the posterior distribution of effective population size at the time of the oldest sample and at the time of the most recent sample, assuming a model of exponential growth or decline during the interval. The effect of changes in number of alleles, number of loci, and sample size on the accuracy of the method is described using test simulations, and it is concluded that these have an approximately equivalent effect. The method is used on three example data sets and problems in interpreting the posterior densities are highlighted and discussed. PMID:12871921

  16. Estimation of genetic parameters for preweaning growth traits of Brahman cattle in Southeastern Mexico.

    PubMed

    Estrada-León, Raciel J; Magaña-Monforte, Juan G; Segura-Correa, José C

    2014-06-01

    The genetic parameters for Brahman cattle under the tropical conditions of Mexico are scarce. Therefore, heritabilities, additive direct and maternal correlations, and genetic correlations for birth weight (BW) and 205 days adjusted weaning weight (WW205) were estimated in four Brahman cattle herds in Yucatan, Mexico. Parameters were estimated fitting a bivariate animal model, with 4,531 animals in the relationship matrix, of which 2,905 had BW and 2,264 had WW205. The number of sires and dams identified for both traits were 122 and 962, respectively. Direct heritability estimates for BW and WW205 were 0.41 ± 0.09 and 0.43 ± 0.09, and maternal heritabilities were 0.15 ± 0.07 and 0.38 ± 0.08, respectively. Genetic correlations between direct additive and maternal genetic effects for BW and WW205 were -0.41 ± 0.22 and -0.50 ± 0.15, respectively. The direct genetic, maternal, and phenotypic correlations between BW and WW205 were 0.77 ± 0.09, 0.61 ± 0.18, and 0.35, respectively. The moderate to high genetic parameter estimates suggest that genetic improvement by selection is possible for those traits. The maternal effects and their correlation with direct effects should be taken into account to reduce bias in genetic evaluations.

  17. A reverse genetic screen in the zebrafish identifies crb2b as a regulator of the glomerular filtration barrier.

    PubMed

    Ebarasi, Lwaki; He, Liqun; Hultenby, Kjell; Takemoto, Minoru; Betsholtz, Christer; Tryggvason, Karl; Majumdar, Arindam

    2009-10-01

    The glomerular filtration barrier is necessary for the selective passage of low molecular weight waste products and the retention of blood plasma proteins. Damage to the filter results in proteinuria. The filtration barrier is the major pathogenic site in almost all glomerular diseases and its study is therefore of clinical significance. We have taken advantage of the zebrafish pronephros as a system for studying glomerular filtration. In order to identify new regulators of filtration barrier assembly, we have performed a reverse genetic screen in the zebrafish testing a group of genes which are enriched in their expression within the mammalian glomerulus. In this novel screen, we have coupled gene knockdown using morpholinos with a physiological glomerular dye filtration assay to test for selective glomerular permeability in living zebrafish larvae. Screening 20 genes resulted in the identification of ralgps1, rapgef2, rabgef1, and crb2b. The crumbs (crb) genes encode a family of evolutionarily conserved proteins important for apical-basal polarity within epithelia. The crb2b gene is expressed in zebrafish podocytes. Electron microscopic analysis of crb2b morphants reveals a gross disorganization of podocyte foot process architecture and loss of slit diaphragms while overall polarity is maintained. Nephrin, a major component of the slit diaphragm, is apically mis-localized in podocytes from crb2b morphants suggesting that crb2b is required for the proper protein trafficking of Nephrin. This report is the first to show a role for crb function in podocyte differentiation. Furthermore, these results suggest a novel link between epithelial polarization and the maintenance of a functional filtration barrier.

  18. Estimated coverage to address financial barriers to HIV preexposure prophylaxis among persons with indications for its use, United States, 2015.

    PubMed

    Smith, Dawn K; Van Handel, Michelle; Huggins, Rebecca

    2017-08-22

    An estimated 1.2 million American adults engage in sexual and drug use behaviors that place them at significant risk of acquiring HIV infection. Engagement in health care for the provision of daily oral antiretroviral medication as preexposure prophylaxis (PrEP), when clinically indicated, could substantially reduce the number of new HIV infections in these persons. However, resources to cover the financial cost of PrEP care is an anticipated barrier for many of the populations with high numbers of new HIV infections. Using nationally representative data, we estimated the current national met and unmet need for financial assistance with covering the cost of PrEP medication, clinical visits, and laboratory costs among adults with indications for its use, overall and by transmission risk population. This study found that, of the 1.2 million adults estimated to have indications for PrEP use, <1% (∼7,300) are in need of financial assistance for both PrEP medication and clinical care, at an estimated annual cost of $89 million. An additional 7% (∼86,300) are in need of financial assistance only for PrEP clinical care at an estimated annual cost of $119 million. This information on PrEP care costs, insurance coverage, and unmet financial need among persons in key HIV transmission risk subpopulations can inform policy makers at all levels as they consider how to address remaining financial barriers to the use of PrEP and accommodate any changes in eligibility for various insurance and financial assistance programs that may occur in coming years.

  19. Estimation of (co)variance components and genetic parameters of greasy fleece weights in Muzaffarnagari sheep.

    PubMed

    Mandal, A; Neser, F W C; Roy, R; Rout, P K; Notter, D R

    2009-02-01

    Variance components and genetic parameters for greasy fleece weights of Muzaffarnagari sheep maintained at the Central Institute for Research on Goats, Makhdoom, Mathura, India, over a period of 29 years (1976 to 2004) were estimated by restricted maximum likelihood (REML), fitting six animal models including various combinations of maternal effects. Data on body weights at 6 (W6) and 12 months (W12) of age were also included in the study. Records of 2807 lambs descended from 160 rams and 1202 ewes were used for the study. Direct heritability estimates for fleece weight at 6 (FW6) and 12 months of age (FW12), and total fleece weights up to 1 year of age (TFW) were 0.14, 0.16 and 0.25, respectively. Maternal genetic and permanent environmental effects did not significantly influence any of the traits under study. Genetic correlations among fleece weights and body weights were obtained from multivariate analyses. Direct genetic correlations of FW6 with W6 and W12 were relatively large, ranging from 0.61 to 0.67, but only moderate genetic correlations existed between FW12 and W6 (0.39) and between FW12 and W12 (0.49). The genetic correlation between FW6 and FW12 was very high (0.95), but the corresponding phenotypic correlation was much lower (0.28). Heritability estimates for all traits were at least 0.15, indicating that there is potential for their improvement by selection. The moderate to high positive genetic correlations between fleece weights and body weights at 6 and 12 months of age suggest that some of the genetic factors that influence animal growth also influence wool growth. Thus selection to improve the body weights or fleece weights at 6 months of age will also result in genetic improvement of fleece weights at subsequent stages of growth.

  20. Population growth rates of reef sharks with and without fishing on the great barrier reef: robust estimation with multiple models.

    PubMed

    Hisano, Mizue; Connolly, Sean R; Robbins, William D

    2011-01-01

    Overfishing of sharks is a global concern, with increasing numbers of species threatened by overfishing. For many sharks, both catch rates and underwater visual surveys have been criticized as indices of abundance. In this context, estimation of population trends using individual demographic rates provides an important alternative means of assessing population status. However, such estimates involve uncertainties that must be appropriately characterized to credibly and effectively inform conservation efforts and management. Incorporating uncertainties into population assessment is especially important when key demographic rates are obtained via indirect methods, as is often the case for mortality rates of marine organisms subject to fishing. Here, focusing on two reef shark species on the Great Barrier Reef, Australia, we estimated natural and total mortality rates using several indirect methods, and determined the population growth rates resulting from each. We used bootstrapping to quantify the uncertainty associated with each estimate, and to evaluate the extent of agreement between estimates. Multiple models produced highly concordant natural and total mortality rates, and associated population growth rates, once the uncertainties associated with the individual estimates were taken into account. Consensus estimates of natural and total population growth across multiple models support the hypothesis that these species are declining rapidly due to fishing, in contrast to conclusions previously drawn from catch rate trends. Moreover, quantitative projections of abundance differences on fished versus unfished reefs, based on the population growth rate estimates, are comparable to those found in previous studies using underwater visual surveys. These findings appear to justify management actions to substantially reduce the fishing mortality of reef sharks. They also highlight the potential utility of rigorously characterizing uncertainty, and applying multiple

  1. Population Growth Rates of Reef Sharks with and without Fishing on the Great Barrier Reef: Robust Estimation with Multiple Models

    PubMed Central

    Hisano, Mizue; Connolly, Sean R.; Robbins, William D.

    2011-01-01

    Overfishing of sharks is a global concern, with increasing numbers of species threatened by overfishing. For many sharks, both catch rates and underwater visual surveys have been criticized as indices of abundance. In this context, estimation of population trends using individual demographic rates provides an important alternative means of assessing population status. However, such estimates involve uncertainties that must be appropriately characterized to credibly and effectively inform conservation efforts and management. Incorporating uncertainties into population assessment is especially important when key demographic rates are obtained via indirect methods, as is often the case for mortality rates of marine organisms subject to fishing. Here, focusing on two reef shark species on the Great Barrier Reef, Australia, we estimated natural and total mortality rates using several indirect methods, and determined the population growth rates resulting from each. We used bootstrapping to quantify the uncertainty associated with each estimate, and to evaluate the extent of agreement between estimates. Multiple models produced highly concordant natural and total mortality rates, and associated population growth rates, once the uncertainties associated with the individual estimates were taken into account. Consensus estimates of natural and total population growth across multiple models support the hypothesis that these species are declining rapidly due to fishing, in contrast to conclusions previously drawn from catch rate trends. Moreover, quantitative projections of abundance differences on fished versus unfished reefs, based on the population growth rate estimates, are comparable to those found in previous studies using underwater visual surveys. These findings appear to justify management actions to substantially reduce the fishing mortality of reef sharks. They also highlight the potential utility of rigorously characterizing uncertainty, and applying multiple

  2. Estimating the purebred-crossbred genetic correlation for uniformity of eggshell color in laying hens.

    PubMed

    Mulder, Han A; Visscher, Jeroen; Fablet, Julien

    2016-05-05

    Uniformity of eggs is an important aspect for retailers because consumers prefer homogeneous products. One of these characteristics is the color of the eggshell, especially for brown eggs. Existence of a genetic component in environmental variance would enable selection for uniformity of eggshell color. Therefore, the objective of this study was to quantify the genetic variance in environmental variance of eggshell color in purebred and crossbred laying hens, to estimate the genetic correlation between environmental variance of eggshell color in purebred and crossbred laying hens and to estimate genetic correlations between environmental variance at different times of the laying period. We analyzed 167,651 and 79,345 eggshell color records of purebred and crossbred laying hens, respectively. The purebred and crossbred laying hens originated mostly from the same sires. Since eggshell color records of crossbred laying hens were collected per cage, these records could be related only to cage and sire family. A double hierarchical generalized linear sire model was used to estimate the genetic variance of the mean of eggshell color and its environmental variance. Approximate standard errors for heritability and the genetic coefficient of variation for environmental variance were derived. The genetic variance in environmental variance at the log scale was equal to 0.077 and 0.067, for purebred and crossbred laying hens, respectively. The genetic coefficient of variation for environmental variance was equal to 0.28 and 0.26, for purebred and crossbred laying hens, respectively. A genetic correlation of 0.70 was found between purebred and crossbred environmental variance of eggshell color, which indicates that there is some reranking of sires for environmental variance of eggshell color in purebred and crossbred laying hens. Genetic correlations between environmental variance of eggshell color in different laying periods were generally higher than 0.85, except between

  3. Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control

    PubMed Central

    Bartha, István; Brumme, Chanson; Harrigan, Richard

    2017-01-01

    We evaluated the fraction of variation in HIV-1 set point viral load attributable to viral or human genetic factors by using joint host/pathogen genetic data from 541 HIV infected individuals. We show that viral genetic diversity explains 29% of the variation in viral load while host factors explain 8.4%. Using a joint model including both host and viral effects, we estimate a total of 30% heritability, indicating that most of the host effects are reflected in viral sequence variation. PMID:28182649

  4. Demographic and genetic factors shaping contemporary metapopulation effective size and its empirical estimation in salmonid fish

    PubMed Central

    Palstra, F P; Ruzzante, D E

    2011-01-01

    The preservation of biodiversity requires an understanding of the maintenance of its components, including genetic diversity. Effective population size determines the amount of genetic variance maintained in populations, but its estimation can be complex, especially when populations are interconnected in a metapopulation. Theory predicts that the effective size of a metapopulation (meta-Ne) can be decreased or increased by population subdivision, but little empirical work has evaluated these predictions. Here, we use neutral genetic markers and simulations to estimate the effective size of a putative metapopulation in Atlantic salmon (Salmo salar). For a weakly structured set of rivers, we find that meta-Ne is similar to the sum of local deme sizes, whereas higher genetic differentiation among demes dramatically reduces meta-Ne estimates. Interdemic demographic processes, such as asymmetrical gene flow, may explain this pattern. However, simulations also suggest that unrecognized population subdivision can also introduce downward bias into empirical estimation, emphasizing the importance of identifying the proper scale of distinct demographic and genetic processes. Under natural patterns of connectivity, evolutionary potential may generally be maintained at higher levels than the local population, with implications for conservation given ongoing species declines and habitat fragmentation. PMID:21522167

  5. Paternal effects on seed germination: a barrier to the genetic assimilation of an endemic plant taxon?

    PubMed

    Andersson, S; Månsby, E; Prentice, H C

    2008-09-01

    We used a crossing experiment to investigate post-zygotic barriers that might limit introgression between a pair of closely-related, gynodioecious plant species--the widespread weed Silene vulgaris and the local Swedish endemic S. uniflora ssp. petraea. The study not only considered the effects of hybridization on conventionally-used (primary) fitness components such as seed set and progeny survival, but also provided a test for the effects of interspecific hybridization on characters with more subtle or habitat-specific effects on fitness. We detected highly significant paternal effects on seed germination properties, with the germination characteristics of hybrid seed resembling those of the species that served as the pollen donor. These paternal effects on germination represent a potentially strong barrier to interspecific introgression in the two species' natural habitats, where an inappropriate germination response in the habitat of the maternal parent may lead to the failure of seedling establishment. Interspecific crosses had weak or variable effects on progeny survival, flowering and sex ratio, but these effects could not be interpreted in terms of barriers to introgression. Our results indicate that nuclear restorers in S. vulgaris have the capacity to suppress cytoplasmic male-sterility genes in its endemic congener.

  6. Estimation of genetic parameters and their sampling variances of quantitative traits in the type 2 modified augmented design

    USDA-ARS?s Scientific Manuscript database

    We proposed a method to estimate the error variance among non-replicated genotypes, thus to estimate the genetic parameters by using replicated controls. We derived formulas to estimate sampling variances of the genetic parameters. Computer simulation indicated that the proposed methods of estimatin...

  7. The problem of estimating recent genetic connectivity in a changing world.

    PubMed

    Samarasin, Pasan; Shuter, Brian J; Wright, Stephen I; Rodd, F Helen

    2017-02-01

    Accurate understanding of population connectivity is important to conservation because dispersal can play an important role in population dynamics, microevolution, and assessments of extirpation risk and population rescue. Genetic methods are increasingly used to infer population connectivity because advances in technology have made them more advantageous (e.g., cost effective) relative to ecological methods. Given the reductions in wildlife population connectivity since the Industrial Revolution and more recent drastic reductions from habitat loss, it is important to know the accuracy of and biases in genetic connectivity estimators when connectivity has declined recently. Using simulated data, we investigated the accuracy and bias of 2 common estimators of migration (movement of individuals among populations) rate. We focused on the timing of the connectivity change and the magnitude of that change on the estimates of migration by using a coalescent-based method (Migrate-n) and a disequilibrium-based method (BayesAss). Contrary to expectations, when historically high connectivity had declined recently: (i) both methods over-estimated recent migration rates; (ii) the coalescent-based method (Migrate-n) provided better estimates of recent migration rate than the disequilibrium-based method (BayesAss); (iii) the coalescent-based method did not accurately reflect long-term genetic connectivity. Overall, our results highlight the problems with comparing coalescent and disequilibrium estimates to make inferences about the effects of recent landscape change on genetic connectivity among populations. We found that contrasting these 2 estimates to make inferences about genetic-connectivity changes over time could lead to inaccurate conclusions. © 2016 Society for Conservation Biology.

  8. Perceived risk following melanoma genetic testing: A 2-year prospective study distinguishing subjective estimates from recall

    PubMed Central

    Aspinwall, Lisa G.; Taber, Jennifer M.; Kohlmann, Wendy; Leaf, Samantha L.; Leachman, Sancy A.

    2014-01-01

    A major goal of predictive genetic testing is to alert people to their risk before illness onset; however, little is known about how risk perceptions change following genetic testing and whether information is recalled accurately over time. In the United States, a CDKN2A/p16 mutation confers 76% lifetime risk of melanoma. Following genetic counseling and test reporting, subjective risk estimates and recall of counselor-provided risk estimates were assessed 5 times over the next 2 years among 60 adult members of 2 extended CDKN2A/p16 kindreds. No sustained changes from baseline in risk perceptions were reported. Unaffected carriers (n=15) consistently reported significantly lower subjective risk estimates (46%) than they were actually given (76%, p < .001) or recalled having been given (60%, p < .001). Noncarriers’ (n=27) risk estimates decreased following results disclosure, but rebounded, with both subjective and recalled estimates subsequently exceeding what they were told by the counselor (both ps < .001). Affected carriers’ (n=18) risk estimates for developing a new melanoma corresponded well to counselor-provided information (p =.362). For all 3 patient groups, results were consistent across multiple risk measures and remained similar when demographic, phenotypic, and baseline behavioral contributors to melanoma risk were statistically controlled. These findings are consistent with other studies of risk perception, but additional studies of more diverse populations are needed to understand the reasons behind both the persistence of initial risk estimates and their divergence from information provided by the counselor during genetic counseling. Additionally, determining whether holding subjective risk perceptions that differ from counselor-provided information ultimately affects adherence to management recommendations will help guide the presentation of risk information in genetic counseling practice. PMID:24322567

  9. Estimates of genetic parameters for daily somatic cell count of Australian dairy cattle.

    PubMed

    Haile-Mariam, M; Goddard, M E; Bowman, P J

    2001-05-01

    Genetic parameters for daily somatic cell counts (SCC) of the first three parities were estimated for Australian Dairy Cattle. Most of the data analyses were carried out with a sire random regression model. The estimates were compared with those from conventional ten-trait analyses and animal models. In the first-parity estimates of heritabilities (h2) were low (0.04 to 0.05) at the beginning of the lactation and higher (0.11 to 0.13) at the end. The average h2 estimated from random regression sire model, random regression animal model and conventional multitrait sire model were 0.09, 0.09, and 0.08, respectively, in the first lactation. The average h2 were 0.09 and 0.11 in the second and third parities, respectively. Genetic correlations between daily log(e) SCC within parity were high for adjacent tests (nearly 1) and low (as low as 0.30) between the beginning and the end of the lactation. Generally, the genetic correlations between parities depend on how far apart they are and on whether they are on the same day in any two parities. Across parities, on average, genetic correlations between parities 1 and 3 were the lowest and those between 1 and 2 intermediate, while those between 2 and 3 were the highest. The estimated environmental correlations were lower than the genetic correlations, but the trends were generally similar. Differences in genetic parameter estimates due to model were small, except for some genetic correlations. The high residual error variances, the low h2, and the inconsistency in genetic correlations that were observed particularly at the beginning of the first lactation suggest that log(e) SCC early in the first lactation may be related to a spike in SCC as result of infection and (or) onset of lactation while SCC later in lactation represents a sustained response to infection. Accounting for the variation in heritabilities and correlations should improve the accuracy of genetic evaluations for SCC based on test day records.

  10. Rats: gnawing through the barriers to understanding genetic susceptibility and breast cancer.

    PubMed

    Blackburn, Anneke C

    2011-10-12

    Advances in genotyping technology have provided us with a large number of genetic loci associated with cancer susceptibility; however, our ability to understand the functional effects of the genetic variants of these loci remains limited. In the previous issue, Smits and colleagues demonstrate the use of congenic rat strains to discover that the Mcs5a breast cancer susceptibility locus is most likely acting through the immune system, via novel transcriptional regulatory mechanisms. This challenges our conventional thinking of cancer susceptibility and gene regulation pathways, and illustrates the potential for rodent models to help us functionally characterize polymorphisms of cancer-associated loci.

  11. The use and abuse of genetic marker-based estimates of relatedness and inbreeding.

    PubMed

    Taylor, Helen R

    2015-08-01

    Genetic marker-based estimators remain a popular tool for measuring relatedness (r xy ) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of r xy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker-based estimators of r xy and F in a species with very low genetic diversity, New Zealand's little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of r xy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated r xy or F is relatively high (Pearson's r = 0.66-0.72 and 0.81-0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker-based estimates of r xy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator's performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of r xy and F debatable.

  12. Estimates of genetic parameters for growth traits in Brahman cattle using random regression and multitrait models.

    PubMed

    Bertipaglia, T S; Carreño, L O D; Aspilcueta-Borquis, R R; Boligon, A A; Farah, M M; Gomes, F J; Machado, C H C; Rey, F S B; da Fonseca, R

    2015-08-01

    Random regression models (RRM) and multitrait models (MTM) were used to estimate genetic parameters for growth traits in Brazilian Brahman cattle and to compare the estimated breeding values obtained by these 2 methodologies. For RRM, 78,641 weight records taken between 60 and 550 d of age from 16,204 cattle were analyzed, and for MTM, the analysis consisted of 17,385 weight records taken at the same ages from 12,925 cattle. All models included the fixed effects of contemporary group and the additive genetic, maternal genetic, and animal permanent environmental effects and the quadratic effect of age at calving (AAC) as covariate. For RRM, the AAC was nested in the animal's age class. The best RRM considered cubic polynomials and the residual variance heterogeneity (5 levels). For MTM, the weights were adjusted for standard ages. For RRM, additive heritability estimates ranged from 0.42 to 0.75, and for MTM, the estimates ranged from 0.44 to 0.72 for both models at 60, 120, 205, 365, and 550 d of age. The maximum maternal heritability estimate (0.08) was at 140 d for RRM, but for MTM, it was highest at weaning (0.09). The magnitude of the genetic correlations was generally from moderate to high. The RRM adequately modeled changes in variance or covariance with age, and provided there was sufficient number of samples, increased accuracy in the estimation of the genetic parameters can be expected. Correlation of bull classifications were different in both methods and at all the ages evaluated, especially at high selection intensities, which could affect the response to selection.

  13. The consistency of quantitative genetic estimates in field and laboratory in the yellow dung fly.

    PubMed

    Blanckenhorn, Wolf U

    2002-03-01

    How consistent quantitative genetic estimates are across environments is unclear and under discussion. Heritability (h2) estimates of hind tibia length (body size), development time and diapause induction in the yellow dung fly, Scathophaga stercoraria, generated with various methods in various environments are reported and compared. Estimates varied considerably within and among studies, but yielded good overall averages. The genetic correlations between the sexes for body size and development time were expectedly high (r(sex) = 0.57-0.78) but clearly less than unity, implying independent evolution of both traits in males and females of this sexually dimorphic species. Genetic and environmental variance components increased in proportion at variable field relative to constant laboratory conditions, resulting in overall similar h(2). Heritabilities for males and females were also similar, and h(2) of the morphological trait hind tibia length was not necessarily greater than that of the two life history traits. Full-sib (broad-sense) estimates (h(2) = 0.7-1.1) were 2-3 times greater than half-sib and parent/offspring (narrow-sense) estimates (h2 = 0-0.6). Common environment (i.e., among-container) variance averaged 38.3% (body size) and 16.8% (development time) of the broad-sense genetic variance in two laboratory studies. The broad-sense h(2), therefore, may contain substantial amounts (12-50%) of dominance variance and/or variance due to maternal effects. A general conclusion emerging from this and similar studies appears to be that whether field and laboratory genetic estimates differ depends on the environment, trait and species under consideration.

  14. Genetic Estimates of Population Age in the Water Flea, Daphnia magna

    PubMed Central

    2012-01-01

    Genetic datasets can be used to date evolutionary events, even on recent time scales if sufficient data are available. We used statistics calculated from multilocus microsatellite datasets to estimate population ages in data generated through coalescent simulations and in samples from populations of known age in a metapopulation of Daphnia magna in Finland. Our simulation results show that age estimates improve with additional loci and define a time frame over which these statistics are most useful. On the most recent time scales, assumptions regarding the model of mutation (infinite sites vs. stepwise mutation) have little influence on estimated ages. In older populations, size homoplasy among microsatellite alleles results in a downwards bias for estimates based on the infinite sites model (ISM). In the Finnish D. magna metapopulation, our genetically derived estimated ages were biased upwards. Potential sources of this bias include the underlying model of mutation, gene flow, founder size, and the possibility of persistent source populations in the system. Our simulated data show that genetic age estimation is possible, even for very young populations, but our empirical data highlight the importance of factors such as migration when these statistics are applied in natural populations. PMID:23129752

  15. Genetic estimates of population age in the water flea, Daphnia magna.

    PubMed

    Robinson, John D; Haag, Christoph R; Hall, David W; Pajunen, V Ilmari; Wares, John P

    2012-01-01

    Genetic datasets can be used to date evolutionary events, even on recent time scales if sufficient data are available. We used statistics calculated from multilocus microsatellite datasets to estimate population ages in data generated through coalescent simulations and in samples from populations of known age in a metapopulation of Daphnia magna in Finland. Our simulation results show that age estimates improve with additional loci and define a time frame over which these statistics are most useful. On the most recent time scales, assumptions regarding the model of mutation (infinite sites vs. stepwise mutation) have little influence on estimated ages. In older populations, size homoplasy among microsatellite alleles results in a downwards bias for estimates based on the infinite sites model (ISM). In the Finnish D. magna metapopulation, our genetically derived estimated ages were biased upwards. Potential sources of this bias include the underlying model of mutation, gene flow, founder size, and the possibility of persistent source populations in the system. Our simulated data show that genetic age estimation is possible, even for very young populations, but our empirical data highlight the importance of factors such as migration when these statistics are applied in natural populations.

  16. Genetic variation in Arizona Mexican Americans: estimation and interpretation of admixture proportions.

    PubMed

    Long, J C; Williams, R C; McAuley, J E; Medis, R; Partel, R; Tregellas, W M; South, S F; Rea, A E; McCormick, S B; Iwaniec, U

    1991-02-01

    Mexican Americans are a numerous and fast growing ethnic population in the United States. Yet little is known about their genetic structure. Since they are a hybrid, it is of interest to identify their parental populations and to estimate the relative contributions of these groups. This information is relevant to historical, biomedical, and evolutionary concerns. New genetic typings on 730 Arizona Mexican Americans for the HLA-A, HLA-B, ABO, Rh, MNSs, Duffy, Kidd, and Kell loci are presented here and they are used to estimate ancestral contributions. We considered both a dihybrid model with Amerindians and Spaniards as proposed ancestors, and a trihybrid model with Amerindians, Spaniards, and Africans as proposed ancestors. A modified weighted least squares method that allows for linkage disequilibrium was used to estimate ancestral contributions for each model. The following admixture estimates were obtained: Amerindian, 0.29 +/- 0.04; Spaniard, 0.68 +/- 0.05; and African, 0.03 +/- 0.02. The interpretation of these results with respect to Amerindian and Spanish ancestry is straightforward. African ancestry is strongly supported by the presence of a marker of African descent, Fy, despite the fact that the standard error of the estimate is as large as the estimated admixture proportion. An evaluation of the sensitivity of these results to a number of variables is presented: 1) our choices of ancestral allele frequencies, 2) the possibility of selection at HLA and the blood groups, and 3) genetic drift in Mexican Americans.

  17. Covariate-Adjusted Precision Matrix Estimation with an Application in Genetical Genomics

    PubMed Central

    Cai, T. Tony; Li, Hongzhe; Liu, Weidong; Xie, Jichun

    2017-01-01

    Summary Motivated by analysis of genetical genomics data, we introduce a sparse high dimensional multivariate regression model for studying conditional independence relationships among a set of genes adjusting for possible genetic effects. The precision matrix in the model specifies a covariate-adjusted Gaussian graph, which presents the conditional dependence structure of gene expression after the confounding genetic effects on gene expression are taken into account. We present a covariate-adjusted precision matrix estimation method using a constrained ℓ1 minimization, which can be easily implemented by linear programming. Asymptotic convergence rates in various matrix norms and sign consistency are established for the estimators of the regression coefficients and the precision matrix, allowing both the number of genes and the number of the genetic variants to diverge. Simulation shows that the proposed method results in significant improvements in both precision matrix estimation and graphical structure selection when compared to the standard Gaussian graphical model assuming constant means. The proposed method is also applied to analyze a yeast genetical genomics data for the identification of the gene network among a set of genes in the mitogen-activated protein kinase pathway.

  18. Estimation of Additive, Dominance, and Imprinting Genetic Variance Using Genomic Data

    PubMed Central

    Lopes, Marcos S.; Bastiaansen, John W. M.; Janss, Luc; Knol, Egbert F.; Bovenhuis, Henk

    2015-01-01

    Traditionally, exploration of genetic variance in humans, plants, and livestock species has been limited mostly to the use of additive effects estimated using pedigree data. However, with the development of dense panels of single-nucleotide polymorphisms (SNPs), the exploration of genetic variation of complex traits is moving from quantifying the resemblance between family members to the dissection of genetic variation at individual loci. With SNPs, we were able to quantify the contribution of additive, dominance, and imprinting variance to the total genetic variance by using a SNP regression method. The method was validated in simulated data and applied to three traits (number of teats, backfat, and lifetime daily gain) in three purebred pig populations. In simulated data, the estimates of additive, dominance, and imprinting variance were very close to the simulated values. In real data, dominance effects account for a substantial proportion of the total genetic variance (up to 44%) for these traits in these populations. The contribution of imprinting to the total phenotypic variance of the evaluated traits was relatively small (1–3%). Our results indicate a strong relationship between additive variance explained per chromosome and chromosome length, which has been described previously for other traits in other species. We also show that a similar linear relationship exists for dominance and imprinting variance. These novel results improve our understanding of the genetic architecture of the evaluated traits and shows promise to apply the SNP regression method to other traits and species, including human diseases. PMID:26438289

  19. Estimates of genetic parameters of body weight in descendants of X-irradiated rat spermatogonia.

    PubMed

    Gianola, D; Chapman, A B; Rutledge, J J

    1977-08-01

    Effects of nine generations of 450r per generation of ancestral spermatogonial X irradiation of inbred rats on genetic parameters of body weight at 3, 6, and 10 weeks of age and of weight gains between these periods were studied. Covariances among relatives were estimated by mixed model and regression techniques in randomly selected lines with (R) and without (C) radiation history. Analyses of the data were based on five linear genetic models combining additive direct, additive indirect (maternal), dominance and environmental effects. Parameters in these models were estimated by generalized least-squares. A model including direct and indirect genetic effects fit more closely to the data in both R and C lines. Overdominance of induced mutations did not seem to be present. Ancestral irradiation increased maternal additive genetic variances of body weights and gains but not direct genetic variances. Theoretically, due to a negative direct-maternal genetic correlation, within full-sib family selection would be ineffective in increasing body weight at six weeks in both R and C lines. However, progress from mass selection would be expected to be faster in the R lines.

  20. State estimation for Markovian jumping genetic regulatory networks with random delays

    NASA Astrophysics Data System (ADS)

    Liu, Jinliang; Tian, Engang; Gu, Zhou; Zhang, Yuanyuan

    2014-07-01

    In this paper, the state estimation problem is investigated for stochastic genetic regulatory networks (GRNs) with random delays and Markovian jumping parameters. The delay considered is assumed to be satisfying a certain stochastic characteristic. Meantime, the delays of GRNs are described by a binary switching sequence satisfying a conditional probability distribution. The aim of this paper is to design a state estimator to estimate the true states of the considered GRNs through the available output measurements. By using Lyapunov functional and some stochastic analysis techniques, the stability criteria of the estimation error systems are obtained in the form of linear matrix inequalities under which the estimation error dynamics is globally asymptotically stable. Then, the explicit expression of the desired estimator is shown. Finally, a numerical example is presented to show the effectiveness of the proposed results.

  1. Short communication: Estimates of genetic parameters for dairy fertility in New Zealand.

    PubMed

    Amer, P R; Stachowicz, K; Jenkins, G M; Meier, S

    2016-10-01

    Reproductive performance of dairy cows in a seasonal calving system is especially important as cows are required to achieve a 365-d calving interval. Prior research with a small data set has identified that the genetic evaluation model for fertility could be enhanced by replacing the binary calving rate trait (CR42), which gives the probability of a cow calving within the first 42d since the planned start of calving at second, third, and fourth calving, with a continuous version, calving season day (CSD), including a heifer calving season day trait expressed at first calving, removing milk yield, retaining a probability of mating trait (PM21) which gives the probability of a cow being mated within the first 21d from the planned start of mating, and first lactation body condition score (BCS), and including gestation length (GL). The aim of this study was to estimate genetic parameters for the proposed new model using a larger data set and compare these with parameters used in the current system. Heritability estimates for CSD and PM21 ranged from 0.013 to 0.019 and from 0.031 to 0.058, respectively. For the 2 traits that correspond with the ones used in the current genetic evaluation system (mating trait, PM21 and BCS) genetic correlations were lower in this study compared with previous estimates. Genetic correlations between CSD and PM21 across different parities were also lower than the correlations between CR42 and PM21 reported previously. The genetic correlation between heifer CSD and CSD in first parity was 0.66. Estimates of genetic correlations of BCS with CSD were higher than those with PM21. For GL, direct heritability was estimated to be 0.67, maternal heritability was 0.11, and maternal repeatability was 0.22. Direct GL had moderate to high and favorable genetic correlations with evaluated fertility traits, whereas corresponding residual correlations remain low, which makes GL a useful candidate predictor trait for fertility in a multiple trait

  2. Bayesian inference in genetic parameter estimation of visual scores in Nellore beef-cattle

    PubMed Central

    2009-01-01

    The aim of this study was to estimate the components of variance and genetic parameters for the visual scores which constitute the Morphological Evaluation System (MES), such as body structure (S), precocity (P) and musculature (M) in Nellore beef-cattle at the weaning and yearling stages, by using threshold Bayesian models. The information used for this was gleaned from visual scores of 5,407 animals evaluated at the weaning and 2,649 at the yearling stages. The genetic parameters for visual score traits were estimated through two-trait analysis, using the threshold animal model, with Bayesian statistics methodology and MTGSAM (Multiple Trait Gibbs Sampler for Animal Models) threshold software. Heritability estimates for S, P and M were 0.68, 0.65 and 0.62 (at weaning) and 0.44, 0.38 and 0.32 (at the yearling stage), respectively. Heritability estimates for S, P and M were found to be high, and so it is expected that these traits should respond favorably to direct selection. The visual scores evaluated at the weaning and yearling stages might be used in the composition of new selection indexes, as they presented sufficient genetic variability to promote genetic progress in such morphological traits. PMID:21637450

  3. An animal breeding approach to the estimation of genetic and environmental trends from field populations.

    PubMed

    Garrick, D J

    2010-04-01

    Observed or phenotypic trends in animal performance can be readily quantified from information collected from research or field populations. Phenotypic performance is determined by the collective impact of systematic effects that vary by trait, but may include herd, year, sex, and age; additive genetic effects; and a remainder that is referred to as the lack-of-fit or unexplained residual. It is of interest to partition observed performance into these respective components to determine the extent to which genetic or environmental trends or both are responsible for any observed phenotypic trends. An animal breeding approach to separate these components from field data involves the use of a linear model that includes fixed effects for systematic terms and random effects for genetic and residual contributions. The fitted random effects are predicted using a shrinkage estimator known as BLUP that relies only on a translation invariant subset of the field data that does not involve the unknown fixed effects. Fixed effects can then be estimated by adjusting observations for estimates of the random effects. Reliable estimation of trends using this approach requires that relevant fixed effects are recorded, cohorts representing different fixed effects classes are genetically related or connected, and that any records used as the basis for selection in the population are included in the data set.

  4. Estimation of the Proportion of Genetic Variation Accounted for by DNA Tests

    USDA-ARS?s Scientific Manuscript database

    An increasingly relevant question in evaluating commercial DNA tests is "What proportion of the additive genetic variation in the target trait is accounted for by the test?" Therefore, several estimators of this quantity were evaluated by simulation of a population of 1000 animals with 100 sires, ea...

  5. Genetic and phenotypic parameter estimates for feed intake and other traits in growing beef cattle

    USDA-ARS?s Scientific Manuscript database

    Genetic parameters for dry matter intake (DMI), residual feed intake (RFI), average daily gain (ADG), mid-period body weight (MBW), gain to feed ratio (G:F) and flight speed (FS) were estimated using 1165 steers from a mixed-breed population using restricted maximum likelihood methodology applied to...

  6. Estimating heritabilities and genetic correlations with marker-based methods: an experimental test in Mimulus guttatus.

    PubMed

    van Kleunen, M; Ritland, K

    2005-01-01

    The calculation of heritabilities and genetic correlations, which are necessary for predicting evolutionary responses, requires knowledge about the relatedness between individuals. This information is often not directly available, especially not for natural populations, but can be inferred by using molecular markers such as allozymes. Several methods based on inferred relatedness from marker data have been developed to estimate heritabilities and genetic correlations in natural populations. Most methods use maximum-likelihood procedures to assign pairs or groups of individuals to predefined discrete relatedness classes (e.g., half sibs and unrelated individuals). The Ritland method, on the other hand, uses method of moments estimators to estimate pairwise relatedness among individuals as continuous values. We tested both the Ritland method and a maximum-likelihood method by applying them to a greenhouse population consisting of seed families of the herb Mimulus guttatus and comparing the results to the ones from a frequently used standard method based on half-sib families. Estimates of genetic correlations were far from accurate, especially when we used the Ritland method. However, this study shows that even with a few variable allozyme loci, it is possible to get qualitatively good indications about the presence of heritable genetic variation from marker-based methods, even though both methods underestimated it.

  7. Estimates of genetic parameters among scale activity scores, growth, and fatness in pigs

    USDA-ARS?s Scientific Manuscript database

    Genetic parameters for scale activity score were estimated from generations 5, 6, and 7 of a randomly selected, composite population composed of Duroc, Large White, and two sources of Landrace (n = 2,186). At approximately 156 d of age, pigs were weighed (WT) and ultrasound backfat measurements (BF1...

  8. Estimates of genetic variation for feed intake and other characteristics in growing beef cattle

    USDA-ARS?s Scientific Manuscript database

    Calves born between 2003 and 2006 at the U.S. Meat Animal Research Center provided data for estimation of genetic and phenotypic parameters for measures of body weight and gain and feed intake during the finishing phase. At average age 278 d, cattle were started on a high-energy diet of corn, alfalf...

  9. Heritability estimates in behavior genetics: wasn't that station passed long ago?

    PubMed

    Crusio, Wim E

    2012-10-01

    Charney describes several mechanisms that will bias estimates of heritability in unpredictable directions. In addition, the mechanisms described by Charney explain the puzzling fact that research in human-behavior genetics routinely reports higher heritabilities than animal studies do. However, I argue that the concept of heritability has no real place in human research anyway.

  10. Estimation of genetic parameters among reproductive and growth traits in yearling heifers.

    PubMed

    Smith, B A; Brinks, J S; Richardson, G V

    1989-11-01

    Growth and reproductive data were obtained on 779 beef heifers at the San Juan Basin Research Center, Hesperus, Co. Genetic parameters were estimated for age of puberty (AOP), age of first calving (AOC), julian day of first calving (DOC), julian day of second calving (DOSC), birth weight, weaning weight, yearling weight, and average daily gain from weaning to yearling and to cycling weights. The least squares model included birth year, age of dam and breed as fixed effects, sire/breed as a random variable, and day of birth and percent inbreeding as covariates. Day of birth was not included in the analyses of AOC, DOC or DOSC. Paternal half-sib estimates of heritability were: AOP, .10 +/- .17; AOC, .01 +/- .12; DOC, .09 +/- .13 and DOSC, .36 +/- .18. Genetic and phenotypic correlations were generally favorable, but genetic correlations were variable with large standard errors. Inbreeding had a detrimental effect on reproductive traits, and a seasonal effect was present for AOP.

  11. Estimation of genetic (co)variances of Gompertz growth function parameters in pigs.

    PubMed

    Coyne, J M; Matilainen, K; Berry, D P; Sevon-Aimonen, M-L; Mäntysaari, E A; Juga, J; Serenius, T; McHugh, N

    2017-04-01

    The objective of this study was to estimate genetic (co)variances for the Gompertz growth function parameters, asymptotic mature weight (A), the ratio of mature weight to birthweight (B) and rate of maturation (k), using alternative modelling approaches. The data set consisted of 51 893 live weight records from 10 201 growing pigs. The growth of each pig was modelled using the Gompertz model employing either a two-step fixed effect or mixed model approach or a one-step mixed model approach using restricted maximum likelihood for the estimation of genetic (co)variance. Heritability estimates for the Gompertz growth function parameters, A (0.40), B (0.69) and k (0.45), were greatest for the one-step approach, compared with the two-step fixed effects approach, A (0.10), B (0.33) and k (0.13), and the two-step mixed model approach, A (0.17), B (0.32) and k (0.18). Inferred genetic correlations (i.e. correlations of estimated breeding values) between growth function parameters within models ranged from -0.78 to 0.76, and across models ranged from 0.28 to 0.73 for parameter A, 0.75 to 0.88 for parameter B and 0.09 to 0.37 for parameter k. Correlations between predicted daily sire live weights based on the Gompertz growth curve parameters' estimated breeding values from 60 to 200 days of age between all three modelled approaches were moderately to strongly correlated (0.75 to 0.95). Results from this study provide heritability estimates for biologically interpretable parameters of pig growth through the quantification of genetic (co)variances, thereby facilitating the estimation of breeding values for inclusion in breeding objectives to aid in breeding and selection decisions.

  12. Landscape barriers reduce gene flow in an invasive carnivore: geographical and local genetic structure of American mink in Scotland.

    PubMed

    Zalewski, Andrzej; Piertney, Stuart B; Zalewska, Hanna; Lambin, Xavier

    2009-04-01

    To be effective, management programmes geared towards halting or reversing the spread of invasive species must focus on defined and defensible areas. This requires knowledge of the dispersal of non-native species targeted for control to better understand invasion and recolonisation scenarios. We investigated the genetic structure of invasive American mink (Neovison vison) in Scotland, and incorporated landscape genetic approaches to examine resultant patterns in relation to geographical features that may influence dispersal. Populations of mink sampled from 10 sites in two regions (Argyll and Northeast Scotland) show a distinct genetic structure. First, the majority of pairwise population comparisons yielded F(ST) values that were significantly greater than zero. Second, AMOVA revealed that most of the genetic variance was attributable to differences among regions. Assignment tests placed 89 or more of individuals into their sampled region. Bayesian clustering methods grouped samples into two clusters according to their region of origin. Wombling approach identified the Cairngorms Mountains as a major impediment to gene flow between the regions. Mantel pairwise correlations between genetic and geographical distances estimated as least-cost distance assuming a linear increase in the cost of movement with increasing elevation were higher than Euclidean distances or distance along waterways. Spatial autocorrelation analyses revealed stronger spatial structuring for females than for males. These results suggest that gene flow by American mink is restricted by landscape features (mountain ranges) and that eradication attempt should in the first instance break down the connectivity between management units separated by mountains.

  13. Genetic analysis of coding SNPs in blood-brain barrier transporter MDR1 in European Parkinson's disease patients.

    PubMed

    Funke, Claudia; Soehn, Anne S; Tomiuk, Juergen; Riess, Olaf; Berg, Daniela

    2009-04-01

    Parkinson's disease (PD) is characterized by the loss of dopaminergic neurons and the presence of intracytoplasmic inclusions (Lewy bodies). Iron, which is elevated in the substantia nigra of PD patients, seems to be of pivotal importance, because of its capacity to enhance the amplification of reactive oxygen species. As iron enters and exits the brain via transport proteins in the blood-brain barrier (BBB), these proteins may represent candidates for a genetic susceptibility to PD. P-glycoprotein (P-gp) is one important efflux pump in the BBB. There is evidence that the function of P-gp is impaired in PD patients. In the current study we examined ten coding single nucleotide polymorphisms in the multidrug resistance gene 1 (MDR1) encoding P-gp to assess whether certain genotypes are associated with PD. However, genotyping of 300 PD patients and 302 healthy controls did not reveal a significant association between coding MDR1 gene polymorphisms and PD.

