A Bayesian model for estimating population means using a link-tracing sampling design

Link-tracing sampling designs can be used to study human populations that contain "hidden" groups who tend to be linked together by a common social trait. These links can be used to increase the sampling intensity of a hidden domain by tracing links from individuals selected in an initial wave of sampling to additional domain members. Chow and Thompson (2003, Survey Methodology 29, 197-205) derived a Bayesian model to estimate the size or proportion of individuals in the hidden population for certain link-tracing designs. We propose an addition to their model that will allow for the modeling of a quantitative response. We assess properties of our model using a constructed population and a real population of at-risk individuals, both of which contain two domains of hidden and nonhidden individuals. Our results show that our model can produce good point and interval estimates of the population mean and domain means when our population assumptions are satisfied.     

Palmar dermatoglyphics as a means of identifying individuals in a baboon population

Dermatoglyphic patterns provide a reliable, permanent means of identifying individual primates in wild populations. Unlike the conventional marking techniques applied in wildlife biology, they are not prone to fading, loss, or distortion. Nonetheless, they have not been previously used for identification in primate field studies. We report here two simple techniques for recording dermatoglyphs in the field and describe an application of the method to a long-term study of population dynamics among baboons (Papio hamadryas, sensu lato)in central Ethiopia. Members of a baboon population were live-trapped, and replicas made of their palmar dermatoglyphics, in 1973, 1982, 1983, and 1984. By comparing the 1973 set with the later samples, we were able to identify four animals, two of each sex. All had been subadult or newly adult in 1973, as determined by dental eruption. Eleven years after their first capture, both females were still members of the same troop, although this had apparently amalgamated with a neighboring group. Both males had migrated. One had moved from one olive baboon group to another; the other (a hybrid) had moved from the hybrid zone described by Nagel (1973) into an olive troop. Ten animals were identified in both the 1983 and the 1984 samples, and one of these had previously been recorded in both 1982 and 1973. Establishing identity by means of dermatoglyphics promises to be a useful tool in studies where sampling episodes are widely separate in time.     

Likelihood analysis for the ratio of means of two independent log-normal distributions

Existing methods for comparing the means of two independent skewed log-normal distributions do not perform well in a range of small-sample settings such as a small-sample bioavailability study. In this article, we propose two likelihood-based approaches-the signed log-likelihood ratio statistic and modified signed log-likelihood ratio statistic-for inference about the ratio of means of two independent log-normal distributions. More specifically, we focus on obtaining p-values for testing the equality of means and also constructing confidence intervals for the ratio of means. The performance of the proposed methods is assessed through simulation studies that show that the modified signed log-likelihood ratio statistic is nearly an exact approach even for very small samples. The methods are also applied to two real-life examples.     

Small-sample inference for the comparison of means of log-normal distributions

We propose a likelihood-based test for comparing the means of two or more log-normal distributions, with possibly unequal variances. A modification to the likelihood ratio test is needed when sample sizes are small. The performance of the proposed procedures is compared with the F-ratio test using Monte Carlo simulations.     

Plug‐in tests for nonequivalence of means of independent normal populations

In this paper, we consider the problem of testing nonequivalence of several independent normal population means. It is a well‐known problem to test the equality of several means using the analysis of variance (ANOVA). Instead of determining the equality, one may consider more flexible homogeneity, which allows a predetermined level of difference. This problem is known as testing nonequivalence of populations. We propose the plug‐in statistics for two different measures of variability: the sum of the absolute deviations and the maximum of the absolute deviations. For each test, the least favorable configuration (LFC) to ensure the maximum rejection probability under the null hypothesis is investigated. Furthermore, we demonstrate the numerical studies based on both simulation and real data to evaluate the plug‐in tests and compare these with the range test.     

Effects of competition on means,variances and covariances in quantitative genetics with an application to general combining ability selection

Summary General expressions are established for means, variances and covariances, taking into account the effect of interactions between individuals. For simplicity, only groups of size two are considered so that interactions are restricted to pairs of individuals; genetic effects are reduced to additivity and to additive × additive interaction between the direct effect of an allele and the associate effect of another. The effect of family structure is studied, and some consequences of interest to plant breeding are discussed by an application to general combining ability selection. From a population genetic point of view, this approach reveals a new application of coefficients of kinship.     

