Malecot's parameters of isolation by distance and the degrees of endogamy in three regions of the Chuvash Republic]

Malecot's parameters of isolation by distance and the degree of endogamy were estimated for individual Village Soviets of the Kanash, Cheboksary, and Morgaushi raions of Chuvashiya. Inbreeding landscape schemes were constructed for the Kanash and Morgaushi raions. The suitability of the Malecot's model of isolation by distance for populations of the Village-Soviet level was analyzed.     

Malecot's Parameters of Isolation by Distance and the Degree of Endogamy in Three Raions of the Chuvash Republic

Malecot's parameters of isolation by distance and the degree of endogamy were estimated for individual village Soviets of the Kanash, Cheboksary, and Morgaushi raions of Chuvashiya. Inbreeding landscape schemes were constructed for the Kanash and Morgaushi raions. The suitability of the Malecot's model of isolation by distance for populations of the village-Soviet level was analyzed.     

Genetic epidemiological study of populations in three regions of Chuvashia Republic

Comprehensive population genetic and medical genetic studies were performed in three raions (districts) of Chuvashia. The population of these districts is more than 90% Chuvash. About 70% of the families that completed reproduction had two or three children. The proportion of families with four or more children was 18%. The duration of generation was 27.6 years. The differential fertility and differential mortality indices in the Chuvash population were estimated at 0.33 and 0.076, respectively. The total index of differential selection was 0.403, which is typical of modern urbanized populations. Mean values of local inbreeding calculated from Malecot's model of isolation by distance were 0.00124 and 0.00377 for the urban and rural populations, respectively, of the districts studied. The prevalence rates of autosomal dominant (AD), autosomal recessive (AR), and X-linked diseases were found to be 0.47, 0.52, and 0.35 per 1000, respectively, in the urban population and 1.62, 1.14, and 0.31 per 1000, respectively, in the rural population. Significant correlation between the local inbreeding and prevalence rates of AD and AR diseases was found. A total of 43 AD and 43 AR diseases were identified. Some of them were not found in previous studies on other populations.     

Genetic Epidemiological Study of Three District Populations in Chuvashia

Comprehensive population genetic and medical genetic studies were performed in three raions (districts) of Chuvashia. The population of these districts is more than 90% Chuvash. About 70% of the families that completed reproduction had two or three children. The proportion of families with four or more children was 18%. The duration of generation was 27.6 years. The differential fertility and differential mortality indices in the Chuvash population were estimated at 0.33 and 0.076, respectively. The total index of differential selection was 0.403, which is typical of modern urbanized populations. Mean values of local inbreeding calculated from Malecot's model of isolation by distance were 0.00124 and 0.00377 for the urban and rural populations, respectively, of the districts studied. The prevalence rates of autosomal dominant (AD), autosomal recessive (AR), and X-linked diseases were found to be 0.47, 0.52, and 0.35 per 1000, respectively, in the urban population and 1.62, 1.14, and 0.31 per 1000, respectively, in the rural population. Significant correlation between the local inbreeding and prevalence rates of AD and AR diseases was found. A total of 43 AD and 43 AR diseases were identified. Some of them were not found in previous studies on other populations.     

The marriage migration characteristics of the Rostov oblast population

Marriage records have been used to study the marriage migration structure of five raions of the Rostov oblast. The mean ethnic marriage assortativeness in the Russian and Ukrainian rural populations are 1.16 and 1.6, respectively. The endogamy index of the urban population varies from 0.19 to 0.34; and that of the rural population, from 0.21 to 0.54. Malecot's isolation by distance parameters have been calculated. Genetic landscapes have been constructed.     

Historical processes and biological structure of the populations. Example from the Island of Korcula

The importance of geographical distance as a determining factor of the population's biological and socio-cultural structure was studied on the island of Korcula, Yugoslavia. Migrational kinship coefficients, biological and linguistic distances were analysed in respect to isolation by distance, using Malecot's model. The fit of the model is highly significant for migrational kinship, linguistic, anthropometrical and physiological distances, while for morphometrical distances of metacarpal bones and dermatoglyphic distances, it is not adequate. The major conclusions reached through this analysis are in concordance with the known historical events in the entire region.     

Dynamics of Horizontal Gene Transfer and the Ecological Risk Assessment of Genetically Engineered Organisms

The extensive published discussion of potential ecological impacts of introduced genetic sequences and genetically engineered organisms has lacked a quantified delineation of the critical questions for the estimation of risk. Ultimately, the ecological risk assessment of introduced gene sequences is the application of evolution, population genetics, and ecology to risk estimation and decision making. This paper provides a framework for the estimation of risk due to introduced sequences in bacteria, and the principles should also hold for many diploid species. Horizontal genetic exchange poses new challenges for ecological risk assessment. Plasmid transfer can occur without any impacts, although the sequence can become ubiquitous in the population. Conversely, the introduction of a plasmid can change the dynamics of the host population, potentially altering the population minimum and maximum characteristics of its dynamics. Because of genetic exchange, new genetic information is unlikely to be constrained among one type of prokaryote. An example of the use of the model is given using genetic exchange data from a series of published soil microcosm experiments. The model demonstrates the increase in plasmid frequency when using experimentally derived conjugation frequencies. Application of these results to ongoing discussion of the risks of genetically engineered organisms is presented. Particular attention is paid to the transfer of genetic material and the resultant changes in host population dynamics.     