  14. The use and abuse of genetic marker-based estimates of relatedness and inbreeding

    PubMed Central

    Taylor, Helen R

    2015-01-01

    Genetic marker-based estimators remain a popular tool for measuring relatedness (rxy) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of rxy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker-based estimators of rxy and F in a species with very low genetic diversity, New Zealand’s little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of rxy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated rxy or F is relatively high (Pearson’s r = 0.66–0.72 and 0.81–0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker-based estimates of rxy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator’s performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of rxy and F debatable. PMID:26357542

  15. Problems and solutions in the estimation of genetic risks from radiation and chemicals

    SciTech Connect

    Russell, W. L.

    1980-01-01

    Extensive investigations with mice on the effects of various physical and biological factors, such as dose rate, sex and cell stage, on radiation-induced mutation have provided an evaluation of the genetics hazards of radiation in man. The mutational results obtained in both sexes with progressive lowering of the radiation dose rate have permitted estimation of the mutation frequency expected under the low-level radiation conditions of most human exposure. Supplementing the studies on mutation frequency are investigations on the phenotypic effects of mutations in mice, particularly anatomical disorders of the skeleton, which allow an estimation of the degree of human handicap associated with the occurrence of parallel defects in man. Estimation of the genetic risk from chemical mutagens is much more difficult, and the research is much less advanced. Results on transmitted mutations in mice indicate a poor correlation with mutation induction in non-mammalian organisms.

  16. Estimating observing locations for advancing beyond the winter predictability barrier of Indian Ocean dipole event predictions

    NASA Astrophysics Data System (ADS)

    Feng, Rong; Duan, Wansuo; Mu, Mu

    2017-02-01

    In this paper, we explored potential observing locations (i.e., the sensitive areas) of positive Indian Ocean dipole (IOD) events to advance beyond the winter predictability barrier (WPB) using the geophysical fluid dynamics laboratory climate model version 2p1 (GFDL CM2p1). The sensitivity analysis is conducted through perfect model predictability experiments, in which the model is assumed to be perfect and so any prediction errors are caused by initial errors. The results show that the initial errors with an east-west dipole pattern are more likely to result in a significant WPB than spatially correlated noises; the areas where the large values of the dipole pattern initial errors are located have great effects on prediction uncertainties in winter and provide useful information regarding the sensitive areas. Further, the prediction uncertainties in winter are more sensitive to the initial errors in the subsurface large value areas than to those in the surface large value areas. The results indicate that the subsurface large value areas are sensitive areas for advancing beyond the WPB of IOD predictions and if we carry out intensive observations across these areas, the prediction errors in winter may be largely reduced. This will lead to large improvements in the skill of wintertime IOD event forecasts.

  17. Tight genetic linkage of prezygotic barrier loci creates a multifunctional speciation island in Petunia.

    PubMed

    Hermann, Katrin; Klahre, Ulrich; Moser, Michel; Sheehan, Hester; Mandel, Therese; Kuhlemeier, Cris

    2013-05-20

    Most flowering plants depend on animal vectors for pollination and seed dispersal. Differential pollinator preferences lead to premating isolation and thus reduced gene flow between interbreeding plant populations. Sets of floral traits, adapted to attract specific pollinator guilds, are called pollination syndromes. Shifts in pollination syndromes have occurred surprisingly frequently, considering that they must involve coordinated changes in multiple genes affecting multiple floral traits. Although the identification of individual genes specifying single pollination syndrome traits is in progress in many species, little is known about the genetic architecture of coadapted pollination syndrome traits and how they are embedded within the genome. Here we describe the tight genetic linkage of loci specifying five major pollination syndrome traits in the genus Petunia: visible color, UV absorption, floral scent production, pistil length, and stamen length. Comparison with other Solanaceae indicates that, in P. exserta and P. axillaris, loci specifying these floral traits have specifically become clustered into a multifunctional "speciation island". Such an arrangement promotes linkage disequilibrium and avoids the dissolution of pollination syndromes by recombination. We suggest that tight genetic linkage provides a mechanism for rapid switches between distinct pollination syndromes in response to changes in pollinator availabilities. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Perceived barriers to Internet-based health communication on human genetics.

    PubMed

    Bernhardt, Jay M; Lariscy, Ruth Ann Weaver; Parrott, Roxanne L; Silk, Kami J; Felter, Elizabeth M

    2002-01-01

    The Internet has emerged as potential vehicle for distributing health communication to millions of individuals because it is interactive, user controlled, and offers breadth and depth of information. However, its widespread use by the public may be limited due to three overarching concerns: privacy and confidentiality, information accuracy and perceptions of credibility, including limited credibility of some government-sponsored web sites. To explore the potential of using the Internet, especially for delivering information on human genetics communication, 15 focus groups and one interview were conducted with African American and European American adult males and females in a southeastern town. We found that the participants recognized great potential in the Internet for health communication on human genetics, but they also voiced concerns about the credibility and accuracy of online information, lack of trust in many web sites, and fear of safeguarding privacy. Their concerns are summarized here, along with potential remedies health communicators could implement and should research further. The Internet cannot achieve its full potential for human genetics communication until the public's concerns are addressed and resolved.

  19. Six genetically distinct clades of Palola (Eunicidae, Annelida) from Lizard Island, Great Barrier Reef, Australia.

    PubMed

    Schulze, Anja

    2015-09-18

    A total of 36 lots of Palola spp. (Eunicidae, Annelida) were collected during the Lizard Island Polychaete Workshop on Lizard Island, Great Barrier Reef, Queensland, Australia. Of these, 21 specimens were sequenced for a portion of the mitochondrial cytochrome c oxidase I gene. These sequences were analysed in conjunction with existing sequences of Palola spp. from other geographic regions. The samples from Lizard Island form six distinct clades, although none of them can clearly be assigned to any of the nominal species. Four of the six Lizard Island clades fall into species group A and the remaining two into species group B (which also includes the type species, Palola viridis). All sequenced specimens were characterized morphologically as far as possible and a dichotomous key was assembled. Based on this key, the remaining samples were identified as belonging to one of the clades.

  20. Indirect genetic effects and kin recognition: estimating IGEs when interactions differ between kin and strangers.

    PubMed

    Alemu, S W; Berg, P; Janss, L; Bijma, P

    2014-02-01

    Social interactions among individuals are widespread, both in natural and domestic populations. As a result, trait values of individuals may be affected by genes in other individuals, a phenomenon known as indirect genetic effects (IGEs). IGEs can be estimated using linear mixed models. The traditional IGE model assumes that an individual interacts equally with all its partners, whether kin or strangers. There is abundant evidence, however, that individuals behave differently towards kin as compared with strangers, which agrees with predictions from kin-selection theory. With a mix of kin and strangers, therefore, IGEs estimated from a traditional model may be incorrect, and selection based on those estimates will be suboptimal. Here we investigate whether genetic parameters for IGEs are statistically identifiable in group-structured populations when IGEs differ between kin and strangers, and develop models to estimate such parameters. First, we extend the definition of total breeding value and total heritable variance to cases where IGEs depend on relatedness. Next, we show that the full set of genetic parameters is not identifiable when IGEs differ between kin and strangers. Subsequently, we present a reduced model that yields estimates of the total heritable effects on kin, on non-kin and on all social partners of an individual, as well as the total heritable variance for response to selection. Finally we discuss the consequences of analysing data in which IGEs depend on relatedness using a traditional IGE model, and investigate group structures that may allow estimation of the full set of genetic parameters when IGEs depend on kin.

  1. Estimates of genetic variance and variance of predicted genetic merits using pedigree or genomic relationship matrices in six Brown Swiss cattle populations for different traits.

    PubMed

    Loberg, A; Dürr, J W; Fikse, W F; Jorjani, H; Crooks, L

    2015-10-01

    The amount of variance captured in genetic estimations may depend on whether a pedigree-based or genomic relationship matrix is used. The purpose of this study was to investigate the genetic variance as well as the variance of predicted genetic merits (PGM) using pedigree-based or genomic relationship matrices in Brown Swiss cattle. We examined a range of traits in six populations amounting to 173 population-trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree-based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as heritability and population size increased. In contrast, variances of predicted genetic merits obtained using a genomic relationship matrix were mostly larger than variances of genetic merit predicted using pedigree-based relationship matrix. The ratio of the genomic to pedigree-based PGM variances decreased as heritability and population size rose. The increased variance among predicted genetic merits is important for animal breeding because this is one of the factors influencing genetic progress.

  2. Fertilization success and the estimation of genetic variance in sperm competitiveness.

    PubMed

    Garcia-Gonzalez, Francisco; Evans, Jonathan P

    2011-03-01

    A key question in sexual selection is whether the ability of males to fertilize eggs under sperm competition exhibits heritable genetic variation. Addressing this question poses a significant problem, however, because a male's ability to win fertilizations ultimately depends on the competitive ability of rival males. Attempts to partition genetic variance in sperm competitiveness, as estimated from measures of fertilization success, must therefore account for stochastic effects due to the random sampling of rival sperm competitors. In this contribution, we suggest a practical solution to this problem. We advocate the use of simple cross-classified breeding designs for partitioning sources of genetic variance in sperm competitiveness and fertilization success and show how these designs can be used to avoid stochastic effects due to the random sampling of rival sperm competitors. We illustrate the utility of these approaches by simulating various scenarios for estimating genetic parameters in sperm competitiveness, and show that the probability of detecting additive genetic variance in this trait is restored when stochastic effects due to the random sampling of rival sperm competitors are controlled. Our findings have important implications for the study of the evolutionary maintenance of polyandry. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

  3. Estimates of genetic parameters for chemical traits of meat quality in Japanese black cattle.

    PubMed

    Sakuma, Hironori; Saito, Kaoru; Kohira, Kimiko; Ohhashi, Fumie; Shoji, Noriaki; Uemoto, Yoshinobu

    2017-02-01

    Genetic parameters for 54 carcass and chemical traits, such as general composition (moisture, crude fat and crude protein), fatty acid composition and water-soluble compounds (free amino acids, peptides, nucleotides and sugars) of 587 commercial Japanese Black cattle were assessed. Heritability estimates for carcass traits and general composition ranged between 0.19-0.28, whereas those for fatty acid composition ranged between 0.11-0.85. Most heritability estimates for water-soluble compounds were lower than 0.30; these traits were affected by aging period. Moderate heritability was observed for glutamine, alanine, taurine, anserine, inosine 5'-monophosphate (IMP), inosine and myo-inositol. In particular, heritability estimates were the highest (0.66) for taurine. Traits with moderate heritability were unaffected by aging period, with the exception of IMP, which was affected by aging period but exhibited moderate heritability (0.47). Although phenotypic correlations of water-soluble compounds with carcass weight (CW), beef marbling standard (BMS) and monounsaturated fatty acid were generally low, genetic correlations between these traits were low to high. At the genetic level, most of the water-soluble compounds were positively correlated with monounsaturated fatty acid but negatively correlated with CW and BMS. Thus, our results indicate that genetic variance and correlations could exist and be captured for some of the water-soluble compounds. © 2016 The Authors. Animal Science Journal published by John Wiley & Sons Australia, Ltd on behalf of Japanese Society of Animal Science.

  4. Estimates of genetic parameters for chemical traits of meat quality in Japanese black cattle

    PubMed Central

    Sakuma, Hironori; Saito, Kaoru; Kohira, Kimiko; Ohhashi, Fumie; Shoji, Noriaki

    2016-01-01

    Abstract Genetic parameters for 54 carcass and chemical traits, such as general composition (moisture, crude fat and crude protein), fatty acid composition and water‐soluble compounds (free amino acids, peptides, nucleotides and sugars) of 587 commercial Japanese Black cattle were assessed. Heritability estimates for carcass traits and general composition ranged between 0.19–0.28, whereas those for fatty acid composition ranged between 0.11–0.85. Most heritability estimates for water‐soluble compounds were lower than 0.30; these traits were affected by aging period. Moderate heritability was observed for glutamine, alanine, taurine, anserine, inosine 5′‐monophosphate (IMP), inosine and myo‐inositol. In particular, heritability estimates were the highest (0.66) for taurine. Traits with moderate heritability were unaffected by aging period, with the exception of IMP, which was affected by aging period but exhibited moderate heritability (0.47). Although phenotypic correlations of water‐soluble compounds with carcass weight (CW), beef marbling standard (BMS) and monounsaturated fatty acid were generally low, genetic correlations between these traits were low to high. At the genetic level, most of the water‐soluble compounds were positively correlated with monounsaturated fatty acid but negatively correlated with CW and BMS. Thus, our results indicate that genetic variance and correlations could exist and be captured for some of the water‐soluble compounds. PMID:27146072

  5. Genetic parameter estimates of live animal ultrasonic measures of retail yield indicators in yearling breeding cattle.

    PubMed

    Shepard, H H; Green, R D; Golden, B L; Hamlin, K E; Perkins, T L; Diles, J B

    1996-04-01

    Ultrasonic measures of backfat thickness (BFT) and longissimus muscle area (LMA) taken on Angus bulls (n = 805) and heifers (n = 877) ranging in age from approximately 8 to 20 mo in a production setting in western Nebraska were used to estimate genetic (co)variances. Further information used in the analyses, including weaning weight (WWT), postweaning ADG, and scrotal circumference (SC), was obtained from the American Angus Association, St. Joseph, MO, for these individuals and for animals from the same herd and contemporary groups. Data were analyzed using single-trait, sire model, restricted maximum likelihood (REML) procedures to estimate starting variances for later two-trait analyses. These two-trait analyses were done to estimate variance components for WWT coupled with BFT, LMA, SC, and ADG, also using REML procedures, but with a sire-maternal grandsire model for WWT and a sire model for the other trait(s). Heritabilities for BFT, LMA, WWT direct, WWT maternal, SC, and ADG were .56, .11, .19, .24, .56, and .51, respectively. Genetic correlations between WWT direct and WWT maternal, WWT direct and LMA, WWT maternal and LMA, WWT maternal and BFT were -.57, .42, .01, and -.69, respectively. Genetic parameters from this study were used to calculate possible genetic change with a typical selection scenario, and it was shown that among WWT, BFT, and LMA, BFT could be affected the most by selection, relative to its mean.

  6. Phenotypic and genetic parameter estimates for reproductive traits in Zandi sheep.

    PubMed

    Mohammadi, Kourosh; Beigi Nassiri, Mohammad Taghi; Rahmatnejad, Enayat; Sheikh, Masoud; Fayazi, Jamal; Karimi Manesh, Amin

    2013-02-01

    This study reports on the phenotypic and genetic (co)variance components for reproductive traits in Zandi sheep, using between 1,859 and 2,588 records obtained from 577 ewes. The data were collected from the Khojir Breeding Station of Zandi sheep in Tehran, Iran from 1994 to 2008. The basic traits were litter size at birth (LSB), litter size at weaning (LSW), litter mean weight per lamb born (LMWLB), and litter mean weight per lamb weaned (LMWLW), and the composite traits were total litter weight at birth (TLWB) and total litter weight at weaning (TLWW). Genetic analyses were carried out using the restricted maximum likelihood method that was explored by fitting the additive direct genetic effects and permanent environmental effects of the ewes as random effects and the ewe age at lambing and lambing year as fixed effects for all of the investigated traits. Akaike's information criterion was used to choose the most appropriate model. LSB, LSW, LMWLB, LMWLW, TLWB, and TLWW direct heritability estimates were 0.07, 0.05, 0.12, 0.10, 0.08, and 0.14, respectively. The estimated fractions of variance due to the permanent environmental effects of the ewe ranged from 0.03 for LMWLB to 0.08 for LMWLW and TLWW. Corresponding repeatability estimates ranged from 0.10 for LSW to 0.22 for TLWW. Direct genetic correlations varied from -0.61 for LSB-LMWLB to 0.88 for LSB-LSW and LSB-TLWB. Results indicate that genetic change depends not only on the heritability of traits, but also on the observed phenotypic variation; therefore, improvement of non-genetic factors should be included in the breeding programs.

  7. A new barrier to dispersal trapped old genetic clines that escaped the Easter Microplate tension zone of the Pacific vent mussels.

    PubMed

    Plouviez, Sophie; Faure, Baptiste; Le Guen, Dominique; Lallier, François H; Bierne, Nicolas; Jollivet, Didier

    2013-01-01

    Comparative phylogeography of deep-sea hydrothermal vent species has uncovered several genetic breaks between populations inhabiting northern and southern latitudes of the East Pacific Rise. However, the geographic width and position of genetic clines are variable among species. In this report, we further characterize the position and strength of barriers to gene flow between populations of the deep-sea vent mussel Bathymodiolus thermophilus. Eight allozyme loci and DNA sequences of four nuclear genes were added to previously published sequences of the cytochrome c oxidase subunit I gene. Our data confirm the presence of two barriers to gene flow, one located at the Easter Microplate (between 21°33'S and 31°S) recently described as a hybrid zone, and the second positioned between 7°25'S and 14°S with each affecting different loci. Coalescence analysis indicates a single vicariant event at the origin of divergence between clades for all nuclear loci, although the clines are now spatially discordant. We thus hypothesize that the Easter Microplate barrier has recently been relaxed after a long period of isolation and that some genetic clines have escaped the barrier and moved northward where they have subsequently been trapped by a reinforcing barrier to gene flow between 7°25'S and 14°S.

  8. A New Barrier to Dispersal Trapped Old Genetic Clines That Escaped the Easter Microplate Tension Zone of the Pacific Vent Mussels

    PubMed Central

    Plouviez, Sophie; Faure, Baptiste; Le Guen, Dominique; Lallier, François H.; Bierne, Nicolas; Jollivet, Didier

    2013-01-01

    Comparative phylogeography of deep-sea hydrothermal vent species has uncovered several genetic breaks between populations inhabiting northern and southern latitudes of the East Pacific Rise. However, the geographic width and position of genetic clines are variable among species. In this report, we further characterize the position and strength of barriers to gene flow between populations of the deep-sea vent mussel Bathymodiolus thermophilus. Eight allozyme loci and DNA sequences of four nuclear genes were added to previously published sequences of the cytochrome c oxidase subunit I gene. Our data confirm the presence of two barriers to gene flow, one located at the Easter Microplate (between 21°33′S and 31°S) recently described as a hybrid zone, and the second positioned between 7°25′S and 14°S with each affecting different loci. Coalescence analysis indicates a single vicariant event at the origin of divergence between clades for all nuclear loci, although the clines are now spatially discordant. We thus hypothesize that the Easter Microplate barrier has recently been relaxed after a long period of isolation and that some genetic clines have escaped the barrier and moved northward where they have subsequently been trapped by a reinforcing barrier to gene flow between 7°25′S and 14°S. PMID:24312557

  9. Population genetic analysis of Streptomyces albidoflavus reveals habitat barriers to homologous recombination in the diversification of streptomycetes.

    PubMed

    Cheng, Kun; Rong, Xiaoying; Pinto-Tomás, Adrián A; Fernández-Villalobos, Marcela; Murillo-Cruz, Catalina; Huang, Ying

    2015-02-01

    Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of Streptomyces albidoflavus derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in S. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φw) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within Streptomyces species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for S. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes.

  10. [Estimation of Genetic Diversity of Romanov Sheep by the Coefficient of Genetic Originality Based on ISSR-Fingerprinting Data].

    PubMed

    Nesteruk, L V; Makarova, N N; Svishcheva, G R; Stolpovsky, Yu A

    2015-07-01

    Estimation of the state of the genetic diversity and the originality of the breed structure is required for the conservation and management of domestic breeds of agricultural animals. The Romanov breed of sheep from the leading breeding and gene pool farms in Yaroslavl oblast (Russia) is the object of our study. ISS R fingerprinting was used as a molecular method of the study of sheep gene pools. Forty-three DNA fragments were detected (25 and 18, respectively) by two primers ((AG)9C and (GA)9C). Of the discovered ISSR markers, 81% were polymorphic. The coefficient of genetic originality was for the first time used for the study of the specificity and originality of the Romanov-breed gene pool. Based on its values, the studied individuals were divided into five classes depending on the frequency of the ISSR fragment. The most original or the rarest, as well as typical genotypes, were singled out in the Romanov sheep gene pool. Use the obtained data on genetic originality was proposed as a means to increase the efficiency of selection and breeding during the breeding of autochthonous breeds of domesticated animal species.

  11. Genetic parameter estimation for major milk fatty acids in Alpine and Saanen primiparous goats.

    PubMed

    Maroteau, C; Palhière, I; Larroque, H; Clément, V; Ferrand, M; Tosser-Klopp, G; Rupp, R

    2014-05-01

    Genetic parameters for 18 fatty acids or groups of fatty acids (FA), milk production traits, and somatic cell score (SCS) were estimated by restricted maximum likelihood with a repeatability animal model, using 45,259 test-day records from the first lactations of 13,677 Alpine and Saanen goats. Fatty acid data were collected as part of an extensive recording scheme (PhénoFinLait), and sample testing was based on mid-infrared spectra estimates. The total predicted FA content in milk was approximately 3.5% in Alpine and Saanen goats. Goat milk fat showed similar saturated FA to cattle and sheep, but higher contents of capric (C10:0) FA (~ 9.7 g/100g of milk fat). Heritability estimates ranged from 0.18 to 0.49 for FA and estimates were generally higher when FA were expressed in g/100g of milk fat compared with g/100g of milk. In general, the 3 specific short- and medium-chain goat FA, caproic acid (C6:0), caprylic acid (C8:0), and especially capric (C10:0) acid, had among the highest heritability estimates (from 0.21 to 0.37; average of 0.30). Heritability estimates for milk yield, fat and protein contents, and SCS were 0.22, 0.23, 0.39, 0.09, and 0.24, 0.20, 0.40, and 0.15, in Alpine and Saanen goats, respectively. When FA were expressed in g/100g of milk, genetic correlations between fat content and all FA were high and positive. Genetic correlations between the fat content and FA groups expressed in g/100g of fat led to further investigation of the association between fat content and FA profile within milk fat. Accordingly, in both Saanen and Alpine breeds, no significant genetic correlations were found between fat content and C16:0, whereas the correlations between fat content and specific goat FA (C6:0 to C10:0) were positive (0.17 to 0.59). In addition, the genetic correlation between fat content and C14:0 was negative (-0.17 to -0.35). The values of the genetic correlations between protein content and individual FA were similar, although genetic correlations

  12. Empirical Bayes procedure for estimating genetic distance between populations and effective population size.

    PubMed Central

    Kitada, S; Hayashi, T; Kishino, H

    2000-01-01

    We developed an empirical Bayes procedure to estimate genetic distances between populations using allele frequencies. This procedure makes it possible to describe the skewness of the genetic distance while taking full account of the uncertainty of the sample allele frequencies. Dirichlet priors of the allele frequencies are specified, and the posterior distributions of the various composite parameters are obtained by Monte Carlo simulation. To avoid overdependence on subjective priors, we adopt a hierarchical model and estimate hyperparameters by maximizing the joint marginal-likelihood function. Taking advantage of the empirical Bayesian procedure, we extend the method to estimate the effective population size using temporal changes in allele frequencies. The method is applied to data sets on red sea bream, herring, northern pike, and ayu broodstock. It is shown that overdispersion overestimates the genetic distance and underestimates the effective population size, if it is not taken into account during the analysis. The joint marginal-likelihood function also estimates the rate of gene flow into island populations. PMID:11102396

  13. How old are you? Genet age estimates in a clonal animal.

    PubMed

    Devlin-Durante, M K; Miller, M W; Precht, W F; Baums, I B

    2016-11-01

    Foundation species such as redwoods, seagrasses and corals are often long-lived and clonal. Genets may consist of hundreds of members (ramets) and originated hundreds to thousands of years ago. As climate change and other stressors exert selection pressure on species, the demography of populations changes. Yet, because size does not indicate age in clonal organisms, demographic models are missing data necessary to predict the resilience of many foundation species. Here, we correlate somatic mutations with genet age of corals and provide the first, preliminary estimates of genet age in a colonial animal. We observed somatic mutations at five microsatellite loci in rangewide samples of the endangered coral, Acropora palmata (n = 3352). Colonies harboured 342 unique mutations in 147 genets. Genet age ranged from 30 to 838 years assuming a mutation rate of 1.195(-04) per locus per year based on colony growth rates and 236 to 6500 years assuming a mutation rate of 1.542(-05) per locus per year based on sea level changes to habitat availability. Long-lived A. palmata genets imply a large capacity to tolerate past environmental change, and yet recent mass mortality events in A. palmata suggest that capacity is now being frequently exceeded. © 2016 John Wiley & Sons Ltd.

  14. Estimating sampling error of evolutionary statistics based on genetic covariance matrices using maximum likelihood.

    PubMed

    Houle, D; Meyer, K

    2015-08-01

    We explore the estimation of uncertainty in evolutionary parameters using a recently devised approach for resampling entire additive genetic variance-covariance matrices (G). Large-sample theory shows that maximum-likelihood estimates (including restricted maximum likelihood, REML) asymptotically have a multivariate normal distribution, with covariance matrix derived from the inverse of the information matrix, and mean equal to the estimated G. This suggests that sampling estimates of G from this distribution can be used to assess the variability of estimates of G, and of functions of G. We refer to this as the REML-MVN method. This has been implemented in the mixed-model program WOMBAT. Estimates of sampling variances from REML-MVN were compared to those from the parametric bootstrap and from a Bayesian Markov chain Monte Carlo (MCMC) approach (implemented in the R package MCMCglmm). We apply each approach to evolvability statistics previously estimated for a large, 20-dimensional data set for Drosophila wings. REML-MVN and MCMC sampling variances are close to those estimated with the parametric bootstrap. Both slightly underestimate the error in the best-estimated aspects of the G matrix. REML analysis supports the previous conclusion that the G matrix for this population is full rank. REML-MVN is computationally very efficient, making it an attractive alternative to both data resampling and MCMC approaches to assessing confidence in parameters of evolutionary interest. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  15. Overcoming the Barrier of Low Efficiency during Genetic Transformation of Streptococcus mitis

    PubMed Central

    Salvadori, Gabriela; Junges, Roger; Morrison, Donald A.; Petersen, Fernanda C.

    2016-01-01

    Objective: Streptococcus mitis is a predominant oral colonizer, but difficulties in genetic manipulation of this species have hampered our understanding of the mechanisms it uses for colonization of oral surfaces. The aim of this study was to reveal optimal conditions for natural genetic transformation in S. mitis and illustrate its application in direct genome editing. Methods: Luciferase reporter assays were used to assess gene expression of the alternative sigma factor (σX) in combination with natural transformation experiments to evaluate the efficiency by which S. mitis activates the competence system and incorporates exogenous DNA. Optimal amounts and sources of donor DNA (chromosomal, amplicon, or replicative plasmid), concentrations of synthetic competence-stimulating peptide, and transformation media were assessed. Results: A semi-defined medium showed much improved results for response to the competence stimulating peptide when compared to rich media. The use of a donor amplicon with large homology flanking regions also provided higher transformation rates. Overall, an increase of transformation efficiencies from 0.001% or less to over 30% was achieved with the developed protocol. We further describe the construction of a markerless mutant based on this high efficiency strategy. Conclusion: We optimized competence development in S. mitis, by use of semi-defined medium and appropriate concentrations of synthetic competence factor. Combined with the use of a large amplicon of donor DNA, this method allowed easy and direct editing of the S. mitis genome, broadening the spectrum of possible downstream applications of natural transformation in this species. PMID:27458432

  16. Estimation of Odds Ratios of Genetic Variants for the Secondary Phenotypes Associated with Primary Diseases

    PubMed Central

    Wang, Jian; Shete, Sanjay

    2011-01-01

    Genetic association studies for binary diseases are designed as case-control studies: the cases are those affected with the primary disease and the controls are free of the disease. At the time of case-control collection, information about secondary phenotypes is also collected. Association studies of secondary phenotype and genetic variants have received a great deal of interest recently. To study the secondary phenotypes, investigators use standard regression approaches, where individuals with secondary phenotypes are coded as cases and those without secondary phenotypes are coded as controls. However, using the secondary phenotype as an outcome variable in a case-control study might lead to a biased estimate of odds ratios (ORs) for genetic variants. The secondary phenotype is associated with the primary disease; therefore, individuals with and without the secondary phenotype are not sampled following the principles of a case-control study. In this article, we demonstrate that such analyses will lead to a biased estimate of OR and propose new approaches to provide more accurate OR estimates of genetic variants associated with the secondary phenotype for both unmatched and frequency-matched (with respect to the secondary phenotype) case-control studies. We also propose a bootstrapping method to estimate the empirical confidence intervals for the corrected ORs. Using simulation studies and analysis of lung cancer data for single-nucleotide polymorphism associated with smoking quantity, we compared our new approaches to standard logistic regression and to an extended version of the inverse-probability-of-sampling-weighted regression. The proposed approaches provide more accurate estimation of the true OR. PMID:21308766

  17. Big mountains but small barriers: Population genetic structure of the Chinese wood frog (Rana chensinensis) in the Tsinling and Daba Mountain region of northern China

    PubMed Central

    Zhan, Aibin; Li, Cheng; Fu, Jinzhong

    2009-01-01

    Background Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Results Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. Conclusion The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may

  18. Big mountains but small barriers: population genetic structure of the Chinese wood frog (Rana chensinensis) in the Tsinling and Daba Mountain region of northern China.

    PubMed

    Zhan, Aibin; Li, Cheng; Fu, Jinzhong

    2009-04-09

    Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may significantly contribute to the

  19. Genome-wide association study of swine farrowing traits. Part I: genetic and genomic parameter estimates.

    PubMed

    Schneider, J F; Rempel, L A; Rohrer, G A

    2012-10-01

    The primary objective of this study was to determine genetic and genomic parameters among swine (Sus scrofa) farrowing traits. Genetic parameters were obtained using MTDFREML. Genomic parameters were obtained using GENSEL. Genetic and residual variances obtained from MTDFREML were used as priors for the Bayes C analysis of GENSEL. Farrowing traits included total number born (TNB), number born alive (NBA), number born dead (NBD), number stillborn (NSB), number of mummies (MUM), litter birth weight (LBW), and average piglet birth weight (ABW). Statistically significant heritabilities included TNB (0.09, P = 0.048), NBA (0.09, P = 0.041), LBW (0.20, P = 0.002), and ABW (0.26, P < 0.0001). Statistically significant genetic correlations included TNB-NBA (0.97, P < 0.0001), TNB-LBW (0.74, P < 0.0001), NBA-LBW (0.56, P < 0.0017), NSB-LBW (0.87, P < 0.0395), and LBW-ABW (0.63, P < 0.0002). Genetic parameters are similar to others found in the literature. The proportion of phenotypic variance explained by genomic markers (GP) generated by GENSEL was TNB (0.04), NBA (0.06), NBD (0.00), NSB (0.01), MUM (0.00), LBW (0.11), and ABW (0.31). Limited information is available in the literature about genomic parameters. Only the GP estimate for NSB is significantly lower than what has been published. The GP estimate for ABW is greater than the estimate for heritability found in this study. Other traits with significant heritability had GP estimates half the value of heritability. This research indicates that significant genetic markers will be found for TNB, NBA, LBW, and ABW that will have either immediate use in industry or provide a roadmap to further research with fine mapping or sequencing of areas of significance. Furthermore, these results indicate that genomic selection implemented at an early age would have similar annual progress as traditional selection, and could be incorporated along with traditional selection procedures to improve genetic progress of litter traits.

  20. Estimates of genetic parameters for stayability to consecutive calvings of Canadian Simmentals by random regression models.

    PubMed

    Jamrozik, J; McGrath, S; Kemp, R A; Miller, S P

    2013-08-01

    Stayability to consecutive calvings was selected as a measure of cow longevity in the Canadian Simmental population. Calving performance data on 188,579 cows and culling information from the Total Herd Reporting System were used to determine whether a cow stayed in a herd for her second and later (up to the eighth) calvings, given that she had calved as 2 yr old. Binary records (n = 1,164,319) were analyzed with animal linear and threshold models including fixed effects of year of birth by season of birth by parity number and age of cow at first calving by parity number and random effects of contemporary group (CG) defined as herd of birth within year by season, animal additive genetic effect, and a cow permanent environmental (PE) effect. All random effects were Legendre polynomial regressions of the same order, defined on the scale from second to the eighth calving. Bayesian methods with Gibbs sampling were used to estimate covariance components and genetic parameters for random effects of models and selected variables on the longitudinal scale. Bayes factors and analyses of mean squared error and correlation between observed and predicted observations indicated that the linear model with regressions of order 3 was most plausible for generating the current data compared with a fixed regression and other random regression (both linear and threshold) models of order up to 4. Estimates of variances for all random effects from the best fitting model changed with the calving number. Estimates of heritability decreased in time: from 0.35 (SD = 0.006) for stayability to second calving to 0.13 (SD = 0.004) for stayability to the eighth calving. Variance due to PE effect constituted the largest part of the total variance of stayability for all longitudinal points followed by genetic and CG components. Genetic effects of stayability to different calvings were relatively highly correlated, from 0.62 (SD = 0.011) to 0.99 (SD = 0.001), and correlation decreased with the time

  1. Compression distance can discriminate animals by genetic profile, build relationship matrices and estimate breeding values.

    PubMed

    Hudson, Nicholas J; Porto-Neto, Laercio; Kijas, James W; Reverter, Antonio

    2015-10-13

    Genetic relatedness is currently estimated by a combination of traditional pedigree-based approaches (i.e. numerator relationship matrices, NRM) and, given the recent availability of molecular information, using marker genotypes (via genomic relationship matrices, GRM). To date, GRM are computed by genome-wide pair-wise SNP (single nucleotide polymorphism) correlations. We describe a new estimate of genetic relatedness using the concept of normalised compression distance (NCD) that is borrowed from Information Theory. Analogous to GRM, the resultant compression relationship matrix (CRM) exploits numerical patterns in genome-wide allele order and proportion, which are known to vary systematically with relatedness. We explored properties of the CRM in two industry cattle datasets by analysing the genetic basis of yearling weight, a phenotype of moderate heritability. In both Brahman (Bos indicus) and Tropical Composite (Bos taurus by Bos indicus) populations, the clustering inferred by NCD was comparable to that based on SNP correlations using standard principal component analysis approaches. One of the versions of the CRM modestly increased the amount of explained genetic variance, slightly reduced the 'missing heritability' and tended to improve the prediction accuracy of breeding values in both populations when compared to both NRM and GRM. Finally, a sliding window-based application of the compression approach on these populations identified genomic regions influenced by introgression of taurine haplotypes. For these two bovine populations, CRM reduced the missing heritability and increased the amount of explained genetic variation for a moderately heritable complex trait. Given that NCD can sensitively discriminate closely related individuals, we foresee CRM having possible value for estimating breeding values in highly inbred populations.

  2. Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars

    PubMed Central

    Shahin, Arwa; Smulders, Marinus J. M.; van Tuyl, Jaap M.; Arens, Paul; Bakker, Freek T.

    2014-01-01

    Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium. PMID:25368628

  3. Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars.

    PubMed

    Shahin, Arwa; Smulders, Marinus J M; van Tuyl, Jaap M; Arens, Paul; Bakker, Freek T

    2014-01-01

    Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium.

  4. Quantitative estimation of activity and quality for collections of functional genetic elements.

    PubMed

    Mutalik, Vivek K; Guimaraes, Joao C; Cambray, Guillaume; Mai, Quynh-Anh; Christoffersen, Marc Juul; Martin, Lance; Yu, Ayumi; Lam, Colin; Rodriguez, Cesar; Bennett, Gaymon; Keasling, Jay D; Endy, Drew; Arkin, Adam P

    2013-04-01

    The practice of engineering biology now depends on the ad hoc reuse of genetic elements whose precise activities vary across changing contexts. Methods are lacking for researchers to affordably coordinate the quantification and analysis of part performance across varied environments, as needed to identify, evaluate and improve problematic part types. We developed an easy-to-use analysis of variance (ANOVA) framework for quantifying the performance of genetic elements. For proof of concept, we assembled and analyzed combinations of prokaryotic transcription and translation initiation elements in Escherichia coli. We determined how estimation of part activity relates to the number of unique element combinations tested, and we show how to estimate expected ensemble-wide part activity from just one or two measurements. We propose a new statistic, biomolecular part 'quality', for tracking quantitative variation in part performance across changing contexts.

  5. Genetic parameter estimates for growth and fleece characteristics in Targhee sheep.

    PubMed

    Notter, D R; Hough, J D

    1997-07-01

    Weaning weights at 60 (WW60) and 120 d (WW120), 60- to 120-d postweaning gains (PWG) for lambs weaned at 60 d, 120- to 365-d postweaning gains (YG) for lambs weaned at 120 d, fleece weights (FWT), and fiber diameters (FD) from 20 Targhee flocks were used to estimate parameters required for multiple-trait genetic evaluation. Flocks from western states (n = 10) recorded primarily WW60 (n = 1,762), WW120 (n = 5,961), YG (n = 2,388), FWT (n = 2,824), and FD (n = 2,000). Eastern flocks primarily recorded WW60 (n = 1,754) and PWG (n = 1,237). Heritability estimates were .01 for WW60 (.00 for western flocks and .07 for eastern flocks), .10 for WW120, .33 for PWG, .20 for YG, .41 for FWT, and .58 for FD. Additive maternal and maternal permanent environmental effects as a proportion of phenotypic variance were .10 and .09, respectively, for WW60 and .05 and .08 for WW120. In western flocks, maternal additive and permanent environmental effects on WW60 and WW120 were highly correlated (> .81), whereas WW120 and YG had a small positive additive genetic correlation (.19) but a negative residual correlation (-.34). Fleece weight had a genetic correlation of .50 with WW120 and YG. Supplemental analyses suggested that the observed genetic relationship between fleece weight and weaning weight arose primarily from a genetic association between additive direct genetic effects on fleece weight and additive maternal effects on weaning weight. Fiber diameter was nearly independent of body weights but had an undesirable additive correlation of .51 with FWT. In eastern flocks, WW60 and PWG had an additive correlation of .71 and a residual correlation of .15.

  6. Simultaneous Estimation of Additive and Mutational Genetic Variance in an Outbred Population of Drosophila serrata.

    PubMed

    McGuigan, Katrina; Aguirre, J David; Blows, Mark W

    2015-11-01

    How new mutations contribute to genetic variation is a key question in biology. Although the evolutionary fate of an allele is largely determined by its heterozygous effect, most estimates of mutational variance and mutational effects derive from highly inbred lines, where new mutations are present in homozygous form. In an attempt to overcome this limitation, middle-class neighborhood (MCN) experiments have been used to assess the fitness effect of new mutations in heterozygous form. However, because MCN populations harbor substantial standing genetic variance, estimates of mutational variance have not typically been available from such experiments. Here we employ a modification of the animal model to analyze data from 22 generations of Drosophila serrata bred in an MCN design. Mutational heritability, measured for eight cuticular hydrocarbons, 10 wing-shape traits, and wing size in this outbred genetic background, ranged from 0.0006 to 0.006 (with one exception), a similar range to that reported from studies employing inbred lines. Simultaneously partitioning the additive and mutational variance in the same outbred population allowed us to quantitatively test the ability of mutation-selection balance models to explain the observed levels of additive and mutational genetic variance. The Gaussian allelic approximation and house-of-cards models, which assume real stabilizing selection on single traits, both overestimated the genetic variance maintained at equilibrium, but the house-of-cards model was a closer fit to the data. This analytical approach has the potential to be broadly applied, expanding our understanding of the dynamics of genetic variance in natural populations.

  7. Simultaneous Estimation of Additive and Mutational Genetic Variance in an Outbred Population of Drosophila serrata

    PubMed Central

    McGuigan, Katrina; Aguirre, J. David; Blows, Mark W.

    2015-01-01

    How new mutations contribute to genetic variation is a key question in biology. Although the evolutionary fate of an allele is largely determined by its heterozygous effect, most estimates of mutational variance and mutational effects derive from highly inbred lines, where new mutations are present in homozygous form. In an attempt to overcome this limitation, middle-class neighborhood (MCN) experiments have been used to assess the fitness effect of new mutations in heterozygous form. However, because MCN populations harbor substantial standing genetic variance, estimates of mutational variance have not typically been available from such experiments. Here we employ a modification of the animal model to analyze data from 22 generations of Drosophila serrata bred in an MCN design. Mutational heritability, measured for eight cuticular hydrocarbons, 10 wing-shape traits, and wing size in this outbred genetic background, ranged from 0.0006 to 0.006 (with one exception), a similar range to that reported from studies employing inbred lines. Simultaneously partitioning the additive and mutational variance in the same outbred population allowed us to quantitatively test the ability of mutation-selection balance models to explain the observed levels of additive and mutational genetic variance. The Gaussian allelic approximation and house-of-cards models, which assume real stabilizing selection on single traits, both overestimated the genetic variance maintained at equilibrium, but the house-of-cards model was a closer fit to the data. This analytical approach has the potential to be broadly applied, expanding our understanding of the dynamics of genetic variance in natural populations. PMID:26384357

  8. Sub-sampling genetic data to estimate black bear population size: A case study

    USGS Publications Warehouse

    Tredick, C.A.; Vaughan, M.R.; Stauffer, D.F.; Simek, S.L.; Eason, T.

    2007-01-01

    Costs for genetic analysis of hair samples collected for individual identification of bears average approximately US$50 [2004] per sample. This can easily exceed budgetary allowances for large-scale studies or studies of high-density bear populations. We used 2 genetic datasets from 2 areas in the southeastern United States to explore how reducing costs of analysis by sub-sampling affected precision and accuracy of resulting population estimates. We used several sub-sampling scenarios to create subsets of the full datasets and compared summary statistics, population estimates, and precision of estimates generated from these subsets to estimates generated from the complete datasets. Our results suggested that bias and precision of estimates improved as the proportion of total samples used increased, and heterogeneity models (e.g., Mh[CHAO]) were more robust to reduced sample sizes than other models (e.g., behavior models). We recommend that only high-quality samples (>5 hair follicles) be used when budgets are constrained, and efforts should be made to maximize capture and recapture rates in the field.

  9. Lack of genetic structure and female-specific effect of dispersal barriers in a rabies vector, the striped skunk (Mephitis mephitis).

    PubMed

    Talbot, Benoit; Garant, Dany; Rioux Paquette, Sébastien; Mainguy, Julien; Pelletier, Fanie

    2012-01-01

    Evaluating the permeability of potential barriers to movement, dispersal and gene exchanges can help describe spreading patterns of wildlife diseases. Here, we used landscape genetics methods to assess the genetic structure of the striped skunk (Mephitis mephitis), which is a frequent vector of rabies, a lethal zoonosis of great concern for public health. Our main objective was to identify landscape elements shaping the genetic structure of this species in Southern Québec, Canada, in an area where the raccoon rabies variant has been detected. We hypothesised that geographic distance and landscape barriers, such as highways and major rivers, would modulate genetic structure. We genotyped a total of 289 individuals sampled across a large area (22,000 km²) at nice microsatellite loci. Genetic structure analyses identified a single genetic cluster in the study area. Major rivers and highways, however, influenced the genetic relatedness among sampled individuals. Sex-specific analyses revealed that rivers significantly limited dispersal only for females while highways only had marginal effects. Rivers and highways did not significantly affect male dispersal. These results support the contention that female skunks are more philopatric than males. Overall, our results suggest that the effects of major rivers and highways on dispersal are sex-specific and rather weak and are thus unlikely to prevent the spread of rabies within and among striped skunk populations.