Theory for modelling means and covariances in a two-breed population with dominance inheritance

This paper presents theory and methods to compute genotypic means and covariances in a two breed population under dominance inheritance, assuming multiple unlinked loci. It is shown that the genotypic mean is a linear function of five location parameters and that the genotypic covariance between relatives is a linear function of 25 dispersion parameters. Recursive procedures are given to compute the necessary identity coefficients. In the absence of inbreeding, the number of parameters for the mean is reduced from five to three and the number for the covariance is reduced from 25 to 12. In a two-breed population, for traits exhibiting dominance, the theory presented here can be used to obtain genetic evaluations by best linear unbiased prediction and to estimate genetic parameters by maximum likelihood.Supported in part by the Illinois Agricultural Experiment Station, Hatch Projects 35-0345 (R.L.F.) and 35-0367 (M.G.). A computer program implementing the methods described here is available upon request to R.L.F.     

Natural focus of leptospirosis in the rice paddies of Krasmodar Territory and the means for its eradication

OFFthe rice fields of the Krasnodar Territory the intensive epizootic of leptospirosis icterohemorrhagica can be observed in the population of Norway rats (995 animals have been examined and 102 cultures obtained) the whole year round. The highest intensity of the epizootic process is known to fall on the end of summer and the beginning of autumn (45-50% of Leptospira carriers). The natural focus of leptospirosis on the rice-growing complex is epidemiologically dangerous. The epizootic process can be suppressed by reducing the population of rats by means of poisoned baits. The alternate use of different poisons ( rotindan , brodifacum ) given in the form of paraffined briquettes has proved to be most expedient.     

Analysing treatment means in plant tissue culture research

Many researchers set up an experiment, make measurements, do an analysis of variance, calculate the mean response for each treatment, and then try to decide if the treatment means are significantly different and why. Much too frequently, Duncan's multiple range test is used to test differences among means. It is only one of a number of techniques that can be used to examine treatment means. Some researchers are unaware of the different techniques and that the interpretation of the results of an experiment is strongly influenced by the technique used i.e. using two different techniques might produce two different interpretations of the results. Selection of the appropriate technique to use for a particular experiment depends upon the nature of the treatments and the objectives of the research. This paper discusses four techniques (ranking treatment means, multiple comparison procedures, fitting response models, and using contrasts to make planned comparisons) that can be used to examine treatment means and presents examples of the use of each one for plant tissue culture research.Abbreviations (IAA) indole-3-acetic acid - (IBA) indole-3-butyric acid - (NAA) naphthalene-acetic acid - (2,4-D) 2, 4-dichlorophenoxyacetic acid - (BA) benzyladenine - (PBA) tetrahydropyranylbenzyladenine - (2iP) 2 isopentenyl adenine - (2iPA) 2 isopentenyl adenosine Journal Paper J-12661 of the Iowa Agriculture and Home Economics Experiment Station, Ames. Project 2210.     

On the origin of species by means of assortative mating.

Assortative mating may split a population even in the absence of natural selection. Here, we study when this happens if mating depends on one or two quantitative traits. Not surprisingly, the modes of assortative mating that can cause sympatric speciation without selection are rather strict. However, some of them may occur in nature. Slow elimination of intermediate individuals caused by the gradual tightening of assortative mating, which evolves owing to relatively weak disruptive selection, provides the alternative scenario for sympatric speciation, in addition to fast elimination of intermediate individuals as a result of the direct action of strong disruptive selection under an invariant mode of assortative mating. Even when assortative mating alone cannot split an initially coherent population, it may be able to prevent the merging of species after their secondary contact.     

The significance of differences between means. A simulation study

1. Three tests of statistical significance: the confidence interval (C), Student's t, and Satterthwaite's corrected t were compared using a computer generated sampling experiment. 2. The C-test was shown to be extremely inefficient at detecting differences between pairs of means. The t-test performed as expected and Satterthwaite's correct t was slightly conservative. 3. When the population variances are different Satterthwaite's corrected t performed extremely well, the t-test was slightly liberal, while the C-test remained extremely insensitive. 4. It is concluded that the C-test should not be used (i.e. against Scheer, 1986, Comp. Biochem. Physiol. 83A, 405-408). 5. It is noted that when many t-tests are performed on one data set, alternative methods are appropriate.     

