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1.
Convergence of genetic distances in a migration matrix model 总被引:2,自引:0,他引:2
J W Wood 《American journal of physical anthropology》1986,71(2):209-219
A recurring problem with the use of migration matrix models of genetic differentiation has to do with their convergence properties. In practice, predictions can be drawn from these models only at equilibrium; but in the case of the standard predictors (most of which are modifications of Wright's FST), it can take an unrealistically large number of generations to approach equilibrium. An alternative set of predictors, the set of all pairwise genetic distances among the populations that define the rows and columns of the migration matrix, is investigated here. These distances are shown analytically to converge much more rapidly than the more commonly used predictors. In an application of the model to migration data on a human population from Papua New Guinea, it takes only about three to four generations for the pairwise distances to converge, in contrast to more than 100 generations for one of the standard predictors. In this case, moreover, the distances predicted by the model at equilibrium are similar to those calculated from the available genetic data. 相似文献
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Kerr RJ Li L Tier B Dutkowski GW McRae TA 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2012,124(7):1271-1282
Mixed models incorporating the inverse of a numerator relationship matrix (NRM) are widely used to estimate genetic parameters
and to predict breeding values in animal breeding. A simple and quick method to directly calculate the inverse of the NRM
has been historically developed for diploid animal species. Mixed models are less used in plant breeding partly because the
existing method for diploids is not applicable to autopolyploid species. This is because of the phenomenon of double reduction
and the possibility that gametes carry alleles which are identical by descent. This paper generalises the NRM and its inverse
for autopolyploid species, so it can be easily incorporated into their genetic analysis. The technique proposed is to first
calculate the kinship coefficient matrix and its inverse as a precursor to calculating the NRM and its inverse. This allows
the NRM to be calculated for populations containing individuals of mixed ploidy levels. This generalization can also accommodate
uncertain parentage by generating the “average” relationship matrix. The possibility that non-inbred parents can produce inbred
progeny (double reduction) is also discussed. Rules are outlined that are applicable for any level of ploidy. Examples of
use of the matrix are provided using simulated pedigrees. 相似文献
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The diffusion equation model and the Lefkovitch matrix model have been employed independently in plant population ecology in order to analyze the dynamics of growth and size structure. The two models describe the dynamics of size structure in biological populations, and thus there must be some relationship between them. In the present paper, we examine the theoretical relationship between these two models. We demonstrate, on a certain assumption, that the one-step Lefkovitch matrix model corresponds to a difference equation of the diffusion equation and that the two- and three-step Lefkovitch matrix model correspond to difference equations of the 4th- and 6th-order Kramers-Moyal expansions, respectively. It is also shown that 2n moments (the first to the 2n-th moments) of growth rate are necessary and sufficient to rewrite uniquely the n-step Lefkovitch matrix model in terms of the linear combination of the moments. We finally discuss the relationship between the species characteristics of census data and the appropriate types of the Lefkovitch matrix. 相似文献
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L D Van Vleck 《Biometrics》1978,34(1):123-127
The genetic fetal effects model shows that the usual sire effect is composed of one-half the direct additive genetic value and one-fourth of the fetal additive genetic value of the sire. The usual sire component of variance is actually the variance of that function. Genetic covariances between records of relatives influenced by fetuses of related sires can easily be written. If the magnitude of fetal sire effects is such that nonrandom use of fetal sires on daughters of sires being evaluated on daughter performance results in bias, the bias can be eliminated (Henderson 1975) by considering the fetal sire effects to be fixed effects. Some reduction in prediction error variance is likely by including fetal sire in the sire evaluation model. 相似文献
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Clark AG 《Genetics》1981,99(1):157-168
Log-linear analysis of contingency tables is applied to trihybrid backcross data to estimate linkage and viability. Whereas nonadditive viability differences perturb recombination estimates in the classical analysis, this statistical procedure yields maximum likelihood crossover frequency estimates in the presence of multiplicative viability effects. Other advantages of this method include: (1) estimation of viability effects of gene substitution at each locus, (2) estimation of asymptotic confidence intervals on recombination frequencies and viabilities, and (3) it tests the null hypothesis of no interference and no viability interactions. Extensions to cover more loci and to allow certain kinds of epistasis are easily made. Relative merits of the proposed and classical methods are discussed. 相似文献
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Representations are based on plant populations, continuously distributed over their habitats according to specified density patterns. Migration of genetic material takes place via pollen and seed dispersal. Monoecious plants with arbitrary rates of self-fertilization and dioecious plants are considered. The model was constructed with the intention of determining coefficients of inbreeding and kinship for all locations within the seed population after its dispersal over the habitat, assuming the respective genetic relationships of the parental generation to be known. To display the consequences of single components hidden in the general result, the following specifications have been treated: finite population size combined with random dispersal of seed, equilibrium states for hypothetically infinite population size with “limited” dispersal of pollen and seed, random dispersal of pollen, and random dispersal of seed. 相似文献
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Estimation of a covariance matrix with zeros 总被引:1,自引:0,他引:1
We consider estimation of the covariance matrix of a multivariaterandom vector under the constraint that certain covariancesare zero. We first present an algorithm, which we call iterativeconditional fitting, for computing the maximum likelihood estimateof the constrained covariance matrix, under the assumption ofmultivariate normality. In contrast to previous approaches,this algorithm has guaranteed convergence properties. Droppingthe assumption of multivariate normality, we show how to estimatethe covariance matrix in an empirical likelihood approach. Theseapproaches are then compared via simulation and on an exampleof gene expression. 相似文献