  10. Lack of Genetic Structure and Female-Specific Effect of Dispersal Barriers in a Rabies Vector, the Striped Skunk (Mephitis mephitis)

    PubMed Central

    Talbot, Benoit; Garant, Dany; Rioux Paquette, Sébastien; Mainguy, Julien; Pelletier, Fanie

    2012-01-01

    Evaluating the permeability of potential barriers to movement, dispersal and gene exchanges can help describe spreading patterns of wildlife diseases. Here, we used landscape genetics methods to assess the genetic structure of the striped skunk (Mephitis mephitis), which is a frequent vector of rabies, a lethal zoonosis of great concern for public health. Our main objective was to identify landscape elements shaping the genetic structure of this species in Southern Québec, Canada, in an area where the raccoon rabies variant has been detected. We hypothesised that geographic distance and landscape barriers, such as highways and major rivers, would modulate genetic structure. We genotyped a total of 289 individuals sampled across a large area (22,000 km2) at nice microsatellite loci. Genetic structure analyses identified a single genetic cluster in the study area. Major rivers and highways, however, influenced the genetic relatedness among sampled individuals. Sex-specific analyses revealed that rivers significantly limited dispersal only for females while highways only had marginal effects. Rivers and highways did not significantly affect male dispersal. These results support the contention that female skunks are more philopatric than males. Overall, our results suggest that the effects of major rivers and highways on dispersal are sex-specific and rather weak and are thus unlikely to prevent the spread of rabies within and among striped skunk populations. PMID:23166760

  11. Influence of priors in Bayesian estimation of genetic parameters for multivariate threshold models using Gibbs sampling

    PubMed Central

    Stock, Kathrin Friederike; Distl, Ottmar; Hoeschele, Ina

    2007-01-01

    Simulated data were used to investigate the influence of the choice of priors on estimation of genetic parameters in multivariate threshold models using Gibbs sampling. We simulated additive values, residuals and fixed effects for one continuous trait and liabilities of four binary traits, and QTL effects for one of the liabilities. Within each of four replicates six different datasets were generated which resembled different practical scenarios in horses with respect to number and distribution of animals with trait records and availability of QTL information. (Co)Variance components were estimated using a Bayesian threshold animal model via Gibbs sampling. The Gibbs sampler was implemented with both a flat and a proper prior for the genetic covariance matrix. Convergence problems were encountered in > 50% of flat prior analyses, with indications of potential or near posterior impropriety between about round 10 000 and 100 000. Terminations due to non-positive definite genetic covariance matrix occurred in flat prior analyses of the smallest datasets. Use of a proper prior resulted in improved mixing and convergence of the Gibbs chain. In order to avoid (near) impropriety of posteriors and extremely poorly mixing Gibbs chains, a proper prior should be used for the genetic covariance matrix when implementing the Gibbs sampler. PMID:17306197

  12. Estimation of atrazine-degrading genetic potential and activity in three French agricultural soils.

    PubMed

    Martin-Laurent, Fabrice; Cornet, Laurent; Ranjard, Lionel; López-Gutiérrez, Juan-Carlos; Philippot, Laurent; Schwartz, Christophe; Chaussod, Rémi; Catroux, Gérard; Soulas, Guy

    2004-06-01

    The impact of organic amendment (sewage sludge or waste water) used to fertilize agricultural soils was estimated on the atrazine-degrading activity, the atrazine-degrading genetic potential and the bacterial community structure of soils continuously cropped with corn. Long-term application of organic amendment did not modify atrazine-mineralizing activity, which was found to essentially depend on the soil type. It also did not modify atrazine-degrading genetic potential estimated by quantitative PCR targeting atzA, B and C genes, which was shown to depend on soil type. The structure of soil bacterial community determined by RISA fingerprinting was significantly affected by organic amendment. These results showed that modification of the structure of soil bacterial community in response to organic amendment is not necessarily accompanied by a modification of atrazine-degrading genetic potential or activity. In addition, these results revealed that different soils showing similar atrazine-degrading genetic potentials may exhibit different atrazine-degrading activities.

  13. Parametric estimation in a genetic mixture model with application to nuclear family data.

    PubMed

    Shoukri, M M; McLachlan, G J

    1994-03-01

    The apparent conflict between the biometrician and Mendelian genetics has been recently resolved by the introduction of a genetic mixed model to analyze continuous traits measured on human families and to elucidate the mechanism of underlying major genes. The mixed model formulated by Elston and Stewart (1971, Human Heredity 21, 523-542), extended by Morton and MacLean (1974, American Journal of Human Genetics 26, 489-503), and reviewed, with further extensions, by Boyle and Elston (1979, Biometrics 35, 55-68) has become an extremely useful tool of wide applicability in the field of genetic epidemiology. This model allows for segregation at a major locus, a polygenic effect, and a sibling environmental variation. The main concern of this paper is with estimating the model parameters by the method of maximum likelihood. The expectation-maximization (EM) algorithm is developed to derive the estimates iteratively. An approximation of the information matrix when using the EM algorithm is given. We illustrate the methodology by fitting the model to the arterial blood pressure data collected by Miall and Oldham (1955, Clinical Science 14, 459-487).

  14. Estimating genetic architectures from artificial-selection responses: a random-effect framework.

    PubMed

    Le Rouzic, Arnaud; Skaug, Hans J; Hansen, Thomas F

    2010-03-01

    Artificial-selection experiments on plants and animals generate large datasets reporting phenotypic changes in the course of time. The dynamics of the changes reflect the underlying genetic architecture, but only simple statistical tools have so far been available to analyze such time series. This manuscript describes a general statistical framework based on random-effect models aiming at estimating key parameters of genetic architectures from artificial-selection responses. We derive explicit Mendelian models (in which the genetic architecture relies on one or two large-effect loci), and compare them with classical polygenic models. With simulations, we show that the models are accurate and powerful enough to provide useful estimates from realistic experimental designs, and we demonstrate that model selection is effective in picking few-locus vs. polygenic genetic architectures even from medium-quality artificial-selection data. The method is illustrated by the analysis of a historical selection experiment, carried on color pattern in rats by Castle et al.

  15. Estimation of heritability and genetic correlations for the major fatty acids in bovine milk.

    PubMed

    Soyeurt, H; Gillon, A; Vanderick, S; Mayeres, P; Bertozzi, C; Gengler, N

    2007-09-01

    The current cattle selection program for dairy cattle in the Walloon region of Belgium does not consider the relative content of the different fatty acids (FA) in milk. However, interest by the local dairy industry in differentiated milk products is increasing. Therefore, farmers may be interested in selecting their animals based on the fat composition. The aim of this study was to evaluate the feasibility of genetic selection to improve the nutritional quality of bovine milk fat. The heritabilities and correlations among milk yield, fat, protein, and major FA contents in milk were estimated. Heritabilities for FA in milk and fat ranged from 5 to 38%. The genetic correlations estimated among FA reflected the common origin of several groups of FA. Given these results, an index including FA contents with the similar metabolic process of production in the mammary gland could be used, for example, to increase the monounsaturated and conjugated fatty acids in milk. Moreover, the genetic correlations between the percentage of fat and the content of C14:0, C12:0, C16:0, and C18:0 in fat were -0.06, 0.55, 0.60, and 0.84, respectively. This result demonstrates that an increase in fat content is not directly correlated with undesirable changes in FA profile in milk for human health. Based on the obtained genetic parameters, a future selection program to improve the FA composition of milk fat could be initiated.

  16. [Modern biotechnologies in estimation of genetic diversity of Ukrainian varieties of hop (Humulus lupulus L.)].

    PubMed

    Syvolap, Iu M; Zakharova, O O; Kozhukhova, N E; Ihnatova, S O; Prystavs'kyĭ, M S; Zelenina, H A

    2010-01-01

    Genetic variety estimation of hop gene pool using DNA-typing of highly polymorphic microsatellite loci and optimization of introduction to the culture of in vitro conditions is the important stage of national varieties resources forming, basis of modern nursery and protect mean of varieties property, and also it is necessary for development of molecular methods of selection of planting-stocks free from pathogens.

  17. Estimating dispersal from genetic isolation by distance in a coral reef fish (Hypoplectrus puella).

    PubMed

    Puebla, Oscar; Bermingham, Eldredge; Guichard, Frédéric

    2009-11-01

    The spatial scale of dispersal in coral reef fishes eludes ecologists despite the importance of this parameter for understanding the dynamics of ecological and evolutionary processes. Genetic isolation by distance (IBD) has been used to estimate dispersal in coral reef fishes, but its application in marine systems has been limited by insufficient sampling at different spatial scales and a lack of information regarding population density. Here, we present an analysis of IBD in the barred hamlet (Hypoplectrus puella, Serranidae) at spatial scales ranging from 10 to 3200 km complemented with SCUBA surveys of population densities covering 94000 m2 of reef. We used 10 hypervariable DNA markers to genotype 854 fish from 15 locations, and our results establish that IBD in H. puella emerges at a spatial scale of 175 km and is preserved up to the regional scale (3200 km). Assuming a normal or a Laplace dispersal function, our data are consistent with mean dispersal distances in H. puella that range between 2 and 14 km. Such small mean dispersal distances is a surprising result given the three-week pelagic larval duration of H. puella and the low level of genetic structure at the Caribbean scale (Wright's fixation index, F(ST), estimate = 0.005). Our data reinforce the importance of considering population density when estimating dispersal from IBD and underscore the relevance of sampling at local scales, even when genetic structure is weak at the regional scale.

  18. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

    PubMed Central

    Beerenwinkel, Niko; Günthard, Huldrych F.; Roth, Volker; Metzner, Karin J.

    2012-01-01

    Many viruses, including the clinically relevant RNA viruses HIV (human immunodeficiency virus) and HCV (hepatitis C virus), exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing (NGS) technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different NGS platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants (SNVs) to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of NGS to estimate viral diversity. PMID:22973268

  19. Estimation of the incidence of a rare genetic disease through a two-tier mutation survey

    SciTech Connect

    Chakraborty, R.; Srinivasan, M.R. ); Raskin, S. Universidade Federal do Parana, Curitiba )

    1993-06-01

    Recent attempts to detect mutations involving single base changes or small deletions that are specific to genetic diseases provide an opportunity to develop a two-tier mutation-screening program through which incidence of rare genetic disorders and gene carriers may be precisely estimated. A two-tier survey consists of mutation screening in a sample of patients with specific genetic disorders and in a second sample of newborns from the same population in which mutation frequency is evaluated. The authors provide the statistical basis for evaluating the incidence of affected and gene carriers in such two-tier mutation-screening surveys, from which the precision of the estimates is derived. Sample-size requirements of such two-tier mutation-screening surveys are evaluated. Considering examples of cystic fibrosis (CF) and medium-chain acyl-CoA dehydrogenase deficiency (MCAD), the two most frequent autosomal recessive diseases in Caucasian populations and the two most frequent mutations ([Delta]F508 and G985) that occur on these disease allele-bearing chromosomes, the authors show that, with 50--100 patients and a 20-fold larger sample of newborns screened for these mutations, the incidence of such diseases and their gene carriers in a population may be quite reliably estimated. The theory developed here is also applicable to rare autosomal dominant diseases for which disease-specific mutations are found. 21 refs., 1 fig., 3 tabs.

  20. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data.

    PubMed

    Beerenwinkel, Niko; Günthard, Huldrych F; Roth, Volker; Metzner, Karin J

    2012-01-01

    Many viruses, including the clinically relevant RNA viruses HIV (human immunodeficiency virus) and HCV (hepatitis C virus), exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing (NGS) technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different NGS platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants (SNVs) to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of NGS to estimate viral diversity.

  1. Estimation of genetic parameters for carcass defects of Japanese Black cattle in Kagoshima.

    PubMed

    Nishi, Kazutaka; Shimogiri, Takeshi; Kusano, Akinori; Sakamoto, Shinichi; Shiromoto, Kiyomi; Kawabe, Kotaro; Okamoto, Shin; Honda, Takeshi; Oyama, Kenji

    2016-05-01

    Cattle exhibit a range of carcass defects, including blood splash (BLS), intramuscular edema (INE), muscle steatosis (MUS), bruising (BR), trim loss (TRL) and others (OTH). These defects lower the carcass value and can result in significant economic loss to producers. We estimated the incidence, relationship with inbreeding coefficients and genetic parameters of carcass defects in Japanese Black cattle using 561 619 carcass records from Kagoshima, Japan during April 1988 through March 2011. The defect incidence ranged from 0.22% for TRL to 5.73% for BR. The incidence of MUS and BR increased from 1.21% to 6.57% and from 1.06% to 9.31%, respectively. The incidence of INE peaked at 7.44% in 1999 and decreased thereafter. We observed a positive linear relationship between the defect incidence and the inbreeding coefficients in MUS, BR and TRL (P < 0.01). The heritabilities estimated by univariate animal model with Gibbs sampling for BLS, INE, MUS, BR and TRL were 0.24, 0.06, 0.18, 0.05 and 0.02, respectively. The contribution of farm variance to phenotypic variance was negligible (0.01 to 0.04). Significant genetic correlations of TRL were estimated with MUS (0.63) and BR (0.63). Our results suggest that genetic factors contribute to the incidence of BLS and MUS. © 2015 Japanese Society of Animal Science.

  2. Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs

    PubMed Central

    2013-01-01

    Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17–29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 ± 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 ± 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 ± 0.06 s.e.), and ADHD and major depressive disorder (0.32 ± 0.07 s.e.), low between schizophrenia and ASD (0.16 ± 0.06 s.e.) and non-significant for other pairs of disorders as well as between psychiatric disorders and the negative control of Crohn’s disease. This empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders. PMID:23933821

  3. Estimation of genetic structure of a Mycosphaerella musicola population using inter-simple sequence repeat markers.

    PubMed

    Peixouto, Y S; Dórea Bragança, C A; Andrade, W B; Ferreira, C F; Haddad, F; Oliveira, S A S; Darosci Brito, F S; Miller, R N G; Amorim, E P

    2015-07-17

    Among the diseases affecting banana (Musa sp), yellow Sigatoka, caused by the fungal pathogen Mycosphaerella musicola Leach, is considered one of the most important in Brazil, causing losses throughout the year. Understanding the genetic structure of pathogen populations will provide insight into the life history of pathogens, including the evolutionary processes occurring in agrosystems. Tools for estimating the possible emergence of pathogen variants with altered pathogenicity, virulence, or aggressiveness, as well as resistance to systemic fungicides, can also be developed from such data. The objective of this study was to analyze the genetic diversity and population genetics of M. musicola in the main banana-producing regions in Brazil. A total of 83 isolates collected from different banana cultivars in the Brazilian states of Bahia, Rio Grande do Norte, and Minas Gerais were evaluated using inter-simple sequence repeat markers. High variability was detected between the isolates, and 85.5% of the haplotypes were singletons in the populations. The highest source of genetic diversity (97.22%) was attributed to variations within populations. Bayesian cluster analysis revealed the presence of 2 probable ancestral groups, however, showed no relationship to population structure in terms of collection site, state of origin, or cultivar. Similarly, we detected noevidence of genetic recombination between individuals within different states, indicating that asexual cycles play a major role in M. musicola reproduction and that long-distance dispersal of the pathogen is the main factor contributing to the lack of population structure in the fungus.

  4. Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.

    PubMed

    Lee, S Hong; Ripke, Stephan; Neale, Benjamin M; Faraone, Stephen V; Purcell, Shaun M; Perlis, Roy H; Mowry, Bryan J; Thapar, Anita; Goddard, Michael E; Witte, John S; Absher, Devin; Agartz, Ingrid; Akil, Huda; Amin, Farooq; Andreassen, Ole A; Anjorin, Adebayo; Anney, Richard; Anttila, Verneri; Arking, Dan E; Asherson, Philip; Azevedo, Maria H; Backlund, Lena; Badner, Judith A; Bailey, Anthony J; Banaschewski, Tobias; Barchas, Jack D; Barnes, Michael R; Barrett, Thomas B; Bass, Nicholas; Battaglia, Agatino; Bauer, Michael; Bayés, Mònica; Bellivier, Frank; Bergen, Sarah E; Berrettini, Wade; Betancur, Catalina; Bettecken, Thomas; Biederman, Joseph; Binder, Elisabeth B; Black, Donald W; Blackwood, Douglas H R; Bloss, Cinnamon S; Boehnke, Michael; Boomsma, Dorret I; Breen, Gerome; Breuer, René; Bruggeman, Richard; Cormican, Paul; Buccola, Nancy G; Buitelaar, Jan K; Bunney, William E; Buxbaum, Joseph D; Byerley, William F; Byrne, Enda M; Caesar, Sian; Cahn, Wiepke; Cantor, Rita M; Casas, Miguel; Chakravarti, Aravinda; Chambert, Kimberly; Choudhury, Khalid; Cichon, Sven; Cloninger, C Robert; Collier, David A; Cook, Edwin H; Coon, Hilary; Cormand, Bru; Corvin, Aiden; Coryell, William H; Craig, David W; Craig, Ian W; Crosbie, Jennifer; Cuccaro, Michael L; Curtis, David; Czamara, Darina; Datta, Susmita; Dawson, Geraldine; Day, Richard; De Geus, Eco J; Degenhardt, Franziska; Djurovic, Srdjan; Donohoe, Gary J; Doyle, Alysa E; Duan, Jubao; Dudbridge, Frank; Duketis, Eftichia; Ebstein, Richard P; Edenberg, Howard J; Elia, Josephine; Ennis, Sean; Etain, Bruno; Fanous, Ayman; Farmer, Anne E; Ferrier, I Nicol; Flickinger, Matthew; Fombonne, Eric; Foroud, Tatiana; Frank, Josef; Franke, Barbara; Fraser, Christine; Freedman, Robert; Freimer, Nelson B; Freitag, Christine M; Friedl, Marion; Frisén, Louise; Gallagher, Louise; Gejman, Pablo V; Georgieva, Lyudmila; Gershon, Elliot S; Geschwind, Daniel H; Giegling, Ina; Gill, Michael; Gordon, Scott D; Gordon-Smith, Katherine; Green, Elaine K; Greenwood, Tiffany A; Grice, Dorothy E; Gross, Magdalena; Grozeva, Detelina; Guan, Weihua; Gurling, Hugh; De Haan, Lieuwe; Haines, Jonathan L; Hakonarson, Hakon; Hallmayer, Joachim; Hamilton, Steven P; Hamshere, Marian L; Hansen, Thomas F; Hartmann, Annette M; Hautzinger, Martin; Heath, Andrew C; Henders, Anjali K; Herms, Stefan; Hickie, Ian B; Hipolito, Maria; Hoefels, Susanne; Holmans, Peter A; Holsboer, Florian; Hoogendijk, Witte J; Hottenga, Jouke-Jan; Hultman, Christina M; Hus, Vanessa; Ingason, Andrés; Ising, Marcus; Jamain, Stéphane; Jones, Edward G; Jones, Ian; Jones, Lisa; Tzeng, Jung-Ying; Kähler, Anna K; Kahn, René S; Kandaswamy, Radhika; Keller, Matthew C; Kennedy, James L; Kenny, Elaine; Kent, Lindsey; Kim, Yunjung; Kirov, George K; Klauck, Sabine M; Klei, Lambertus; Knowles, James A; Kohli, Martin A; Koller, Daniel L; Konte, Bettina; Korszun, Ania; Krabbendam, Lydia; Krasucki, Robert; Kuntsi, Jonna; Kwan, Phoenix; Landén, Mikael; Långström, Niklas; Lathrop, Mark; Lawrence, Jacob; Lawson, William B; Leboyer, Marion; Ledbetter, David H; Lee, Phil H; Lencz, Todd; Lesch, Klaus-Peter; Levinson, Douglas F; Lewis, Cathryn M; Li, Jun; Lichtenstein, Paul; Lieberman, Jeffrey A; Lin, Dan-Yu; Linszen, Don H; Liu, Chunyu; Lohoff, Falk W; Loo, Sandra K; Lord, Catherine; Lowe, Jennifer K; Lucae, Susanne; MacIntyre, Donald J; Madden, Pamela A F; Maestrini, Elena; Magnusson, Patrik K E; Mahon, Pamela B; Maier, Wolfgang; Malhotra, Anil K; Mane, Shrikant M; Martin, Christa L; Martin, Nicholas G; Mattheisen, Manuel; Matthews, Keith; Mattingsdal, Morten; McCarroll, Steven A; McGhee, Kevin A; McGough, James J; McGrath, Patrick J; McGuffin, Peter; McInnis, Melvin G; McIntosh, Andrew; McKinney, Rebecca; McLean, Alan W; McMahon, Francis J; McMahon, William M; McQuillin, Andrew; Medeiros, Helena; Medland, Sarah E; Meier, Sandra; Melle, Ingrid; Meng, Fan; Meyer, Jobst; Middeldorp, Christel M; Middleton, Lefkos; Milanova, Vihra; Miranda, Ana; Monaco, Anthony P; Montgomery, Grant W; Moran, Jennifer L; Moreno-De-Luca, Daniel; Morken, Gunnar; Morris, Derek W; Morrow, Eric M; Moskvina, Valentina; Muglia, Pierandrea; Mühleisen, Thomas W; Muir, Walter J; Müller-Myhsok, Bertram; Murtha, Michael; Myers, Richard M; Myin-Germeys, Inez; Neale, Michael C; Nelson, Stan F; Nievergelt, Caroline M; Nikolov, Ivan; Nimgaonkar, Vishwajit; Nolen, Willem A; Nöthen, Markus M; Nurnberger, John I; Nwulia, Evaristus A; Nyholt, Dale R; O'Dushlaine, Colm; Oades, Robert D; Olincy, Ann; Oliveira, Guiomar; Olsen, Line; Ophoff, Roel A; Osby, Urban; Owen, Michael J; Palotie, Aarno; Parr, Jeremy R; Paterson, Andrew D; Pato, Carlos N; Pato, Michele T; Penninx, Brenda W; Pergadia, Michele L; Pericak-Vance, Margaret A; Pickard, Benjamin S; Pimm, Jonathan; Piven, Joseph; Posthuma, Danielle; Potash, James B; Poustka, Fritz; Propping, Peter; Puri, Vinay; Quested, Digby J; Quinn, Emma M; Ramos-Quiroga, Josep Antoni; Rasmussen, Henrik B; Raychaudhuri, Soumya; Rehnström, Karola; Reif, Andreas; Ribasés, Marta; Rice, John P; Rietschel, Marcella; Roeder, Kathryn; Roeyers, Herbert; Rossin, Lizzy; Rothenberger, Aribert; Rouleau, Guy; Ruderfer, Douglas; Rujescu, Dan; Sanders, Alan R; Sanders, Stephan J; Santangelo, Susan L; Sergeant, Joseph A; Schachar, Russell; Schalling, Martin; Schatzberg, Alan F; Scheftner, William A; Schellenberg, Gerard D; Scherer, Stephen W; Schork, Nicholas J; Schulze, Thomas G; Schumacher, Johannes; Schwarz, Markus; Scolnick, Edward; Scott, Laura J; Shi, Jianxin; Shilling, Paul D; Shyn, Stanley I; Silverman, Jeremy M; Slager, Susan L; Smalley, Susan L; Smit, Johannes H; Smith, Erin N; Sonuga-Barke, Edmund J S; St Clair, David; State, Matthew; Steffens, Michael; Steinhausen, Hans-Christoph; Strauss, John S; Strohmaier, Jana; Stroup, T Scott; Sutcliffe, James S; Szatmari, Peter; Szelinger, Szabocls; Thirumalai, Srinivasa; Thompson, Robert C; Todorov, Alexandre A; Tozzi, Federica; Treutlein, Jens; Uhr, Manfred; van den Oord, Edwin J C G; Van Grootheest, Gerard; Van Os, Jim; Vicente, Astrid M; Vieland, Veronica J; Vincent, John B; Visscher, Peter M; Walsh, Christopher A; Wassink, Thomas H; Watson, Stanley J; Weissman, Myrna M; Werge, Thomas; Wienker, Thomas F; Wijsman, Ellen M; Willemsen, Gonneke; Williams, Nigel; Willsey, A Jeremy; Witt, Stephanie H; Xu, Wei; Young, Allan H; Yu, Timothy W; Zammit, Stanley; Zandi, Peter P; Zhang, Peng; Zitman, Frans G; Zöllner, Sebastian; Devlin, Bernie; Kelsoe, John R; Sklar, Pamela; Daly, Mark J; O'Donovan, Michael C; Craddock, Nicholas; Sullivan, Patrick F; Smoller, Jordan W; Kendler, Kenneth S; Wray, Naomi R

    2013-09-01

    Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17-29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 ± 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 ± 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 ± 0.06 s.e.), and ADHD and major depressive disorder (0.32 ± 0.07 s.e.), low between schizophrenia and ASD (0.16 ± 0.06 s.e.) and non-significant for other pairs of disorders as well as between psychiatric disorders and the negative control of Crohn's disease. This empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders.

  5. Application of DNA markers to estimate genetic diversity of Mycobacterium tuberculosis strains.

    PubMed

    Korzekwa, Karol; Polok, Kornelia; Zieliński, Roman

    2006-01-01

    The obligatory human pathogen, Mycobacterium tuberculosis, is the most important etiological factor of tuberculosis. Unfortunately, there is little information about genetic diversity of this pathogen. The main aim of this research was the estimation of genetic diversity of M. tuberculosis on the basis of various categories of DNA markers. The genome of 32 strains were scanned by DNA markers such RAPD, IS6110 and catalase-peroxidase katG gene. All 162 identified loci were polymorphic. The genetic diversity coefficient (HT) of M. tuberculosis was 0.32 for RAPD and 0.27 for IS 6110. There were 14 alleles in katG gene. All strains were characterised by the individual molecular pattern. Genetic similarity varied from 0.13 to 0.94 (RAPD markers) and from 0 to 1 for (IS6110). M. tuberculosis strains did not represent a clonal structure, single source of transmission and epidemiological relationships as well. The applied DNA markers proved to be highly efficient for analysis of genetic structure of M. tuberculosis.

  6. Genetic Differentiation among Wild Populations of Tribolium castaneum Estimated Using Microsatellite Markers

    PubMed Central

    Siniard, Ashley L.; Wade, Michael J.

    2009-01-01

    We report our characterization of the genetic variation within and differentiation among wild-collected populations of the red flour beetle, Tribolium castaneum, using microsatellite loci identified from its genome sequence. We find that global differentiation, estimated as the average FST across all loci and between all population pairs, is 0.180 (95% confidence intervals of 0.142 and 0.218). A majority of our pairwise population comparisons (>70%) were significant even though this species is considered an excellent colonizer by virtue of its pest status. Regional genetic variation between Tribolium populations is 2–3 times that observed in the fruit fly, Drosophila melanogaster. There was a weak positive correlation between genetic distance [FST/(1 − FST)] and geographic distance [ln(km)]; pairs of populations with the highest degree of genetic differentiation (FST > 0.29) have been shown to exhibit significant postzygotic reproductive isolation when crossed in previous studies. We discuss the possibility that local extinction and kin-structured colonization have increased the level of genetic differentiation between Tribolium populations. PMID:19734259

  7. Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate.

    PubMed

    Hardy, Olivier J

    2016-01-01

    Nowadays, the population genetics analysis of autopolyploid species faces many difficulties due to (i) limited development of population genetics tools under polysomic inheritance, (ii) difficulties to assess allelic dosage when genotyping individuals and (iii) a form of inbreeding resulting from the mechanism of 'double reduction'. Consequently, few data analysis computer programs are applicable to autopolyploids. To contribute bridging this gap, this article first derives theoretical expectations for the inbreeding and identity disequilibrium coefficients under polysomic inheritance in a mixed mating model. Moment estimators of these coefficients are proposed when exact genotypes or just markers phenotypes (i.e. allelic dosage unknown) are available. This led to the development of estimators of the selfing rate based on adult genotypes or phenotypes and applicable to any even-ploidy level. Their statistical performances and robustness were assessed by numerical simulations. Contrary to inbreeding-based estimators, the identity disequilibrium-based estimator using phenotypes is robust (absolute bias generally < 0.05), even in the presence of double reduction, null alleles or biparental inbreeding due to isolation by distance. A fairly good precision of the selfing rate estimates (root mean squared error < 0.1) is already achievable using a sample of 30-50 individuals phenotyped at 10 loci bearing 5-10 alleles each, conditions reachable using microsatellite markers. Diallelic markers (e.g. SNP) can also perform satisfactorily in diploids and tetraploids but more polymorphic markers are necessary for higher ploidy levels. The method is implemented in the software SPAGeDi and should contribute to reduce the lack of population genetics tools applicable to autopolyploids. © 2015 John Wiley & Sons Ltd.

  8. Genetic Parameter Estimates of Carcass Traits under National Scale Breeding Scheme for Beef Cattle

    PubMed Central

    Do, ChangHee; Park, ByungHo; Kim, SiDong; Choi, TaeJung; Yang, BohSuk; Park, SuBong; Song, HyungJun

    2016-01-01

    Carcass and price traits of 72,969 Hanwoo cows, bulls and steers aged 16 to 80 months at slaughter collected from 2002 to 2013 at 75 beef packing plants in Korea were analyzed to determine heritability, correlation and breeding value using the Multi-Trait restricted maximum likelihood (REML) animal model procedure. The traits included carcass measurements, scores and grades at 24 h postmortem and bid prices at auction. Relatively high heritability was found for maturity (0.41±0.031), while moderate heritability estimates were obtained for backfat thickness (0.20±0.018), longissimus muscle (LM) area (0.23±0.020), carcass weight (0.28±0.019), yield index (0.20±0.018), yield grade (0.16±0.017), marbling (0.28±0.021), texture (0.14±0.016), quality grade (0.26±0.016) and price/kg (0.24±0.025). Relatively low heritability estimates were observed for meat color (0.06±0.013) and fat color (0.06±0.012). Heritability estimates for most traits were lower than those in the literature. Genetic correlations of carcass measurements with characteristic scores or quality grade of carcass ranged from −0.27 to +0.21. Genetic correlations of yield grade with backfat thickness, LM area and carcass weight were 0.91, −0.43, and −0.09, respectively. Genetic correlations of quality grade with scores of marbling, meat color, fat color and texture were −0.99, 0.48, 0.47, and 0.98, respectively. Genetic correlations of price/kg with LM area, carcass weight, marbling, meat color, texture and maturity were 0.57, 0.64, 0.76, −0.41, −0.79, and −0.42, respectively. Genetic correlations of carcass price with LM area, carcass weight, marbling and texture were 0.61, 0.57, 0.64, and −0.73, respectively, with standard errors ranging from ±0.047 to ±0.058. The mean carcass weight breeding values increased by more than 8 kg, whereas the mean marbling scores decreased by approximately 0.2 from 2000 through 2009. Overall, the results suggest that genetic improvement of

  9. Estimates of genetic parameters for fatty acid compositions in the longissimus dorsi muscle of Hanwoo cattle.

    PubMed

    Bhuiyan, M S A; Lee, D H; Kim, H J; Lee, S H; Cho, S H; Yang, B S; Kim, S D

    2017-08-10

    We estimated the heritabilities (h 2) and genetic and phenotypic correlations among individual and groups of fatty acids, as well as their correlations with six important carcass and meat-quality traits in Korean Hanwoo cattle. Meat samples were collected from the longissimus dorsi muscles of 1000 Hanwoo steers that were 30-month-old (progeny of 85 proven Hanwoo bulls) to determine intramuscular fatty acid profiles. Phenotypic data on carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), marbling score (MS), Warner-Bratzler shear force (WBSF) and intramuscular fat content (IMF) were also investigated using this half-sib population. Variance and covari.ance components were estimated using restricted maximum likelihood procedures under univariate and pairwise bivariate animal models. Oleic acid (C18:1n-9) was the most abundant fatty acid, accounting for 50.69% of all investigated fatty acids, followed by palmitic (C16:0; 27.33%) and stearic acid (C18:0; 10.96%). The contents of saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs) and polyunsaturated fatty acids (PUFAs) were 41.64%, 56.24% and 2.10%, respectively, and the MUFA/SFA ratio, PUFA/SFA ratio, desaturation index (DI) and elongation index (EI) were 1.36, 0.05, 0.59 and 0.66, respectively. The h 2 estimates for individual fatty acids ranged from very low to high (0.03±0.14 to 0.63±0.14). The h 2 estimates for SFAs, MUFAs, PUFAs, DI and EI were 0.53±0.14, 0.49±0.14, 0.23±0.10, 0.51±0.13 and 0.53±0.13, respectively. The genetic and phenotypic correlations among individual fatty acids and fatty acid classes varied widely (-0.99 to 0.99). Notably, C18:1n-9 had favourable (negative) genetic correlations with two detrimental fatty acids, C14:0 (-0.76) and C16:0 (-0.92). Genetic correlations of individual and group fatty acids with CWT, EMA, BFT, MS, WBSF and IMF ranged from low to moderate (both positive and negative) with the exception of low-concentration PUFAs. Low or near

  10. Evolutionary Estimation of Diffusion Models in Multi-Generation NAND Flash Memory Using Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Li, Yiming; Chiang, Su-Yun; Liou, Kuen-Ying

    2007-11-01

    In this paper, using the realistic market data of NAND flash memory in the past decade, we provide theoretical arguments and empirical evidence for how genetic algorithms (GA) can be used for efficient estimation of macro-level diffusion models. Under the comparison of two methods, we perform two parts; one is the estimation of growth of single generation of NAND flash memory and the other is the estimation of growth of multi-generation NAND flash memory. In the first part, we find the estimated ability of GA is as good as nonlinear least square (NLS), but GA can overcome initial guess problems that NLS couldn't. In the second part, we find the result of estimation by NLS method cannot converge. Thus, GA is superior to NLS when we perform the estimation of multi-generation flash memory. According to the preliminary results above, we could conclude that GA is suited for estimation of diffusion model than that of the NLS; in particular, for multi-generation NAND flash memory.

  11. Estimation of variance components and genetic trends for twinning rate in Holstein dairy cattle of Iran.

    PubMed

    Ghavi Hossein-Zadeh, N; Nejati-Javaremi, A; Miraei-Ashtiani, S R; Kohram, H

    2009-07-01

    Calving records from the Animal Breeding Center of Iran, collected from January 1991 to December 2007 and comprising 1,163,594 Holstein calving events from 2,552 herds, were analyzed using a linear animal model, linear sire model, threshold animal model, and threshold sire model to estimate variance components, heritabilities, genetic correlations, and genetic trends for twinning rate in the first, second, and third parities. The overall twinning rate was 3.01%. Mean incidence of twins increased from first to fourth and later parities: 1.10, 3.20, 4.22, and 4.50%, respectively. For first-parity cows, a maximum frequency of twinning was observed from January through April (1.36%), and second- and third-parity cows showed peaks from July to September (at 3.35 and 4.55%, respectively). The phenotypic rate of twinning decreased from 1991 to 2007 for the first, second, and third parities. Sire predicted transmitting abilities were estimated using linear sire model and threshold sire model analyses. Sire transmitting abilities for twinning rate in the first, second, and third parities ranged from -0.30 to 0.42, -0.32 to 0.31, and -0.27 to 0.30, respectively. Heritability estimates of twinning rate for parities 1, 2, and 3 ranged from 1.66 to 10.6%, 1.35 to 9.0%, and 1.10 to 7.3%, respectively, using different models for analysis. Heritability estimates for twinning rate, obtained from the analysis of threshold models, were greater than the estimates of linear models. Solutions for age at calving for the first, second, and third parities demonstrated that cows older at calving were more likely to have twins. Genetic correlations for twinning rate between parities 2 and 3 were greater than correlations between parities 1 and 2 and between parities 1 and 3. There was a slightly increasing trend for twinning rate in parities 1, 2, and 3 over time with the analysis of linear animal and linear sire models, but the trend for twinning rate in parities 1, 2, and 3 with threshold

  12. Estimating genetic parameters for fertility in dairy cows from in-line milk progesterone profiles.

    PubMed

    Tenghe, A M M; Bouwman, A C; Berglund, B; Strandberg, E; Blom, J Y; Veerkamp, R F

    2015-08-01

    The aim of this study was to define endocrine fertility traits from in-line milk progesterone (P4) records and to estimate genetic parameters for these traits. Correlations of classical fertility (calving interval and calving to first service) and milk production traits with endocrine fertility traits were also estimated. In-line milk P4 records (n=160,952) collected from June 2009 through November 2013 for 2,273 lactations of 1,561 Holstein-Friesian cows in 12 commercial herds in the Netherlands were analyzed for (the log of) the number of days from calving till commencement of luteal activity (lnC-LA), proportion of samples between 25 and 60 d in milk with luteal activity (PLA), presence or absence of luteal activity for a cow between 25 and 60 d in milk, interval from commencement of luteal activity to first service (CLAFS), first luteal phase length, length of first interluteal interval, and length of first interovulatory interval. Milk P4 records were sampled, on average, every 2 d. Genetic parameters were estimated using a mixed linear animal model. Heritability estimates (±SE) of endocrine fertility traits were 0.12±0.05 for lnC-LA, 0.12±0.05 for PLA, and 0.11±0.06 for CLAFS, and their repeatability estimates were 0.29±0.04, 0.21±0.04, and 0.15±0.06, respectively. The genetic correlation of lnC-LA with PLA was -0.91±0.06 and with CLAFS was -0.56±0.25. The genetic correlations of lnC-LA were 0.26±0.33 with calving interval and 0.37±0.21 with calving to first service. Genetic correlations of the milk production traits with lnC-LA ranged from 0.04 to 0.18 and 0.07 to 0.65 with classical fertility traits. The phenotypic correlations of all endocrine fertility traits with milk production traits were close to zero (0.01 to 0.07). This study shows that in-line P4 records can be used to define and explore several heritable endocrine fertility traits in dairy cows and might help in selection for improved fertility. Copyright © 2015 American Dairy Science

  13. Genetic parameter estimates for prenatal and postnatal mortality in Nellore cattle.

    PubMed

    Magalhães Silva, L C; Baldi, F; Aboujaoude, C; Venturini, G C; Albuquerque, L G; Paranhos da Costa, M J R

    2017-02-01

    The aim of this study was to estimate genetic parameters for prenatal (PRE) and postnatal (POS) mortality in Nellore cattle. A total of 13 141 (PRE) and 17 818 (POS) records from Nellore females were used. PRE and POS were recorded using binary scale scores: a score of '1' was given to calves that were born alive (PRE) and those that were alive at weaning (POS), and a score of '0' was given to calves that were not alive at or around birth (PRE), as well as to those weighed at birth but not at weaning (POS). The relationship matrix included 698 sires, 107 paternal grandsires and 69 maternal grandsires. Data were analysed using Bayesian inference and a sire-maternal grandsire threshold model, including contemporary groups as random effects, and the classes of dam age at the beginning of mating season (for PRE), and dam age at calving and birthweight (linear covariable) (for POS), as fixed effects. For both traits, the covariance between direct and maternal effects (rD,M ) was estimated (rD,M ≠ 0) or fixed at zero (rD,M  = 0). PRE and POS rates were 3.00 and 4.04%, respectively. Estimates of direct and maternal heritability were 0.07 and 0.17, respectively, for PRE, and 0.02 and 0.07, respectively, for POS, assuming rD,M  = 0. For rD,M  ≠ 0, these estimates were 0.07 and 0.12, respectively, for PRE, and 0.03 and 0.07, respectively, for POS. The correlation estimates between direct and maternal effects were -0.71 (PRE) and -0.33 (POS). PRE and POS show low genetic variability, indicating that these traits probably suffer major environmental influences. Additionally, our study shows that the maternal genetic component affects preweaning calf mortality twice as much (or more) as the direct genetic component. A large number of offspring per sire is necessary in progeny tests to genetically decrease calf mortality.

  14. Genetic assignment of recruits reveals short- and long-distance larval dispersal in Pocillopora damicornis on the Great Barrier Reef.

    PubMed

    Torda, G; Lundgren, P; Willis, B L; van Oppen, M J H

    2013-12-01

    Understanding connectivity of coral populations among and within reefs over ecologically significant timescales is essential for developing evidence-based management strategies, including the design of marineprotected areas. Here, we present the first assessment of contemporary connectivity among populations of two Molecular Operational Taxonomic Units (MOTUs) of the brooding coral Pocillopora damicornis. We used individual-based genetic assignment methods to identify the proportions of philopatric and migrant larval recruits, settling over 12 months at sites around Lizard Island (northern Great Barrier Reef [GBR]) and over 24 months at sites around the Palms Islands (central GBR). Overall, we found spatially and temporally variable rates of self-recruitment and dispersal, demonstrating the importance of variation in local physical characteristics in driving dispersal processes. Recruitment patterns and inferred dispersal distances differed between the two P. damicornis MOTUs, with type α recruits exhibiting predominantly philopatric recruitment, while the majority of type β recruits were either migrants from identified putative source populations or assumed migrants based on genetic exclusion from all known populations. While P. damicornis invests much energy into brooding clonal larvae, we found that only 15% and 7% of type α and type β recruits, respectively, were clones of sampled adult colonies or other recruits, challenging the hypothesis that reproduction is predominantly asexual in this species on the GBR. We explain high rates of self-recruitment and low rates of clonality in these MOTUs by suggesting that locally retained larvae originate predominantly from spawned gametes, while brooded larvae are mainly vagabonds.

  15. Estimating groundwater recharge using the SMAR conceptual model calibrated by genetic algorithm

    NASA Astrophysics Data System (ADS)

    Fazal, M. A.; Imaizumi, M.; Ishida, S.; Kawachi, T.; Tsuchihara, T.

    2005-03-01

    Proper groundwater management of a contaminated aquifer requires the accurate estimation of groundwater recharge, which carries the contaminated load. There are many direct and indirect methods and sophisticated models for estimating recharge. However, most of them require many field data or model parameters, which limit their actual field application. To overcome this limitation, the Soil Moisture Accounting and Routing (SMAR), a conceptual rainfall-runoff model, is employed. The SMAR model has the potential for estimating recharge using only rainfall, evaporation and groundwater level data. However, for an aquifer having prominent horizontal groundwater flow, this model cannot be used directly. For this reason a horizontal flow component is added to this model. Model parameters are calibrated by the Genetic Algorithm (GA) optimization technique. Sensitivity of calibrated parameters to model efficiency and estimated recharge, and parameter interdependence are investigated. This model is applied to 11 observation locations in four catchment areas of Miyakojima Island, Japan, where groundwater nitrate contamination is a threat. The effectiveness of the model is evaluated using the model efficiency ( R2), the mean of the sum of square errors (MSE), plots of observed versus estimated groundwater levels, scatter plots of observed versus estimated groundwater levels, measure of timing of the peaks, and the correlation between monthly rainfall and monthly estimated recharge. All show that this technique is very efficient for estimation of recharge. Model efficiency ( R2) up to 92%, minimum MSE 0.32 m 2/day, average relative error of timing of the peaks 4.13%, and coefficient of determination ( r2) up to 0.92 are obtained for the study area. The estimated recharge is 45% of the mean annual rainfall and agrees with other finding. It is thus concluded that the SMAR model could be a viable alternative since it can estimate dependable recharge with a minimum of input data.

  16. Estimating aquifer recharge in Mission River watershed, Texas: model development and calibration using genetic algorithms

    NASA Astrophysics Data System (ADS)

    Uddameri, V.; Kuchanur, M.

    2007-01-01

    Soil moisture balance studies provide a convenient approach to estimate aquifer recharge when only limited site-specific data are available. A monthly mass-balance approach has been utilized in this study to estimate recharge in a small watershed in the coastal bend of South Texas. The developed lumped parameter model employs four adjustable parameters to calibrate model predicted stream runoff to observations at a gaging station. A new procedure was developed to correctly capture the intermittent nature of rainfall. The total monthly rainfall was assigned to a single-equivalent storm whose duration was obtained via calibration. A total of four calibrations were carried out using an evolutionary computing technique called genetic algorithms as well as the conventional gradient descent (GD) technique. Ordinary least squares and the heteroscedastic maximum likelihood error (HMLE) based objective functions were evaluated as part of this study as well. While the genetic algorithm based calibrations were relatively better in capturing the peak runoff events, the GD based calibration did slightly better in capturing the low flow events. Treating the Box-Cox exponent in the HMLE function as a calibration parameter did not yield better estimates and the study corroborates the suggestion made in the literature of fixing this exponent at 0.3. The model outputs were compared against available information and results indicate that the developed modeling approach provides a conservative estimate of recharge.