Effect of recombination in the parent populations on the means and combining ability variances in hybrid populations of maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

Recombination of selected genotypes plays a key role in plant breeding for generating new base populations. We investigated the influence of recombination in two parent populations on the means and combining ability variances of their hybrid population by (1) quantitative genetic theory and (2) experiments with maize. The two parent populations were founded by four early flint and four early dent inbred lines, respectively. Each population was studied in three generations: Syn-0, the four inbred lines themselves; Syn*-1, the six intrapool single crosses (SC); and Syn*-2, the three intrapool double crosses (DC). Four interpool hybrid populations were created: (1) all 16 SC and (2) all 36 DC were produced from generations Syn-0 and Syn*-1, respectively, (3) 168 biparental progenies (BIP) of type flint x dent (female x male), and (4) 168 BIP of type dent x flint were produced according to NC-design I with randomly sampled plants of generation Syn*-2. The half-sib and full-sib families obtained in this manner were evaluated for grain yield, dry matter concentration and plant height. According to theoretical results, differences in the population means of these hybrid populations indicate the presence of various types of epistasis. Changes in combining ability variances from SC to DC reflect different levels of parental inbreeding (F = 1 vs F = 0), whereas changes from DC to BIP only reflect the effects of recombination and are attributable to covariances between additive and dominance effects caused by linkage disequilibrium in the Syn-0 generations. The experimental results showed a significant decline in yield from DC to BIP due to a loss of gene combinations with favourable epistatic effects. Estimates of sigma(2)(GCA) attributable to flint or dent lines decreased or remained unchanged from SC to DC, but generally increased in the BIP populations. The consequences of these trends for developing improved interpool hybrids are discussed.     

Models for mating disruption by means of pheromone for insect pest control

Models are presented to investigate the population dynamic behavior of a pest population with the release of pheromone for mating disruption. Three mechanisms of mating disruption are considered: (i) confusion of males, (ii) competition with female pheromone trails yielding false trail following, (iii) emigration of males prior to mating. In addition, several refinements to confusion are considered. Confusion and emigration of males were found to be very similar both quantitatively and dynamically; also, a combination of both mechanisms was very little more efficient than either one separately. False trail following is difficult to compare with the other two, since competition with wild females is involved and thus the total population size enters the equations. Density dependence of the action of pheromones results in some cases in which mating disruption cannot control the pest population. Similarly, aggregation of the pest population decreases the efficiency of the method unless the pheromone action is density independent. Delayed mating of females makes control easier, and may constitute one mechanism for mating disruption.     

A natural focus of icterohemorrhagic leptospirosis in the floodplain of the lower Don and means for its eradication

An active natural focus of icterohemorrhagic leptospirosis has been detected in the area of fish-breeding ponds in Rostov Province, where the intensive epizootic among the population of Norway rats is observed the whole year round (574 animals have been examined, 56 cultures have been isolated). The epizootic process reaches its highest intensity in autumn (the proportion of infected animals exceeds 50%). This natural focus in the area of fish-breeding ponds is epidemiologically dangerous. The limitation of its infectious potential is possible by means of poisoned baits.     

运用PRINS和体细胞杂种克隆板对猪新微卫星的定位

In this study, two new microsatellites HAU02 and HAU06, which are screened and cloned. HUA02 and HAU06 are repectively mapped in lq23-27 and 6q11-21 by means of PRINS (primed in situ labeling) and somatic cell hybrid (SCH) panel techniques, we discussed their advantage and disadvantage in gene mapping. These two means provide us more techniques in gene mapping, and the locations of these new microsatellites accumulate more resource for Porcine Physical Map.     

Estimation of the direction and intensity of natural selection in relation to human intelligence by means of the intrinsic rate of natural increase

Abstract

A follow‐up study was made of 979 white individuals born in 1916 or 1917 who took the Terman Group Intelligence Test in the sixth grade while attending the Kalamazoo Public School System. It is the first study to take into account all of the variables that affect population growth (fertility, mortality, and generation length) by means of the intrinsic rate of natural increase when estimating the direction and intensity of natural selection in relation to human intelligence. When all the variables affecting population growth have been taken into account, the population under study has probably been in equilibrium with respect to the genetic factors favoring high intelligence, or more likely, has experienced a slight increase in the frequency of the genetic factors favoring high intelligence.     

Conserving the gene pool of Far Eastern plants by means of seed cryopreservation

Cryotolerance of seeds has been studied in 103 plant species of 33 families from five regions of the Russian Far East. In 89.1% of these species, seed viability has not decreased in the course of cryogenic storage. Six species have shown interpopulation variation in the seed response to extremely low temperature (?196°C). Freezing in liquid nitrogen, which results in deep anabiosis, can be used as a means for long-term seed storage. A preliminary assessment of genetic diversity at the population level provides for the maximum possible mobilization of the species gene pool. The results of this study contribute to the development of a scientific basis for creating a seed bank of the Far Eastern flora with the purpose to conserve and restore biological resources of the region.     