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Dabrowska DM 《The international journal of biostatistics》2012,8(1):Article 15
Semi-Markov and modulated renewal processes provide a large class of multi-state models which can be used for analysis of longitudinal failure time data. In biomedical applications, models of this kind are often used to describe evolution of a disease and assume that patient may move among a finite number of states representing different phases in the disease progression. Several authors proposed extensions of the proportional hazard model for regression analysis of these processes. In this paper, we consider a general class of censored semi-Markov and modulated renewal processes and propose use of transformation models for their analysis. Special cases include modulated renewal processes with interarrival times specified using transformation models, and semi-Markov processes with with one-step transition probabilities defined using copula-transformation models. We discuss estimation of finite and infinite dimensional parameters and develop an extension of the Gaussian multiplier method for setting confidence bands for transition probabilities and related parameters. A transplant outcome data set from the Center for International Blood and Marrow Transplant Research is used for illustrative purposes. 相似文献
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H R Gregorius 《Theoretical population biology》1975,8(3):331-345
Representations are based on plant populations, continuously distributed over their habitats according to specified density patterns. Migration of genetic material takes place via pollen and seed dispersal. Monoecious plants with arbitrary rates of self-fertilization and dioecious plants are considered. The model was constructed with the intention of determining coefficients of inbreeding and kinship for all locations within the seed population after its dispersal over the habitat, assuming the respective genetic relationships of the parental generation to be known. To display the consequences of single components hidden in the general result, the following specifications have been treated: finite population size combined with random dispersal of seed, equilibrium states for hypothetically infinite population size with “limited” dispersal of pollen and seed, random dispersal of pollen, and random dispersal of seed. 相似文献
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This study presents a new approach to obtain dominance estimates without using the full Henderson's mixed model equations (MMEs) related to an additive plus dominance animal model. This reduction could decrease substantially the computing time and hence its cost. In contrast to a procedure that we proposed before, the method developed in this paper does not require D(-1) and provides best linear unbiased prediction (BLUP) of genetic values that is close to that given by processing the full MMEs. In the previous study, we also elaborated an algorithm (denoted xi-REML) in order to approximate restricted maximum likelihood estimation of variance components via the expectation maximization (EM) algorithm. The xi-REML algorithm has been modified to be adapted to our new resolution approach. Through a numerical example, we show that there is a good agreement between REML-(EM), xi-REML and modified xi-REML estimates and that the latter algorithm is more efficient than our first proposition in terms of computing time and memory conservation. 相似文献
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Many species display a mixture of close inbreeding and outbreeding which is referred to as mixed mating. For selfing species,
models predict that such mixed mating systems can be stable. Conversely, models considering separate sex species have not
been able to explain mixed mating systems. This failure may be a result of the unrealistic assumption that recurrent inbreeding
does not increase the inbreeding coefficient. Here we show that mixed mating is expected in separate sex systems when recurrent
inbreeding is taken into account. A female that allows her brother to sibmate with her gives an extra mating opportunity to
said brother. This kin selective advantage should be strongest in genetic systems where the male is more related to the female.
In support of this idea, we find that inbreeding evolves most easily in selfers, followed by diploid sibmating, followed by
haplodiploid sibmating. Consideration of published values for the regression of fitness on inbreeding coefficient suggests
that many species fall in a range where some selfing/sibmating is optimal. 相似文献
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V. Tranchida‐Lombardo M. Roy E. Bugot G. Santoro Ü. Püttsepp M. Selosse S. Cozzolino 《Plant biology (Stuttgart, Germany)》2010,12(4):659-667
Several green orchids of the Neottieae tribe acquire organic carbon both from their mycorrhizal fungi and from photosynthesis. This strategy may represent an intermediate evolutionary step towards mycoheterotrophy of some non‐photosynthetic (albino) orchids. Mixed populations of green and albino individuals possibly represent a transient evolutionary stage offering opportunities to understand the evolution of mycoheterotrophy. In order to understand the emergence of albinos, we investigated patterns of spatial and genetic relationships among green and albino individuals in three mixed populations of Cephalanthera damasonium and one of C. longifolia using spatial repartition and Amplified fragment length polymorphism (AFLP) markers. Two of these populations were monitored over two consecutive flowering seasons. In spatial repartition analyses, albino individuals did not aggregate more than green individuals. Genetic analyses revealed that, in all sampled populations, albino individuals did not represent a unique lineage, and that albinos were often closer related to green individuals than to other albinos from the same population. Genetic and spatial comparison of genets from the 2‐year monitoring revealed that: (i) albinos had lower survival than green individuals; (ii) accordingly, albinos detected in the first year did not correspond to the those sampled in the second year; and (iii) with one possible exception, all examined albinos did not belong to any green genet from the same and/or from the previous year, and vice versa. Our results support a scenario of repeated insurgence of the albino phenotypes within the populations, but unsuccessful transition between the two contrasting phenotypes. Future studies should try to unravel the genetic and ecological basis of the two phenotypes. 相似文献
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We consider a matrix model to describe the population dynamics of the Indian paper waspRopalidia marginata, a eusocial insect species of peninsular India. We obtain the stable class distribution of this model and apply it to compute the worker-brood genetic relatedness of the colony. Our results are compared with those obtained by observational studies. Further, we study the effect of changes in turnover rates and survival rates on the genetic relatedness coefficient with the help of the theoretical formulae. 相似文献
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Estimation efficiency in a binary mixed-effects model setting 总被引:3,自引:0,他引:3