  17. Estimation of genetic parameters for novel functional traits in Brown Swiss cattle.

    PubMed

    Kramer, M; Erbe, M; Bapst, B; Bieber, A; Simianer, H

    2013-09-01

    The aim of this study was to estimate genetic parameters and accuracies of breeding values for a set of functional, behavior, and conformation traits in Brown Swiss cattle. These traits were milking speed, udder depth, position of labia, rank order in herd, general temperament, aggressiveness, milking temperament, and days to first heat. Data of 1,799 phenotyped Brown Swiss cows from 40 Swiss dairy herds were analyzed taking the complete pedigree into account. Estimated heritabilities were within the ranges reported in literature, with results at the high end of the reported values for some traits (e.g., milking speed: 0.42±0.06, udder depth: 0.42±0.06), whereas other traits were of low heritability and heritability estimates were of low accuracy (e.g., milking temperament: 0.04±0.04, days to first heat: 0.02±0.04). For most behavior traits, we found relatively high heritabilities (general temperament: 0.38±0.07, aggressiveness: 0.12±0.08, and rank order in herd: 0.16±0.06). Position of labia, arguably an indicator trait for pathological urovagina, was genetically analyzed in this study for the first time, and a moderate heritability (0.28±0.06) was estimated. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  18. Genetic versus census estimators of the opportunity for sexual selection in the wild.

    PubMed

    Dunn, Stacey J; Waits, Lisette P; Byers, John A

    2012-04-01

    Abstract The existence of a direct link between intensity of sexual selection and mating-system type is widely accepted. However, the quantification of sexual selection has proven problematic. Several measures of sexual selection have been proposed, including the operational sex ratio (OSR), the breeding sex ratio (BSR), and the opportunity for sexual selection (I(mates)). For a wild population of pronghorn (Antilocapra americana), we calculated OSR and BSR. We estimated I(mates) from census data on the spatial and temporal distribution of receptive females in rut and from a multigenerational genetic pedigree. OSR and BSR indicated weak sexual selection on males, but census and pedigree I(mates) suggested stronger sexual selection on males than on females. OSR and BSR correlated with census but not pedigree estimates of I(mates), and census I(mates) did not correlate with pedigree estimates. This suggests that the behavioral mating system, as deduced from the spatial and temporal distribution of females, does not predict the genetic mating system of pronghorn. The differences we observed between estimators were primarily due to female mate sampling and choice and to the sex ratio. For most species, behavioral data are not perfectly accurate and therefore will be an insufficient alternative to using multigenerational pedigrees to quantify sexual selection.

  19. Limitations to estimating bacterial cross-speciestransmission using genetic and genomic markers: inferencesfrom simulation modeling

    USGS Publications Warehouse

    Julio Andre, Benavides; Cross, Paul C.; Luikart, Gordon; Scott, Creel

    2014-01-01

    Cross-species transmission (CST) of bacterial pathogens has major implications for human health, livestock, and wildlife management because it determines whether control actions in one species may have subsequent effects on other potential host species. The study of bacterial transmission has benefitted from methods measuring two types of genetic variation: variable number of tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). However, it is unclear whether these data can distinguish between different epidemiological scenarios. We used a simulation model with two host species and known transmission rates (within and between species) to evaluate the utility of these markers for inferring CST. We found that CST estimates are biased for a wide range of parameters when based on VNTRs and a most parsimonious reconstructed phylogeny. However, estimations of CST rates lower than 5% can be achieved with relatively low bias using as low as 250 SNPs. CST estimates are sensitive to several parameters, including the number of mutations accumulated since introduction, stochasticity, the genetic difference of strains introduced, and the sampling effort. Our results suggest that, even with whole-genome sequences, unbiased estimates of CST will be difficult when sampling is limited, mutation rates are low, or for pathogens that were recently introduced.

  20. Estimates of (co)variance components and genetic parameters for growth traits of Avikalin sheep.

    PubMed

    Prince, Leslie Leo L; Gowane, Gopal R; Chopra, Ashish; Arora, Amrit L

    2010-08-01

    (Co)variance components and genetic parameters for various growth traits of Avikalin sheep maintained at Central Sheep and Wool Research Institute, Avikanagar, Rajasthan, India, were estimated by Restricted Maximum Likelihood, fitting six animal models with various combinations of direct and maternal effects. Records of 3,840 animals descended from 257 sires and 1,194 dams were taken for this study over a period of 32 years (1977-2008). Direct heritability estimates (from best model as per likelihood ratio test) for weight at birth, weaning, 6 and 12 months of age, and average daily gain from birth to weaning, weaning to 6 months, and 6 to 12 months were 0.28 +/- 0.03, 0.20 +/- 0.03, 0.28 +/- 0.07, 0.15 +/- 0.04, 0.21 +/- 0.03, 0.16 and 0.03 +/- 0.03, respectively. Maternal heritability for traits declined as animal grows older and it was not at all evident at adult age and for post-weaning daily gain. Maternal permanent environmental effect (c(2)) declined significantly with advancement of age of animal. A small effect of c(2) on post-weaning weights was probably a carryover effect of pre-weaning maternal influence. A significant large negative genetic correlation was observed between direct and maternal genetic effects for all the traits, indicating antagonistic pleiotropy, which needs special care while formulating breeding plans. A fair rate of genetic progress seems possible in the flock by selection for all traits, but direct and maternal genetic correlation needs to be taken in to consideration.

  1. Ocean currents influence the genetic structure of an intertidal mollusc in southeastern Australia - implications for predicting the movement of passive dispersers across a marine biogeographic barrier.

    PubMed

    Miller, Adam D; Versace, Vincent L; Matthews, Ty G; Montgomery, Steven; Bowie, Kate C

    2013-05-01

    Major disjunctions among marine communities in southeastern Australia have been well documented, although explanations for biogeographic structuring remain uncertain. Converging ocean currents, environmental gradients, and habitat discontinuities have been hypothesized as likely drivers of structuring in many species, although the extent to which species are affected appears largely dependent on specific life histories and ecologies. Understanding these relationships is critical to the management of native and invasive species, and the preservation of evolutionary processes that shape biodiversity in this region. In this study we test the direct influence of ocean currents on the genetic structure of a passive disperser across a major biogeographic barrier. Donax deltoides (Veneroida: Donacidae) is an intertidal, soft-sediment mollusc and an ideal surrogate for testing this relationship, given its lack of habitat constraints in this region, and its immense dispersal potential driven by year-long spawning and long-lived planktonic larvae. We assessed allele frequencies at 10 polymorphic microsatellite loci across 11 sample locations spanning the barrier region and identified genetic structure consistent with the major ocean currents of southeastern Australia. Analysis of mitochondrial DNA sequence data indicated no evidence of genetic structuring, but signatures of a species range expansion corresponding with historical inundations of the Bassian Isthmus. Our results indicate that ocean currents are likely to be the most influential factor affecting the genetic structure of D. deltoides and a likely physical barrier for passive dispersing marine fauna generally in southeastern Australia.

  2. Ocean currents influence the genetic structure of an intertidal mollusc in southeastern Australia – implications for predicting the movement of passive dispersers across a marine biogeographic barrier

    PubMed Central

    Miller, Adam D; Versace, Vincent L; Matthews, Ty G; Montgomery, Steven; Bowie, Kate C

    2013-01-01

    Major disjunctions among marine communities in southeastern Australia have been well documented, although explanations for biogeographic structuring remain uncertain. Converging ocean currents, environmental gradients, and habitat discontinuities have been hypothesized as likely drivers of structuring in many species, although the extent to which species are affected appears largely dependent on specific life histories and ecologies. Understanding these relationships is critical to the management of native and invasive species, and the preservation of evolutionary processes that shape biodiversity in this region. In this study we test the direct influence of ocean currents on the genetic structure of a passive disperser across a major biogeographic barrier. Donax deltoides (Veneroida: Donacidae) is an intertidal, soft-sediment mollusc and an ideal surrogate for testing this relationship, given its lack of habitat constraints in this region, and its immense dispersal potential driven by year-long spawning and long-lived planktonic larvae. We assessed allele frequencies at 10 polymorphic microsatellite loci across 11 sample locations spanning the barrier region and identified genetic structure consistent with the major ocean currents of southeastern Australia. Analysis of mitochondrial DNA sequence data indicated no evidence of genetic structuring, but signatures of a species range expansion corresponding with historical inundations of the Bassian Isthmus. Our results indicate that ocean currents are likely to be the most influential factor affecting the genetic structure of D. deltoides and a likely physical barrier for passive dispersing marine fauna generally in southeastern Australia. PMID:23762511

  3. Heritability estimates of the Big Five personality traits based on common genetic variants.

    PubMed

    Power, R A; Pluess, M

    2015-07-14

    According to twin studies, the Big Five personality traits have substantial heritable components explaining 40-60% of the variance, but identification of associated genetic variants has remained elusive. Consequently, knowledge regarding the molecular genetic architecture of personality and to what extent it is shared across the different personality traits is limited. Using genomic-relatedness-matrix residual maximum likelihood analysis (GREML), we here estimated the heritability of the Big Five personality factors (extraversion, agreeableness, conscientiousness, neuroticism and openness for experience) in a sample of 5011 European adults from 527,469 single-nucleotide polymorphisms across the genome. We tested for the heritability of each personality trait, as well as for the genetic overlap between the personality factors. We found significant and substantial heritability estimates for neuroticism (15%, s.e. = 0.08, P = 0.04) and openness (21%, s.e. = 0.08, P < 0.01), but not for extraversion, agreeableness and conscientiousness. The bivariate analyses showed that the variance explained by common variants entirely overlapped between neuroticism and openness (rG = 1.00, P < 0.001), despite low phenotypic correlation (r = - 0.09, P < 0.001), suggesting that the remaining unique heritability may be determined by rare or structural variants. As far as we are aware of, this is the first study estimating the shared and unique heritability of all Big Five personality traits using the GREML approach. Findings should be considered exploratory and suggest that detectable heritability estimates based on common variants is shared between neuroticism and openness to experiences.

  4. Blood vitamin d levels in relation to genetic estimation of African ancestry.

    PubMed

    Signorello, Lisa B; Williams, Scott M; Zheng, Wei; Smith, Jeffrey R; Long, Jirong; Cai, Qiuyin; Hargreaves, Margaret K; Hollis, Bruce W; Blot, William J

    2010-09-01

    African-Americans generally have lower circulating levels of 25 hydroxyvitamin D [25(OH)D] than Whites, attributed to skin pigmentation and dietary habits. Little is known about the genetic determinants of 25(OH)D levels nor whether the degree of African ancestry associates with circulating 25(OH)D. With the use of a panel of 276 ancestry informative genetic markers, we estimated African and European admixture for a sample of 758 African-American and non-Hispanic White Southern Community Cohort Study participants. For African-Americans, cut points of <85%, 85% to 95%, and >or=95% defined low, medium, and high African ancestry, respectively. We estimated the association between African ancestry and 25(OH)D and also explored whether vitamin D exposure (sunlight, diet) had varying effects on 25(OH)D levels dependent on ancestry level. The mean serum 25(OH)D levels among Whites and among African-Americans of low, medium, and high African ancestry were 27.2, 19.5, 18.3, and 16.5 ng/mL, respectively. Serum 25(OH)D was estimated to decrease by 1.0 to 1.1 ng/mL per 10% increase in African ancestry. The effect of high vitamin D exposure from sunlight and diet was 46% lower among African-Americans with high African ancestry than among those with low/medium ancestry. We found novel evidence that the level of African ancestry may play a role in clinical vitamin D status. This is the first study to describe how 25(OH)D levels vary in relation to genetic estimation of African ancestry. Further study is warranted to replicate these findings and uncover the potential pathways involved. (c)2010 AACR.

  5. Genetic parameter estimates for carcass traits and visual scores including or not genomic information.

    PubMed

    Gordo, D G M; Espigolan, R; Tonussi, R L; Júnior, G A F; Bresolin, T; Magalhães, A F Braga; Feitosa, F L; Baldi, F; Carvalheiro, R; Tonhati, H; de Oliveira, H N; Chardulo, L A L; de Albuquerque, L G

    2016-05-01

    The objective of this study was to determine whether visual scores used as selection criteria in Nellore breeding programs are effective indicators of carcass traits measured after slaughter. Additionally, this study evaluated the effect of different structures of the relationship matrix ( and ) on the estimation of genetic parameters and on the prediction accuracy of breeding values. There were 13,524 animals for visual scores of conformation (CS), finishing precocity (FP), and muscling (MS) and 1,753, 1,747, and 1,564 for LM area (LMA), backfat thickness (BF), and HCW, respectively. Of these, 1,566 animals were genotyped using a high-density panel containing 777,962 SNP. Six analyses were performed using multitrait animal models, each including the 3 visual scores and 1 carcass trait. For the visual scores, the model included direct additive genetic and residual random effects and the fixed effects of contemporary group (defined by year of birth, management group at yearling, and farm) and the linear effect of age of animal at yearling. The same model was used for the carcass traits, replacing the effect of age of animal at yearling with the linear effect of age of animal at slaughter. The variance and covariance components were estimated by the REML method in analyses using the numerator relationship matrix () or combining the genomic and the numerator relationship matrices (). The heritability estimates for the visual scores obtained with the 2 methods were similar and of moderate magnitude (0.23-0.34), indicating that these traits should response to direct selection. The heritabilities for LMA, BF, and HCW were 0.13, 0.07, and 0.17, respectively, using matrix and 0.29, 0.16, and 0.23, respectively, using matrix . The genetic correlations between the visual scores and carcass traits were positive, and higher correlations were generally obtained when matrix was used. Considering the difficulties and cost of measuring carcass traits postmortem, visual scores of

  6. RAPD and pedigree-based genetic diversity estimates in cultivated diploid potato hybrids.

    PubMed

    Sun, Genlou; Wang-Pruski, Gefu; Mayich, Michael; Jong, Hielke

    2003-06-01

    In this study, RAPD and pedigree data were used to investigate the genetic relationships in a group of 45 diploid hybrid potato clones used in the breeding and genetics program of the Agriculture and Agri-Food Canada Potato Research Centre in Fredericton, New Brunswick, and used for the potato after-cooking darkness program at the Nova Scotia Agricultural College. These hybrids were derived from crossing primitive cultivated South American diploid species such as Solanum phureja or Solanum stenotomum and wild diploid species such as Solanum chacoense and other wild Argentine species with haploids of Solanum tuberosum. These hybrids have subsequently undergone up to 30 years of breeding and selection, for adaptation to local growing and storage conditions, processing traits and pest resistances. The objectives of this study were to estimate the level of genetic similarity (GS) among these sets of clones and to investigate the correlation between RAPD-based GS and f, based on pedigree information. Genetic similarity coefficients varied from 0.29 to 0.90 with a mean of 0.65 when based on the RAPD data, whereas the coefficient of parentage varied from zero to 0.75 with a mean of 0.11. The degree of relationship between the similarity matrices based on RAPD and pedigree was measured by comparing the similarity matrices with the normalized Mantel test. A low positive correlation (R = 0.104, p = 0.999) between the two matrices was observed. Cluster analysis using GS divided the clones into many subgroups that did not correspond well with the grouping based on pedigree. The level of genetic variation present in this set of potato clones is very high. Rigorous selection pressure aimed at different breeding purposes may result in the genetic differentiation of the clones from the same origin.

  7. A method for estimating population sex ratio for sage-grouse using noninvasive genetic samples.

    PubMed

    Baumgardt, J A; Goldberg, C S; Reese, K P; Connelly, J W; Musil, D D; Garton, E O; Waits, L P

    2013-05-01

    Population sex ratio is an important metric for wildlife management and conservation, but estimates can be difficult to obtain, particularly for sexually monomorphic species or for species that differ in detection probability between the sexes. Noninvasive genetic sampling (NGS) using polymerase chain reaction (PCR) has become a common method for identifying sex from sources such as hair, feathers or faeces, and is a potential source for estimating sex ratio. If, however, PCR success is sex-biased, naively using NGS could lead to a biased sex ratio estimator. We measured PCR success rates and error rates for amplifying the W and Z chromosomes from greater sage-grouse (Centrocercus urophasianus) faecal samples, examined how success and error rates for sex identification changed in response to faecal sample exposure time, and used simulation models to evaluate precision and bias of three sex assignment criteria for estimating population sex ratio with variable sample sizes and levels of PCR replication. We found PCR success rates were higher for females than males and that choice of sex assignment criteria influenced the bias and precision of corresponding sex ratio estimates. Our simulations demonstrate the importance of considering the interplay between the sex bias of PCR success, number of genotyping replicates, sample size, true population sex ratio and accuracy of assignment rules for designing future studies. Our results suggest that using faecal DNA for estimating the sex ratio of sage-grouse populations has great potential and, with minor adaptations and similar marker evaluations, should be applicable to numerous species.

  8. Genetic polymorphisms for estimating risk of atrial fibrillation: a literature-based meta-analysis

    PubMed Central

    Smith, J. Gustav; Almgren, Peter; Engström, Gunnar; Hedblad, Bo; Platonov, Pyotr G.; Newton-Cheh, Christopher; Melander, Olle

    2013-01-01

    Objectives Genome-wide association studies have recently identified genetic polymorphisms associated with common, etiologically complex diseases, for which direct-to-consumer genetic testing with provision of absolute genetic risk estimates is marketed by commercial companies. Polymorphisms associated with atrial fibrillation (AF) have shown relatively large risk estimates but the robustness of such estimates across populations and study designs has not been studied. Design A systematic literature review with meta-analysis and assessment of between-study heterogeneity was performed for single nucleotide polymorphisms (SNPs) in the six genetic regions associated with AF in genome-wide or candidate gene studies. Results Data from 18 samples of European ancestry (n=12,100 cases; 115,702 controls) were identified for the SNP on chromosome 4q25 (rs220733), 16 samples (n=12,694 cases; 132,602 controls) for the SNP on 16q22 (rs2106261) and 4 samples (n=5,272 cases; 59,725 controls) for the SNP in KCNH2 (rs1805123). Only the discovery studies were identified for SNPs on 1q21 and in GJA5 and IL6R, why no meta-analyses were performed for those SNPs. In overall random-effects meta-analyses, association with AF was observed for both SNPs from genome-wide studies on 4q25 (OR 1.67, 95% CI=1.50–1.86, p=2×10−21) and 16q22 (OR 1.21, 95% CI=1.13–1.29, p=1×10−8), but not the SNP in KCNH2 from candidate gene studies (p=0.15). There was substantial effect heterogeneity across case-control and cross-sectional studies for both polymorphisms (I2=0.50–0.78, p<0.05), but not across prospective cohort studies (I2=0.39, p=0.15). Both polymorphisms were robustly associated with AF for each study design individually (p<0.05). Conclusions In meta-analyses including up to 150,000 individuals, polymorphisms in two genetic regions were robustly associated with AF across all study designs but with substantial context-dependency of risk estimates. PMID:22690879

  9. Accounting for missing data in the estimation of contemporary genetic effective population size (N(e) ).

    PubMed

    Peel, D; Waples, R S; Macbeth, G M; Do, C; Ovenden, J R

    2013-03-01

    Theoretical models are often applied to population genetic data sets without fully considering the effect of missing data. Researchers can deal with missing data by removing individuals that have failed to yield genotypes and/or by removing loci that have failed to yield allelic determinations, but despite their best efforts, most data sets still contain some missing data. As a consequence, realized sample size differs among loci, and this poses a problem for unbiased methods that must explicitly account for random sampling error. One commonly used solution for the calculation of contemporary effective population size (N(e) ) is to calculate the effective sample size as an unweighted mean or harmonic mean across loci. This is not ideal because it fails to account for the fact that loci with different numbers of alleles have different information content. Here we consider this problem for genetic estimators of contemporary effective population size (N(e) ). To evaluate bias and precision of several statistical approaches for dealing with missing data, we simulated populations with known N(e) and various degrees of missing data. Across all scenarios, one method of correcting for missing data (fixed-inverse variance-weighted harmonic mean) consistently performed the best for both single-sample and two-sample (temporal) methods of estimating N(e) and outperformed some methods currently in widespread use. The approach adopted here may be a starting point to adjust other population genetics methods that include per-locus sample size components.

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

    PubMed

    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.

  11. Multivariable Mendelian Randomization: The Use of Pleiotropic Genetic Variants to Estimate Causal Effects

    PubMed Central

    Burgess, Stephen; Thompson, Simon G.

    2015-01-01

    A conventional Mendelian randomization analysis assesses the causal effect of a risk factor on an outcome by using genetic variants that are solely associated with the risk factor of interest as instrumental variables. However, in some cases, such as the case of triglyceride level as a risk factor for cardiovascular disease, it may be difficult to find a relevant genetic variant that is not also associated with related risk factors, such as other lipid fractions. Such a variant is known as pleiotropic. In this paper, we propose an extension of Mendelian randomization that uses multiple genetic variants associated with several measured risk factors to simultaneously estimate the causal effect of each of the risk factors on the outcome. This “multivariable Mendelian randomization” approach is similar to the simultaneous assessment of several treatments in a factorial randomized trial. In this paper, methods for estimating the causal effects are presented and compared using real and simulated data, and the assumptions necessary for a valid multivariable Mendelian randomization analysis are discussed. Subject to these assumptions, we demonstrate that triglyceride-related pathways have a causal effect on the risk of coronary heart disease independent of the effects of low-density lipoprotein cholesterol and high-density lipoprotein cholesterol. PMID:25632051

  12. Multivariable Mendelian randomization: the use of pleiotropic genetic variants to estimate causal effects.

    PubMed

    Burgess, Stephen; Thompson, Simon G

    2015-02-15

    A conventional Mendelian randomization analysis assesses the causal effect of a risk factor on an outcome by using genetic variants that are solely associated with the risk factor of interest as instrumental variables. However, in some cases, such as the case of triglyceride level as a risk factor for cardiovascular disease, it may be difficult to find a relevant genetic variant that is not also associated with related risk factors, such as other lipid fractions. Such a variant is known as pleiotropic. In this paper, we propose an extension of Mendelian randomization that uses multiple genetic variants associated with several measured risk factors to simultaneously estimate the causal effect of each of the risk factors on the outcome. This "multivariable Mendelian randomization" approach is similar to the simultaneous assessment of several treatments in a factorial randomized trial. In this paper, methods for estimating the causal effects are presented and compared using real and simulated data, and the assumptions necessary for a valid multivariable Mendelian randomization analysis are discussed. Subject to these assumptions, we demonstrate that triglyceride-related pathways have a causal effect on the risk of coronary heart disease independent of the effects of low-density lipoprotein cholesterol and high-density lipoprotein cholesterol.

  13. Estimate of genetic gain in popcorn after cycles of phenotypic recurrent selection.

    PubMed

    Ematné, H J; Nunes, J A R; Dias, K O G; Prado, P E R; Souza, J C

    2016-05-20

    Popcorn is widely consumed in Brazil, yet there are few breeding programs for this crop. Recurrent selection (RS) is a viable breeding alternative for popcorn; however, the gains achieved must be frequently checked. The aim of this study was to assess the effect of selection for grain type (round and pointed) after four cycles of phenotypic RS on the main agronomic traits of popcorn, to estimate the genetic gain achieved for the trait of expansion volume (EV), and to obtain estimates of phenotypic correlations for the main traits of the crop in the UFLA E and UFLA R populations. The zero, one, two, and three cycles of the UFLA E and UFLA R populations, the fourth cycle, and the controls IAC-112 and IAC-125 were used. The experiments were conducted at the experimental farm of Universidade Federal de Lavras (UFLA; Environment 1) and at the experimental area of the Genetics and Plant Breeding Sector of the Department of Biology at UFLA (Environment 2) in the 2010/11 crop season. Nine agronomic traits were evaluated, including EV and grain yield (GY). The UFLA R and UFLA E populations showed similar behavior for all evaluated traits. The type of grain did not affect the genetic gain for EV, which was 5 and 3.7% in each cycle carried out in the UFLA E and UFLA R population, respectively. Phenotypic selection carried out during recombination for EV is an effective method for increasing expression of the trait. EV and GY did not show a linear association.

  14. Genetic Risk and Longitudinal Disease Activity in Systemic Lupus Erythematosus Using Targeted Maximum Likelihood Estimation

    PubMed Central

    Gianfrancesco, Milena A.; Balzer, Laura; Taylor, Kimberly E.; Trupin, Laura; Nititham, Joanne; Seldin, Michael F.; Singer, Amanda Wheeler; Criswell, Lindsey A.; Barcellos, Lisa F.

    2016-01-01

    Systemic lupus erythematous (SLE) is a chronic autoimmune disease associated with genetic and environmental risk factors. However, the extent to which genetic risk is causally associated with disease activity is unknown. We utilized longitudinal targeted maximum likelihood estimation to estimate the causal association between a genetic risk score (GRS) comprised of 41 established SLE variants and clinically important disease activity as measured by the validated systemic lupus activity questionnaire (SLAQ) in a multi-ethnic cohort of 942 individuals with SLE. We did not find evidence of a clinically important SLAQ score difference (> 4.0) for individuals with a high GRS compared to those with a low GRS across nine timepoints after controlling for sex, ancestry, renal status, dialysis, disease duration, treatment, depression, smoking, and education, as well as time-dependent confounding of missing visits. Individual SNP analyses revealed that 12 of the 41 variants were significantly associated with clinically relevant changes in SLAQ scores across timepoints 8 and 9 after controlling for multiple testing. Results based on sophisticated causal modeling of longitudinal data in a large patient cohort suggest that individual SLE risk variants may influence disease activity over time. Our findings also emphasize a role for other biological or environmental factors. PMID:27467283

  15. Genetic risk and longitudinal disease activity in systemic lupus erythematosus using targeted maximum likelihood estimation.

    PubMed

    Gianfrancesco, M A; Balzer, L; Taylor, K E; Trupin, L; Nititham, J; Seldin, M F; Singer, A W; Criswell, L A; Barcellos, L F

    2016-09-01

    Systemic lupus erythematous (SLE) is a chronic autoimmune disease associated with genetic and environmental risk factors. However, the extent to which genetic risk is causally associated with disease activity is unknown. We utilized longitudinal-targeted maximum likelihood estimation to estimate the causal association between a genetic risk score (GRS) comprising 41 established SLE variants and clinically important disease activity as measured by the validated Systemic Lupus Activity Questionnaire (SLAQ) in a multiethnic cohort of 942 individuals with SLE. We did not find evidence of a clinically important SLAQ score difference (>4.0) for individuals with a high GRS compared with those with a low GRS across nine time points after controlling for sex, ancestry, renal status, dialysis, disease duration, treatment, depression, smoking and education, as well as time-dependent confounding of missing visits. Individual single-nucleotide polymorphism (SNP) analyses revealed that 12 of the 41 variants were significantly associated with clinically relevant changes in SLAQ scores across time points eight and nine after controlling for multiple testing. Results based on sophisticated causal modeling of longitudinal data in a large patient cohort suggest that individual SLE risk variants may influence disease activity over time. Our findings also emphasize a role for other biological or environmental factors.

  16. Polygenic risk score and heritability estimates reveals a genetic relationship between ASD and OCD.

    PubMed

    Guo, W; Samuels, J F; Wang, Y; Cao, H; Ritter, M; Nestadt, P S; Krasnow, J; Greenberg, B D; Fyer, A J; McCracken, J T; Geller, D A; Murphy, D L; Knowles, J A; Grados, M A; Riddle, M A; Rasmussen, S A; McLaughlin, N C; Nurmi, E L; Askland, K D; Cullen, B A; Piacentini, J; Pauls, D L; Bienvenu, O J; Stewart, S E; Goes, F S; Maher, B; Pulver, A E; Valle, D; Mattheisen, M; Qian, J; Nestadt, G; Shugart, Y Y

    2017-07-01

    Obsessive-compulsive disorder (OCD) and Autism spectrum disorder (ASD) are both highly heritable neurodevelopmental disorders that conceivably share genetic risk factors. However, the underlying genetic determinants remain largely unknown. In this work, the authors describe a combined genome-wide association study (GWAS) of ASD and OCD. The OCD dataset includes 2998 individuals in nuclear families. The ASD dataset includes 6898 individuals in case-parents trios. GWAS summary statistics were examined for potential enrichment of functional variants associated with gene expression levels in brain regions. The top ranked SNP is rs4785741 (chromosome 16) with P value=6.9×10(-7) in our re-analysis. Polygenic risk score analyses were conducted to investigate the genetic relationship within and across the two disorders. These analyses identified a significant polygenic component of ASD, predicting 0.11% of the phenotypic variance in an independent OCD data set. In addition, we examined the genomic architecture of ASD and OCD by estimating heritability on different chromosomes and different allele frequencies, analyzing genome-wide common variant data by using the Genome-wide Complex Trait Analysis (GCTA) program. The estimated global heritability of OCD is 0.427 (se=0.093) and 0.174 (se=0.053) for ASD in these imputed data. Published by Elsevier B.V.

  17. Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L.)

    PubMed Central

    Smith, Brad L.; Lu, Ching-Ping; García-Cortés, Blanca; Viñas, Jordi; Yeh, Shean-Ya; Alvarado Bremer, Jaime R.

    2015-01-01

    Previous genetic studies of Atlantic swordfish (Xiphias gladius L.) revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs) within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise FST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish. PMID:26057382

  18. Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L.).

    PubMed

    Smith, Brad L; Lu, Ching-Ping; García-Cortés, Blanca; Viñas, Jordi; Yeh, Shean-Ya; Alvarado Bremer, Jaime R

    2015-01-01

    Previous genetic studies of Atlantic swordfish (Xiphias gladius L.) revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs) within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise FST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish.

  19. Estimation of genetic variance for macro- and micro-environmental sensitivity using double hierarchical generalized linear models.

    PubMed

    Mulder, Han A; Rönnegård, Lars; Fikse, W Freddy; Veerkamp, Roel F; Strandberg, Erling

    2013-07-04

    Genetic variation for environmental sensitivity indicates that animals are genetically different in their response to environmental factors. Environmental factors are either identifiable (e.g. temperature) and called macro-environmental or unknown and called micro-environmental. The objectives of this study were to develop a statistical method to estimate genetic parameters for macro- and micro-environmental sensitivities simultaneously, to investigate bias and precision of resulting estimates of genetic parameters and to develop and evaluate use of Akaike's information criterion using h-likelihood to select the best fitting model. We assumed that genetic variation in macro- and micro-environmental sensitivities is expressed as genetic variance in the slope of a linear reaction norm and environmental variance, respectively. A reaction norm model to estimate genetic variance for macro-environmental sensitivity was combined with a structural model for residual variance to estimate genetic variance for micro-environmental sensitivity using a double hierarchical generalized linear model in ASReml. Akaike's information criterion was constructed as model selection criterion using approximated h-likelihood. Populations of sires with large half-sib offspring groups were simulated to investigate bias and precision of estimated genetic parameters. Designs with 100 sires, each with at least 100 offspring, are required to have standard deviations of estimated variances lower than 50% of the true value. When the number of offspring increased, standard deviations of estimates across replicates decreased substantially, especially for genetic variances of macro- and micro-environmental sensitivities. Standard deviations of estimated genetic correlations across replicates were quite large (between 0.1 and 0.4), especially when sires had few offspring. Practically, no bias was observed for estimates of any of the parameters. Using Akaike's information criterion the true genetic

  20. Estimation of genetic variance for macro- and micro-environmental sensitivity using double hierarchical generalized linear models

    PubMed Central

    2013-01-01

    Background Genetic variation for environmental sensitivity indicates that animals are genetically different in their response to environmental factors. Environmental factors are either identifiable (e.g. temperature) and called macro-environmental or unknown and called micro-environmental. The objectives of this study were to develop a statistical method to estimate genetic parameters for macro- and micro-environmental sensitivities simultaneously, to investigate bias and precision of resulting estimates of genetic parameters and to develop and evaluate use of Akaike’s information criterion using h-likelihood to select the best fitting model. Methods We assumed that genetic variation in macro- and micro-environmental sensitivities is expressed as genetic variance in the slope of a linear reaction norm and environmental variance, respectively. A reaction norm model to estimate genetic variance for macro-environmental sensitivity was combined with a structural model for residual variance to estimate genetic variance for micro-environmental sensitivity using a double hierarchical generalized linear model in ASReml. Akaike’s information criterion was constructed as model selection criterion using approximated h-likelihood. Populations of sires with large half-sib offspring groups were simulated to investigate bias and precision of estimated genetic parameters. Results Designs with 100 sires, each with at least 100 offspring, are required to have standard deviations of estimated variances lower than 50% of the true value. When the number of offspring increased, standard deviations of estimates across replicates decreased substantially, especially for genetic variances of macro- and micro-environmental sensitivities. Standard deviations of estimated genetic correlations across replicates were quite large (between 0.1 and 0.4), especially when sires had few offspring. Practically, no bias was observed for estimates of any of the parameters. Using Akaike

  1. Estimation of genetic parameters for resistance to gastro-intestinal nematodes in pure blood Arabian horses.

    PubMed

    Kornaś, Sławomir; Sallé, Guillaume; Skalska, Marta; David, Ingrid; Ricard, Anne; Cabaret, Jacques

    2015-03-01

    Equine internal parasites, mostly cyathostomins, affect both horse welfare and performance. The appearance of anthelmintic-resistant parasites creates a pressing need for optimising drenching schemes. This optimization may be achieved by identifying genetic markers associated with host susceptibility to infection and then to drench carriers of these markers. The aim of our study was to characterise the genetics of horse resistance to strongyle infection by estimating heritability of this trait in an Arabian pure blood population. A population of 789 Arabian pure blood horses from the Michałów stud farm, Poland were measured for strongyle egg excretion twice a year, over 8 years. Low repeatability values were found for faecal egg counts. Our analyses showed that less than 10% of the observed variation for strongyle faecal egg counts in this population had a genetic origin. However, additional analyses highlighted an age-dependent increase in heritability which was 0.04 (±0.02) in young horses (up to 3 years of age) but 0.21 (±0.04) in older ones. These results suggest that a significant part of the inter-individual variation has a genetic origin. This paves the way to a genomic dissection of horse-nematode interactions which might provide predictive markers of susceptibility, allowing individualised drenching schemes. Copyright © 2015 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  2. Assumption-free estimation of the genetic contribution to refractive error across childhood

    PubMed Central

    St Pourcain, Beate; McMahon, George; Timpson, Nicholas J.; Evans, David M.; Williams, Cathy

    2015-01-01

    Purpose Studies in relatives have generally yielded high heritability estimates for refractive error: twins 75–90%, families 15–70%. However, because related individuals often share a common environment, these estimates are inflated (via misallocation of unique/common environment variance). We calculated a lower-bound heritability estimate for refractive error free from such bias. Methods Between the ages 7 and 15 years, participants in the Avon Longitudinal Study of Parents and Children (ALSPAC) underwent non-cycloplegic autorefraction at regular research clinics. At each age, an estimate of the variance in refractive error explained by single nucleotide polymorphism (SNP) genetic variants was calculated using genome-wide complex trait analysis (GCTA) using high-density genome-wide SNP genotype information (minimum N at each age=3,404). Results The variance in refractive error explained by the SNPs (“SNP heritability”) was stable over childhood: Across age 7–15 years, SNP heritability averaged 0.28 (SE=0.08, p<0.001). The genetic correlation for refractive error between visits varied from 0.77 to 1.00 (all p<0.001) demonstrating that a common set of SNPs was responsible for the genetic contribution to refractive error across this period of childhood. Simulations suggested lack of cycloplegia during autorefraction led to a small underestimation of SNP heritability (adjusted SNP heritability=0.35; SE=0.09). To put these results in context, the variance in refractive error explained (or predicted) by the time participants spent outdoors was <0.005 and by the time spent reading was <0.01, based on a parental questionnaire completed when the child was aged 8–9 years old. Conclusions Genetic variation captured by common SNPs explained approximately 35% of the variation in refractive error between unrelated subjects. This value sets an upper limit for predicting refractive error using existing SNP genotyping arrays, although higher-density genotyping in

  3. Estimates of genetic parameters for Holstein cows for test-day yield traits with a random regression cubic spline model.

    PubMed

    DeGroot, B J; Keown, J F; Van Vleck, L D; Kachman, S D

    2007-06-30

    Genetic parameters were estimated with restricted maximum likelihood for individual test-day milk, fat, and protein yields and somatic cell scores with a random regression cubic spline model. Test-day records of Holstein cows that calved from 1994 through early 1999 were obtained from Dairy Records Management Systems in Raleigh, North Carolina, for the analysis. Estimates of heritability for individual test-days and estimates of genetic and phenotypic correlations between test-days were obtained from estimates of variances and covariances from the cubic spline analysis. Estimates were calculated of genetic parameters for the averages of the test days within each of the ten 30-day test intervals. The model included herd test-day, age at first calving, and bovine somatropin treatment as fixed factors. Cubic splines were fitted for the overall lactation curve and for random additive genetic and permanent environmental effects, with five predetermined knots or four intervals between days 0, 50, 135, 220, and 305. Estimates of heritability for lactation one ranged from 0.10 to 0.15, 0.06 to 0.10, 0.09 to 0.15, and 0.02 to 0.06 for test-day one to test-day 10 for milk, fat, and protein yields and somatic cell scores, respectively. Estimates of heritability were greater in lactations two and three. Estimates of heritability increased over the course of the lactation. Estimates of genetic and phenotypic correlations were smaller for test-days further apart.

  4. A Genetic Algorithm Method for Direct estimation of paleostress states from heterogeneous fault-slip observations

    NASA Astrophysics Data System (ADS)

    Srivastava, D. C.

    2016-12-01

    A Genetic Algorithm Method for Direct estimation of paleostress states from heterogeneous fault-slip observationsDeepak C. Srivastava, Prithvi Thakur and Pravin K. GuptaDepartment of Earth Sciences, Indian Institute of Technology Roorkee, Roorkee 247667, India. Abstract Paleostress estimation from a group of heterogeneous fault-slip observations entails first the classification of the observations into homogeneous fault sets and then a separate inversion of each homogeneous set. This study combines these two issues into a nonlinear inverse problem and proposes a heuristic search method that inverts the heterogeneous fault-slip observations. The method estimates different paleostress states in a group of heterogeneous fault-slip observations and classifies it into homogeneous sets as a byproduct. It uses the genetic algorithm operators, elitism, selection, encoding, crossover and mutation. These processes translate into a guided search that finds successively fitter solutions and operate iteratively until the termination criteria is met and the globally fittest stress tensors are obtained. We explain the basic steps of the algorithm on a working example and demonstrate validity of the method on several synthetic and a natural group of heterogeneous fault-slip observations. The method is independent of any user-defined bias or any entrapment of solution in a local optimum. It succeeds even in the difficult situations where other classification methods are found to fail.

  5. Phenotypic and genetic parameter estimates for racing traits of Arabian horses in Turkey.

    PubMed

    Ekiz, B; Kocak, O

    2005-10-01

    The racing records for Arabian horses used in the study were obtained from the Turkish Jockey Club. The traits used in the study were racing time, best racing time, rank, annual earnings, earnings per start, log annual earnings and log earnings per start. Genetic parameters were estimated by the restricted maximum likelihood (REML) procedure using the DFREML program. The effects of age, sex and origin of horse were significant for each trait. The effect of year was significant on time and earning traits, but not rank. The effect of month on time traits was also significant. Heritability estimates of the entire data set were 0.280, 0.281, 0.069, 0.139, 0.174, 0.152 and 0.171 for racing time, best racing time, rank, annual earnings, earnings per start, log annual earnings and log earnings per start respectively. Estimates of repeatability varied from 0.349 to 0.500 for racing time, from 0.430 to 0.524 for best racing time and from 0.129 to 0.171 for rank depending on the data set used in the analyses. Best racing time was the most appropriate trait for selection in this study, as this might lead to genetic improvement than other traits.

  6. Three-dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity.

    PubMed

    Milanesi, P; Holderegger, R; Bollmann, K; Gugerli, F; Zellweger, F

    2017-02-01

    Estimating connectivity among fragmented habitat patches is crucial for evaluating the functionality of ecological networks. However, current estimates of landscape resistance to animal movement and dispersal lack landscape-level data on local habitat structure. Here, we used a landscape genetics approach to show that high-fidelity habitat structure maps derived from Light Detection and Ranging (LiDAR) data critically improve functional connectivity estimates compared to conventional land cover data. We related pairwise genetic distances of 128 Capercaillie (Tetrao urogallus) genotypes to least-cost path distances at multiple scales derived from land cover data. Resulting β values of linear mixed effects models ranged from 0.372 to 0.495, while those derived from LiDAR ranged from 0.558 to 0.758. The identification and conservation of functional ecological networks suffering from habitat fragmentation and homogenization will thus benefit from the growing availability of detailed and contiguous data on three-dimensional habitat structure and associated habitat quality.

  7. Estimation of genetic diversity in Gute sheep: pedigree and microsatellite analyses of an ancient Swedish breed.

    PubMed

    Rochus, Christina M; Johansson, Anna M

    2017-01-01

    Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep. Three datasets were analysed: pedigree information of the whole population, pedigree information for 100 animals of the population, and microsatellite genotypes for 94 of the 100 animals. The average inbreeding coefficient for lambs born during a six year time period (2007-2012) did not increase during that time period. The inbreeding calculated from the entire pedigree (0.038) and for a sample of the population (0.018) was very low. Sheep were more heterozygous at the microsatellite markers than expected (average multilocus heterozygosity and Ritland inbreeding estimates 1.01845 and -0.03931) and five of seven microsatellite markers were not in Hardy Weinberg equilibrium due to heterozygosity excess. The total effective population size estimated from the pedigree information was 155.4 and the average harmonic mean effective population size estimated from microsatellites was 88.3. Pedigree and microsatellite genotype estimations of inbreeding were consistent with a breeding program with the purpose of reducing inbreeding. Our results showed that current breeding programs of the Swedish Gute sheep are consistent with efforts of keeping this breed viable and these breeding programs are an example for other small local breeds in conserving breeds for the future.

  8. Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China

    PubMed Central

    Dou, Hailong; Yang, Haitao; Feng, Limin; Mou, Pu; Wang, Tianming; Ge, Jianping

    2016-01-01

    Over the past century, the endangered Amur tiger (Panthera tigris altaica) has experienced a severe contraction in demography and geographic range because of habitat loss, poaching, and prey depletion. In its historical home in Northeast China, there appears to be a single tiger population that includes tigers in Southwest Primorye and Northeast China; however, the current demographic status of this population is uncertain. Information on the abundance, distribution and genetic diversity of this population for assessing the efficacy of conservation interventions are scarce. We used noninvasive genetic detection data from scats, capture-recapture models and an accumulation curve method to estimate the abundance of Amur tigers in Northeast China. We identified 11 individual tigers (6 females and 5 males) using 10 microsatellite loci in three nature reserves between April 2013 and May 2015. These tigers are confined primarily to a Hunchun Nature Reserve along the border with Russia, with an estimated population abundance of 9–11 tigers during the winter of 2014–2015. They showed a low level of genetic diversity. The mean number of alleles per locus was 2.60 and expected and observed heterozygosity were 0.42 and 0.49, respectively. We also documented long-distance dispersal (~270 km) of a male Amur tiger to Huangnihe Nature Reserve from the border, suggesting that the expansion of neighboring Russian populations may eventually help sustain Chinese populations. However, the small and isolated population recorded by this study demonstrate that there is an urgent need for more intensive regional management to create a tiger-permeable landscape and increased genetic connectivity with other populations. PMID:27100387

  9. Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China.

    PubMed

    Dou, Hailong; Yang, Haitao; Feng, Limin; Mou, Pu; Wang, Tianming; Ge, Jianping

    2016-01-01

    Over the past century, the endangered Amur tiger (Panthera tigris altaica) has experienced a severe contraction in demography and geographic range because of habitat loss, poaching, and prey depletion. In its historical home in Northeast China, there appears to be a single tiger population that includes tigers in Southwest Primorye and Northeast China; however, the current demographic status of this population is uncertain. Information on the abundance, distribution and genetic diversity of this population for assessing the efficacy of conservation interventions are scarce. We used noninvasive genetic detection data from scats, capture-recapture models and an accumulation curve method to estimate the abundance of Amur tigers in Northeast China. We identified 11 individual tigers (6 females and 5 males) using 10 microsatellite loci in three nature reserves between April 2013 and May 2015. These tigers are confined primarily to a Hunchun Nature Reserve along the border with Russia, with an estimated population abundance of 9-11 tigers during the winter of 2014-2015. They showed a low level of genetic diversity. The mean number of alleles per locus was 2.60 and expected and observed heterozygosity were 0.42 and 0.49, respectively. We also documented long-distance dispersal (~270 km) of a male Amur tiger to Huangnihe Nature Reserve from the border, suggesting that the expansion of neighboring Russian populations may eventually help sustain Chinese populations. However, the small and isolated population recorded by this study demonstrate that there is an urgent need for more intensive regional management to create a tiger-permeable landscape and increased genetic connectivity with other populations.

