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At least 973 records · Page 54Linked to original sources
PubMed1998

Signatures of population expansion in microsatellite repeat data.

To examine the signature of population expansion on genetic variability at microsatellite loci, we consider a population that evolves according to the time-continuous Moran model, with growing population size and mutations that follow a general asymmetric stepwise mutation model. We present calculations of expected allele-size variance and homozygosity at a locus in such a model for several variants of growth, including stepwise, exponential, and logistic growth. These calculations in particular prove that population bottleneck followed by growth in size causes an imbalance between allele size variance and heterozygosity, characterized by the variance being transiently higher than expected under equilibrium conditions. This effect is, in a sense, analogous to that demonstrated before for the infinite allele model, where the number of alleles transiently increases after a stepwise growth of population. We analyze a set of data on tetranucleotide repeats that reveals the imbalance expected under the assumption of bottleneck followed by population growth in two out of three major racial groups. The imbalance is strongest in Asians, intermediate in Europeans, and absent in Africans. This finding is consistent with previous findings by others concerning the population expansion of modern humans, with the bottleneck event being most ancient in Africans, most recent in Asians, and intermediate in Europeans. Nevertheless, the imbalance index alone cannot reliably estimate the time of initiation of population expansion.

Genetics, Population↗
PubMed2006

Method for mapping population-based case-control studies: an application using generalized additive models.

BACKGROUND: Mapping spatial distributions of disease occurrence and risk can serve as a useful tool for identifying exposures of public health concern. Disease registry data are often mapped by town or county of diagnosis and contain limited data on covariates. These maps often possess poor spatial resolution, the potential for spatial confounding, and the inability to consider latency. Population-based case-control studies can provide detailed information on residential history and covariates. RESULTS: Generalized additive models (GAMs) provide a useful framework for mapping point-based epidemiologic data. Smoothing on location while controlling for covariates produces adjusted maps. We generate maps of odds ratios using the entire study area as a reference. We smooth using a locally weighted regression smoother (loess), a method that combines the advantages of nearest neighbor and kernel methods. We choose an optimal degree of smoothing by minimizing Akaike's Information Criterion. We use a deviance-based test to assess the overall importance of location in the model and pointwise permutation tests to locate regions of significantly increased or decreased risk. The method is illustrated with synthetic data and data from a population-based case-control study, using S-Plus and ArcView software. CONCLUSION: Our goal is to develop practical methods for mapping population-based case-control and cohort studies. The method described here performs well for our synthetic data, reproducing important features of the data and adequately controlling the covariate. When applied to the population-based case-control data set, the method suggests spatial confounding and identifies statistically significant areas of increased and decreased odds ratios.

Case-Control Studies↗
PubMed2004

How old is the most recent ancestor of two copies of an allele?

An important clue to the evolutionary history of an allele is the structure of the neighboring region of the genome, which we term the genomic background of the allele. Consider two copies of the allele. How similar we expect their genomic background to be is strongly influenced by the age of their most recent common ancestor (MRCA). We apply diffusion theory, first used by Motoo Kimura as a tool for predicting the changes in allele frequencies over time and developed by him in many articles in this journal, to prove a variety of new results on the age of the MRCA under the simplest demographic assumptions. In particular, we show that the expected age of the MRCA of two copies of an allele with population frequency f is just 2Nf generations, where N is the effective population size. Our results are a first step in running exact coalescent simulations, where we also simulate the history of the population frequency of an allele.

Alleles↗
PubMed1983

[Effect of a complex system of controlling influenza on a citywide scale on the etiological structure of acute respiratory diseases].

Materials on the etiological structure of acute respiratory diseases (ARD) and the spread of respiratory virus infection among the population of the city under the conditions of mass vaccinal prophylaxis and chemoprophylaxis are presented. These materials indicate that the proportion of influenza A virus in the etiological structure of ARD decreased by half as the result of introducing the complex system of influenza control in the city. The proportion of other causative agents of ARD before and after introducing the complex system of influenza control irregularly varied among different age groups of the population without statistical significance. The indices characterizing the spread of influenza A virus infection among the population of the whole city were found to be significantly decreased during the second period of observation.

Adolescent↗
PubMed2006

On identifiability in capture-recapture models.

We study the issue of identifiability of mixture models in the context of capture-recapture abundance estimation for closed populations. Such models are used to take account of individual heterogeneity in capture probabilities, but their validity was recently questioned by Link (2003, Biometrics 59, 1123-1130) on the basis of their nonidentifiability. We give a general criterion for identifiability of the mixing distribution, and apply it to establish identifiability within families of mixing distributions that are commonly used in this context, including finite and beta mixtures. Our analysis covers binomial and geometrically distributed outcomes. In an example we highlight the difference between the identifiability issue considered here and that in classical binomial mixture models.

Animals↗
PubMed1998

Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history.