Analysis of the effect of inoculum characteristics on the first stages of a growing yeast population in beer fermentations by means of an individual-based model

The yeast Saccharomyces cerevisiae has a limited replicative lifespan. The cell mass at division is partitioned unequally between a larger, old parent cell and a smaller, new daughter cell. Industrial beer fermentations maintain and reuse yeast. At the end of fermentation a portion of the yeast is ‘cropped’ from the vessel for ‘serial repitching’. Harvesting yeast may select a population with an imbalance of young and aged individuals, but the output of any bioprocess is dependent on the physiology of each single cell in the population. Unlike continuous models, individual-based modelling is an approach that considers each microbe as an individual, a unique and discrete entity, with characteristics that change throughout its life. The aim of this contribution is to explore, by means of individual-based simulations, the effects of inoculum size and cell genealogical age on the dynamics of virtual yeast fermentation, focussing on: (1) the first stages of population growth, (2) the mean biomass evolution of the population, (3) the rate of glucose uptake and ethanol production, and (4) the biomass and genealogical age distributions. The ultimate goal is to integrate these results in order to make progress in the understanding of the composition of yeast populations and their temporal evolution in beer fermentations. Simulation results show that there is a clear influence of these initial features of the inocula on the subsequent growth dynamics. By contrasting both the individual and global properties of yeast cells and populations, we gain insight into the interrelation between these two types of data, which helps us to deal with the macroscopic behaviour observed in experimental research.     

Comparisons of treatment means when factors do not interact in two-factorial studies

Scientists in the fields of nutrition and other biological sciences often design factorial studies to test the hypotheses of interest and importance. In the case of two-factorial studies, it is widely recognized that the analysis of factor effects is generally based on treatment means when the interaction of the factors is statistically significant, and involves multiple comparisons of treatment means. However, when the two factors do not interact, a common understanding among biologists is that comparisons among treatment means cannot or should not be made. Here, we bring this misconception into the attention of researchers. Additionally, we indicate what kind of comparisons among the treatment means can be performed when there is a nonsignificant interaction among two factors. Such information should be useful in analyzing the experimental data and drawing meaningful conclusions.     

Effect of gametic disequilibrium on means and on genetic variances of autotetraploid synthetic varieties

Summary The occurrence and effects of a gametic disequilibrium (DSE) in the first generation of a theoretical two-population synthetic variety were investigated. Theoretical development was limited to the genetics at a single locus with two alleles in an autotetraploid species with random chromosome inheritance. Algebraic expressions were developed for the differences between the mean genotypic values of the two-population synthetic variety at generation one and in random mating equilibrium (RME). For the situation where both parents of the synthetic were in RME, a numerical analysis was performed for all possible allele frequencies assuming the following types of genic action: monoplex dominance, partial monoplex dominance, duplex dominance, partial duplex dominance, and additive. The result indicated that with non-additive genic action the DSE could, in some cases, greatly depress or inflate the mean genotypic value of the first generation (Syn-1_(RME)). Thus, any change of means over advancing generations with loss of DSE could be positive or negative. When additive genic action was assumed, there was no effect associated with DSE and when both parents had the same allele frequencies there was no DSE. The DSE, with only a minor exception, decreased the genetic variance and in numerous cases forced it near zero. Expressions were developed for mean genotypic values of a first generation synthetic with DSE in one parent (Syn-1_(DSE/RME)) or both parents (Syn-1_(DSE)). The deviation of these means from those of Syn-1_(RME) was a function of digenic and quadragenic population effects. An inspection of the response equations for Syn-1_(RME) indicated that in a series of crosses with one common parent the rankings of first generation means would be the same as the ranking of populations at equilibrium though the individual means would be biased. More importantly with DSE of one or both parents there are situations when a ranking of first generation mean genotypic values would not reflect relative frequency of desirable alleles in the populations. These results indicate that statistical analyses and selections based on means of the Syn-1 generation can have an error which is not avoidable by improvement in precision of evaluation.Cooperative investigations of the Alfalfa Production Research Unit, United States Department of Agriculture, Agricultural Research Service, and the Nevada Agricultural Experiment Station, Reno, Nevada, USAPaper No. 590 Scientific Journal Series, Nevada Agricultural Experiment Station