  10. The effect of RAD allele dropout on the estimation of genetic variation within and between populations.

    PubMed

    Gautier, Mathieu; Gharbi, Karim; Cezard, Timothee; Foucaud, Julien; Kerdelhué, Carole; Pudlo, Pierre; Cornuet, Jean-Marie; Estoup, Arnaud

    2013-06-01

    Inexpensive short-read sequencing technologies applied to reduced representation genomes is revolutionizing genetic research, especially population genetics analysis, by allowing the genotyping of massive numbers of single-nucleotide polymorphisms (SNP) for large numbers of individuals and populations. Restriction site-associated DNA (RAD) sequencing is a recent technique based on the characterization of genomic regions flanking restriction sites. One of its potential drawbacks is the presence of polymorphism within the restriction site, which makes it impossible to observe the associated SNP allele (i.e. allele dropout, ADO). To investigate the effect of ADO on genetic variation estimated from RAD markers, we first mathematically derived measures of the effect of ADO on allele frequencies as a function of different parameters within a single population. We then used RAD data sets simulated using a coalescence model to investigate the magnitude of biases induced by ADO on the estimation of expected heterozygosity and F(ST) under a simple demographic model of divergence between two populations. We found that ADO tends to overestimate genetic variation both within and between populations. Assuming a mutation rate per nucleotide between 10(-9) and 10(-8), this bias remained low for most studied combinations of divergence time and effective population size, except for large effective population sizes. Averaging F(ST) values over multiple SNPs, for example, by sliding window analysis, did not correct ADO biases. We briefly discuss possible solutions to filter the most problematic cases of ADO using read coverage to detect markers with a large excess of null alleles. © 2012 John Wiley & Sons Ltd.

  11. Estimation of genetic effects in the presence of multicollinearity in multibreed beef cattle evaluation.

    PubMed

    Roso, V M; Schenkel, F S; Miller, S P; Schaeffer, L R

    2005-08-01

    Breed additive, dominance, and epistatic loss effects are of concern in the genetic evaluation of a multibreed population. Multiple regression equations used for fitting these effects may show a high degree of multicollinearity among predictor variables. Typically, when strong linear relationships exist, the regression coefficients have large SE and are sensitive to changes in the data file and to the addition or deletion of variables in the model. Generalized ridge regression methods were applied to obtain stable estimates of direct and maternal breed additive, dominance, and epistatic loss effects in the presence of multicollinearity among predictor variables. Preweaning weight gains of beef calves in Ontario, Canada, from 1986 to 1999 were analyzed. The genetic model included fixed direct and maternal breed additive, dominance, and epistatic loss effects, fixed environmental effects of age of the calf, contemporary group, and age of the dam x sex of the calf, random additive direct and maternal genetic effects, and random maternal permanent environment effect. The degree and the nature of the multicollinearity were identified and ridge regression methods were used as an alternative to ordinary least squares (LS). Ridge parameters were obtained using two different objective methods: 1) generalized ridge estimator of Hoerl and Kennard (R1); and 2) bootstrap in combination with cross-validation (R2). Both ridge regression methods outperformed the LS estimator with respect to mean squared error of predictions (MSEP) and variance inflation factors (VIF) computed over 100 bootstrap samples. The MSEP of R1 and R2 were similar, and they were 3% less than the MSEP of LS. The average VIF of LS, R1, and R2 were equal to 26.81, 6.10, and 4.18, respectively. Ridge regression methods were particularly effective in decreasing the multicollinearity involving predictor variables of breed additive effects. Because of a high degree of confounding between estimates of maternal

  12. Genetic Structure of the Tree Peony (Paeonia rockii) and the Qinling Mountains as a Geographic Barrier Driving the Fragmentation of a Large Population

    PubMed Central

    Yuan, Jun–hui; Cheng, Fang–Yun; Zhou, Shi–Liang

    2012-01-01

    Background Tree peonies are great ornamental plants associated with a rich ethnobotanical history in Chinese culture and have recently been used as an evolutionary model. The Qinling Mountains represent a significant geographic barrier in Asia, dividing mainland China into northern (temperate) and southern (semi–tropical) regions; however, their flora has not been well analyzed. In this study, the genetic differentiation and genetic structure of Paeonia rockii and the role of the Qinling Mountains as a barrier that has driven intraspecific fragmentation were evaluated using 14 microsatellite markers. Methodology/Principal Findings Twenty wild populations were sampled from the distributional range of P. rockii. Significant population differentiation was suggested (FST value of 0.302). Moderate genetic diversity at the population level (HS of 0.516) and high population diversity at the species level (HT of 0.749) were detected. Significant excess homozygosity (FIS of 0.076) and recent population bottlenecks were detected in three populations. Bayesian clusters, population genetic trees and principal coordinate analysis all classified the P. rockii populations into three genetic groups and one admixed Wenxian population. An isolation-by-distance model for P. rockii was suggested by Mantel tests (r = 0.6074, P<0.001) and supported by AMOVA (P<0.001), revealing a significant molecular variance among the groups (11.32%) and their populations (21.22%). These data support the five geographic boundaries surrounding the Qinling Mountains and adjacent areas that were detected with Monmonier's maximum-difference algorithm. Conclusions/Significance Our data suggest that the current genetic structure of P. rockii has resulted from the fragmentation of a formerly continuously distributed large population following the restriction of gene flow between populations of this species by the Qinling Mountains. This study provides a fundamental genetic profile for the conservation

  13. Genetic analysis of the age at menopause by using estimating equations and Bayesian random effects models.

    PubMed

    Do, K A; Broom, B M; Kuhnert, P; Duffy, D L; Todorov, A A; Treloar, S A; Martin, N G

    2000-05-15

    Multi-wave self-report data on age at menopause in 2182 female twin pairs (1355 monozygotic and 827 dizygotic pairs), were analysed to estimate the genetic, common and unique environmental contribution to variation in age at menopause. Two complementary approaches for analysing correlated time-to-onset twin data are considered: the generalized estimating equations (GEE) method in which one can estimate zygosity-specific dependence simultaneously with regression coefficients that describe the average population response to changing covariates; and a subject-specific Bayesian mixed model in which heterogeneity in regression parameters is explicitly modelled and the different components of variation may be estimated directly. The proportional hazards and Weibull models were utilized, as both produce natural frameworks for estimating relative risks while adjusting for simultaneous effects of other covariates. A simple Markov chain Monte Carlo method for covariate imputation of missing data was used and the actual implementation of the Bayesian model was based on Gibbs sampling using the freeware package BUGS. Copyright 2000 John Wiley & Sons, Ltd.

  14. Estimating Modifying Effect of Age on Genetic and Environmental Variance Components in Twin Models.

    PubMed

    He, Liang; Sillanpää, Mikko J; Silventoinen, Karri; Kaprio, Jaakko; Pitkäniemi, Janne

    2016-04-01

    Twin studies have been adopted for decades to disentangle the relative genetic and environmental contributions for a wide range of traits. However, heritability estimation based on the classical twin models does not take into account dynamic behavior of the variance components over age. Varying variance of the genetic component over age can imply the existence of gene-environment (G×E) interactions that general genome-wide association studies (GWAS) fail to capture, which may lead to the inconsistency of heritability estimates between twin design and GWAS. Existing parametricG×Einteraction models for twin studies are limited by assuming a linear or quadratic form of the variance curves with respect to a moderator that can, however, be overly restricted in reality. Here we propose spline-based approaches to explore the variance curves of the genetic and environmental components. We choose the additive genetic, common, and unique environmental variance components (ACE) model as the starting point. We treat the component variances as variance functions with respect to age modeled by B-splines or P-splines. We develop an empirical Bayes method to estimate the variance curves together with their confidence bands and provide an R package for public use. Our simulations demonstrate that the proposed methods accurately capture dynamic behavior of the component variances in terms of mean square errors with a data set of >10,000 twin pairs. Using the proposed methods as an alternative and major extension to the classical twin models, our analyses with a large-scale Finnish twin data set (19,510 MZ twins and 27,312 DZ same-sex twins) discover that the variances of the A, C, and E components for body mass index (BMI) change substantially across life span in different patterns and the heritability of BMI drops to ∼50% after middle age. The results further indicate that the decline of heritability is due to increasing unique environmental variance, which provides more

  15. Comparison of different models for estimation of genetic parameters of early growth traits in the Mehraban sheep.

    PubMed

    Zamani, P; Mohammadi, H

    2008-02-01

    Genetic parameters for birth weight (BW), weaning weight (WW) and pre-weaning daily gain (PWDG) in Iranian Mehraban sheep were estimated using restricted maximum likelihood (REML) procedure. Six different animal models were fitted, differentiated by including or excluding maternal effects, with and without covariance between maternal and direct genetic effects. The estimates for direct heritability ranged from 0.26 to 0.53, 0.18 to 0.32 and 0.15 to 0.33 for BW, WW and PWDG respectively. The estimates were substantially higher when maternal effects, either genetic or environmental, were ignored in the model. The results of this study show that full models with maternal genetic and environmental effects gave the most accurate estimates for early growth traits.

  16. Estimation of genetic parameters for body weight and egg production traits in Mazandaran native chicken.

    PubMed

    Niknafs, Shahram; Nejati-Javaremi, Ardeshir; Mehrabani-Yeganeh, Hassan; Fatemi, Seyed Abolghasem

    2012-10-01

    Native chicken breeding station of Mazandaran was established in 1988 with two main objectives: genetic improvement through selection programs and dissemination of indigenous Mazandarani birds. (Co)variance components and genetic parameters for economically important traits were estimated using (bi) univariate animal models with ASREML procedure in Mazandarani native chicken. The data were from 18 generations of selection (1988-2009). Heritability estimates for body weight at different ages [at hatch (bw1), 8 (bw8), 12 (bw12) weeks of ages and sex maturation (wsm)] ranged from 0.24 ± 0.00 to 0.47 ± 0.01. Heritability for reproductive traits including age at sex maturation (asm); egg number (en); weight of first egg (ew1); average egg weight at 28 (ew28), 30 (ew30), and 32 (ew32) weeks of age; their averages (av); average egg weight for the first 12 weeks of production (ew12); egg mass (em); and egg intensity (eint) varied from 0.16 ± 0.01 to 0.43 ± 0.01. Generally, the magnitudes of heritability for the investigated traits were moderate. However, egg production traits showed smaller heritability compared with growth traits. Genetic correlations among egg weight at different ages were mostly higher than 0.8. On the one hand, body weight at different ages showed positive and relatively moderate genetic correlations with egg weight traits (ew1, ew28, ew30, ew32, ew12, and av) and varied from 0.30 ± 0.03 to 0.59 ± 0.02. On the other hand, low negative genetic correlations were obtained between body weight traits (bw1, bw8, bw12, and wsm) and egg number (en). Also, there is low negative genetic correlation (-24 ± 0.04 to -29 ± 0.05) between egg number and egg weight. Therefore, during simultaneous selection process for both growth and egg production traits, probable reduction in egg production due to low reduction in egg number may be compensated by increases in egg weight.

  17. National Estimates of Genetic Testing in Women With a History of Breast or Ovarian Cancer.

    PubMed

    Childers, Christopher P; Childers, Kimberly K; Maggard-Gibbons, Melinda; Macinko, James

    2017-08-18

    Purpose In the United States, 3.8 million women have a history of breast (BC) or ovarian cancer (OC). Up to 15% of cases are attributable to heritable mutations, which, if identified, provide critical knowledge for treatment and preventive care. It is unknown how many patients who are at high risk for these mutations have not been tested and how rates vary by risk criteria. Methods We used pooled cross-sectional data from three Cancer Control Modules (2005, 2010, 2015) of the National Health Interview Survey, a national in-person household interview survey. Eligible patients were adult females with a history of BC and/or OC meeting select 2017 National Comprehensive Cancer Network eligibility criteria on the basis of age of diagnosis and family history. Outcomes included the proportion of individuals reporting a history of discussing genetic testing with a health professional, being advised to undergo genetic testing, or undergoing genetic testing for BC or OC. Results Of 47,218 women, 2.7% had a BC history and 0.4% had an OC history. For BC, 35.6% met one or more select eligibility criteria; of those, 29.0% discussed, 20.2% were advised to undergo, and 15.3% underwent genetic testing. Testing rates for individual eligibility criteria ranged from 6.2% (relative with OC) to 18.2% (diagnosis ≤ 45 years of age). For OC, 15.1% discussed, 13.1% were advised to undergo, and 10.5% underwent testing. Using only four BC eligibility criteria and all patients with OC, an estimated 1.2 to 1.3 million individuals failed to receive testing. Conclusion Fewer than one in five individuals with a history of BC or OC meeting select National Cancer Comprehensive Network criteria have undergone genetic testing. Most have never discussed testing with a health care provider. Large national efforts are warranted to address this unmet need.

  18. Estimation of genetic parameters and breeding values across challenged environments to select for robust pigs.

    PubMed

    Herrero-Medrano, J M; Mathur, P K; ten Napel, J; Rashidi, H; Alexandri, P; Knol, E F; Mulder, H A

    2015-04-01

    Robustness is an important issue in the pig production industry. Since pigs from international breeding organizations have to withstand a variety of environmental challenges, selection of pigs with the inherent ability to sustain their productivity in diverse environments may be an economically feasible approach in the livestock industry. The objective of this study was to estimate genetic parameters and breeding values across different levels of environmental challenge load. The challenge load (CL) was estimated as the reduction in reproductive performance during different weeks of a year using 925,711 farrowing records from farms distributed worldwide. A wide range of levels of challenge, from favorable to unfavorable environments, was observed among farms with high CL values being associated with confirmed situations of unfavorable environment. Genetic parameters and breeding values were estimated in high- and low-challenge environments using a bivariate analysis, as well as across increasing levels of challenge with a random regression model using Legendre polynomials. Although heritability estimates of number of pigs born alive were slightly higher in environments with extreme CL than in those with intermediate levels of CL, the heritabilities of number of piglet losses increased progressively as CL increased. Genetic correlations among environments with different levels of CL suggest that selection in environments with extremes of low or high CL would result in low response to selection. Therefore, selection programs of breeding organizations that are commonly conducted under favorable environments could have low response to selection in commercial farms that have unfavorable environmental conditions. Sows that had experienced high levels of challenge at least once during their productive life were ranked according to their EBV. The selection of pigs using EBV ignoring environmental challenges or on the basis of records from only favorable environments

  19. Estimating the probability of allelic drop-out of STR alleles in forensic genetics.

    PubMed

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt; Morling, Niels

    2009-09-01

    In crime cases with available DNA evidence, the amount of DNA is often sparse due to the setting of the crime. In such cases, allelic drop-out of one or more true alleles in STR typing is possible. We present a statistical model for estimating the per locus and overall probability of allelic drop-out using the results of all STR loci in the case sample as reference. The methodology of logistic regression is appropriate for this analysis, and we demonstrate how to incorporate this in a forensic genetic framework.

  20. Estimation of genetic parameters for heat stress, including dominance gene effects, on milk yield in Thai Holstein dairy cattle.

    PubMed

    Boonkum, Wuttigrai; Duangjinda, Monchai

    2015-03-01

    Heat stress in tropical regions is a major cause that strongly negatively affects to milk production in dairy cattle. Genetic selection for dairy heat tolerance is powerful technique to improve genetic performance. Therefore, the current study aimed to estimate genetic parameters and investigate the threshold point of heat stress for milk yield. Data included 52 701 test-day milk yield records for the first parity from 6247 Thai Holstein dairy cattle, covering the period 1990 to 2007. The random regression test day model with EM-REML was used to estimate variance components, genetic parameters and milk production loss. A decline in milk production was found when temperature and humidity index (THI) exceeded a threshold of 74, also it was associated with the high percentage of Holstein genetics. All variance component estimates increased with THI. The estimate of heritability of test-day milk yield was 0.231. Dominance variance as a proportion to additive variance (0.035) indicated that non-additive effects might not be of concern for milk genetics studies in Thai Holstein cattle. Correlations between genetic and permanent environmental effects, for regular conditions and due to heat stress, were - 0.223 and - 0.521, respectively. The heritability and genetic correlations from this study show that simultaneous selection for milk production and heat tolerance is possible. © 2014 Japanese Society of Animal Science.

  1. Estimating Genetic and Environmental Influences on Depressive Symptoms in Adolescence: Differing Effects on Higher and Lower Levels of Symptoms

    ERIC Educational Resources Information Center

    Rende, Richard; Slomkowski, Cheryl; Lloyd-Richardson, Elizabeth; Stroud, Laura; Niaura, Raymond

    2006-01-01

    We estimate the relative effect sizes of genetic and environmental influences on both higher and lower levels of depressive symptoms with attention to persistence over a 1-year period in the genetically informative subsample of adolescents participating in the National Longitudinal Study of Adolescent Health (Add Health). Shared environmental…

  2. Estimating Genetic and Environmental Influences on Depressive Symptoms in Adolescence: Differing Effects on Higher and Lower Levels of Symptoms

    ERIC Educational Resources Information Center

    Rende, Richard; Slomkowski, Cheryl; Lloyd-Richardson, Elizabeth; Stroud, Laura; Niaura, Raymond

    2006-01-01

    We estimate the relative effect sizes of genetic and environmental influences on both higher and lower levels of depressive symptoms with attention to persistence over a 1-year period in the genetically informative subsample of adolescents participating in the National Longitudinal Study of Adolescent Health (Add Health). Shared environmental…

  3. Grizzly Bear Noninvasive Genetic Tagging Surveys: Estimating the Magnitude of Missed Detections.

    PubMed

    Fisher, Jason T; Heim, Nicole; Code, Sandra; Paczkowski, John

    2016-01-01

    Sound wildlife conservation decisions require sound information, and scientists increasingly rely on remotely collected data over large spatial scales, such as noninvasive genetic tagging (NGT). Grizzly bears (Ursus arctos), for example, are difficult to study at population scales except with noninvasive data, and NGT via hair trapping informs management over much of grizzly bears' range. Considerable statistical effort has gone into estimating sources of heterogeneity, but detection error-arising when a visiting bear fails to leave a hair sample-has not been independently estimated. We used camera traps to survey grizzly bear occurrence at fixed hair traps and multi-method hierarchical occupancy models to estimate the probability that a visiting bear actually leaves a hair sample with viable DNA. We surveyed grizzly bears via hair trapping and camera trapping for 8 monthly surveys at 50 (2012) and 76 (2013) sites in the Rocky Mountains of Alberta, Canada. We used multi-method occupancy models to estimate site occupancy, probability of detection, and conditional occupancy at a hair trap. We tested the prediction that detection error in NGT studies could be induced by temporal variability within season, leading to underestimation of occupancy. NGT via hair trapping consistently underestimated grizzly bear occupancy at a site when compared to camera trapping. At best occupancy was underestimated by 50%; at worst, by 95%. Probability of false absence was reduced through successive surveys, but this mainly accounts for error imparted by movement among repeated surveys, not necessarily missed detections by extant bears. The implications of missed detections and biased occupancy estimates for density estimation-which form the crux of management plans-require consideration. We suggest hair-trap NGT studies should estimate and correct detection error using independent survey methods such as cameras, to ensure the reliability of the data upon which species management and

  4. Reinforcement genetic approach to coefficient estimation for multivariable nonlinear discrete-time dynamical systems

    NASA Astrophysics Data System (ADS)

    Chang, Wei-Der; Yan, Jun-Juh

    2006-10-01

    In this paper, we propose a novel genetic algorithm (GA) with a multi-crossover fashion to estimate the associated coefficients for a class of nonlinear discrete-time multivariable dynamical systems. Unlike the traditional crossover method of using two chromosomes, the proposed method uses three chromosomes to achieve a crossover. According to the adjusting direction by crossing three chromosomes, more excellent offspring can be produced. To solve the identification problem of multivariable nonlinear discrete-time systems, each of estimated system coefficients represents a gene, and a collection of genes is referred to as a chromosome in the view of GA. The chromosomes in the population are then evolved using the proposed multi-crossover method. An illustrative example of multivariable nonlinear systems is given to demonstrate the effectiveness, as compared with the traditional crossover method, of the proposed method.

  5. Genetic algorithm to estimate the input parameters of Klatt and HLSyn formant-based speech synthesizers.

    PubMed

    Araújo, Fabíola; Filho, José; Klautau, Aldebaro

    2016-12-01

    Voice imitation basically consists in estimating a synthesizer's input parameters to mimic a target speech signal. This is a difficult inverse problem because the mapping is time-varying, non-linear and from many to one. It typically requires considerable amount of time to be done manually. This work presents the evolution of a system based on a genetic algorithm (GA) to automatically estimate the input parameters of the Klatt and HLSyn formant synthesizers using an analysis-by-synthesis process. Results are presented for natural (human-generated) speech for three male speakers. The results obtained with the GA-based system outperform those obtained with the baseline Winsnoori with respect to four objective figures of merit and a subjective test. The GA with Klatt synthesizer generated similar voices to the target and the subjective tests indicate an improvement in the quality of the synthetic voices when compared to the ones produced by the baseline.

  6. Estimating structure of multivariate systems with genetic algorithms for nonlinear prediction

    NASA Astrophysics Data System (ADS)

    Suzuki, Tomoya; Ueoka, Yuta; Sato, Haruki

    2009-12-01

    Although we can often observe time-series data of many elements, these elements do not always interact with each other. This paper proposes a scheme to estimate the interdependency among observed elements only by time-series data, which is useful for selecting essential elements to optimize multivariate prediction model. Because this estimation is a sort of combinatorial optimization problems, we applied the genetic algorithm as a method to moderate this problem. Through some simulations, we confirmed performance of our method, which can identify interaction of multivariate system and can improve its prediction accuracy. Especially, our method can be applied to predict real foreign-exchange markets even if system has nonstational property and its structure changes dynamically.

  7. Model-based spectral estimation of Doppler signals using parallel genetic algorithms.

    PubMed

    Solano González, J; Rodríguez Vázquez, K; García Nocetti, D F

    2000-05-01

    Conventional spectral analysis methods use a fast Fourier transform (FFT) on consecutive or overlapping windowed data segments. For Doppler ultrasound signals, this approach suffers from an inadequate frequency resolution due to the time segment duration and the non-stationarity characteristics of the signals. Parametric or model-based estimators can give significant improvements in the time-frequency resolution at the expense of a higher computational complexity. This work describes an approach which implements in real-time a parametric spectral estimator method using genetic algorithms (GAs) in order to find the optimum set of parameters for the adaptive filter that minimises the error function. The aim is to reduce the computational complexity of the conventional algorithm by using the simplicity associated to GAs and exploiting its parallel characteristics. This will allow the implementation of higher order filters, increasing the spectrum resolution, and opening a greater scope for using more complex methods.

  8. Genetic parameters for hoof health traits estimated with linear and threshold models using alternative cohorts.

    PubMed

    Malchiodi, F; Koeck, A; Mason, S; Christen, A M; Kelton, D F; Schenkel, F S; Miglior, F

    2017-04-01

    A national genetic evaluation program for hoof health could be achieved by using hoof lesion data collected directly by hoof trimmers. However, not all cows in the herds during the trimming period are always presented to the hoof trimmer. This preselection process may not be completely random, leading to erroneous estimations of the prevalence of hoof lesions in the herd and inaccuracies in the genetic evaluation. The main objective of this study was to estimate genetic parameters for individual hoof lesions in Canadian Holsteins by using an alternative cohort to consider all cows in the herd during the period of the hoof trimming sessions, including those that were not examined by the trimmer over the entire lactation. A second objective was to compare the estimated heritabilities and breeding values for resistance to hoof lesions obtained with threshold and linear models. Data were recorded by 23 hoof trimmers serving 521 herds located in Alberta, British Columbia, and Ontario. A total of 73,559 hoof-trimming records from 53,654 cows were collected between 2009 and 2012. Hoof lesions included in the analysis were digital dermatitis, interdigital dermatitis, interdigital hyperplasia, sole hemorrhage, sole ulcer, toe ulcer, and white line disease. All variables were analyzed as binary traits, as the presence or the absence of the lesions, using a threshold and a linear animal model. Two different cohorts were created: Cohort 1, which included only cows presented to hoof trimmers, and Cohort 2, which included all cows present in the herd at the time of hoof trimmer visit. Using a threshold model, heritabilities on the observed scale ranged from 0.01 to 0.08 for Cohort 1 and from 0.01 to 0.06 for Cohort 2. Heritabilities estimated with the linear model ranged from 0.01 to 0.07 for Cohort 1 and from 0.01 to 0.05 for Cohort 2. Despite a low heritability, the distribution of the sire breeding values showed large and exploitable variation among sires. Higher breeding

  9. Central Role of the Gut Epithelial Barrier in the Pathogenesis of Chronic Intestinal Inflammation: Lessons Learned from Animal Models and Human Genetics

    PubMed Central

    Pastorelli, Luca; De Salvo, Carlo; Mercado, Joseph R.; Vecchi, Maurizio; Pizarro, Theresa T.

    2013-01-01

    The gut mucosa is constantly challenged by a bombardment of foreign antigens and environmental microorganisms. As such, the precise regulation of the intestinal barrier allows the maintenance of mucosal immune homeostasis and prevents the onset of uncontrolled inflammation. In support of this concept, emerging evidence points to defects in components of the epithelial barrier as etiologic factors in the pathogenesis of inflammatory bowel diseases (IBDs). In fact, the integrity of the intestinal barrier relies on different elements, including robust innate immune responses, epithelial paracellular permeability, epithelial cell integrity, as well as the production of mucus. The purpose of this review is to systematically evaluate how alterations in the aforementioned epithelial components can lead to the disruption of intestinal immune homeostasis, and subsequent inflammation. In this regard, the wealth of data from mouse models of intestinal inflammation and human genetics are pivotal in understanding pathogenic pathways, for example, that are initiated from the specific loss of function of a single protein leading to the onset of intestinal disease. On the other hand, several recently proposed therapeutic approaches to treat human IBD are targeted at enhancing different elements of gut barrier function, further supporting a primary role of the epithelium in the pathogenesis of chronic intestinal inflammation and emphasizing the importance of maintaining a healthy and effective intestinal barrier. PMID:24062746

  10. Bayesian estimation of genetic parameters for multivariate threshold and continuous phenotypes and molecular genetic data in simulated horse populations using Gibbs sampling

    PubMed Central

    Stock, Kathrin F; Distl, Ottmar; Hoeschele, Ina

    2007-01-01

    Background Requirements for successful implementation of multivariate animal threshold models including phenotypic and genotypic information are not known yet. Here simulated horse data were used to investigate the properties of multivariate estimators of genetic parameters for categorical, continuous and molecular genetic data in the context of important radiological health traits using mixed linear-threshold animal models via Gibbs sampling. The simulated pedigree comprised 7 generations and 40000 animals per generation. Additive genetic values, residuals and fixed effects for one continuous trait and liabilities of four binary traits were simulated, resembling situations encountered in the Warmblood horse. Quantitative trait locus (QTL) effects and genetic marker information were simulated for one of the liabilities. Different scenarios with respect to recombination rate between genetic markers and QTL and polymorphism information content of genetic markers were studied. For each scenario ten replicates were sampled from the simulated population, and within each replicate six different datasets differing in number and distribution of animals with trait records and availability of genetic marker information were generated. (Co)Variance components were estimated using a Bayesian mixed linear-threshold animal model via Gibbs sampling. Residual variances were fixed to zero and a proper prior was used for the genetic covariance matrix. Results Effective sample sizes (ESS) and biases of genetic parameters differed significantly between datasets. Bias of heritability estimates was -6% to +6% for the continuous trait, -6% to +10% for the binary traits of moderate heritability, and -21% to +25% for the binary traits of low heritability. Additive genetic correlations were mostly underestimated between the continuous trait and binary traits of low heritability, under- or overestimated between the continuous trait and binary traits of moderate heritability, and

  11. Comparative landscape genetic analyses show a Belgian motorway to be a gene flow barrier for red deer (Cervus elaphus), but not wild boars (Sus scrofa).

    PubMed

    Frantz, A C; Bertouille, S; Eloy, M C; Licoppe, A; Chaumont, F; Flamand, M C

    2012-07-01

    While motorways are often assumed to influence the movement behaviour of large mammals, there are surprisingly few studies that show an influence of these linear structures on the genetic make-up of wild ungulate populations. Here, we analyse the spatial genetic structure of red deer (Cervus elaphus) and wild boars (Sus scrofa) along a stretch of motorway in the Walloon part of Belgium. Altogether, 876 red deer were genotyped at 13 microsatellite loci, and 325 wild boars at 14 loci. In the case of the red deer, different genetic clustering tools identified two genetic subpopulations whose borders matched the motorway well. Conversely, no genetic structure was identified in the case of the wild boar. Analysis of isolation-by-distance patterns of pairs of individuals on the same side and on different sides of the motorway also suggested that the road was a barrier to red deer, but not to wild boar movement. While telemetry studies seem to confirm that red deer are more affected by motorways than wild boar, the red deer sample size was also much larger than that of the wild boars. We therefore repeated the analysis of genetic structure in the red deer with randomly sub-sampled data sets of decreasing size. The power to detect the genetic structure using clustering methods decreased with decreasing sample size.

  12. Using a genetic algorithm to estimate the details of earthquake slip distributions from point surface displacements

    NASA Astrophysics Data System (ADS)

    Lindsay, A.; McCloskey, J.; Nic Bhloscaidh, M.

    2016-03-01

    Examining fault activity over several earthquake cycles is necessary for long-term modeling of the fault strain budget and stress state. While this requires knowledge of coseismic slip distributions for successive earthquakes along the fault, these exist only for the most recent events. However, overlying the Sunda Trench, sparsely distributed coral microatolls are sensitive to tectonically induced changes in relative sea levels and provide a century-spanning paleogeodetic and paleoseismic record. Here we present a new technique called the Genetic Algorithm Slip Estimator to constrain slip distributions from observed surface deformations of corals. We identify a suite of models consistent with the observations, and from them we compute an ensemble estimate of the causative slip. We systematically test our technique using synthetic data. Applying the technique to observed coral displacements for the 2005 Nias-Simeulue earthquake and 2007 Mentawai sequence, we reproduce key features of slip present in previously published inversions such as the magnitude and location of slip asperities. From the displacement data available for the 1797 and 1833 Mentawai earthquakes, we present slip estimates reproducing observed displacements. The areas of highest modeled slip in the paleoearthquake are nonoverlapping, and our solutions appear to tile the plate interface, complementing one another. This observation is supported by the complex rupture pattern of the 2007 Mentawai sequence, underlining the need to examine earthquake occurrence through long-term strain budget and stress modeling. Although developed to estimate earthquake slip, the technique is readily adaptable for a wider range of applications.

  13. Estimation of fugitive landfill methane emissions using surface emission monitoring and Genetic Algorithms optimization.

    PubMed

    Kormi, Tarek; Mhadhebi, Safa; Bel Hadj Ali, Nizar; Abichou, Tarek; Green, Roger

    2016-11-22

    As municipal solid waste (MSW) landfills can generate significant amounts of methane, there is considerable interest in quantifying fugitive methane emissions at such facilities. A variety of methods exist for the estimation of methane emissions from landfills. These methods are either based on analytical emission models or on measurements. This paper presents a method to estimate methane emissions using ambient air methane measurements obtained on the surface of a landfill. Genetic Algorithms based optimization combined with the standard Gaussian dispersion model is employed to identify locations as well as emission rates of potential emission sources throughout a municipal solid waste landfill. Four case studies are employed in order to evaluate the performance of the proposed methodology. It is shown that the proposed approach enables estimation of landfill methane emissions and localization of major emission hotspots in the studied landfills. The proposed source-locating-scheme could be seen as a cost effective method assisting landfill operators to reasonably estimate and locate major methane emissions. Copyright © 2016. Published by Elsevier Ltd.

  14. Inference of biological S-system using the separable estimation method and the genetic algorithm.

    PubMed

    Liu, Li-Zhi; Wu, Fang-Xiang; Zhang, W J

    2012-01-01

    Reconstruction of a biological system from its experimental time series data is a challenging task in systems biology. The S-system which consists of a group of nonlinear ordinary differential equations (ODEs) is an effective model to characterize molecular biological systems and analyze the system dynamics. However, inference of S-systems without the knowledge of system structure is not a trivial task due to its nonlinearity and complexity. In this paper, a pruning separable parameter estimation algorithm (PSPEA) is proposed for inferring S-systems. This novel algorithm combines the separable parameter estimation method (SPEM) and a pruning strategy, which includes adding an l₁ regularization term to the objective function and pruning the solution with a threshold value. Then, this algorithm is combined with the continuous genetic algorithm (CGA) to form a hybrid algorithm that owns the properties of these two combined algorithms. The performance of the pruning strategy in the proposed algorithm is evaluated from two aspects: the parameter estimation error and structure identification accuracy. The results show that the proposed algorithm with the pruning strategy has much lower estimation error and much higher identification accuracy than the existing method.

  15. Genetic and phenotypic parameters estimated from Nebraska specific-pathogen-free swine field records.

    PubMed

    David, P J; Johnson, R K; Socha, T E

    1983-11-01

    Records collected during 1971 through 1979 from 101,606 hogs raised in 18 Nebraska Specific Pathogen Free herds were analyzed. Traits considered were backfat at 100 kg (BF), weight at 140 d of age (WT) and, in some analyses, number of live pigs/litter at birth (NBA). The phenotypic correlation of BF and WT, averaged across herds, was -.07. The correlations between BF and NBA and between WT and NBA were .04 and -.05, respectively. Average phenotypic standard deviations for BF, WT and NBA were 2.6 mm, 8.8 kg and 2.0 pigs. Estimates of the heritability of BF and WT were lower than most estimates reported from university research herds. Within breed, herd and sex estimates of heritability ranged from -.22 and .51 (unweighted mean = .16 +/- .025) for BF and ranged from -.28 to .49 (mean = .16 +/- .016) for WT. Estimates of the genetic correlation between BF and WT were extremely variable (mean = -.62 +/- 14.3, range = -9.42 to 1.30) among breed-herd-sex subclasses.

  16. Estimating Modifying Effect of Age on Genetic and Environmental Variance Components in Twin Models

    PubMed Central

    He, Liang; Sillanpää, Mikko J.; Silventoinen, Karri; Kaprio, Jaakko; Pitkäniemi, Janne

    2016-01-01

    Twin studies have been adopted for decades to disentangle the relative genetic and environmental contributions for a wide range of traits. However, heritability estimation based on the classical twin models does not take into account dynamic behavior of the variance components over age. Varying variance of the genetic component over age can imply the existence of gene–environment (G × E) interactions that general genome-wide association studies (GWAS) fail to capture, which may lead to the inconsistency of heritability estimates between twin design and GWAS. Existing parametric G × E interaction models for twin studies are limited by assuming a linear or quadratic form of the variance curves with respect to a moderator that can, however, be overly restricted in reality. Here we propose spline-based approaches to explore the variance curves of the genetic and environmental components. We choose the additive genetic, common, and unique environmental variance components (ACE) model as the starting point. We treat the component variances as variance functions with respect to age modeled by B-splines or P-splines. We develop an empirical Bayes method to estimate the variance curves together with their confidence bands and provide an R package for public use. Our simulations demonstrate that the proposed methods accurately capture dynamic behavior of the component variances in terms of mean square errors with a data set of >10,000 twin pairs. Using the proposed methods as an alternative and major extension to the classical twin models, our analyses with a large-scale Finnish twin data set (19,510 MZ twins and 27,312 DZ same-sex twins) discover that the variances of the A, C, and E components for body mass index (BMI) change substantially across life span in different patterns and the heritability of BMI drops to ∼50% after middle age. The results further indicate that the decline of heritability is due to increasing unique environmental variance, which provides

  17. Estimates of genetic parameters for reproductive traits in Brahman cattle breed.

    PubMed

    Cavani, L; Garcia, D A; Carreño, L O D; Ono, R K; Pires, M P; Farah, M M; Ventura, H T; Millen, D D; Fonseca, R

    2015-07-01

    This study was designed to estimate genetic parameters for the following traits of Brahman cattle in Brazil: age at first calving (AFC), calving interval (CI), rebreeding (REB), and stayability (STAY). For REB, the value 1 was assigned to heifers that rebred and calved after first calving and the value 0 was assigned to heifers that failed to rebreed after first calving. Likewise, for STAY, the value 1 was assigned to cows that calved at least 3 times by the time they reach 6 yr of age; otherwise, the value 0 was assigned. A bivariate analysis was used to estimate covariances components by using linear animal model for CI and AFC and threshold animal model for REB and STAY. The mean h(2) were 0.10, 0.02, 0.22, and 0.10 for AFC, CI, REB, and STAY, respectively. The genetic correlations were –0.13 between AFC and CI, –0.35 between AFC and REB, –0.57 between AFC and STAY, and 0.32 between REB and STAY, which reveal that cows that remain productive for longer periods in the herd also start breeding younger and present greater chances to REB. The selection of Brahman cattle for reproductive traits, such as AFC, CI, REB, and STAY, will render low magnitude and long-term responses.

  18. Estimation of parameters of a biochemically based model of photosynthesis using a genetic algorithm.

    PubMed

    Su, Yonghong; Zhu, Gaofeng; Miao, Zewei; Feng, Qi; Chang, Zongqiang

    2009-12-01

    Photosynthesis response to carbon dioxide concentration can provide data on a number of important parameters related to leaf physiology. The genetic algorithm (GA), which is a robust stochastic evolutionary computational algorithm inspired by both natural selection and natural genetics, is proposed to simultaneously estimate the parameters [including maximum carboxylation rate allowed by ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco) carboxylation rate (V(cmax)), potential light-saturated electron transport rate (J(max)), triose-phosphate utilization (TPU), leaf dark respiration in the light (R(d)) and mesophyll conductance (g(m))] of the photosynthesis models presented by Farquhar, von Caemmerer and Berry, and Ethier and Livingston. The results show that by properly constraining the parameter bounds the GA-based estimate methods can effectively and efficiently obtain globally (or, at least near globally) optimal solutions, which are as good as or better than those obtained by non-linear curve fitting methods used in previous studies. More complicated problems such as taking the g(m) variation response to CO(2) into account can be easily formulated and solved by using GA. The influence of the crossover probability (P(c)), mutation probability (P(m)), population size and generation on the performance of GA was also investigated.

  19. Estimating Information Processing in a Memory System: The Utility of Meta-analytic Methods for Genetics

    PubMed Central

    Yildizoglu, Tugce; Weislogel, Jan-Marek; Mohammad, Farhan; Chan, Edwin S.-Y.; Assam, Pryseley N.; Claridge-Chang, Adam

    2015-01-01

    Genetic studies in Drosophila reveal that olfactory memory relies on a brain structure called the mushroom body. The mainstream view is that each of the three lobes of the mushroom body play specialized roles in short-term aversive olfactory memory, but a number of studies have made divergent conclusions based on their varying experimental findings. Like many fields, neurogenetics uses null hypothesis significance testing for data analysis. Critics of significance testing claim that this method promotes discrepancies by using arbitrary thresholds (α) to apply reject/accept dichotomies to continuous data, which is not reflective of the biological reality of quantitative phenotypes. We explored using estimation statistics, an alternative data analysis framework, to examine published fly short-term memory data. Systematic review was used to identify behavioral experiments examining the physiological basis of olfactory memory and meta-analytic approaches were applied to assess the role of lobular specialization. Multivariate meta-regression models revealed that short-term memory lobular specialization is not supported by the data; it identified the cellular extent of a transgenic driver as the major predictor of its effect on short-term memory. These findings demonstrate that effect sizes, meta-analysis, meta-regression, hierarchical models and estimation methods in general can be successfully harnessed to identify knowledge gaps, synthesize divergent results, accommodate heterogeneous experimental design and quantify genetic mechanisms. PMID:26647168

  20. Grizzly Bear Noninvasive Genetic Tagging Surveys: Estimating the Magnitude of Missed Detections

    PubMed Central

    Fisher, Jason T.; Heim, Nicole; Code, Sandra; Paczkowski, John

    2016-01-01

    Sound wildlife conservation decisions require sound information, and scientists increasingly rely on remotely collected data over large spatial scales, such as noninvasive genetic tagging (NGT). Grizzly bears (Ursus arctos), for example, are difficult to study at population scales except with noninvasive data, and NGT via hair trapping informs management over much of grizzly bears’ range. Considerable statistical effort has gone into estimating sources of heterogeneity, but detection error–arising when a visiting bear fails to leave a hair sample–has not been independently estimated. We used camera traps to survey grizzly bear occurrence at fixed hair traps and multi-method hierarchical occupancy models to estimate the probability that a visiting bear actually leaves a hair sample with viable DNA. We surveyed grizzly bears via hair trapping and camera trapping for 8 monthly surveys at 50 (2012) and 76 (2013) sites in the Rocky Mountains of Alberta, Canada. We used multi-method occupancy models to estimate site occupancy, probability of detection, and conditional occupancy at a hair trap. We tested the prediction that detection error in NGT studies could be induced by temporal variability within season, leading to underestimation of occupancy. NGT via hair trapping consistently underestimated grizzly bear occupancy at a site when compared to camera trapping. At best occupancy was underestimated by 50%; at worst, by 95%. Probability of false absence was reduced through successive surveys, but this mainly accounts for error imparted by movement among repeated surveys, not necessarily missed detections by extant bears. The implications of missed detections and biased occupancy estimates for density estimation–which form the crux of management plans–require consideration. We suggest hair-trap NGT studies should estimate and correct detection error using independent survey methods such as cameras, to ensure the reliability of the data upon which species

  1. Estimating genetic and phenotypic parameters of cellular immune-associated traits in dairy cows.

    PubMed

    Denholm, Scott J; McNeilly, Tom N; Banos, Georgios; Coffey, Mike P; Russell, George C; Bagnall, Ainsley; Mitchell, Mairi C; Wall, Eileen

    2017-04-01

    Data collected from an experimental Holstein-Friesian research herd were used to determine genetic and phenotypic parameters of innate and adaptive cellular immune-associated traits. Relationships between immune-associated traits and production, health, and fertility traits were also investigated. Repeated blood leukocyte records were analyzed in 546 cows for 9 cellular immune-associated traits, including percent T cell subsets, B cells, NK cells, and granulocytes. Variance components were estimated by univariate analysis. Heritability estimates were obtained for all 9 traits, the highest of which were observed in the T cell subsets percent CD4(+), percent CD8(+), CD4(+):CD8(+) ratio, and percent NKp46(+) cells (0.46, 0.41, 0.43 and 0.42, respectively), with between-individual variation accounting for 59 to 81% of total phenotypic variance. Associations between immune-associated traits and production, health, and fertility traits were investigated with bivariate analyses. Strong genetic correlations were observed between percent NKp46(+) and stillbirth rate (0.61), and lameness episodes and percent CD8(+) (-0.51). Regarding production traits, the strongest relationships were between CD4(+):CD8(+) ratio and weight phenotypes (-0.52 for live weight; -0.51 for empty body weight). Associations between feed conversion traits and immune-associated traits were also observed. Our results provide evidence that cellular immune-associated traits are heritable and repeatable, and the noticeable variation between animals would permit selection for altered trait values, particularly in the case of the T cell subsets. The associations we observed between immune-associated, health, fertility, and production traits suggest that genetic selection for cellular immune-associated traits could provide a useful tool in improving animal health, fitness, and fertility.

  2. Estimation of genetic parameters and environmental factors on early growth traits for Lori breed sheep using single trait animal model.