Since the 1920s, population geneticists have had measures that describe how genetic variation is distributed spatially within a species' geographical range. Modern genetic survey techniques frequently yield information on the evolutionary relationships among the alleles or haplotypes as well as information on allele frequencies and their spatial distributions. This evolutionary information is often expressed in the form of an estimated haplotype or allele tree. Traditional statistics of population structure, such as F statistics, do not make use of evolutionary genealogical information, so it is necessary to develop new statistical estimators and tests that explicitly incorporate information from the haplotype tree. One such technique is to use the haplotype tree to define a nested series of branches (clades), thereby allowing an evolutionary nested analysis of the spatial distribution of genetic variation. Such a nested analysis can be performed regarding the geographical sampling locations either as categorical or continuous variables (i.e. some measure of spatial distance). It is shown that such nested phylogeographical analyses have more power to detect geographical associations than traditional, nonhistorical analyses and, as a consequence, allow a broader range of gene-flow parameters to be estimated in a precise fashion. More importantly, such nested analyses can discriminate between phylogeographical associations due to recurrent but restricted gene flow vs. historical events operating at the population level (e.g. past fragmentation, colonization, or range expansion events). Restricted gene flow and historical events can be intertwined, and the cladistic analyses can reconstruct their temporal juxtapositions, thereby yielding great insight into both the evolutionary history and population structure of the species. Examples are given that illustrate these properties, concentrating on the detection of range expansion events.

Alleles↗
PubMed1999

[Epidemiologic study of regional inequalities].

The technological achievements of the recent years and the need for more advanced control of the processes within the health sector have supported the geographical epidemiology to become a distinct branch of epidemiology. The combined application of the simple standardized rates, statistical tests and different corrected risk parameters is able to describe the health status for geographically defined, small populations. Several statistical processes have been elaborated to estimate the number of the false positive results and to evaluate the role of chance in predicting the observed geographical pattern. These data completed with the usual risk measures quantify the risk difference within a broader region and determine the actual risk levels for the investigated small areas. The routine data processing system operating as a part of the public health surveillance identifies the high risk areas (the clusters) and without leaving the framework of routine data handling investigates the association between basic exposure data and health risks producing additional data about the nature of the aggregation of health related events. All the spetially varying etiological factors (environmental effects, social status, traditions, regional features of the health sector etc.) are ready to elicit regional alterations in the health status. The aim of the geographical information system is to cover the consequences of the uneven distribution of these factors. Since these kind of etiological factors play significant role in the generation of the most important public health problems in Hungary, and it is known that the small area inequalities are profound for these health impairments, the more extensive application of geographical information systems is expected to improve the efficiency of the control for public health problems and the performance of preventive medicine.

Data Interpretation, Statistical↗
PubMed1983

A graphical analysis of the interrelationships among waterborne asbestos, digestive system cancer and population density.

Five statistical procedures were used to partial the correlation between waterborne asbestos and digestive site cancer for the putative effects of population density. These include: analysis based on a data subset with roughly homogeneous population density; standard residual analysis (partial correlation); conditional probability integral transformation; analysis based upon ranked data, and use of logarithmic transformation. Nonparametric regression graphical techniques are applied to examine the nature or shape of the asbestos-cancer dose-response curve. Evidence is presented that suggests that there is considerable difference between analyses involving nonhigh-density tracts and non-San Francisco tracts. Evidence is also presented that the modal-type nonparametric regression curve forks or bifurcates when adjustment is made for population density.

Asbestos↗
PubMed2004

Estimation of fish abundance indices based on scientific research trawl surveys.

The fish abundance index over an ocean region is defined here to be the integral of expected catch per unit effort (CPUE), approximated by the sum of expected CPUE over grid squares. When trawl surveys are done within grid squares selected according to a probability sampling design, several other sources of variation such as the fish population dynamics and the catching process are also involved. In such situations model-assisted methods for estimating abundance, assessed under both design and model perspectives, have some advantages over purely design-based methods such as the Horvitz-Thompson (HT) estimator or purely model-based prediction approaches. This article develops model-assisted empirical likelihood (EL) methods via loglinear regression and nonparametric smoothing. The methods are applied to grid surveys of the Grand Bank region carried out annually by Fishery Products International from 1996 through 2002. The HT and EL methods produce similar point estimates of abundance indices. Simulation results, however, indicate that the EL estimator under local linear smoothing is associated with smaller standard errors.

Animals↗
PubMed1997

The Michigan equine monitoring system. I. Design, implementation and population estimates.

The Michigan equine monitoring system (MEMS) was designed and implemented in the State of Michigan, starting in 1991. The program was designed systematically to track the State's equine population, its health, and its economic implications to the equine industry. The MEMS was designed as a two-phase program. Phase I (the population and economic survey; the subject of this paper) was designed to provide new and statistically valid information describing the size, composition, location and economic characteristics of the Michigan equine industry. A standardized questionnaire was used to collect data via mail, telephone and personal interviews. Of the 3000 randomly selected list-frame samples, 2800 (93%) participated. However, 650 of these had no equids. There were 129,932 equids reported compared with 160,000 in 1984. The American Quarter Horse, Standardbred and Arabian breeds were the most numerous. Detailed results, including the size of equine operations/herds, uses, geographical distribution and the financial structure of the industry, are presented. A detailed account of the strategies used in designing and implementing the system is provided.

Animal Husbandry↗