    PubMed

    Lavvaf, A; Noshary, A

    2008-01-01

    The effects of different environmental factors and estimation of genetic parameters on early growth traits for Lori breed sheep including birth weight, weaning weight and body weight at 6 months of age using 19960 records from 35 herds of Lorestan Jahad Agriculture Organization were studied in the cities of Aleshtar, Khorramabad and Poldokhtar from 1995 to 2003. The effect of herd, sex of lambs, dam age and birth year on all traits and birth type had significant effect only on weaning weight. Different single trait animal models estimated the components of direct additive genetic variance, maternal genetic variance and maternal permanent environment variance through restricted maximum likelihood using environmental factors as a fixe effect and different random effects. The results showed that direct additive genetic effect had additionally significant effect on all traits moreover maternal additive genetic and maternal permanent environment effects. Results also revealed that the maternal permanent environment variance for all traits is higher than maternal genetic variance. Also the direct heritability for all traits was higher than maternal heritability. Estimation of the direct heritability from the birth to 6 months of age showed a reducing trend that could arise from high dependence of birth and weaning weight on maternal environment conditions as compared with the age conditions afterward. The genetic assessment of growth traits in Lori breed sheep without inclusion of maternal effect in animal model causes decreased selection accuracy and incorrect genetic assessment of the lambs.

  3. Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage.

    PubMed

    Zukurov, Jean P; do Nascimento-Brito, Sieberth; Volpini, Angela C; Oliveira, Guilherme C; Janini, Luiz Mario R; Antoneli, Fernando

    2016-01-01

    In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motivation for this work is to better understand the genetic diversity of viruses with high rates of nucleotide substitution, as HIV-1 and Influenza. Most methods for viral diversity estimation proposed so far are intended to take benefit of the longer reads produced by some next-generation sequencing platforms in order to estimate a population of haplotypes which represent the diversity of the original population. The method proposed here is custom-made to take advantage of the very low error rate and extremely deep coverage per site, which are the main features of some neglected technologies that have not received much attention due to the short length of its reads, which precludes haplotype estimation. This approach allowed us to avoid some hard problems related to haplotype reconstruction (need of long reads, preliminary error filtering and assembly). We propose to measure genetic diversity of a viral population through a family of multinomial probability distributions indexed by the sites of the virus genome, each one representing the distribution of nucleic bases per site. Moreover, the implementation of the method focuses on two main optimization strategies: a read mapping/alignment procedure that aims at the recovery of the maximum possible number of short-reads; the inference of the multinomial parameters in a Bayesian framework with smoothed Dirichlet estimation. The Bayesian approach provides conditional probability distributions for the multinomial parameters allowing one to take into account the prior information of the control experiment and providing a natural way to separate signal from noise, since it automatically furnishes Bayesian confidence intervals and thus avoids the drawbacks of preliminary error filtering. The methods described in this

  4. Genetic variability of lactoferrin content estimated by mid-infrared spectrometry in bovine milk.

    PubMed

    Soyeurt, H; Colinet, F G; Arnould, V M-R; Dardenne, P; Bertozzi, C; Renaville, R; Portetelle, D; Gengler, N

    2007-09-01

    The effects of lactoferrin (LF) on the immune system have already been shown by many studies. Unfortunately, the current methods used to measure LF levels in milk do not permit the study of the genetic variability of lactoferrin or the performance of routine genetic evaluations. The first aim of this research was to derive a calibration equation permitting the prediction of LF in milk by mid-infrared spectrometry (MIR). The calibration with partial least squares on 69 samples showed a ratio of standard error of cross-validation to standard deviation equal to 1.98. Based on this value, the calibration equation was used to establish an LF indicator trait (predicted LF; pLF) on a large number of milk samples (n = 7,690). A subsequent study of its variability was conducted, which confirmed that stage of lactation and lactation number influence the overall pLF level. Small differences in mean pLF among 7 dairy breeds were also observed. The pLF content of Jersey milk was significantly higher than that in Holstein milk. Therefore, the choice of breed could change the expected LF level. Heritability estimated for pLF was 19.7%. The genetic and phenotypic correlations between somatic cell score and pLF were 0.04 and 0.26, respectively. As somatic cell score increases in presence of mastitis, this observation seems to indicate that pLF, or a function of observed pLF, compared with expected LF might have potential as an indicator of mastitis. The negative genetic correlation (-0.36) between milk yield and pLF could indicate an undesirable effect of selection for high milk production on the overall LF level.

  5. Combining direct and indirect genetic methods to estimate dispersal for informing wildlife disease management decisions.

    PubMed

    Cullingham, C I; Pond, B A; Kyle, C J; Rees, E E; Rosatte, R C; White, B N

    2008-11-01

    Epidemiological models are useful tools for management to predict and control wildlife disease outbreaks. Dispersal behaviours of the vector are critical in determining patterns of disease spread, and key variables in epidemiological models, yet they are difficult to measure. Raccoon rabies is enzootic over the eastern seaboard of North America and management actions to control its spread are costly. Understanding dispersal behaviours of raccoons can contribute to refining management protocols to reduce economic impacts. Here, estimates of dispersal were obtained through parentage and spatial genetic analyses of raccoons in two areas at the front of the raccoon rabies epizootic in Ontario; Niagara (N = 296) and St Lawrence (N = 593). Parentage analysis indicated the dispersal distance distribution is highly positively skewed with 85% of raccoons, both male and female, moving < 3 km. The tail of this distribution indicated a small proportion (< 4%) moves more than 20 km. Analysis of spatial genetic structure provided a similar assessment as the spatial genetic correlation coefficient dropped sharply after 1 km. Directionality of dispersal would have important implications for control actions; however, evidence of directional bias was not found. Separating the data into age and sex classes the spatial genetic analyses detected female philopatry. Dispersal distances differed significantly between juveniles and adults, while juveniles in the Niagara region were significantly more related to each other than adults were to each other. Factors that may contribute to these differences include kin association, and spring dispersal. Changes to the timing and area covered by rabies control operations in Ontario are indicated based on these dispersal data.

  6. A weighted genetic risk score using all known susceptibility variants to estimate rheumatoid arthritis risk

    PubMed Central

    Yarwood, Annie; Han, Buhm; Raychaudhuri, Soumya; Bowes, John; Lunt, Mark; Pappas, Dimitrios A; Kremer, Joel; Greenberg, Jeffrey D; Plenge, Robert; Worthington, Jane; Barton, Anne; Eyre, Steve

    2015-01-01

    Background There is currently great interest in the incorporation of genetic susceptibility loci into screening models to identify individuals at high risk of disease. Here, we present the first risk prediction model including all 46 known genetic loci associated with rheumatoid arthritis (RA). Methods A weighted genetic risk score (wGRS) was created using 45 RA non-human leucocyte antigen (HLA) susceptibility loci, imputed amino acids at HLA-DRB1 (11, 71 and 74), HLA-DPB1 (position 9) HLA-B (position 9) and gender. The wGRS was tested in 11 366 RA cases and 15 489 healthy controls. The risk of developing RA was estimated using logistic regression by dividing the wGRS into quintiles. The ability of the wGRS to discriminate between cases and controls was assessed by receiver operator characteristic analysis and discrimination improvement tests. Results Individuals in the highest risk group showed significantly increased odds of developing anti-cyclic citrullinated peptide-positive RA compared to the lowest risk group (OR 27.13, 95% CI 23.70 to 31.05). The wGRS was validated in an independent cohort that showed similar results (area under the curve 0.78, OR 18.00, 95% CI 13.67 to 23.71). Comparison of the full wGRS with a wGRS in which HLA amino acids were replaced by a HLA tag single-nucleotide polymorphism showed a significant loss of sensitivity and specificity. Conclusions Our study suggests that in RA, even when using all known genetic susceptibility variants, prediction performance remains modest; while this is insufficiently accurate for general population screening, it may prove of more use in targeted studies. Our study has also highlighted the importance of including HLA variation in risk prediction models. PMID:24092415

  7. Parameter Estimation for the Phenomenological Model of Hysteresis Using Efficient Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Xiaomin, Xue; Ling, Zhang; Qing, Sun

    2010-05-01

    Magnetorheological (MR) dampers provide an ideal candidate for diverse applications including structural vibration suppression as well as shock absorption and vibration control in vehicle systems in recent years. To understand the dynamic characteristics of MR damper, many researchers have utilized some useful models to illustrate the behavior of the MR damper, which are Bingham model, polynomial curve-fitting model using sigmoid function, Bouc-Wen phenomenological model, etc. The Bouc-Wen differential model is one of the most widely accepted phenomenological models due to its capability to capture a range of shapes of hysteretic cycles which can match the behavior of a MR damper. As a result, it is the tendency of this model being used to describe hysteretic phenomena. However, this model has an obvious shortcoming, its complicated equation expression, which seems to be a big problem for multi-parameter estimation simultaneously. With the development of the computer technology, a powerful multi-processing algorithm is found out possible to solve these complicated problems efficiently. Thus, this paper devotes to the use of an efficient Genetic Algorithm (GA) to estimate the multi-parameter of the Bouc-Wen model efficiently. A modified GA is adopted and improved by effective methods including adaptive genetic operators and appropriate termination criteria. The modified GA has greatly improved the performance of the traditional GA. Finally, experimental data of the MR damper are used to verify the proposed approaches with satisfactory parameter estimation results and highly efficient computational capability. Meanwhile, the algorithm and the results proposed herein also throw light on development and characterization of other novel smart dampers.

  8. Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms.

    PubMed

    Murrugarra, David; Miller, Jacob; Mueller, Alex N

    2016-01-01

    Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS) are a modeling framework that considers two propensity parameters for updating each node and uses one when the update has a positive impact on the variable, that is, when the update causes the variable to increase its value, and uses the other when the update has a negative impact, that is, when the update causes it to decrease its value. This framework offers additional features for simulations but also adds a complexity in parameter estimation of the propensities. This paper presents a method for estimating the propensity parameters for SDDS. The method is based on adding noise to the system using the Google PageRank approach to make the system ergodic and thus guaranteeing the existence of a stationary distribution. Then with the use of a genetic algorithm, the propensity parameters are estimated. Approximation techniques that make the search algorithms efficient are also presented and Matlab/Octave code to test the algorithms are available at http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html.

  9. Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms

    PubMed Central

    Murrugarra, David; Miller, Jacob; Mueller, Alex N.

    2016-01-01

    Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS) are a modeling framework that considers two propensity parameters for updating each node and uses one when the update has a positive impact on the variable, that is, when the update causes the variable to increase its value, and uses the other when the update has a negative impact, that is, when the update causes it to decrease its value. This framework offers additional features for simulations but also adds a complexity in parameter estimation of the propensities. This paper presents a method for estimating the propensity parameters for SDDS. The method is based on adding noise to the system using the Google PageRank approach to make the system ergodic and thus guaranteeing the existence of a stationary distribution. Then with the use of a genetic algorithm, the propensity parameters are estimated. Approximation techniques that make the search algorithms efficient are also presented and Matlab/Octave code to test the algorithms are available at http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html. PMID:27891072

  10. Population genetic and field-ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian.

    PubMed

    Wang, Ian J; Shaffer, H Bradley

    2017-07-01

    The explosive growth of empirical population genetics has seen a proliferation of analytical methods leading to a steady increase in our ability to accurately measure key population parameters, including genetic isolation, effective population size, and gene flow, in natural systems. Assuming they yield similar results, population genetic methods offer an attractive complement to, or replacement of, traditional field-ecological studies. However, empirical assessments of the concordance between direct field-ecological and indirect population genetic studies of the same populations are uncommon in the literature. In this study, we investigate genetic isolation, rates of dispersal, and population sizes for the endangered California tiger salamander, Ambystoma californiense, across multiple breeding seasons in an intact vernal pool network. We then compare our molecular results to a previously published study based on multiyear, mark-recapture data from the same breeding sites. We found that field and genetic estimates of population size were only weakly correlated, but dispersal rates were remarkably congruent across studies and methods. In fact, dispersal probability functions derived from genetic data and traditional field-ecological data were a significant match, suggesting that either method can be used effectively to assess population connectivity. These results provide one of the first explicit tests of the correspondence between landscape genetic and field-ecological approaches to measuring functional population connectivity and suggest that even single-year genetic samples can return biologically meaningful estimates of natural dispersal and gene flow.

  11. THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps.

    PubMed

    Cheema, Jitender; Ellis, T H Noel; Dicks, Jo

    2010-07-01

    The estimation of genetic linkage maps is a key component in plant and animal research, providing both an indication of the genetic structure of an organism and a mechanism for identifying candidate genes associated with traits of interest. Because of this importance, several computational solutions to genetic map estimation exist, mostly implemented as stand-alone software packages. However, the estimation process is often largely hidden from the user. Consequently, problems such as a program crashing may occur that leave a user baffled. THREaD Mapper Studio (http://cbr.jic.ac.uk/threadmapper) is a new web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers. The rationale behind the web site is to make the estimation process as transparent and robust as possible, while also allowing users to use their expert knowledge during analysis. Indeed, the 3D visual nature of the tool allows users to spot features in a data set, such as outlying markers and potential structural rearrangements that could cause problems with the estimation procedure and to account for them in their analysis. Furthermore, THREaD Mapper Studio facilitates the visual comparison of genetic map solutions from third party software, aiding users in developing robust solutions for their data sets.

  12. THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps

    PubMed Central

    Cheema, Jitender; Ellis, T. H. Noel; Dicks, Jo

    2010-01-01

    The estimation of genetic linkage maps is a key component in plant and animal research, providing both an indication of the genetic structure of an organism and a mechanism for identifying candidate genes associated with traits of interest. Because of this importance, several computational solutions to genetic map estimation exist, mostly implemented as stand-alone software packages. However, the estimation process is often largely hidden from the user. Consequently, problems such as a program crashing may occur that leave a user baffled. THREaD Mapper Studio (http://cbr.jic.ac.uk/threadmapper) is a new web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers. The rationale behind the web site is to make the estimation process as transparent and robust as possible, while also allowing users to use their expert knowledge during analysis. Indeed, the 3D visual nature of the tool allows users to spot features in a data set, such as outlying markers and potential structural rearrangements that could cause problems with the estimation procedure and to account for them in their analysis. Furthermore, THREaD Mapper Studio facilitates the visual comparison of genetic map solutions from third party software, aiding users in developing robust solutions for their data sets. PMID:20494977

  13. Elevation as a barrier: genetic structure for an Atlantic rain forest tree (Bathysa australis) in the Serra do Mar mountain range, SE Brazil

    PubMed Central

    Reis, Talita Soares; Ciampi-Guillardi, Maísa; Bajay, Miklos Maximiliano; de Souza, Anete Pereira; dos Santos, Flavio Antonio Maës

    2015-01-01

    Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self-compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80–216 m) and an upland site (1010–1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (FST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation-by-distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ∼10-20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence

  14. Estimating Typhoon Rainfall over Sea from SSM/I Satellite Data Using an Improved Genetic Programming

    NASA Astrophysics Data System (ADS)

    Yeh, K.; Wei, H.; Chen, L.; Liu, G.

    2010-12-01

    Estimating Typhoon Rainfall over Sea from SSM/I Satellite Data Using an Improved Genetic Programming Keh-Chia Yeha, Hsiao-Ping Weia,d, Li Chenb, and Gin-Rong Liuc a Department of Civil Engineering, National Chiao Tung University, Hsinchu, Taiwan, 300, R.O.C. b Department of Civil Engineering and Engineering Informatics, Chung Hua University, Hsinchu, Taiwan, 300, R.O.C. c Center for Space and Remote Sensing Research, National Central University, Tao-Yuan, Taiwan, 320, R.O.C. d National Science and Technology Center for Disaster Reduction, Taipei County, Taiwan, 231, R.O.C. Abstract This paper proposes an improved multi-run genetic programming (GP) and applies it to predict the rainfall using meteorological satellite data. GP is a well-known evolutionary programming and data mining method, used to automatically discover the complex relationships among nonlinear systems. The main advantage of GP is to optimize appropriate types of function and their associated coefficients simultaneously. This study makes an improvement to enhance escape ability from local optimums during the optimization procedure. The GP continuously runs several times by replacing the terminal nodes at the next run with the best solution at the current run. The current novel model improves GP, obtaining a highly nonlinear mathematical equation to estimate the rainfall. In the case study, this improved GP described above combining with SSM/I satellite data is employed to establish a suitable method for estimating rainfall at sea surface during typhoon periods. These estimated rainfalls are then verified with the data from four rainfall stations located at Peng-Jia-Yu, Don-Gji-Dao, Lan-Yu, and Green Island, which are four small islands around Taiwan. From the results, the improved GP can generate sophisticated and accurate nonlinear mathematical equation through two-run learning procedures which outperforms the traditional multiple linear regression, empirical equations and back-propagated network

  15. Can estimates of genetic effective population size contribute to fisheries stock assessments?

    PubMed

    Ovenden, J R; Leigh, G M; Blower, D C; Jones, A T; Moore, A; Bustamante, C; Buckworth, R C; Bennett, M B; Dudgeon, C L

    2016-12-01

    Sustainable exploitation of fisheries populations is challenging to achieve when the size of the population prior to exploitation and the actual numbers removed over time and across fishing zones are not clearly known. Quantitative fisheries' modeling is able to address this problem, but accurate and reliable model outcomes depend on high quality input data. Much of this information is obtained through the operation of the fishery under consideration, but while this seems appropriate, biases may occur. For example, poorly quantified changes in fishing methods that increase catch rates can erroneously suggest that the overall population size is increasing. Hence, the incorporation of estimates of abundance derived from independent data sources is preferable. We review and evaluate a fisheries-independent method of indexing population size; inferring adult abundance from estimates of the genetic effective size of a population (Ne ). Recent studies of elasmobranch species have shown correspondence between Ne and ecologically determined estimates of the population size (N). Simulation studies have flagged the possibility that the range of Ne /N ratios across species may be more restricted than previously thought, and also show that declines in Ne track declines in the abundance of model fisheries species. These key developments bring this new technology closer to implementation in fisheries science, particularly for data-poor fisheries or species of conservation interest. © 2016 The Fisheries Society of the British Isles.

  16. Multi Population Genetic Algorithm to estimate snow properties from GPR data

    NASA Astrophysics Data System (ADS)

    Godio, A.

    2016-08-01

    Multi-population genetic algorithms (DGA or MGA) are based on the partition of the population into several semi-isolated subpopulations (demes). Each sub-population is associated to an independent GA and explores different promising regions of the search space. We evaluate the sensitivity of some parameters to solve a non-linear problem in georadar data analysis. Particularly, we adapt the DGAs to optimize the model parameters of a data set of variable-offset data, collected in variable offset modality with Ground Penetrating Radar, to estimate porosity, saturation and density of snowpack in a glacial environment. The data set comes from investigation on glaciers to estimate the thickness and density of the seasonal snow. The main strategies to select the best parameters of the optimization process are outlined. We analyze the sensitivity on the solution of the optimization problems of some parameters of DGA; we deal with the effects of population and sub-population, and mutation properties. We consider the reflection traveltimes in a layered medium including a relationship between the traveltimes, porosity and saturation of the snow. We solve the problem for the layer thickness and the porosity, saturation and structural exponent of the snow. Reliable results are obtained in the snow density estimating, while the evaluation of free water content into the snow still remains challenging.

  17. Genetic progress estimation strategy for upright common bean plants using recurrent selection.

    PubMed

    Pereira, L A; Abreu, A F B; Júnior, I C Vieira; Pires, L P M; Ramalho, M A P

    2017-03-22

    Common bean producers in Brazil tend to grow plants as upright as possible. Because the control of this trait involves a large number of genes, recurrent selection (RS) is the best approach for successful plant improvement. Because plant architecture (PA) is evaluated using scores and usually has high heritability, RS for PA is performed through visual selection in generation S0. The aim of the present study was to evaluate selection progress and investigate whether this progress varies with the number of selected progenies or the generation evaluated. In addition, the effect of RS for the upright (PA) trait on progeny grain yield (GY) was investigated. Data of progenies S0:3 and S0:4 of the fifth, eighth, and twelfth cycles were used. A combined analysis of variance was performed using the adjusted means of the 47 best progenies from each generation and cycle, using two control cultivars as reference. A joint analysis of the two generations used during the evaluation of progenies for the different cycles was also performed. The genetic progress (GP) was estimated by fitting a linear regression equation to the relationship between the adjusted mean of each cycle and the number of cycles. We found that RS was efficient and the estimated GP of the evaluated progenies was 4.5%. Based on the GY heritability estimates, in more advanced generation selection for GY can be successfully performed on progenies. Thus, the selection already done for PA in F2 could be associated to the most productive progenies.

  18. Estimation of male gene flow from measures of nuclear and female genetic differentiation.

    PubMed

    Hedrick, Philip W; Allendorf, Fred W; Baker, C Scott

    2013-01-01

    An approach is provided to estimate male gene flow and the ratio of male to female gene flow, given that there are estimates of diploid, nuclear gene flow and haploid, female gene flow. This approach can be applied to estimates of differentiation (F ST ) from biparentally and maternally inherited markers, assuming the equilibrium island model and equal effective numbers of males and females. Corrections to formulas used previously for California sea lions (González-Suárez M, Flatz R, Aurioles-Gamboa D, Hedrick PW, Gerber LR. 2009. Isolation by distance among California sea lion populations in Mexico: redefining management stocks. Mol Ecol. 18:1088-1099.) and American bison (Halbert ND, Gogan PJP, Hedrick PW, Wahl L, Derr JN. 2012. Genetic population substructure in bison in Yellowstone National Park. J Hered. 103:360-370.) are given and revised values for those species are calculated. The effect of unequal male and female effective population sizes, nonequilibrium conditions, and approximations of differentiation formulas are briefly discussed.

  19. Inrush Current Simulation of Power Transformer using Machine Parameters Estimated by Design Procedure of Winding Structure and Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Tokunaga, Yoshitaka

    This paper presents estimation techniques of machine parameters for power transformer using design procedure of transformer and genetic algorithm with real coding. Especially, it is very difficult to obtain machine parameters for transformers in customers' facilities. Using estimation techniques, machine parameters could be calculated from the only nameplate data of these transformers. Subsequently, EMTP-ATP simulation of the inrush current was carried out using machine parameters estimated by techniques developed in this study and simulation results were reproduced measured waveforms.

  20. Genetic and least squares algorithms for estimating spectral EIS parameters of prostatic tissues.

    PubMed

    Halter, Ryan J; Hartov, Alex; Paulsen, Keith D; Schned, Alan; Heaney, John

    2008-06-01

    We employed electrical impedance spectroscopy (EIS) to evaluate the electrical properties of prostatic tissues. We collected freshly excised prostates from 23 men immediately following radical prostatectomy. The prostates were sectioned into 3 mm slices and electrical property measurements of complex resistivity were recorded from each of the slices using an impedance probe over the frequency range of 100 Hz to 100 kHz. The area probed was marked so that following tissue fixation and slide preparation, histological assessment could be correlated directly with the recorded EIS spectra. Prostate cancer (CaP), benign prostatic hyperplasia (BPH), non-hyperplastic glandular tissue and stroma were the primary prostatic tissue types probed. Genetic and least squares parameter estimation algorithms were implemented for fitting a Cole-type resistivity model to the measured data. The four multi-frequency-based spectral parameters defining the recorded spectrum (rho(infinity), Deltarho, f(c) and alpha) were determined using these algorithms and statistically analyzed with respect to the tissue type. Both algorithms fit the measured data well, with the least squares algorithm having a better average goodness of fit (95.2 mOmega m versus 109.8 mOmega m) and a faster execution time (80.9 ms versus 13 637 ms) than the genetic algorithm. The mean parameters, from all tissue samples, estimated using the genetic algorithm ranged from 4.44 to 5.55 Omega m, 2.42 to 7.14 Omega m, 3.26 to 6.07 kHz and 0.565 to 0.654 for rho(infinity), Deltarho, f(c) and alpha, respectively. These same parameters estimated using the least squares algorithm ranged from 4.58 to 5.79 Omega m, 2.18 to 6.98 Omega m, 2.97 to 5.06 kHz and 0.621 to 0.742 for rho(infinity), Deltarho, f(c) and alpha, respectively. The ranges of these parameters were similar to those reported in the literature. Further, significant differences (p < 0.01) were observed between CaP and BPH for the spectral parameters Deltarho and f

  1. Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants.

    PubMed

    Mohd Ali, Noorlin; Tsuboi, Ryo; Matsumoto, Yuta; Koishi, Daisuke; Inoue, Kentaro; Maeda, Kazuhiro; Kurata, Hiroyuki

    2016-07-01

    Computational analysis of metabolic fluxes is essential in understanding the structure and function of a metabolic network and in rationally designing genetically modified mutants for an engineering purpose. We had presented the genetic modification flux (GMF) that predicts the flux distribution of a broad range of genetically modified mutants. To enhance the feasibility and usability of GMF, we have developed a web application with a metabolic network database to predict a flux distribution of genetically modified mutants. One hundred and twelve data sets of Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Chinese hamster ovary were registered as standard models.

  2. Fine-scale genetic breaks driven by historical range dynamics and ongoing density-barrier effects in the estuarine seaweed Fucus ceranoides L.

    PubMed

    Neiva, João; Pearson, Gareth A; Valero, Myriam; Serrão, Ester A

    2012-06-06

    Factors promoting the emergence of sharp phylogeographic breaks include restricted dispersal, habitat discontinuity, physical barriers, disruptive selection, mating incompatibility, genetic surfing and secondary contact. Disentangling the role of each in any particular system can be difficult, especially when species are evenly distributed across transition zones and dispersal barriers are not evident. The estuarine seaweed Fucus ceranoides provides a good example of highly differentiated populations along its most persistent distributional range at the present rear edge of the species distribution, in NW Iberia. Intrinsic dispersal restrictions are obvious in this species, but have not prevented F. ceranoides from vastly expanding its range northwards following the last glaciation, implying that additional factors are responsible for the lack of connectivity between neighbouring southern populations. In this study we analyze 22 consecutive populations of F. ceranoides along NW Iberia to investigate the processes generating and maintaining the observed high levels of regional genetic divergence. Variation at seven microsatellite loci and at mtDNA spacer sequences was concordant in revealing that Iberian F. ceranoides is composed of three divergent genetic clusters displaying nearly disjunct geographical distributions. Structure and AFC analyses detected two populations with an admixed nuclear background. Haplotypic diversity was high in the W sector and very low in the N sector. Within each genetic cluster, population structure was also pervasive, although shallower. The deep divergence between sectors coupled with the lack of support for a role of oceanographic barriers in defining the location of breaks suggested 1) that the parapatric genetic sectors result from the regional reassembly of formerly vicariant sub-populations, and 2) that the genetic discontinuities at secondary contact zones (and elsewhere) are maintained despite normal migration rates. We

  3. Fine-scale genetic breaks driven by historical range dynamics and ongoing density-barrier effects in the estuarine seaweed Fucus ceranoides L.

    PubMed Central

    2012-01-01

    Background Factors promoting the emergence of sharp phylogeographic breaks include restricted dispersal, habitat discontinuity, physical barriers, disruptive selection, mating incompatibility, genetic surfing and secondary contact. Disentangling the role of each in any particular system can be difficult, especially when species are evenly distributed across transition zones and dispersal barriers are not evident. The estuarine seaweed Fucus ceranoides provides a good example of highly differentiated populations along its most persistent distributional range at the present rear edge of the species distribution, in NW Iberia. Intrinsic dispersal restrictions are obvious in this species, but have not prevented F. ceranoides from vastly expanding its range northwards following the last glaciation, implying that additional factors are responsible for the lack of connectivity between neighbouring southern populations. In this study we analyze 22 consecutive populations of F. ceranoides along NW Iberia to investigate the processes generating and maintaining the observed high levels of regional genetic divergence. Results Variation at seven microsatellite loci and at mtDNA spacer sequences was concordant in revealing that Iberian F. ceranoides is composed of three divergent genetic clusters displaying nearly disjunct geographical distributions. Structure and AFC analyses detected two populations with an admixed nuclear background. Haplotypic diversity was high in the W sector and very low in the N sector. Within each genetic cluster, population structure was also pervasive, although shallower. Conclusions The deep divergence between sectors coupled with the lack of support for a role of oceanographic barriers in defining the location of breaks suggested 1) that the parapatric genetic sectors result from the regional reassembly of formerly vicariant sub-populations, and 2) that the genetic discontinuities at secondary contact zones (and elsewhere) are maintained despite

  4. Estimation of the genetic correlations between twisted legs and growth or conformation traits in broiler chickens.

    PubMed

    Bihan-Duval, E L; Beaumont, C; Colleau, J J

    1997-01-12

    Genetic correlations between two types of leg deformities, valgus and varus angulations, and some growth or conformation traits were estimated in two commercial broiler strains. 14 264 chickens of both sexes in line A were measured for leg defects at 6 weeks and body weight at 3 (BW3) or 6 (BW6) weeks. The same measures were taken in line B on 8 164 chickens, as well as breast angle (BRA) and breast meat yield (BRM) at 6 weeks on 70% of the male birds. The multinomial logit model previously developed for the genetic analysis of valgus and varus deformities was extended to deal with the joint analysis of one unordered categorical trait and one continuous variable. The model assumed a competition between latent susceptibility variates related to the various deformities and linearly dependent on the continuous performances. Location parameters for latent susceptibilities and continuous trait were estimated by the 'Maximum A Posteriori' approach and dispersion parameters by the 'Maximum Marginal Likelihood' using a tilda-hat approximation. The genetic model took into account the effects of the sire, maternal grandsire and dam within maternal grandsire. As described in a previous study, leg deformities showed moderate heritabilities. Mean heritability estimate for both lines, based on the sire/maternal-grandsire (S/MGS) component, was equal to 0.22 for valgus and varus; when based on the dam component, mean estimates were equal to 0.37 and 0.29 for the two deformities respectively. Except for BRA, heritability of growth and conformation traits appeared to be smaller when based on S/MGS component (from 0.18 to 0.47) than on dam component (from 0.41 to 0.63). Very low genetic correlations were found between susceptibilities to leg deformities and growth performances: average estimates for both lines of the genetic correlation with BW3 were -0.03 and -0.05 for valgus and varus respectively. Respective genetic correlations with BW6 were estimated to be +0.05 and +0

  5. Bayesian estimates of genetic parameters for pre-conception traits, gestation length and calving interval in beef cattle.

    PubMed

    Yagüe, G; Goyache, F; Becerra, J; Moreno, C; Sánchez, L; Altarriba, J

    2009-08-01

    A total of 5253 records obtained from 2081 Rubia Gallega beef cows managed using artificial insemination as the only reproduction system were analysed to estimate genetic parameters for days to first insemination (DFI), days from first insemination to conception (FIC), number of inseminations per conception (IN), days open (DO), gestation length (GL) and calving interval (CI) via multitrait Bayesian procedures. Estimates of the mean of posterior distribution of the heritability of DFI, FIC, IN, DO, GL and CI were, respectively, 0.050, 0.078, 0.071, 0.053, 0.037 and 0.085 and the corresponding estimates for repeatability of these traits were 0.116, 0.129, 0.147, 0.138, 0.082 and 0.132, respectively. No significant genetic correlations associated to DFI or GL were found. However, genetic correlations between the other four analysed traits were high and significant. Genetic correlations between FIC and IN, DO and CI were similar and higher than 0.85. Genetic correlations of IN-DO and IN-CI were over 0.65. The highest genetic correlation was estimated for the pair DO-CI (0.992) that can be considered the same trait in genetic terms. Results indicated that DFI can be highly affected by non-genetic factors thus limiting its usefulness to be used as an earlier indicator of reproductive performance in beef cattle. Moreover, GL could not be associated to the reproductive performance of the cow before conception. The other four analysed traits, FIC, IN, DO and CI, have close genetic relationships. The inclusion of IN as an earlier indicator of fertility in beef cattle improvement programs using artificial insemination as the main reproductive system can be advisable due to the low additional recording effort needed.

  6. Estimates of phenotypic and genetic parameters for birth weight of Brown Swiss calves in Turkey using an animal model.

    PubMed

    Sahin, A; Ulutas, Z; Yilmaz Adkinson, A; Adkinson, R W

    2012-06-01

    A study was conducted to assess the influence of genetic and environmental factors on Brown Swiss calf birth weight, and to estimate variance components, genetic parameters, and breeding values. Data were collected on 1,761 Brown Swiss calves born from 1990 to 2005 in the Konuklar State Farm in Turkey. Mean birth weight for all calves was 39.3 ± 0.09 kg. Least squares mean birth weights for male and female Brown Swiss calves were 40.3 ± 0.02 and 39.0 ± 0.02 kg, respectively. Variance components, genetic parameters, and breeding values for birth weight in Brown Swiss calves were estimated by restricted error maximum likelihood (REML)-best linear unbiased prediction(BLUP) procedures using an MTDFREML (multiple trait derivative free restricted maximum likelihood) program employing an animal model. Direct heritability (h(d)(2)), maternal heritability (h(m)(2)), total heritability (h(T)(2)), r(am) and c(am) estimates were 0.12, 0.09, 0.23, -0.58, and -0.06, respectively. The estimated maternal permanent environmental variance expressed as a proportion of the phenotypic variance (c(2)) was 0.05. Breeding values were estimated for the trait and used to evaluate genetic trends across the time period investigated. The genetic trend linear regression was not different from zero. No genetic trend for birth weight was expected, since there had been no direct selection pressure on the trait. Absence of a trend confirms that there was no change due to selection pressure on correlated traits. Genetic and environmental parameter estimates were similar to literature values indicating that effective selection methods used in more developed improvement programs would be effective in Turkey as well.

  7. Genetic parameters and estimated breeding values of insect bite hypersensitivity in Belgian Warmblood horses.

    PubMed

    Peeters, Liesbet M; Janssens, Steven; Brebels, Machteld; Buys, Nadine

    2015-12-01

    Genetic factors involved in susceptibility to insect bite hypersensitivity (IBH) in Belgian Warmblood horses (BWP) were investigated. Data relating to 3409 horses were collected using a questionnaire, administered to owners during sport competitions, BWP breeding days, breeder visits and after phone calls. Horses were classified as IBH-affected or unaffected, based on two 'disease classifiers': a lifetime record, based on owner information (life_status) and another based on whether or not the horse was showing clinical signs at the time of questioning (clin_status). IBH prevalence was 10% based on life_status, and 6.2% based on clin_status. The heritabilities estimated using threshold animal models varied from 0.65 to 0.78 on the underlying scale (0.18-0.26 on the observed scale). These research findings indicate that susceptibility to IBH is a heritable trait in BWP. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Genetic and phenotypic parameter estimates for body weights and egg production in Horro chicken of Ethiopia

    PubMed Central

    vander Waaij, E. H.; van Arendonk, Johan A. M.

    2010-01-01

    A breeding program has been established in 2008 to improve productivity of Horro chicken, an indigenous population in the western highlands of Ethiopia. The pedigree descended from 26 sires and 260 dams. Body weights were measured every 2 weeks from hatch to 8 weeks then every 4 weeks for the next 8 weeks. Egg production was recorded to 44 weeks of age for one generation. Genetic parameters were estimated using animal model fitted with common environmental effects for growth traits and ignoring common environment for egg production traits. Direct heritabilities ranged from low (0.15 ± 0.08), for body weight at 6 weeks, to moderate (0.40 ± 0.23), for hatch weight. Heritabilities of common environmental effects on growth were high at hatch (0.39 ± 0.10) and remained low afterwards. Age at first egg showed a very low heritability (0.06 ± 0.15). Heritabilities of egg numbers in the first, second, third, and fourth months of laying were 0.32 (±0.13), 0.20 (±0.16), 0.56 (±0.15), and 0.25 (±0.14), respectively. Heritabilities of cumulative of monthly records of egg numbers were from 0.24 ± 0.16 (for the first 2 months, EP12) to 0.35 ± 0.16 (over the 6 months, EP16). Body weight at 16 weeks of age (BW16) has a strong genetic correlation with the cumulative of monthly records: 0.92 (with EP12), 0.69 (with EP36), and 0.73 (with EP16). Besides their strong association, BW16 and EP16 showed higher heritability, relative to their respective trait categories. These two traits seemed to have common genes and utilizing them as selection traits would be expected to improve both egg production and growth performance of local chicken. However, the standard errors of estimates in this study were mostly high indicating that the estimates have low precision. Parameter estimations based on more data are needed before applying the current results in breeding programs. PMID:20625931

  9. A hybrid neural networks-fuzzy logic-genetic algorithm for grade estimation

    PubMed Central

    Tahmasebi, Pejman; Hezarkhani, Ardeshir

    2012-01-01

    The grade estimation is a quite important and money/time-consuming stage in a mine project, which is considered as a challenge for the geologists and mining engineers due to the structural complexities in mineral ore deposits. To overcome this problem, several artificial intelligence techniques such as Artificial Neural Networks (ANN) and Fuzzy Logic (FL) have recently been employed with various architectures and properties. However, due to the constraints of both methods, they yield the desired results only under the specific circumstances. As an example, one major problem in FL is the difficulty of constructing the membership functions (MFs).Other problems such as architecture and local minima could also be located in ANN designing. Therefore, a new methodology is presented in this paper for grade estimation. This method which is based on ANN and FL is called “Coactive Neuro-Fuzzy Inference System” (CANFIS) which combines two approaches, ANN and FL. The combination of these two artificial intelligence approaches is achieved via the verbal and numerical power of intelligent systems. To improve the performance of this system, a Genetic Algorithm (GA) – as a well-known technique to solve the complex optimization problems – is also employed to optimize the network parameters including learning rate, momentum of the network and the number of MFs for each input. A comparison of these techniques (ANN, Adaptive Neuro-Fuzzy Inference System or ANFIS) with this new method (CANFIS–GA) is also carried out through a case study in Sungun copper deposit, located in East-Azerbaijan, Iran. The results show that CANFIS–GA could be a faster and more accurate alternative to the existing time-consuming methodologies for ore grade estimation and that is, therefore, suggested to be applied for grade estimation in similar problems. PMID:25540468

  10. A hybrid neural networks-fuzzy logic-genetic algorithm for grade estimation

    NASA Astrophysics Data System (ADS)

    Tahmasebi, Pejman; Hezarkhani, Ardeshir

    2012-05-01

    The grade estimation is a quite important and money/time-consuming stage in a mine project, which is considered as a challenge for the geologists and mining engineers due to the structural complexities in mineral ore deposits. To overcome this problem, several artificial intelligence techniques such as Artificial Neural Networks (ANN) and Fuzzy Logic (FL) have recently been employed with various architectures and properties. However, due to the constraints of both methods, they yield the desired results only under the specific circumstances. As an example, one major problem in FL is the difficulty of constructing the membership functions (MFs).Other problems such as architecture and local minima could also be located in ANN designing. Therefore, a new methodology is presented in this paper for grade estimation. This method which is based on ANN and FL is called "Coactive Neuro-Fuzzy Inference System" (CANFIS) which combines two approaches, ANN and FL. The combination of these two artificial intelligence approaches is achieved via the verbal and numerical power of intelligent systems. To improve the performance of this system, a Genetic Algorithm (GA) - as a well-known technique to solve the complex optimization problems - is also employed to optimize the network parameters including learning rate, momentum of the network and the number of MFs for each input. A comparison of these techniques (ANN, Adaptive Neuro-Fuzzy Inference System or ANFIS) with this new method (CANFIS-GA) is also carried out through a case study in Sungun copper deposit, located in East-Azerbaijan, Iran. The results show that CANFIS-GA could be a faster and more accurate alternative to the existing time-consuming methodologies for ore grade estimation and that is, therefore, suggested to be applied for grade estimation in similar problems.

  11. Estimates of population genetic diversity in brown bullhead catfish by DNA fingerprinting

    SciTech Connect

    Roth, A.C.; Wessendarp, T.K.; Gordon, D.A.; Smith, M.K.; Lattier, D.L.; Hertzberg, V.; Leonard, A.

    1994-12-31

    Estimates of population genetic diversity may be a sensitive indicator of environmental impact, since limiting the effective breeding population by any means will result in loss of some variant genotypes, as has been demonstrated by allozyme analysis. DNA fingerprinting techniques are also coming into use for population analyses, and the authors chose to apply fingerprinting analysis three populations of brown bullhead catfish collected in Northern Ohio. DNA was isolated from the red blood cells of individual fish. Purified DNAs were digested with EcoR1 restriction enzyme; the digests were then sized on a 1% agarose gel, transferred to nylon membranes and probed with a radiolabeled M13 probe using the Westneat hybridization protocol (Southern blotting). This method effects fragments containing VNTR (variable number of tandem repeat) sequences complementary to the M13, which are highly variable among individual catfish. Hybridized bands were visualized by a Molecular Dynamics phosphorimager and recorded and analyzed with its proprietary Imagequant image analysis program, Excel and SAS. A total of 10 variable bands were identified and their presence or absence scored in each individual. These data were analyzed to determine between and within-population similarity indices as well as population heterozygosity and genetic diversity measures.

  12. Estimation of genetic parameters for growth, carcass and overfeeding traits in a white geese strain

    PubMed Central

    Larzul, Catherine; Rouvier, Roger; Rousselot-Pailley, Daniel; Guy, Gérard

    2000-01-01

    In an experimental strain of white plumage geese created in 1989, two experiments were carried out from 1993 to 1995 in order to estimate genetic parameters for growth, and carcass composition traits in non-overfed animals, and genetic parameters for growth and fatty liver formation in overfed animals. Four hundred and thirty-one non-overfed animals were bred and slaughtered at 11 weeks of age; they were measured for forearm length, keel bone length, chest circumference and breast depth before and after slaughtering. The carcasses were partly dissected in order weigh breast, breast muscle and skin + fat, and abdominal fat. Four hundred and seventy-seven overfed animals were slaughtered at 20 weeks of age; they were measured for "paletot" (breast meat, bone and meat from wings, bone and meat from thigh and legs) weight and liver weight. In these two experiments, the weights had moderate to high heritability values. Breast depth measured on live animals showed a low heritability value. In overfed animals, liver weight showed a high heritability value. Liver weight could be increased by selection without a great effect on "paletot" weight. Thus, obtaining a white plumage geese strain for fatty liver production by selection would be difficult because only 20% of overfed animals had fatty liver. The results did not allow to conclude on the influence of selection on liver weight on carcass traits such as muscle or fatty tissue weight. PMID:14736387

  13. Estimation of Genetic Associations between Production and Meat Quality Traits in Duroc Pigs.

    PubMed

    Cabling, M M; Kang, H S; Lopez, B M; Jang, M; Kim, H S; Nam, K C; Choi, J G; Seo, K S

    2015-08-01

    Data collected from 690 purebred Duroc pigs from 2009 to 2012 were used to estimate the heritability, and genetic and phenotypic correlations between production and meat quality traits. Variance components were obtained through the restricted maximum likelihood procedure using Wombat and SAS version 9.0. Animals were raised under the same management in five different breeding farms. The average daily gain, loin muscle area (LMA), backfat thickness (BF), and lean percent (LP) were measured as production traits. Meat quality traits included pH, cooking loss, lightness (L*), redness (a*), yellowness (b*), marbling score (MS), moisture content (MC), water holding capacity (WHC), and shear force. The results showed that the heritability estimates for meat quality traits varied largely from 0.19 to 0.79. Production traits were moderate to highly heritable from 0.41 to 0.73. Genotypically, the BF was positively correlated (p<0.05) with MC (0.786), WHC (0.904), and pH (0.328) but negatively correlated with shear force (-0.533). The results of genetic correlations indicated that selection for less BF could decrease pH, moisture content, and WHC and increase the shear force of meat. Additionally, a significant positive correlation was recorded between average daily gain and WHC, which indicates pork from faster-growing animals has higher WHC. Furthermore, selection for larger LMA and LP could increase MS and lightness color of meat. The meat quality and production traits could be improved simultaneously if desired. Hence, to avoid further deterioration of pork characteristics, appropriate selection of traits should be considered.

  14. Estimates of (co)variance components and genetic parameters for growth traits in Sirohi goat.

    PubMed

    Gowane, Gopal R; Chopra, Ashish; Prakash, Ved; Arora, A L

    2011-01-01

    Data were collected over a period of 21 years (1988-2008) to estimate (co)variance components for birth weight (BWT), weaning weight (WWT), 6-month weight (6WT), 9-month weight (9WT), 12-month weight (12WT), average daily gain from birth to weaning (ADG1), weaning to 6WT (ADG2), and from 6WT to 12WT (ADG3) in Sirohi goats maintained at the Central Sheep and Wool Research Institute, Avikanagar, Rajasthan, India. Analyses were carried out by restricted maximum likelihood, fitting six animal models with various combinations of direct and maternal effects. The best model was chosen after testing the improvement of the log-likelihood values. Heritability estimates for BWT, WWT, 6WT, 9WT, 12WT, ADG1, ADG2, and ADG3 were 0.39 ± 0.05, 0.09 ± 0.03, 0.06 ± 0.02, 0.09 ± 0.03, 0.11 ± 0.03, 0.10 ± 0.3, 0.04 ± 0.02, and 0.01 ± 0.01, respectively. For BWT and ADG1, only direct effects were significant. Estimate of maternal permanent environmental effect were important for body weights from weaning to 12WT and also for ADG2 and ADG3. However, direct maternal effects were not significant throughout. Estimate of c (2) were 0.06 ± 0.02, 0.03 ± 0.02, 0.06 ± 0.02, 0.05 ± 0.02, 0.02 ± 0.02, and 0.02 ± 0.02 for 3WT, 6WT, 9WT, 12WT, ADG2, and ADG3, respectively. The estimated repeatabilities across years of ewe effects on kid body weights were 0.10, 0.08, 0.05, 0.08, and 0.08 at birth, weaning, 6, 9, and 12 months of age, respectively. Results suggest possibility of modest rate of genetic progress for body weight traits and ADG1 through selection, whereas only slow progress will be possible for post-weaning gain. Genetic and phenotypic correlations between body weight traits were high and positive. High genetic correlation between 6WT and 9WT suggests that selection of animals at 6 months can be carried out instead of present practice of selection at 9 months.

  15. Analytical and simulation methods for estimating the potential predictive ability of genetic profiling: a comparison of methods and results.

    PubMed

    Kundu, Suman; Karssen, Lennart C; Janssens, A Cecile J W

    2012-12-01

    Various modeling methods have been proposed to estimate the potential predictive ability of polygenic risk variants that predispose to various common diseases. However, it is unknown whether differences between them affect their conclusions on predictive ability. We reviewed input parameters, assumptions and output of the five most common methods and compared their estimates of the area under the receiver operating characteristic (ROC) curve (AUC) using hypothetical data representing effect sizes and frequencies of genetic variants, population disease risk and number of variants. To assess the accuracy of the estimated AUCs, we aimed to reproduce the AUCs of published empirical studies. All methods assumed that the combined effect of genetic variants on disease risk followed a multiplicative risk model of independent genetic effects, but they either assumed per allele, per genotype or dominant/recessive effects for the genetic variants. Modeling strategy and input parameters differed. Methods used simulation analysis or analytical formulas with effect sizes quantified by odds ratios (ORs) or relative risks. Estimated AUC values were similar for lower ORs (<1.2). When AUCs were larger (>0.7) due to variants with strong effects, differences in estimated AUCs between methods increased. The simulation methods accurately reproduced the AUC values of empirical studies, but the analytical methods did not. We conclude that despite differences in input parameters, the modeling methods estimate similar AUC for realistic values of the ORs. When one or more variants have stronger effects and AUC values are higher, the simulation methods tend to be more accurate.

  16. Genetic differentiation among populations of Brachytrupes portentosus (Lichtenstein 1796) (Orthoptera: Gryllidae) in Thailand and the Lao PDR: the Mekong River as a biogeographic barrier.

    PubMed

    Tantrawatpan, C; Saijuntha, W; Pilab, W; Sakdakham, K; Pasorn, P; Thanonkeo, S; Thiha; Satrawaha, R; Petney, T

    2011-12-01

    The Mekong River is known to act as a boundary between a number of terrestrial and freshwater species, including various parasites and their intermediate hosts as well as endangered mammal species. Little information is available, however, on the genetic differentiation between terrestrial invertebrates to the east and the west of this wide river. The genetic diversity among eight natural populations of Brachytrupes portentosus (Lichtenstein, 1796) (Orthoptera: Gryllidae) collected from Thailand and the Lao People's Democratic Republic (PDR) were analyzed by multilocus enzyme electrophoresis. The allelic profiles of 20 enzymes encoding 23 loci were analyzed. An average of 41% fixed differences was detected between the populations from Thailand and Lao PDR, which are separated by the Mekong River. The percent fixed differences ranged between 4% and 26% within the populations from Thailand and between 4% and 22% within the populations from Lao PDR. A phenogram shows that the eight populations fell into two major clusters based on the Thai and Lao sampling sites. The genetic distance between the samples within Thailand and within Lao PDR was related to the distances between sampling areas. The genetic variability between populations of this cricket indicates that genetic relationships are influenced by a natural barrier as well as by the geographical distance between these allopatric populations.

  17. Stochastic dynamic simulation modeling including multitrait genetics to estimate genetic, technical, and financial consequences of dairy farm reproduction and selection strategies.

    PubMed

    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

  18. Experimental Design for Groundwater Pumping Estimation Using a Genetic Algorithm (GA) and Proper Orthogonal Decomposition (POD)

    NASA Astrophysics Data System (ADS)

    Siade, A. J.; Cheng, W.; Yeh, W. W.

    2010-12-01

    This study optimizes observation well locations and sampling frequencies for the purpose of estimating unknown groundwater extraction in an aquifer system. Proper orthogonal decomposition (POD) is used to reduce the groundwater flow model, thus reducing the computation burden and data storage space associated with solving this problem for heavily discretized models. This reduced model can store a significant amount of system information in a much smaller reduced state vector. Along with the sensitivity equation method, the proposed approach can efficiently compute the Jacobian matrix that forms the information matrix associated with the experimental design. The criterion adopted for experimental design is the maximization of the trace of the weighted information matrix. Under certain conditions, this is equivalent to the classical A-optimality criterion established in experimental design. A genetic algorithm (GA) is used to optimize the observation well locations and sampling frequencies for maximizing the collected information from the hydraulic head sampling at the observation wells. We applied the proposed approach to a hypothetical 30,000-node groundwater aquifer system. We studied the relationship among the number of observation wells, observation well locations, sampling frequencies, and the collected information for estimating unknown groundwater extraction.

  19. Estimates of genetics and phenotypics parameters for the yield and quality of soybean seeds.

    PubMed

    Zambiazzi, E V; Bruzi, A T; Guilherme, S R; Pereira, D R; Lima, J G; Zuffo, A M; Ribeiro, F O; Mendes, A E S; Godinho, S H M; Carvalho, M L M

    2017-09-27

    Estimating genotype x environment (GxE) parameters for quality and yield in soybean seed grown in different environments in Minas Gerais State was the goal of this study, as well as to evaluate interaction effects of GxE for soybean seeds yield and quality. Seeds were produced in three locations in Minas Gerais State (Lavras, Inconfidentes, and Patos de Minas) in 2013/14 and 2014/15 seasons. Field experiments were conducted in randomized blocks in a factorial 17 x 6 (GxE), and three replications. Seed yield and quality were evaluated for germination in substrates paper and sand, seedling emergence, speed emergency index, mechanical damage by sodium hypochlorite, electrical conductivity, speed aging, vigor and viability of seeds by tetrazolium test in laboratory using completely randomized design. Quadratic component genotypic, GXE variance component, genotype determination coefficient, genetic variation coefficient and environmental variation coefficient were estimated using the Genes software. Percentage analysis of genotypes contribution, environments and genotype x environment interaction were conducted by sites combination two by two and three sites combination, using the R software. Considering genotypes selection of broad adaptation, TMG 1179 RR, CD 2737 RR, and CD 237 RR associated better yield performance at high physical and physiological potential of seed. Environmental effect was more expressive for most of the characters related to soybean seed quality. GxE interaction effects were expressive though genotypes did not present coincidental behavior in different environments.

  20. Diversity and genetic parameter estimates for yield and its components in Jatropha curcas L.

    PubMed

    Freitas, R G; Dias, L A S; Cardoso, P M R; Evaristo, A B; Silva, M F; Araújo, N M

    2016-03-24

    Jatropha curcas L. is one of the most promising oilseeds for biodiesel and biokerosene production, but few basic studies or breeding programs have been conducted for the species. We estimated genetic parameters and diversity based on 10 yield traits in 77 half-sib progenies of J. curcas after 52 months in the field, and evaluated correlations between them and the oil content of the seeds. The mean grain yield per plant was 377.9 g (ranging from 169.8 to 772.1 g) and the mean oil content was 36.2% (ranging from 30 to 39.6%). Moderate estimates of heritability at the mean progeny level were obtained for the length of the fruit (84.7%), length (69.1%) and width (68.2%) of the seed, and grain yield per plant (62.2%). Oil content was only positively and significantly correlated with 100-seed weight. Our study revealed a range of possible crosses to be investigated in J. curcas. Progeny production should be evaluated over several crop seasons for the accurate selection of the best progenies.

  1. Breed effects and genetic parameter estimates for calving difficulty and birth weight in a multibreed population.

    PubMed

    Ahlberg, C M; Kuehn, L A; Thallman, R M; Kachman, S D; Snelling, W M; Spangler, M L

    2016-05-01

    Birth weight (BWT) and calving difficulty (CD) were recorded on 4,579 first-parity females from the Germplasm Evaluation Program at the U.S. Meat Animal Research Center (USMARC). Both traits were analyzed using a bivariate animal model with direct and maternal effects. Calving difficulty was transformed from the USMARC scores to corresponding -scores from the standard normal distribution based on the incidence rate of the USMARC scores. Breed fraction covariates were included to estimate breed differences. Heritability estimates (SE) for BWT direct, CD direct, BWT maternal, and CD maternal were 0.34 (0.10), 0.29 (0.10), 0.15 (0.08), and 0.13 (0.08), respectively. Calving difficulty direct breed effects deviated from Angus ranged from -0.13 to 0.77 and maternal breed effects deviated from Angus ranged from -0.27 to 0.36. Hereford-, Angus-, Gelbvieh-, and Brangus-sired calves would be the least likely to require assistance at birth, whereas Chiangus-, Charolais-, and Limousin-sired calves would be the most likely to require assistance at birth. Maternal breed effects for CD were least for Simmental and Charolais and greatest for Red Angus and Chiangus. Results showed that the diverse biological types of cattle have different effects on both BWT and CD. Furthermore, results provide a mechanism whereby beef cattle producers can compare EBV for CD direct and maternal arising from disjoined and breed-specific genetic evaluations.

  2. Ionizing radiation and genetic risks. XIII. Summary and synthesis of papers VI to XII and estimates of genetic risks in the year 2000.

    PubMed

    Sankaranarayanan, K; Chakraborty, R

    2000-10-16

    This paper recapitulates the advances in the field of genetic risk estimation that have occurred during the past decade and using them as a basis, presents revised estimates of genetic risks of exposure to radiation. The advances include: (i) an upward revision of the estimates of incidence for Mendelian diseases (2.4% now versus 1.25% in 1993); (ii) the introduction of a conceptual change for calculating doubling doses; (iii) the elaboration of methods to estimate the mutation component (i.e. the relative increase in disease frequency per unit relative increase in mutation rate) and the use of the estimates obtained through these methods for assessing the impact of induced mutations on the incidence of Mendelian and chronic multifactorial diseases; (iv) the introduction of an additional factor called the "potential recoverability correction factor" in the risk equation to bridge the gap between radiation-induced mutations that have been recovered in mice and the risk of radiation-inducible genetic disease in human live births and (v) the introduction of the concept that the adverse effects of radiation-induced genetic damage are likely to be manifest predominantly as multi-system developmental abnormalities in the progeny. For all classes of genetic disease (except congenital abnormalities), the estimates of risk have been obtained using a doubling dose of 1 Gy. For a population exposed to low LET, chronic/ low dose irradiation, the current estimates for the first generation progeny are the following (all estimates per million live born progeny per Gy of parental irradiation): autosomal dominant and X-linked diseases, approximately 750-1500 cases; autosomal recessive, nearly zero and chronic multifactorial diseases, approximately 250-1200 cases. For congenital abnormalities, the estimate is approximately 2000 cases and is based on mouse data on developmental abnormalities. The total risk per Gy is of the order of approximately 3000-4700 cases which represent

  3. Genetic trends for fertility, udder health and protein yield in Swedish red cattle estimated with different models.

    PubMed

    Eriksson, S; Johansson, K; Hansen Axelsson, H; Fikse, W F

    2017-02-20

    The aim of this study was to estimate and compare genetic trends in Swedish Red cattle using a full multiple-trait (MT) model and trait-group-wise models for female fertility, udder health and protein yield. Field data for maiden heifers from 1989 and cows with a first and second lactation between 1990 and 2007 were included. (Co)variance components were estimated prior to prediction of breeding values. The estimated genetic trends were clearly favourable for protein yield and udder conformation, and in most cases neutral to favourable for clinical mastitis and calving to first insemination. In maiden heifers, the trends were neutral for number of inseminations per service period. Unfavourable genetic trends were estimated for number of inseminations in the first two lactations, but the trends seemed less unfavourable from evaluations within trait groups compared with when using the full MT model. Excluding maiden heifer data affected genetic trends less than using trait-group-wise analyses instead of a full MT model. Unfavourable genetic trends in functional traits may be missed unless the traits are evaluated in a MT model including traits under strong selection.

  4. Random regression test day models to estimate genetic parameters for milk yield and milk components in Philippine dairy buffaloes.

    PubMed

    Flores, E B; van der Werf, J

    2015-08-01

    Heritabilities and genetic correlations for milk production traits were estimated from first-parity test day records on 1022 Philippine dairy buffalo cows. Traits analysed included milk (MY), fat (FY) and protein (PY) yields, and fat (Fat%) and protein (Prot%) concentrations. Varying orders of Legendre polynomials (Leg(m)) as well as the Wilmink function (Wil) were used in random regression models. These various models were compared based on log likelihood, Akaike's information criterion, Bayesian information criterion and genetic variance estimates. Six residual variance classes were sufficient for MY, FY, PY and Fat%, while seven residual classes for Prot%. Multivariate analysis gave higher estimates of genetic variance and heritability compared with univariate analysis for all traits. Heritability estimates ranged from 0.25 to 0.44, 0.13 to 0.31 and 0.21 to 0.36 for MY, FY and PY, respectively. Wilmink's function was the better fitting function for additive genetic effects for all traits. It was also the preferred function for permanent environment effects for Fat% and Prot%, but for MY, FY and PY, the Legm was the appropriate function. Genetic correlations of MY with FY and PY were high and they were moderately negative with Fat% and Prot%. To prevent deterioration in Fat% and Prot% and improve milk quality, more weight should be applied to milk component traits.

  5. Short-Term Genetic Changes: Evaluating Effective Population Size Estimates in a Comprehensively Described Brown Trout (Salmo trutta) Population

    PubMed Central

    Serbezov, Dimitar; Jorde, Per Erik; Bernatchez, Louis; Olsen, Esben Moland; Vøllestad, L. Asbjørn

    2012-01-01

    The effective population size (Ne) is notoriously difficult to accurately estimate in wild populations as it is influenced by a number of parameters that are difficult to delineate in natural systems. The different methods that are used to estimate Ne are affected variously by different processes at the population level, such as the life-history characteristics of the organism, gene flow, and population substructure, as well as by the frequency patterns of genetic markers used and the sampling design. Here, we compare Ne estimates obtained by different genetic methods and from demographic data and elucidate how the estimates are affected by various factors in an exhaustively sampled and comprehensively described natural brown trout (Salmo trutta) system. In general, the methods yielded rather congruent estimates, and we ascribe that to the adequate genotyping and exhaustive sampling. Effects of violating the assumptions of the different methods were nevertheless apparent. In accordance with theoretical studies, skewed allele frequencies would underestimate temporal allele frequency changes and thereby upwardly bias Ne if not accounted for. Overlapping generations and iteroparity would also upwardly bias Ne when applied to temporal samples taken over short time spans. Gene flow from a genetically not very dissimilar source population decreases temporal allele frequency changes and thereby acts to increase estimates of Ne. Our study reiterates the importance of adequate sampling, quantification of life-history parameters and gene flow, and incorporating these data into the Ne estimation. PMID:22466040

  6. Genetics

    MedlinePlus

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  7. Estimation of genetic parameters and response to selection for a continuous trait subject to culling before testing.

    PubMed

    Arnason, T; Albertsdóttir, E; Fikse, W F; Eriksson, S; Sigurdsson, A

    2012-02-01

    The consequences of assuming a zero environmental covariance between a binary trait 'test-status' and a continuous trait on the estimates of genetic parameters by restricted maximum likelihood and Gibbs sampling and on response from genetic selection when the true environmental covariance deviates from zero were studied. Data were simulated for two traits (one that culling was based on and a continuous trait) using the following true parameters, on the underlying scale: h² = 0.4; r(A) = 0.5; r(E) = 0.5, 0.0 or -0.5. The selection on the continuous trait was applied to five subsequent generations where 25 sires and 500 dams produced 1500 offspring per generation. Mass selection was applied in the analysis of the effect on estimation of genetic parameters. Estimated breeding values were used in the study of the effect of genetic selection on response and accuracy. The culling frequency was either 0.5 or 0.8 within each generation. Each of 10 replicates included 7500 records on 'test-status' and 9600 animals in the pedigree file. Results from bivariate analysis showed unbiased estimates of variance components and genetic parameters when true r(E) = 0.0. For r(E) = 0.5, variance components (13-19% bias) and especially (50-80%) were underestimated for the continuous trait, while heritability estimates were unbiased. For r(E) = -0.5, heritability estimates of test-status were unbiased, while genetic variance and heritability of the continuous trait together with were overestimated (25-50%). The bias was larger for the higher culling frequency. Culling always reduced genetic progress from selection, but the genetic progress was found to be robust to the use of wrong parameter values of the true environmental correlation between test-status and the continuous trait. Use of a bivariate linear-linear model reduced bias in genetic evaluations, when data were subject to culling. © 2011 Blackwell Verlag GmbH.

  8. Estimation of total genetic effects for survival time in crossbred laying hens showing cannibalism, using pedigree or genomic information.

    PubMed

    Brinker, T; Raymond, B; Bijma, P; Vereijken, A; Ellen, E D

    2017-02-01

    Mortality of laying hens due to cannibalism is a major problem in the egg-laying industry. Survival depends on two genetic effects: the direct genetic effect of the individual itself (DGE) and the indirect genetic effects of its group mates (IGE). For hens housed in sire-family groups, DGE and IGE cannot be estimated using pedigree information, but the combined effect of DGE and IGE is estimated in the total breeding value (TBV). Genomic information provides information on actual genetic relationships between individuals and might be a tool to improve TBV accuracy. We investigated whether genomic information of the sire increased TBV accuracy compared with pedigree information, and we estimated genetic parameters for survival time. A sire model with pedigree information (BLUP) and a sire model with genomic information (ssGBLUP) were used. We used survival time records of 7290 crossbred offspring with intact beaks from four crosses. Cross-validation was used to compare the models. Using ssGBLUP did not improve TBV accuracy compared with BLUP which is probably due to the limited number of sires available per cross (~50). Genetic parameter estimates were similar for BLUP and ssGBLUP. For both BLUP and ssGBLUP, total heritable variance (T(2) ), expressed as a proportion of phenotypic variance, ranged from 0.03 ± 0.04 to 0.25 ± 0.09. Further research is needed on breeding value estimation for socially affected traits measured on individuals kept in single-family groups.

  9. Genetic diversity estimates point to immediate efforts for conserving the endangered Tibetan sheep of India

    PubMed Central

    Sharma, Rekha; Kumar, Brijesh; Arora, Reena; Ahlawat, Sonika; Mishra, A.K.; Tantia, M.S.

    2016-01-01

    Tibetan is a valuable Himalayan sheep breed classified as endangered. Knowledge of the level and distribution of genetic diversity in Tibetan sheep is important for designing conservation strategies for their sustainable survival and to preserve their evolutionary potential. Thus, for the first time, genetic variability in the Tibetan population was accessed with twenty five inter-simple sequence repeat markers. All the microsatellites were polymorphic and a total of 148 alleles were detected across these loci. The observed number of alleles across all the loci was more than the effective number of alleles and ranged from 3 (BM6506) to 11 (BM6526) with 5.920 ± 0.387 mean number of alleles per locus. The average observed heterozygosity was less than the expected heterozygosity. The observed and expected heterozygosity values ranged from 0.150 (BM1314) to 0.9 (OarCP20) with an overall mean of 0.473 ± 0.044 and from 0.329 (BM8125) to 0.885 (BM6526) with an overall mean 0.672 ± 0.030, respectively. The lower heterozygosity pointed towards diminished genetic diversity in the population. Thirteen microsatellite loci exhibited significant (P < 0.05) departures from the Hardy–Weinberg proportions in the population. The estimate of heterozygote deficiency varied from − 0.443 (OarCP20) to 0.668 (OarFCB128) with a mean positive value of 0.302 ± 0.057. A normal ‘L’ shaped distribution of mode-shift test and non-significant heterozygote excess on the basis of different models suggested absence of recent bottleneck in the existing Tibetan population. In view of the declining population of Tibetan sheep (less than 250) in the breeding tract, need of the hour is immediate scientific management of the population so as to increase the population hand in hand with retaining the founder alleles to the maximum possible extent. PMID:27014586

  10. Origin and number of founders in an introduced insular primate: estimation from nuclear genetic data.

    PubMed

    Bonhomme, M; Blancher, A; Cuartero, S; Chikhi, L; Crouau-Roy, B

    2008-02-01

    Cynomolgus macaques (Macaca fascicularis) were introduced on the island of Mauritius between 400 and 500 years ago and underwent a strong population expansion after a probable initial founding event. However, in practice, little is known of the geographical origin of the individuals that colonized the island, on how many individuals were introduced, and of whether the following demographic expansion erased any signal of this putative bottleneck. In this study, we asked whether the current nuclear genome of the Mauritius population retained a signature that would allow us to answer these questions. Altogether, 21 polymorphic autosomal and sex-linked microsatellites were surveyed from 81 unrelated Mauritius individuals and 173 individuals from putative geographical sources in Southeast Asia: Java, the Philippines islands and the Indochinese peninsula. We found that (i) the Mauritius population was closer to different populations depending on the markers we used, which suggests a possible mixed origin with Java playing most probably a major role; and (ii) the level of diversity was lower than the other populations but there was no clear and consistent bottleneck signal using either summary statistics or full-likelihood methods. However, summary statistics strongly suggest that Mauritius is not at mutation-drift equilibrium and favours an expansion rather than a bottleneck. This suggests that on a short time scale, population decline followed by growth can be difficult to deduce from genetic data based on mutation-drift theory. We then used a simple Bayesian rejection algorithm to estimate the number of founders under different demographic models (exponential, logistic and logistic with lag) and pure genetic drift. This new method uses current population size estimates and expected heterozygosity of Mauritius and source population(s). Our results indicate that a simple exponential growth is unlikely and that, under the logistic models, the population may have expanded

  11. Estimates of fission barrier heights for neutron-deficient Po to Ra nuclei produced in fusion reactions

    NASA Astrophysics Data System (ADS)

    Sagaidak, Roman

    2017-09-01

    The cross section data for fission and evaporation residue production in fusion reactions leading to nuclei from Po to Ra have been considered in a systematic way in the framework of the conventional barrier-passing (fusion) model coupled with the statistical model. The cross section data obtained in very asymmetric projectile-target combinations can be described within these models rather well with the adjusted model parameters. In particular, one can scale and fix the macroscopic (liquid-drop) fission barrier heights (FBHs) for nuclei involved in the de-excitation of compound nuclei produced in the reactions. The macroscopic FBHs for nuclei from Po to Ra have been derived in the framework of such analysis and compared with the predictions of various theoretical models.

  12. Genetic correlation estimates between beef fatty acid profile with meat and carcass traits in Nellore cattle finished in feedlot.

    PubMed

    Feitosa, Fabieli Loise Braga; Olivieri, Bianca Ferreira; Aboujaoude, Carolyn; Pereira, Angélica Simone Cravo; de Lemos, Marcos Vinicius Antunes; Chiaia, Hermenegildo Lucas Justino; Berton, Mariana Piatto; Peripolli, Elisa; Ferrinho, Adrielle Matias; Mueller, Lenise Freitas; Mazalli, Mônica Roberta; de Albuquerque, Lucia Galvão; de Oliveira, Henrique Nunes; Tonhati, Humberto; Espigolan, Rafael; Tonussi, Rafael Lara; de Oliveira Silva, Rafael Medeiros; Gordo, Daniel Gustavo Mansan; Magalhães, Ana Fabrícia Braga; Aguilar, Ignacio; Baldi, Fernando

    2017-02-01

    The objective of this study was to estimate the genetic-quantitative relationships between the beef fatty acid profile with the carcass and meat traits of Nellore cattle. A total of 1826 bulls finished in feedlot conditions and slaughtered at 24 months of age on average were used. The following carcass and meat traits were analysed: subcutaneous fat thickness (BF), shear force (SF) and total intramuscular fat (IMF). The fatty acid (FA) profile of the Longissimus thoracis samples was determined. Twenty-five FAs (18 individuals and seven groups of FAs) were selected due to their importance for human health. The animals were genotyped with the BovineHD BeadChip and, after quality control for single nucleotide polymorphisms (SNPs), only 470,007 SNPs from 1556 samples remained. The model included the random genetic additive direct effect, the fixed effect of the contemporary group and the animal's slaughter age as a covariable. The (co)variances and genetic parameters were estimated using the REML method, considering an animal model (single-step GBLUP). A total of 25 multi-trait analyses, with four traits, were performed considering SF, BF and IMF plus each individual FA. The heritability estimates for individual saturated fatty acids (SFA) varied from 0.06 to 0.65, for monounsaturated fatty acids (MUFA) it varied from 0.02 to 0.14 and for polyunsaturated fatty acids (PUFA) it ranged from 0.05 to 0.68. The heritability estimates for Omega 3, Omega 6, SFA, MUFA and PUFA sum were low to moderate, varying from 0.09 to 0.20. The carcass and meat traits, SF (0.06) and IMF (0.07), had low heritability estimates, while BF (0.17) was moderate. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with BF were 0.04, 0.64 and -0.41, respectively. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with SF were 0.29, -0.06 and -0.04, respectively. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with IMF were 0.24, 0

  13. Estimation of biotransformation and sorption of emerging organic compounds (EOCs) during artificial recharge through a reactive barrier.

    NASA Astrophysics Data System (ADS)

    Valhondo, C.; Martinez-Landa, L.; Carrera, J.; Hidalgo, J. J.; Ayora, C.

    2016-12-01

    The reuse of lesser quality water such as effluents from wastewater treatment plants or effluent-receiving water bodies has been promoted due to the water shortages affecting many regions of the world. Artificial recharge through infiltration basins is known to improve several water quality parameters including the attenuation of emerging organic compounds (EOCs). Many of these contaminants exhibit redox dependent biotransformation because the redox state is one of the factors controlling microbial community development. Together with biotransformation, sorption also affects the behavior of EOCs in their passage through the soil. We studied EOCs attenuation in an infiltration system is located in Sant Vicenç dells Horts on the Llobregat delta (Barcelona, Spain), where the local water agency has an artificial recharge pilot project . The Llobregat river water used for the artificial recharge is affected by treatment plant effluents which contain EOCs. A reactive barrier consisting of vegetable compost, clay, and iron oxide was installed in the bottom of the infiltration basin to enhance biotransformation and sorption of EOCs. The barrier releases dissolved organic carbon, which favors the development of a broad range of redox environments, and supplies neutral, cationic, and anionic surfaces to favor sorption of different types of contaminants. Results were excellent, but quantitative evaluation of the EOCs attenuation requires knowledge of the residence time distribution of infiltrated water. A tracer test was performed by adding tracers to the infiltration water and interpreting the breakthrough curves at diverse monitoring points with a 2D multilayer numerical model. The calibrated model quantify degradation, as a first order law, and sorption through a linear distribution coefficient for ten selected EOCs. Results indicate higher degradation rates and sorption coefficients in the reactive barrier than in the rest of the aquifer for nine and eight of the ten

  14. Estimation of genetic parameters for longevity traits in dairy cattle: a review with focus on the characteristics of analytical models.

    PubMed

    Sasaki, Osamu

    2013-06-01

    Longevity is an economically important trait of dairy cattle for increasing the profitability of dairy management. The reasons for culling can be either voluntary (primarily productivity) or involuntary (primarily health and fertility). Longevity characteristics include: (i) true longevity (all culling reasons, including productivity); and (ii) functional longevity (all culling reasons, except productivity). Improvements to longevity are made to decrease the rate of involuntary culling rather than extend the herd life (HL). The proportional hazard model is useful for evaluating genetic ability for HL. However, the differences between estimates made using the proportional hazard model and those made using linear single or multiple-trait animal models are not clear. The model commonly used for evaluation differs among countries. Productive traits, udder traits, and feet and legs traits are genetically correlated with longevity, and consequently these traits are used to indirectly evaluate longevity. The reliability of estimates of genetic ability for longevity is increased by combining direct and indirect estimates. In Japan, HL is evaluated using the multiple-traits model. The genetic correlations between HL and other traits vary with the birth year. Therefore, these genetic correlations need to be reviewed regularly.

  15. Experimental and kinetic study for lead removal via photosynthetic consortia using genetic algorithms to parameter estimation.

    PubMed

    Hernández-Melchor, Dulce Jazmín; López-Pérez, Pablo A; Carrillo-Vargas, Sergio; Alberto-Murrieta, Alvaro; González-Gómez, Evanibaldo; Camacho-Pérez, Beni

    2017-09-06

    This work presents an experimental-theoretical strategy for a batch process for lead removal by photosynthetic consortium, conformed by algae and bacteria. Photosynthetic consortium, isolated from a treatment plant wastewater of Tecamac (Mexico), was used as inoculum in bubble column photobioreactors. The consortium was used to evaluate the kinetics of lead removal at different initial concentrations of metal (15, 30, 40, 50, and 60 mgL(-1)), carried out in batch culture with a hydraulic residence time of 14 days using Bold's Basal mineral medium. The photobioreactor was operated under the following conditions: aeration of 0.5 vvm, 80 μmol m(-2) s(-1) of photon flux density and a photoperiod light/dark 12:12. After determining the best growth kinetics of biomass and metal removal, they were tested under different ratios (30 and 60%) of wastewater-culture medium. Additionally, the biomass growth (X), nitrogen consumption (N), chemical oxygen demand (COD), and metal removal (Pb) were quantified. Achieved lead removal was 97.4% when the initial lead concentration was up to 50 mgL(-1) using 60% of wastewater. Additionally, an unstructured-type mathematical model was developed to simulate COD, X, N, and lead removal. Furthermore, a comparison between the Levenberg-Marquardt (L-M) optimization approach and Genetic Algorithms (GA) was carried out for parameter estimation. Also, it was concluded that GA has a slightly better performance and possesses better convergence and computational time than L-M. Hence, the proposed method might be applied for parameter estimation of biological models and be used for the monitoring and control process.

  16. Evaluating alternate models to estimate genetic parameters of calving traits in United Kingdom Holstein-Friesian dairy cattle

    PubMed Central

    2012-01-01

    Background The focus in dairy cattle breeding is gradually shifting from production to functional traits and genetic parameters of calving traits are estimated more frequently. However, across countries, various statistical models are used to estimate these parameters. This study evaluates different models for calving ease and stillbirth in United Kingdom Holstein-Friesian cattle. Methods Data from first and later parity records were used. Genetic parameters for calving ease, stillbirth and gestation length were estimated using the restricted maximum likelihood method, considering different models i.e. sire (−maternal grandsire), animal, univariate and bivariate models. Gestation length was fitted as a correlated indicator trait and, for all three traits, genetic correlations between first and later parities were estimated. Potential bias in estimates was avoided by acknowledging a possible environmental direct-maternal covariance. The total heritable variance was estimated for each trait to discuss its theoretical importance and practical value. Prediction error variances and accuracies were calculated to compare the models. Results and discussion On average, direct and maternal heritabilities for calving traits were low, except for direct gestation length. Calving ease in first parity had a significant and negative direct-maternal genetic correlation. Gestation length was maternally correlated to stillbirth in first parity and directly correlated to calving ease in later parities. Multi-trait models had a slightly greater predictive ability than univariate models, especially for the lowly heritable traits. The computation time needed for sire (−maternal grandsire) models was much smaller than for animal models with only small differences in accuracy. The sire (−maternal grandsire) model was robust when additional genetic components were estimated, while the equivalent animal model had difficulties reaching convergence. Conclusions For the evaluation of

  17. Estimation of genetic parameters for functional longevity in the South African Holstein cattle using a piecewise Weibull proportional hazards model.

    PubMed

    Imbayarwo-Chikosi, V E; Ducrocq, V; Banga, C B; Halimani, T E; van Wyk, J B; Maiwashe, A; Dzama, K

    2017-03-14

    Non-genetic factors influencing functional longevity and the heritability of the trait were estimated in South African Holsteins using a piecewise Weibull proportional hazards model. Data consisted of records of 161,222 of daughters of 2,051 sires calving between 1995 and 2013. The reference model included fixed time-independent age at first calving and time-dependent interactions involving lactation number, region, season and age of calving, within-herd class of milk production, fat and protein content, class of annual variation in herd size and the random herd-year effect. Random sire and maternal grandsire effects were added to the model to estimate genetic parameters. The within-lactation Weibull baseline hazards were assumed to change at 0, 270, 380 days and at drying date. Within-herd milk production class had the largest contribution to the relative risk of culling. Relative culling risk increased with lower protein and fat per cent production classes and late age at first calving. Cows in large shrinking herds also had high relative risk of culling. The estimate of the sire genetic variance was 0.0472 ± 0.0017 giving a theoretical heritability estimate of 0.11 in the complete absence of censoring. Genetic trends indicated an overall decrease in functional longevity of 0.014 standard deviation from 1995 to 2007. There are opportunities for including the trait in the breeding objective for South African Holstein cattle.

  18. Genetic and phenotypic parameter estimates for feed intake and other traits in growing beef cattle, and opportunities for selection

    USDA-ARS?s Scientific Manuscript database

    Growth, feed intake, and temperament indicator data, collected over 5 yr on a total of 1,141 to 1,183 mixed-breed steers, were used to estimate genetic and phenotypic parameters. All steers had a portion of either Hereford or Angus or both plus varying percentages also of Simmental, Charolais, Limo...

  19. Genome-based, mechanism-driven computational modeling of risks of ionizing radiation: The next frontier in genetic risk estimation?

    PubMed

    Sankaranarayanan, K; Nikjoo, H

    2015-01-01

    Research activity in the field of estimation of genetic risks of ionizing radiation to human populations started in the late 1940s and now appears to be passing through a plateau phase. This paper provides a background to the concepts, findings and methods of risk estimation that guided the field through the period of its growth to the beginning of the 21st century. It draws attention to several key facts: (a) thus far, genetic risk estimates have been made indirectly using mutation data collected in mouse radiation studies; (b) important uncertainties and unsolved problems remain, one notable example being that we still do not know the sensitivity of human female germ cells to radiation-induced mutations; and (c) the concept that dominated the field thus far, namely, that radiation exposures to germ cells can result in single gene diseases in the descendants of those exposed has been replaced by the concept that radiation exposure can cause DNA deletions, often involving more than one gene. Genetic risk estimation now encompasses work devoted to studies on DNA deletions induced in human germ cells, their expected frequencies, and phenotypes and associated clinical consequences in the progeny. We argue that the time is ripe to embark on a human genome-based, mechanism-driven, computational modeling of genetic risks of ionizing radiation, and we present a provisional framework for catalyzing research in the field in the 21st century.

  20. Early detection of population declines: high power of genetic monitoring using effective population size estimators

    PubMed Central

    Antao, Tiago; Pérez-Figueroa, Andrés; Luikart, Gordon

    2011-01-01

    Early detection of population declines is essential to prevent extinctions and to ensure sustainable harvest. We evaluated the performance of two Ne estimators to detect population declines: the two-sample temporal method and a one-sample method based on linkage disequilibrium (LD). We used simulated data representing a wide range of population sizes, sample sizes and number of loci. Both methods usually detect a population decline only one generation after it occurs if Ne drops to less than approximately 100, and 40 microsatellite loci and 50 individuals are sampled. However, the LD method often out performed the temporal method by allowing earlier detection of less severe population declines (Ne approximately 200). Power for early detection increased more rapidly with the number of individuals sampled than with the number of loci genotyped, primarily for the LD method. The number of samples available is therefore an important criterion when choosing between the LD and temporal methods. We provide guidelines regarding design of studies targeted at monitoring for population declines. We also report that 40 single nucleotide polymorphism (SNP) markers give slightly lower precision than 10 microsatellite markers. Our results suggest that conservation management and monitoring strategies can reliably use genetic based methods for early detection of population declines. PMID:25567959

  1. Making medical decisions in dependence of genetic background: estimation of the utility of DNA testing in clinical, pharmaco-epidemiological or genetic studies.

    PubMed

    Nguyen, Thuy Trang; Schäfer, Helmut; Timmesfeld, Nina

    2013-05-01

    An index measuring the utility of testing a DNA marker before deciding between two alternative treatments is proposed which can be estimated from pharmaco-epidemiological case-control or cohort studies. In the case-control design, external estimates of the prevalence of the disease and of the frequency of the genetic risk variant are required for estimating the utility index. Formulas for point and interval estimates are derived. Empirical coverage probabilities of the confidence intervals were estimated under different scenarios of disease prevalence, prevalence of drug use, and population frequency of the genetic variant. To illustrate our method, we re-analyse pharmaco-epidemiological case-control data on oral contraceptive intake and venous thrombosis in carriers and non-carriers of the factor V Leiden mutation. We also re-analyse cross-sectional data from the Framingham study on a gene-diet interaction between an APOA2 polymorphism and high saturated fat intake on obesity. We conclude that the utility index may be helpful to evaluate and appraise the potential clinical and public health relevance of gene-environment interaction effects detected in genomic and candidate gene association studies and may be a valuable decision support for designing prospective studies on the clinical utility. © 2013 Wiley Periodicals, Inc.

  2. The first step toward genetic selection for host tolerance to infectious pathogens: obtaining the tolerance phenotype through group estimates

    PubMed Central

    Doeschl-Wilson, Andrea B.; Villanueva, Beatriz; Kyriazakis, Ilias

    2012-01-01

    Reliable phenotypes are paramount for meaningful quantification of genetic variation and for estimating individual breeding values on which genetic selection is based. In this paper, we assert that genetic improvement of host tolerance to disease, although desirable, may be first of all handicapped by the ability to obtain unbiased tolerance estimates at a phenotypic level. In contrast to resistance, which can be inferred by appropriate measures of within host pathogen burden, tolerance is more difficult to quantify as it refers to change in performance with respect to changes in pathogen burden. For this reason, tolerance phenotypes have only been specified at the level of a group of individuals, where such phenotypes can be estimated using regression analysis. However, few stsudies have raised the potential bias in these estimates resulting from confounding effects between resistance and tolerance. Using a simulation approach, we demonstrate (i) how these group tolerance estimates depend on within group variation and co-variation in resistance, tolerance, and vigor (performance in a pathogen free environment); and (ii) how tolerance estimates are affected by changes in pathogen virulence over the time course of infection and by the timing of measurements. We found that in order to obtain reliable group tolerance estimates, it is important to account for individual variation in vigor, if present, and that all individuals are at the same stage of infection when measurements are taken. The latter requirement makes estimation of tolerance based on cross-sectional field data challenging, as individuals become infected at different time points and the individual onset of infection is unknown. Repeated individual measurements of within host pathogen burden and performance would not only be valuable for inferring the infection status of individuals in field conditions, but would also provide tolerance estimates that capture the entire time course of infection. PMID

  3. Variance in estimated pairwise genetic distance under high versus low coverage sequencing: The contribution of linkage disequilibrium.

    PubMed

    Shpak, Max; Ni, Yang; Lu, Jie; Müller, Peter

    2017-10-01

    The mean pairwise genetic distance among haplotypes is an estimator of the population mutation rate θ and a standard measure of variation in a population. With the advent of next-generation sequencing (NGS) methods, this and other population parameters can be estimated under different modes of sampling. One approach is to sequence individual genomes with high coverage, and to calculate genetic distance over all sample pairs. The second approach, typically used for microbial samples or for tumor cells, is sequencing a large number of pooled genomes with very low individual coverage. With low coverage, pairwise genetic distances are calculated across independently sampled sites rather than across individual genomes. In this study, we show that the variance in genetic distance estimates is reduced with low coverage sampling if the mean pairwise linkage disequilibrium weighted by allele frequencies is positive. Practically, this means that if on average the most frequent alleles over pairs of loci are in positive linkage disequilibrium, low coverage sequencing results in improved estimates of θ, assuming similar per-site read depths. We show that this result holds under the expected distribution of allele frequencies and linkage disequilibria for an infinite sites model at mutation-drift equilibrium. From simulations, we find that the conditions for reduced variance only fail to hold in cases where variant alleles are few and at very low frequency. These results are applied to haplotype frequencies from a lung cancer tumor to compute the weighted linkage disequilibria and the expected error in estimated genetic distance using high versus low coverage. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Dynamics of hepatitis B virus quasispecies heterogeneity and virologic response in patients receiving low-to-moderate genetic barrier nucleoside analogs.

    PubMed

    Peveling-Oberhag, J; Herrmann, E; Kronenberger, B; Farnik, H; Susser, S; Sarrazin, C; Zeuzem, S; Hofmann, W-P

    2013-04-01

    We characterized the early dynamics of hepatitis B virus (HBV) quasispecies evolution during the first weeks of antiviral therapy with low-to-moderate genetic barrier antiviral drugs and associated these data with antiviral response patterns. Fifteen chronic hepatitis B patients (men, 10; mean age, 34; HBeAg positive, 6) who received lamivudine or telbivudine for at least 52 weeks were included. HBV DNA was extracted from serum, and a 910-bp fragment covering domains A-F of the reverse transcriptase region was amplified, cloned and sequenced. Parameters of quasispecies heterogeneity, genetic diversity and complexity were calculated and were correlated with complete virologic response, defined as undetectable HBV DNA at week 52. Nine patients achieved complete virologic response during the observational period. While baseline HBV DNA levels and HBeAg status were associated with virologic response, baseline quasispecies complexity and diversity of responders showed no significant difference to those of nonresponders (P > 0.05). However, at week 4, quasispecies complexity of nonresponders was significantly higher compared with that of responders on the nucleotide level (P = 0.01) and the aa level (P = 0.04). The number of synonymous substitutions per synonymous site dropped significantly in responders at week 4 (P = 0.04), while there was no difference in nonresponders. The HBV quasispecies complexity at the early stage of antiviral therapy (week 4) with the low-to-moderate genetic barrier nucleoside analogs lamivudine or telbivudine was associated with subsequent virologic response. Further studies are needed to confirm HBV quasispecies evolution as additional predictive marker for beneficial treatment outcome.

  5. Similar estimates of population genetic composition and sex ratio derived from carcasses and faeces of Eurasian otter Lutra lutra.

    PubMed

    Dallas, John F; Coxon, Karen E; Sykes, Tim; Chanin, Paul R F; Marshall, Freda; Carss, David N; Bacon, Philip J; Piertney, Stuart B; Racey, Paul A

    2003-01-01

    Collecting faeces is viewed as a potentially efficient way to sample elusive animals. Nonetheless, any biases in estimates of population composition associated with such sampling remain uncharacterized. The goal of this study was to compare estimates of genetic composition and sex ratio derived from Eurasian otter Lutra lutra spraints (faeces) with estimates derived from carcasses. Twenty per cent of 426 wild-collected spraints from SW England yielded composite genotypes for 7-9 microsatellites and the SRY gene. The expected number of incorrect spraint genotypes was negligible, given the proportions of allele dropout and false allele detection estimated using paired blood and spraint samples of three captive otters. Fifty-two different spraint genotypes were detected and compared with genotypes of 70 otter carcasses from the same area. Carcass and spraint genotypes did not differ significantly in mean number of alleles, mean unbiased heterozygosity or sex ratio, although statistical power to detect all but large differences in sex ratio was low. The genetic compositions of carcass and spraint genotypes were very similar according to confidence intervals of theta and two methods for assigning composite genotypes to groups. A distinct group of approximately 11 carcass and spraint genotypes was detected using the latter methods. The results suggest that spraints can yield unbiased estimates of population genetic composition and sex ratio.

  6. Mechanisms and genetic control of interspecific crossing barriers in lycopersicon. Progress report, First year, August 1, 1992

    SciTech Connect

    Mutschler, M.A.; McCormick, S.

    1992-12-31

    The goal of this program is to use Lycopersica esculentum and L. pennellii as a model system to study the interspecific reproductive barriers unilateral incongruity (UI), hybrid breakdown and interspecific aberrant ratio syndrome (IARS). Specifically we seek to determine the functional basis of UI including the timing of the failure of incongruous crosses, the developmental step(s) interrupted by UI, the tissue and genomes involved in UI.

  7. Estimation of state-of-charge of Li-ion batteries in EV using the genetic particle filter

    NASA Astrophysics Data System (ADS)

    Bi, Jun; Gao, Hang; Wang, Yongxing; Zhao, Xiaomei

    2017-08-01

    Estimating the state of charge (SOC) of electric vehicle (EV) batteries accurately and timely is of great significance to the safe trip of pure EV. Based on the nonlinear properties of the battery, and the standard particle filter (PF) has certain adaptability for this feature, so it can be used to accurately estimate the SOC of the batteries. However, the standard PF has particle degeneracy phenomenon, which will make the accuracy of prediction lower. Therefore, in this paper, the genetic algorithm is applied to the standard PF, and the estimation of SOC is optimized, which makes the improved filter algorithm more accurate. Based on the measured data of Beijing pure electric sanitation vehicle, an experiment is defined to verify the algorithm. The experimental results show that the genetic particle filter (GPF) can increase the diversity of particles and has better prediction accuracy and timeliness than the PF.

  8. Estimating the risks of cancer mortality and genetic defects resulting from exposures to low levels of ionizing radiation

    SciTech Connect

    Buhl, T.E.; Hansen, W.R.

    1984-05-01

    Estimators for calculating the risk of cancer and genetic disorders induced by exposure to ionizing radiation have been recommended by the US National Academy of Sciences Committee on the Biological Effects of Ionizing Radiations, the UN Scientific Committee on the Effects of Atomic Radiation, and the International Committee on Radiological Protection. These groups have also considered the risks of somatic effects other than cancer. The US National Council on Radiation Protection and Measurements has discussed risk estimate procedures for radiation-induced health effects. The recommendations of these national and international advisory committees are summarized and compared in this report. Based on this review, two procedures for risk estimation are presented for use in radiological assessments performed by the US Department of Energy under the National Environmental Policy Act of 1969 (NEPA). In the first procedure, age- and sex-averaged risk estimators calculated with US average demographic statistics would be used with estimates of radiation dose to calculate the projected risk of cancer and genetic disorders that would result from the operation being reviewed under NEPA. If more site-specific risk estimators are needed, and the demographic information is available, a second procedure is described that would involve direct calculation of the risk estimators using recommended risk-rate factors. The computer program REPCAL has been written to perform this calculation and is described in this report. 25 references, 16 tables.

  9. Estimation of Genetic parameters of the Productive and Reproductive Traits in Ethiopian Holstein using Multi-trait Models.

    PubMed

    Ayalew, Wondossen; Aliy, Mohammed; Negussie, Enyew

    2017-06-27

    The objective of this study was to estimate genetic parameters for productive and reproductive traits. The data included production and reproduction records of animals that have calved between 1979 and 2013. The genetic parameters were estimated using multivariate mixed models (DMU) package, fitting univariate and multivariate mixed models with average information restricted maximum likelihood (AI-REML) algorithm. The estimates of heritability for milk production traits from the first three lactation records were 0.03±0.03 for lactation length (LL), 0.17±0.04 for lactation milk yield (LMY) and 0.15±0.04 for 305 days milk yield (305-dMy). For reproductive traits the heritability estimates were, 0.09±0.03 for DO (days open), 0.11±0.04 for CI (calving interval) and 0.47±0.06 for AFC (age at first calving). The repeatability estimates for production traits were 0.12±0.02, for LL, 0.39±0.02 for LMY and 0.25±0.02 for 305-dMy. For reproductive traits the estimates of repeatability were 0.19±0.02 for DO, and to 0.23±0.02 for CI. The phenotypic correlations between production and reproduction traits ranged from 0.08±0.04 for LL and AFC to 0.42±0.02 for LL and DO. The genetic correlation among production traits were generally high (> 0.7) and between reproductive traits the estimates ranged from 0.06±0.13 for AFC and DO to 0.99±0.01 between CI and DO. Genetic correlations of productive traits with reproductive traits were ranged from -0.02 to 0.99. The high heritability estimates observed for AFC indicated that reasonable genetic improvement for this trait might be possible through selection. The h2 and r estimates for reproductive traits were slightly different from single versus multi-trait analyses of reproductive traits with production traits. As single-trait method is biased due to selection on milk yield, a multi-trait evaluation of fertility with milk yield is recommended.

  10. kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.

    PubMed

    Murray, Kevin D; Webers, Christfried; Ong, Cheng Soon; Borevitz, Justin; Warthmann, Norman

    2017-09-01

    Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

  11. Genetic Structure of Chinese Indigenous Goats and the Special Geographical Structure in the Southwest China as a Geographic Barrier Driving the Fragmentation of a Large Population

    PubMed Central

    Xu, Lingyang; Liu, Gang; Wang, Zhigang; Zhao, Fuping; Zhang, Li; Han, Xu; Du, Lixin; Liu, Chousheng

    2014-01-01

    Background China has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demograogic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers. Methodology/Principal Findings Forty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (HS of 0.644) and high population diversity at the species level (HT value of 0.737) were estimated. Significant moderate population differentiation was detected (FST value of 0.129). Significant excess homozygosity (FIS of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China. Conclusions/Significance Our results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human’s migration history throughout China. This study

  12. Genetic structure of Chinese indigenous goats and the special geographical structure in the Southwest China as a geographic barrier driving the fragmentation of a large population.

    PubMed

    Wei, Caihong; Lu, Jian; Xu, Lingyang; Liu, Gang; Wang, Zhigang; Zhao, Fuping; Zhang, Li; Han, Xu; Du, Lixin; Liu, Chousheng

    2014-01-01

    China has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demographic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers. Forty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (H(S) of 0.644) and high population diversity at the species level (H(T) value of 0.737) were estimated. Significant moderate population differentiation was detected (F(ST) value of 0.129). Significant excess homozygosity (F(IS) of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China. Our results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human's migration history throughout China. This study provides a fundamental genetic profile for the conservation of

  13. Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments

    PubMed Central

    Kumar, Satish; Molloy, Claire; Muñoz, Patricio; Daetwyler, Hans; Chagné, David; Volz, Richard

    2015-01-01

    The nonadditive genetic effects may have an important contribution to total genetic variation of phenotypes, so estimates of both the additive and nonadditive effects are desirable for breeding and selection purposes. Our main objectives were to: estimate additive, dominance and epistatic variances of apple (Malus × domestica Borkh.) phenotypes using relationship matrices constructed from genome-wide dense single nucleotide polymorphism (SNP) markers; and compare the accuracy of genomic predictions using genomic best linear unbiased prediction models with or without including nonadditive genetic effects. A set of 247 clonally replicated individuals was assessed for six fruit quality traits at two sites, and also genotyped using an Illumina 8K SNP array. Across several fruit quality traits, the additive, dominance, and epistatic effects contributed about 30%, 16%, and 19%, respectively, to the total phenotypic variance. Models ignoring nonadditive components yielded upwardly biased estimates of additive variance (heritability) for all traits in this study. The accuracy of genomic predicted genetic values (GEGV) varied from about 0.15 to 0.35 for various traits, and these were almost identical for models with or without including nonadditive effects. However, models including nonadditive genetic effects further reduced the bias of GEGV. Between-site genotypic correlations were high (>0.85) for all traits, and genotype-site interaction accounted for <10% of the phenotypic variability. The accuracy of prediction, when the validation set was present only at one site, was generally similar for both sites, and varied from about 0.50 to 0.85. The prediction accuracies were strongly influenced by trait heritability, and genetic relatedness between the training and validation families. PMID:26497141

  14. Coronaviruses resistant to a 3C-like protease inhibitor are attenuated for replication and pathogenesis, revealing a low genetic barrier but high fitness cost of resistance.

    PubMed

    Deng, Xufang; StJohn, Sarah E; Osswald, Heather L; O'Brien, Amornrat; Banach, Bridget S; Sleeman, Katrina; Ghosh, Arun K; Mesecar, Andrew D; Baker, Susan C

    2014-10-01

    Viral protease inhibitors are remarkably effective at blocking the replication of viruses such as human immunodeficiency virus and hepatitis C virus, but they inevitably lead to the selection of inhibitor-resistant mutants, which may contribute to ongoing disease. Protease inhibitors blocking the replication of coronavirus (CoV), including the causative agents of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), provide a promising foundation for the development of anticoronaviral therapeutics. However, the selection and consequences of inhibitor-resistant CoVs are unknown. In this study, we exploited the model coronavirus, mouse hepatitis virus (MHV), to investigate the genotype and phenotype of MHV quasispecies selected for resistance to a broad-spectrum CoV 3C-like protease (3CLpro) inhibitor. Clonal sequencing identified single or double mutations within the 3CLpro coding sequence of inhibitor-resistant virus. Using reverse genetics to generate isogenic viruses with mutant 3CLpros, we found that viruses encoding double-mutant 3CLpros are fully resistant to the inhibitor and exhibit a significant delay in proteolytic processing of the viral replicase polyprotein. The inhibitor-resistant viruses also exhibited postponed and reduced production of infectious virus particles. Biochemical analysis verified double-mutant 3CLpro enzyme as impaired for protease activity and exhibiting reduced sensitivity to the inhibitor and revealed a delayed kinetics of inhibitor hydrolysis and activity restoration. Furthermore, the inhibitor-resistant virus was shown to be highly attenuated in mice. Our study provides the first insight into the pathogenicity and mechanism of 3CLpro inhibitor-resistant CoV mutants, revealing a low genetic barrier but high fitness cost of resistance. Importance: RNA viruses are infamous for their ability to evolve in response to selective pressure, such as the presence of antiviral drugs. For coronaviruses such as

  15. Estimation of genetic parameters for body weights, scrotal circumference, and testicular volume measured at different ages in Nellore cattle.

    PubMed

    Boligon, A A; Silva, J A V; Sesana, R C; Sesana, J C; Junqueira, J B; Albuquerque, L G

    2010-04-01

    Data from 129,575 Nellore cattle born between 1993 and 2006, belonging to the Jacarezinho cattle-raising farm, were used to estimate genetic parameters for scrotal circumference measured at 9 (SC9), 12 (SC12), and 18 (SC18) mo of age and testicular volume measured at the same ages (TV9, TV12, and TV18) and to determine their correlation with weaning weight (WW) and yearling weight (YW), to provide information for the definition of selection criteria in beef cattle. Estimates of (co)variance components were calculated by the REML method applying an animal model in single- and multiple-trait analysis. The following heritability estimates and their respective SE were obtained for WW, YW, SC9, SC12, SC18, TV9, TV12, and TV18: 0.33 +/- 0.02, 0.37 +/- 0.03, 0.29 +/- 0.03, 0.39 +/- 0.04, 0.42 +/- 0.03, 0.19 +/- 0.04, 0.26 +/- 0.05, and 0.39 +/- 0.04, respectively. The genetic correlation between WW and YW was positive and high (0.80 +/- 0.04), indicating that these traits are mainly determined by the same genes. Genetic correlations between the growth traits and scrotal circumference measures were positive and of low to moderate magnitude, ranging from 0.23 +/- 0.04 to 0.38 +/- 0.04. On the other hand, increased genetic associations were estimated between scrotal circumference and testicular volume at different ages (0.61 +/- 0.04 to 0.86 +/- 0.04). Selection for greater scrotal circumference in males should result in greater WW, YW, and testicular volume. In conclusion, in view of the difficulty in measuring testicular volume, there is no need to change the selection criterion from scrotal circumference to testicular volume in genetic breeding programs of Zebu breeds.

  16. Estimates of genetic parameters for total milk yield over multiple ages in Brazilian Murrah buffaloes using different models.

    PubMed

    Sesana, R C; Baldi, F; Borquis, R R A; Bignardi, A B; Hurtado-Lugo, N A; El Faro, L; Albuquerque, L G; Tonhati, H

    2014-04-14

    The objective of this study was to estimate variance components and genetic parameters for accumulated 305-day milk yield (MY305) over multiple ages, from 24 to 120 months of age, applying random regression (RRM), repeatability (REP) and multi-trait (MT) models. A total of 4472 lactation records from 1882 buffaloes of the Murrah breed were utilized. The contemporary group (herd-year-calving season) and number of milkings (two levels) were considered as fixed effects in all models. For REP and RRM, additive genetic, permanent environmental and residual effects were included as random effects. MT considered the same random effects as did REP and RRM with the exception of permanent environmental effect. Residual variances were modeled by a step function with 1, 4, and 6 classes. The heritabilities estimated with RRM increased with age, ranging from 0.19 to 0.34, and were slightly higher than that obtained with the REP model. For the MT model, heritability estimates ranged from 0.20 (37 months of age) to 0.32 (94 months of age). The genetic correlation estimates for MY305 obtained by RRM (L23.res4) and MT models were very similar, and varied from 0.77 to 0.99 and from 0.77 to 0.99, respectively. The rank correlation between breeding values for MY305 at different ages predicted by REP, MT, and RRM were high. It seems that a linear and quadratic Legendre polynomial to model the additive genetic and animal permanent environmental effects, respectively, may be sufficient to explain more parsimoniously the changes in MY305 genetic variation with age.

  17. Estimation of genetic connectedness diagnostics based on prediction errors without the prediction error variance-covariance matrix.

    PubMed

    Holmes, John B; Dodds, Ken G; Lee, Michael A

    2017-03-02

    An important issue in genetic evaluation is the comparability of random effects (breeding values), particularly between pairs of animals in different contemporary groups. This is usually referred to as genetic connectedness. While various measures of connectedness have been proposed in the literature, there is general agreement that the most appropriate measure is some function of the prediction error variance-covariance matrix. However, obtaining the prediction error variance-covariance matrix is computationally demanding for large-scale genetic evaluations. Many alternative statistics have been proposed that avoid the computational cost of obtaining the prediction error variance-covariance matrix, such as counts of genetic links between contemporary groups, gene flow matrices, and functions of the variance-covariance matrix of estimated contemporary group fixed effects. In this paper, we show that a correction to the variance-covariance matrix of estimated contemporary group fixed effects will produce the exact prediction error variance-covariance matrix averaged by contemporary group for univariate models in the presence of single or multiple fixed effects and one random effect. We demonstrate the correction for a series of models and show that approximations to the prediction error matrix based solely on the variance-covariance matrix of estimated contemporary group fixed effects are inappropriate in certain circumstances. Our method allows for the calculation of a connectedness measure based on the prediction error variance-covariance matrix by calculating only the variance-covariance matrix of estimated fixed effects. Since the number of fixed effects in genetic evaluation is usually orders of magnitudes smaller than the number of random effect levels, the computational requirements for our method should be reduced.

  18. Estimate Landslide Volume with Genetic Algorithms and Image Similarity Method from Single Satellite Image

    NASA Astrophysics Data System (ADS)

    Yu, Ting-To

    2013-04-01

    It is important to acquire the volume of landslide in short period of time. For hazard mitigation and also emergency response purpose, the traditional method takes much longer time than expected. Due to the weather limit, traffic accessibility and many regulations of law, it take months to handle these process before the actual carry out of filed work. Remote sensing imagery can get the data as long as the visibility allowed, which happened only few day after the event. While traditional photometry requires a stereo pairs images to produce the post event DEM for calculating the change of volume. Usually have to wait weeks or even months for gathering such data, LiDAR or ground GPS measurement might take even longer period of time with much higher cost. In this study we use one post event satellite image and pre-event DTM to compare the similarity between these by alter the DTM with genetic algorithms. The outcome of smartest guess from GAs shall remove or add exact values of height at each location, which been converted into shadow relief viewgraph to compare with satellite image. Once the similarity threshold been make then the guessing work stop. It takes only few hours to finish the entire task, the computed accuracy is around 70% by comparing to the high resolution LiDAR survey at a landslide, southern Taiwan. With extra GCPs, the estimate accuracy can improve to 85% and also within few hours after the receiving of satellite image. Data of this demonstration case is a 5 m DTM at 2005, 2M resolution FormoSat optical image at 2009 and 5M LiDAR at 2010. The GAs and image similarity code is developed on Matlab at windows PC.

  19. Estimation of genetic trend in a selected population with and without the use of a control population.

    PubMed

    Blair, H T; Pollak, E J

    1984-04-01

    Data from a selection experiment conducted with sheep at Massey University, New Zealand, were analyzed to obtain an evaluation of selection response. Selection was for heavy 14-mo greasy fleece weight. Approximately seven generations of selection were represented in the data. Three estimates of genetic superiority of the selected line to the control line were obtained. All three estimates were obtained from a mixed model evaluation using the individual animal model for predicting breeding values from own and relatives' records. The estimators were 1) deviation of selected line predicted yearly phenotypes from control line predicted yearly phenotypes, 2) deviation of the predicted yearly phenotype for the selected line from the year estimate in the control line and 3) the mean yearly breeding value from the analysis of the selected line only. The realized heritability using the first approach was .20. However, the control line was found to have a slight positive drift; hence, this estimate was biased downward. Using Approach 2, accounting for drift, the realized heritability was .23. The same realized heritability, .23, was obtained from an analysis of the selected line ignoring the control (Approach 3), when a prior heritability of .30 was assumed for the mixed model evaluation. The estimate of genetic trend from predicted breeding values in the latter approach is, however, quite dependent on the assumed heritability.

  20. Estimates of genetic parameters for faecal egg count of Haemonchus contortus infection and relationship with growth traits in Avikalin sheep.

    PubMed

    Prince, Leslie Leo L; Gowane, G R; Swarnkar, C P; Singh, D; Arora, A L

    2010-04-01

    Genetic parameters for faecal egg count were estimated in naturally challenged Avikalin sheep developed and maintained at Central Sheep & Wool Research Institute, Avikanagar, India, over a period of 4 years (2004-2007). The data on faecal egg count for 433 animals descended from 41 sires, and 151 dams were used for the study. Genetic analyses were carried out using restricted maximum likelihood, fitting an animal model and ignoring or including maternal genetic or permanent environmental effects. Direct heritability for the trait was 0.149 +/- 0.096 when maternal effects were ignored. In the model which takes in to account direct genetic, maternal genetic and maternal permanent environment effect together, it was observed that maternal heritability (m(2)) accounts for 0.6% of total variation whereas maternal permanent environmental effect (c(2)) accounts for 6.14% of total phenotypic variation. Effect of faecal egg count on the growth characteristics was observed to be significant. It was seen that wherever FEC was high, body weight or average daily gain declined in active infective stage. After termination of the infection, these effects were found to be non-significant. Result suggests that direct genetic and maternal permanent environmental effects were important for this trait; thus, they need to be considered for improvement in the trait.

  1. Estimates of heritability and genetic correlations for milk coagulation properties and individual laboratory cheese yield in Sarda ewes.

    PubMed

    Puledda, A; Gaspa, G; Manca, M G; Serdino, J; Urgeghe, P P; Dimauro, C; Negrini, R; Macciotta, N P P

    2017-06-01

    Objective of this study was to estimate genetic parameters of milk coagulation properties (MCPs) and individual laboratory cheese yield (ILCY) in a sample of 1018 Sarda breed ewes farmed in 47 flocks. Rennet coagulation time (RCT), curd-firming time (k 20) and curd firmness (a 30) were measured using Formagraph instrument, whereas ILCY were determined by a micromanufacturing protocol. About 10% of the milk samples did not coagulate within 30 min and 13% had zero value for k 20. The average ILCY was 36%. (Co)variance components of considered traits were estimated by fitting both single- and multiple-trait animal models. Flock-test date explained from 13% to 28% of the phenotypic variance for MCPs and 26% for ILCY, respectively. The largest value of heritability was estimated for RCT (0.23±0.10), whereas it was about 0.15 for the other traits. Negative genetic correlations between RCT and a 30 (-0.80±0.12), a 30 and k 20 (-0.91±0.09), and a 30 and ILCY (-0.67±0.08) were observed. Interesting genetic correlations between MCPs and milk composition (r G>0.40) were estimated for pH, NaCl and casein. Results of the present study suggest to use only one out of three MCPs to measure milk renneting ability, due to high genetic correlations among them. Moreover, negative correlations between ILCY and MCPs suggest that great care should be taken when using these methods to estimate cheese yield from small milk samples.

  2. sGD software for estimating spatially explicit indices of genetic diversity

    Treesearch

    A. J. Shirk; Samuel Cushman

    2011-01-01

    Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is...

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

    USDA-ARS?s Scientific Manuscript database

    Genome-wide molecular markers are readily being applied 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 polymorp...

  4. Genetic diversity in three natural populations of Pitcairnia flammea (l.) John (Bromeliaceae) estimated by ISSR markers.

    PubMed

    Souza-Sobreira, F B; Souza, G B; Rosado, C C G; Miranda, F D; Soares, T C B; Gontijo, A B P L

    2015-12-03

    Bromeliads are greatly represented in the Atlantic Forest, although many species are threatened with extinction owing to habitat fragmentation and intense extraction for ornamental purposes. Therefore, it is necessary to conduct studies generating knowledge about genetic diversity and the distribution of this diversity among and within natural populations to establish conservation strategies. These studies can be performed with the use of molecular markers. Molecular markers are advantageous for studies of natural populations, for conservation programs, and to aid in properly classifying plant species. This study aimed to evaluate the genetic diversity among and within natural populations of Pitcairnia flammea, occurring in three fragments of the Atlantic Forest in the southern State of Espírito Santo through the use of inter-simple sequence repeat (ISSR) markers. DNA samples from 55 individuals were amplified with 18 ISSR primers, generating 180 bands, 159 of which were polymorphic. The Shannon genetic diversity index ranged from 0.348 to 0.465, with an average of 0.412. The Bayesian approach for the molecular data indicated the existence of two genetic groups. Analysis of molecular variance indicated the existence of 90.3% diversity within the population and 9.74% among populations. The amount of genetic differentiation of populations was moderate (0.0974), indicating that gene flow rates may be enough to counteract the effects of genetic drift. Greater genetic variability found in population B indicates that this area is an important source of genetic variability.

  5. Non-monophyly and deep genetic differentiation across low-elevation barriers in a Neotropical montane bird (Basileuterus tristriatus; Aves: Parulidae).

    PubMed

    Gutiérrez-Pinto, Natalia; Cuervo, Andrés M; Miranda, Jhonathan; Pérez-Emán, Jorge L; Brumfield, Robb T; Cadena, Carlos Daniel

    2012-07-01

    Most widespread birds of Neotropical cloud forests exhibit phenotypic variation that is partitioned geographically suggesting allopatric divergence, but little is known about the extent to which such phenotypic differentiation is consistent with genetic variation. We studied geographic patterns of genetic differentiation in the Three-striped Warbler (Basileuterus tristriatus), a polytypic and widespread understory bird of the foothills and mid-elevation zone of the tropical Andes and adjacent mountains of Central and South America. We sequenced mitochondrial DNA for 196 samples covering the entire range of B. tristriatus, as well as 22 samples of its putative closest relatives: the Three-banded (B. trifasciatus) and Santa Marta (B. basilicus) warblers. We found deep genetic structure across the range of B. tristriatus, which consisted of ten major clades including B. trifasciatus, a species that was nested within B. tristriatus. In contrast, B. basilicus was not closely related to B. tristriatus but part of a clade of Myiothlypis warblers. Geographic boundaries among clades were clearly related to lowland gaps separating subspecies groups. The subspecies melanotis of the mountains of Central America was sister to a large clade including B. t. tacarcunae, and the rest of South American clades, including B. trifasciatus. Five clades are found in the northern Andes, where no signs of gene flow were found across barriers such as the Táchira Depression or the Magdalena valley. Our study highlights the importance of valleys in promoting and maintaining divergence in a lower montane forest bird. The substantial genetic and phenotypic differentiation, and the paraphyly uncovered in B. tristriatus, may call for revising its species boundaries. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Historical and contemporary factors shape the population genetic structure of the broadcast spawning coral, Acropora millepora, on the Great Barrier Reef.

    PubMed

    Van Oppen, Madeleine J H; Peplow, Lesa M; Kininmonth, Stuart; Berkelmans, Ray

    2011-12-01

    Effective management of reef corals requires knowledge of the extent to which populations are open or closed and the scales over which genetic exchange occurs, information which is commonly derived from population genetic data. Such data are sparse for Great Barrier Reef (GBR) corals and other organisms, with the studies that are available being mostly based on a small number of sampling locations spanning only part of the GBR. Using 11 microsatellite loci, we genotyped 947 colonies of the reef-building coral Acropora millepora from 20 sites spanning almost the full length of the GBR (∼12° of latitude and ∼1550 km). The results show a major divide between the southernmost central to southern offshore populations and all other sampled populations. We interpret this divide as a signature of allopatric divergence in northern and southern refugia during the Pleistocene glaciations, from which the GBR was subsequently recolonized. Superimposed on this pattern is a cross-shelf genetic division, as well as a separation of inshore populations south of the Cape Clifton Front at ∼21.5-22°S. Most inshore populations north of this, as well as mid-shelf populations in the northern and far northern GBR, are open, exchanging recruits frequently. In contrast, inshore populations south of the Cape Clifton Front and offshore populations in the central and southern GBR are largely self-seeding, at least within the spatial resolution that was achieved given our sampling intensity. Populations that have been impacted by recent disturbance events causing extensive coral mortality show no evidence of reduced genetic diversity.

  7. NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data.

    PubMed

    Do, C; Waples, R S; Peel, D; Macbeth, G M; Tillett, B J; Ovenden, J R

    2014-01-01

    NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.

  8. Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates.

    PubMed

    García-Verdugo, C; Sajeva, M; La Mantia, T; Harrouni, C; Msanda, F; Caujapé-Castells, J

    2015-02-01

    Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island-mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long-standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N = 66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations.

  9. Modeling lactation curves and estimation of genetic parameters in Holstein cows using multiple-trait random regression models.

    PubMed

    Kheirabadi, Khabat; Rashidi, Amir; Alijani, Sadegh; Imumorin, Ikhide

    2014-11-01

    We compared the goodness of fit of three mathematical functions (including: Legendre polynomials, Lidauer-Mäntysaari function and Wilmink function) for describing the lactation curve of primiparous Iranian Holstein cows by using multiple-trait random regression models (MT-RRM). Lactational submodels provided the largest daily additive genetic (AG) and permanent environmental (PE) variance estimates at the end and at the onset of lactation, respectively, as well as low genetic correlations between peripheral test-day records. For all models, heritability estimates were highest at the end of lactation (245 to 305 days) and ranged from 0.05 to 0.26, 0.03 to 0.12 and 0.04 to 0.24 for milk, fat and protein yields, respectively. Generally, the genetic correlations between traits depend on how far apart they are or whether they are on the same day in any two traits. On average, genetic correlations between milk and fat were the lowest and those between fat and protein were intermediate, while those between milk and protein were the highest. Results from all criteria (Akaike's and Schwarz's Bayesian information criterion, and -2*logarithm of the likelihood function) suggested that a model with 2 and 5 coefficients of Legendre polynomials for AG and PE effects, respectively, was the most adequate for fitting the data.

  10. Random regression models on Legendre polynomials to estimate genetic parameters for weights from birth to adult age in Canchim cattle.

    PubMed

    Baldi, F; Albuquerque, L G; Alencar, M M

    2010-08-01

    The objective of this work was to estimate covariance functions for direct and maternal genetic effects, animal and maternal permanent environmental effects, and subsequently, to derive relevant genetic parameters for growth traits in Canchim cattle. Data comprised 49,011 weight records on 2435 females from birth to adult age. The model of analysis included fixed effects of contemporary groups (year and month of birth and at weighing) and age of dam as quadratic covariable. Mean trends were taken into account by a cubic regression on orthogonal polynomials of animal age. Residual variances were allowed to vary and were modelled by a step function with 1, 4 or 11 classes based on animal's age. The model fitting four classes of residual variances was the best. A total of 12 random regression models from second to seventh order were used to model direct and maternal genetic effects, animal and maternal permanent environmental effects. The model with direct and maternal genetic effects, animal and maternal permanent environmental effects fitted by quadric, cubic, quintic and linear Legendre polynomials, respectively, was the most adequate to describe the covariance structure of the data. Estimates of direct and maternal heritability obtained by multi-trait (seven traits) and random regression models were very similar. Selection for higher weight at any age, especially after weaning, will produce an increase in mature cow weight. The possibility to modify the growth curve in Canchim cattle to obtain animals with rapid growth at early ages and moderate to low mature cow weight is limited.

  11. Molecular genetic variation of boll weevil populations in North America estimated with microsatellites: implications for patterns of dispersal.

    PubMed

    Kim, Kyung Seok; Sappington, Thomas W

    2006-05-01

    The boll weevil (Anthonomus grandis Boheman) is an insect pest of cotton that underwent a well-documented range expansion across the southeastern U.S. from Mexico beginning about 110 years ago. Eleven microsatellite loci were surveyed to infer the magnitude and pattern of genetic differentiation among boll weevil populations from 18 locations across eight U.S. states and northeast Mexico. Estimates of genetic diversity (allelic diversity and heterozygosity) were greater in Southern than Northern populations, and were greater in the west than the east among Northern populations. Boll weevil populations were genetically structured as a whole across the geographic range sampled, with a global F (ST) of 0.241. South-central populations exhibit classic isolation by distance, but evidence suggests that populations within the Eastern and Western regions have not yet reached genetic equilibrium. Gene flow appears to be relatively high among populations within the Eastern region. Population assignment data and estimates of gene flow indicate that migration between locations separated by < 300 km is frequent. The database of microsatellite genotypes generated in this study now makes it possible, through population assignment techniques, to identify the most likely geographic source of a boll weevil reintroduced to an eradication zone, which will help action agencies decide the most appropriate mitigation response.

  12. A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef.

    PubMed

    van Oppen, Madeleine J H; Lukoschek, Vimoksalehi; Berkelmans, Ray; Peplow, Lesa M; Jones, Alison M

    2015-01-01

    Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR) in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative isolation and contributes

  13. TNFA Haplotype Genetic Testing Improves HLA in Estimating the Risk of Celiac Disease in Children

    PubMed Central

    Zambon, Carlo-Federico; Navaglia, Filippo; Greco, Eliana; Pelloso, Michela; Artuso, Serena; Padoan, Andrea; Pescarin, Matilde; Aita, Ada; Bozzato, Dania; Moz, Stefania; Cananzi, Mara; Guariso, Graziella; Plebani, Mario

    2015-01-01

    Background TNF-α and IFN-γ play a role in the development of mucosal damage in celiac disease (CD). Polymorphisms of TNFA and IFNG genes, as well as of the TNFRSF1A gene, encoding the TNF-α receptor 1, might underlie different inter-individual disease susceptibility over a common HLA risk background. The aims of this study were to ascertain whether five SNPs in the TNFA promoter (-1031T>C,-857C>T,-376G>A,-308G>A,-238G>A), sequence variants of the TNFRSF1A gene and IFNG +874A>T polymorphism are associated with CD in a HLA independent manner. Methods 511 children (244 CD, 267 controls) were genotyped for HLA, TNFA and INFG (Real Time PCR). TNFRSF1A variants were studied (DHPLC and sequence). Results Only the rare TNFA-1031C (OR=0.65, 95% CI:0.44-0.95), -857T (OR=0.42, 95% CI:0.27-0.65), -376A (OR=2.25, 95% CI:1.12-4.51) and -308A (OR=4.76, 95% CI:3.12-7.26) alleles were significantly associated with CD. One TNFRSF1A variant was identified (c.625+10A>G, rs1800693), but not associated with CD. The CD-correlated TNFA SNPs resulted in six haplotypes. Two haplotypes were control-associated (CCGG and TTGG) and three were CD-associated (CCAG, TCGA and CCGA). The seventeen inferred haplotype combinations were grouped (A to E) based on their frequencies among CD. Binary logistic regression analysis documented a strong association between CD and HLA (OR for intermediate risk haplotypes=178; 95% CI:24-1317; OR for high risk haplotypes=2752; 95% CI:287-26387), but also an HLA-independent correlation between CD and TNFA haplotype combination groups. The CD risk for patients carrying an intermediate risk HLA haplotype could be sub-stratified by TNFA haplotype combinations. Conclusion TNFA promoter haplotypes associate with CD independently from HLA. We suggest that their evaluation might enhance the accuracy in estimating the CD genetic risk. PMID:25915602

  14. Estimates for genetic variance components in reciprocal recurrent selection in populations derived from maize single-cross hybrids.

    PubMed

    dos Reis, Matheus Costa; Pádua, José Maria Villela; Abreu, Guilherme Barbosa; Guedes, Fernando Lisboa; Balbi, Rodrigo Vieira; de Souza, João Cândido

    2014-01-01

    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 (σ τ (2)) and the covariance between these and their intrapopulation additive effects (Cov Aτ) 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.

  15. Estimates of genetic parameters for stayability and their associations with traits of economic interest in Gir dairy cows.

    PubMed

    Silva, R M O; Boligon, A A; Fernandes, A R; Vercesi Filho, A E; El Faro, L; Tonhati, H; Albuquerque, L G; Fraga, A B

    2016-02-19

    The objective of the present study was to estimate genetic parameters for stayability at 60 months of age (STAY60) and its association with first lactation cumulative milk yield (P305), age at first calving (AFC), and first calving interval (FCI), in order to adopt these traits as selection criteria for longevity in Gir dairy cattle. Records for 2770 cows born between 1982 and 2008 from six herds in the Brazilian states of Minas Gerais, São Paulo, and Paraíba were analyzed. The (co)variance components were estimated by a Bayesian approach using bivariate animal models. The heritability estimates were 0.37 ± 0.09, 0.23 ± 0.04, 0.26 ± 0.06, and 0.07 ± 0.03 for STAY60, P305, AFC, and FCI, respectively. The genetic correlations of STAY60 with P305, AFC, and FCI were moderate to high, with values of 0.61 (0.17), -0.44 (0.23), and 0.88 (0.13), respectively. STAY60, P305, and AFC exhibited additive genetic variability, and these traits should be considered in selection indices. The indirect selection for longevity through the correlated responses of early-expression traits, such as milk production at first lactation, could be used to improve the ability of animals to remain in the herd.

  16. Estimates for Genetic Variance Components in Reciprocal Recurrent Selection in Populations Derived from Maize Single-Cross Hybrids

    PubMed Central

    dos Reis, Matheus Costa; Pádua, José Maria Villela; Abreu, Guilherme Barbosa; Guedes, Fernando Lisboa; Balbi, Rodrigo Vieira; de Souza, João Cândido

    2014-01-01

    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 (σ τ 2) 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. PMID:25009831

  17. Behavioural linear standardized scoring system of the Lidia cattle breed by testing in herd: estimation of genetic parameters.

    PubMed

    Pelayo, R; Solé, M; Sánchez, M J; Molina, A; Valera, M

    2016-10-01

    Docility is very important for cattle production, and many behavioural tests to measure this trait have been developed. However, very few objective behavioural tests to measure the opposite approach 'aggressive behaviour' have been described. Therefore, the aim of this work was to validate in the Lidia cattle breed a behavioural linear standardized scoring system that measure the aggressiveness and enable genetic analysis of behavioural traits expressing fearless and fighting ability. Reproducibility and repeatability measures were calculated for the 12 linear traits of this scoring system to assess its accuracy, and ranged from 85.3 and 94.2%, and from 66.7 to 97.9%, respectively. Genetic parameters were estimated using an animal model with a Bayesian approach. A total of 1202 behavioural records were used. The pedigree matrix contained 5001 individuals. Heritability values (with standard deviations) ranged between 0.13 (0.04) (Falls of the bull) and 0.41 (0.08) (Speed of approach to horse). Genetic correlations varied from 0.01 (0.07) to 0.90 (0.13). Finally, an exploratory factor analysis using the genetic correlation matrix was calculated. Three main factors were retained to describe the traditional genetic indexes aggressiveness, strength and mobility.

  18. Genetic distances between popcorn populations based on molecular markers and correlations with heterosis estimates made by diallel analysis of hybrids.

    PubMed

    Munhoz, R E F; Prioli, A J; Amaral, A T; Scapim, C A; Simon, G A

    2009-08-11

    Diallel analysis was used to obtain information on combining ability, heterosis, estimates of genetic distances by random amplified polymorphic DNA (RAPD) and on their correlations with heterosis, for the popcorn varieties RS 20, UNB2, CMS 43, CMS 42, Zélia, UEM J1, UEM M2, Beija-Flor, and Viçosa, which were crossed to obtain all possible combinations, without reciprocals. The genitors and the 36 F(1) hybrids were evaluated in field trials in Maringá during two growing seasons in a randomized complete block design with three replications. Based on the results, strategies for further studies were developed, including the construction of composites by joining varieties with high general combining ability for grain yield (UNB2 and CMS 42) with those with high general combining ability for popping expansion (Zélia, RS 20 and UEM M2). Based on the RAPD markers, UEM J1 and Zélia were the most genetically distant and RS 20 and UNB2 were the most similar. The low correlation between heterosis and genetic distances may be explained by the random dispersion of the RAPD markers, which were insufficient for the exploitation of the popcorn genome. We concluded that an association between genetic dissimilarity and heterosis based only on genetic distance is not expected without considering the effect of dominant loci.

  19. Efficient multiple-trait association and estimation of genetic correlation using the matrix-variate linear mixed model.

    PubMed

    Furlotte, Nicholas A; Eskin, Eleazar

    2015-05-01

    Multiple-trait association mapping, in which multiple traits are used simultaneously in the identification of genetic variants affecting those traits, has recently attracted interest. One class of approaches for this problem builds on classical variance component methodology, utilizing a multitrait version of a linear mixed model. These approaches both increase power and provide insights into the genetic architecture of multiple traits. In particular, it is possible to estimate the genetic correlation, which is a measure of the portion of the total correlation between traits that is due to additive genetic effects. Unfortunately, the practical utility of these methods is limited since they are computationally intractable for large sample sizes. In this article, we introduce a reformulation of the multiple-trait association mapping approach by defining the matrix-variate linear mixed model. Our approach reduces the computational time necessary to perform maximum-likelihood inference in a multiple-trait model by utilizing a data transformation. By utilizing a well-studied human cohort, we show that our approach provides more than a 10-fold speedup, making multiple-trait association feasible in a large population cohort on the genome-wide scale. We take advantage of the efficiency of our approach to analyze gene expression data. By decomposing gene coexpression into a genetic and environmental component, we show that our method provides fundamental insights into the nature of coexpressed genes. An implementation of this method is available at http://genetics.cs.ucla.edu/mvLMM. Copyright © 2015 by the Genetics Society of America.

  20. Simulation analysis to test the influence of model adequacy and data structure on the estimation of genetic parameters for traits with direct and maternal effects.

    PubMed

    Clément, V; Bibé, B; Verrier, E; Elsen, J M; Manfredi, E; Bouix, J; Hanocq, E

    2001-01-01

    Simulations were used to study the influence of model adequacy and data structure on the estimation of genetic parameters for traits governed by direct and maternal effects. To test model adequacy, several data sets were simulated according to different underlying genetic assumptions and analysed by comparing the correct and incorrect models. Results showed that omission of one of the random effects leads to an incorrect decomposition of the other components. If maternal genetic effects exist but are neglected, direct heritability is overestimated, and sometimes more than double. The bias depends on the value of the genetic correlation between direct and maternal effects. To study the influence of data structure on the estimation of genetic parameters, several populations were simulated, with different degrees of known paternity and different levels of genetic connectedness between flocks. Results showed that the lack of connectedness affects estimates when flocks have different genetic means because no distinction can be made between genetic and environmental differences between flocks. In this case, direct and maternal heritabilities are under-estimated, whereas maternal environmental effects are overestimated. The insufficiency of pedigree leads to biased estimates of genetic parameters.

  1. Simulation analysis to test the influence of model adequacy and data structure on the estimation of genetic parameters for traits with direct and maternal effects

    PubMed Central

    Clément, Virginie; Bibé, Bernard; Verrier, Étienne; Elsen, Jean-Michel; Manfredi, Eduardo; Bouix, Jacques; Hanocq, Éric

    2001-01-01

    Simulations were used to study the influence of model adequacy and data structure on the estimation of genetic parameters for traits governed by direct and maternal effects. To test model adequacy, several data sets were simulated according to different underlying genetic assumptions and analysed by comparing the correct and incorrect models. Results showed that omission of one of the random effects leads to an incorrect decomposition of the other components. If maternal genetic effects exist but are neglected, direct heritability is overestimated, and sometimes more than double. The bias depends on the value of the genetic correlation between direct and maternal effects. To study the influence of data structure on the estimation of genetic parameters, several populations were simulated, with different degrees of known paternity and different levels of genetic connectedness between flocks. Results showed that the lack of connectedness affects estimates when flocks have different genetic means because no distinction can be made between genetic and environmental differences between flocks. In this case, direct and maternal heritabilities are under-estimated, whereas maternal environmental effects are overestimated. The insufficiency of pedigree leads to biased estimates of genetic parameters. PMID:11563370

  2. Multiple-trait estimates of genetic parameters for metabolic disease traits, fertility disorders, and their predictors in Canadian Holsteins.

    PubMed

    Jamrozik, J; Koeck, A; Kistemaker, G J; Miglior, F

    2016-03-01

    Producer-recorded health data for metabolic disease traits and fertility disorders on 35,575 Canadian Holstein cows were jointly analyzed with selected indicator traits. Metabolic diseases included clinical ketosis (KET) and displaced abomasum (DA); fertility disorders were metritis (MET) and retained placenta (RP); and disease indicators were fat-to-protein ratio, milk β-hydroxybutyrate, and body condition score (BCS) in the first lactation. Traits in first and later (up to fifth) lactations were treated as correlated in the multiple-trait (13 traits in total) animal linear model. Bayesian methods with Gibbs sampling were implemented for the analysis. Estimates of heritability for disease incidence were low, up to 0.06 for DA in first lactation. Among disease traits, the environmental herd-year variance constituted 4% of the total variance for KET and less for other traits. First- and later-lactation disease traits were genetically correlated (from 0.66 to 0.72) across all traits, indicating different genetic backgrounds for first and later lactations. Genetic correlations between KET and DA were relatively strong and positive (up to 0.79) in both first- and later-lactation cows. Genetic correlations between fertility disorders were slightly lower. Metritis was strongly genetically correlated with both metabolic disease traits in the first lactation only. All other genetic correlations between metabolic and fertility diseases were statistically nonsignificant. First-lactation KET and MET were strongly positively correlated with later-lactation performance for these traits due to the environmental herd-year effect. Indicator traits were moderately genetically correlated (from 0.30 to 0.63 in absolute values) with both metabolic disease traits in the first lactation. Smaller and mostly nonsignificant genetic correlations were among indicators and metabolic diseases in later lactations. The only significant genetic correlations between indicators and fertility

  3. Estimating genetic effect sizes under joint disease-endophenotype models in presence of gene-environment interactions

    PubMed Central

    Bureau, Alexandre; Croteau, Jordie; Couture, Christian; Vohl, Marie-Claude; Bouchard, Claude; Pérusse, Louis

    2015-01-01

    Effects of genetic variants on the risk of complex diseases estimated from association studies are typically small. Nonetheless, variants may have important effects in presence of specific levels of environmental exposures, and when a trait related to the disease (endophenotype) is either normal or impaired. We propose polytomous and transition models to represent the relationship between disease, endophenotype, genotype and environmental exposure in family studies. Model coefficients were estimated using generalized estimating equations and were used to derive gene-environment interaction effects an