Estimating confidence of European WFD ecological status class and WISER Bioassessment Uncertainty Guidance Software (WISERBUGS)

The Water Framework Directive (WFD) requires estimates of the confidence and precision associated with any scheme for assessing and monitoring the ecological status class of any European rivers, lakes, transitional or coastal waters. This is a complex important issue, especially for waterbody assessments based on multiple metrics and/or two or more taxonomic groups. This paper aims to contribute towards improving understanding and providing practical approaches to assessing confidence of class by (i) discussing the various sources and causes of uncertainty, (ii) using UK rivers macroinvertebrate datasets to illustrate the estimation of replicate, temporal and spatial variance components and the implications for water body metric precision, confidence of class and optimal sampling design, (iii) introducing new freely available general software WISER Bioassessment Uncertainty Guidance Software (WISERBUGS) which uses prior sampling uncertainty estimates with user-specified metrics, class limits and metric combination rules to simulate the joint sampling uncertainty in metric EQR values and provide estimates of confidence of class based on individual metrics, (optionally weighted) multi-metric indices and/or multi-metric classification rules (worst case, mean or median class) based on one or more WFD biological quality elements.     

Use of Tissue Culture and Biotechnology for the Genetic Improvement of Watermelon

Watermelon is an important vegetable crop world-wide with over 81 million metric tons produced annually. Despite these high production figures, million of metric tons of fruit are lost in fields to disease. Genetic improvement through tissue culture and biotechnology offer potential routes of improving fruit harvest by offering higher quality products, like seedless fruit, or by introducing recombinant genes or generating somaclonal variants with improved resistance to biotic or abiotic stresses. The purpose of this review is to highlight how tissue culture and biotechnology have been used for the genetic improvement of watermelon and provide suggestions for future application of these methods to facilitate further genetic improvement.     

Genetic demography of Ukrainian urban populations in the 1990s: the ethnic composition of the migration flow in the Kharkov population

Marriage records were used to study the dynamics of the migration flow into the population of Kharkov in 1960-1993. The decrease in the migration rate was accompanied by changes in the ethnic composition of the migrants. The entire migration flow from the republics of the Baltic region consisted of Russians and Ukrainians. The increase in the migration flow from Transcaucasia was mainly accounted for by the migration activity of indigenous populations. Most migrants from Moldova, Central Asia, Kazakhstan, and Kyrgyzstan were also representatives of the respective indigenous populations. Malecot's coefficient of isolation by distance (b) decreased from 0.00123 to 0.0081.     

Simulation of Quantitative Characters by Genes with Biochemically Definable Action. VI. Modifications of a Simple Model

Investigations on metric characters of defined genotypes of Matthiola incana, and application of different linear models for the estimation of genetic parameters, indicate that the use of midparental value as a reference point results in parameter estimates that do not correspond to the actual biological situation. Use of the most recessive genotype as a reference point causes all of the contributions of single loci to be unidirectional and positive, and all the allelic and nonallelic interactions to be unidirectional and negative, in accord with our Model 2.2. The results indicate that the phenotypic response to allelic substitutions follows the characteristics of a saturation curve. The possibility is discussed that the saturation character results from regulating processes, whereas deviations of single measurements from the response curve, or response surface, reflect real interactions between allelic and nonallelic genes.     

Genetic structure of the Udmurt population

Integrated study of the genetic structure of the Udmurt population with respect to different genetic systems has been performed. Data on the genes of genetic diseases, abiotic parameters analyzed by population statistic methods, and DNA polymorphism are summarized. The populations of six raions (districts) of Udmurt Republic (the Mozhga, Malaya Purga, Sharkan, Debesy, Igra, and Glazov raions) have been studied. The total population studied was 267,655 people (an urban population of 150,119 people and a rural population of 117,536 people), including 155,346 Udmurts. The population structure has been studied in six districts on the basis of the vital statistics, Crow's indices, Malecot's isolation by distance parameters, ethnically assortative marriage parameters, endogamy indices, inbreeding-endogamy (ie) indices, and frequencies of the genotype and allele frequencies of four DNA markers (17 alleles). The prevalences of hereditary diseases have been calculated for different population groups: urban and rural populations, Udmurts and other ethnic groups. These groups, especially the urban and rural populations, substantially differed from one another in the prevalences of autosomal dominant (AR) and autosomal recessive (AR) diseases. The correlation between the prevalence of AD and AR diseases and the ie index is positive and significant. The spectrum of hereditary diseases detected in six districts of Udmurtia comprises 149 diseases (80, 57, and 12 AD, AR, and X-linked diseases, respectively). Accumulation of individual diseases in districts of Udmurtia and accumulation of diseases in Udmurtia as compared to regions studied earlier has been found. Cluster analysis of the frequencies of genes of AD and AR diseases and DNA markers has determined the gene geographic position of Udmurts.     

ESTIMATING RELATEDNESS USING GENETIC MARKERS

A new method is described for estimating genetic relatedness from genetic markers such as protein polymorphisms. It is based on Grafen's (1985) relatedness coefficient and is most easily interpreted in terms of identity by descent rather than as a genetic regression. It has several advantages over methods currently in use: it eliminates a downward bias for small sample sizes; it improves estimation of relatedness for subsets of population samples; and it allows estimation of relatedness for a single group or for a single pair of individuals. Individual estimates of relatedness tend to be highly variable but, in aggregate, can still be very useful as data for nonparametric tests. Such tests allow testing for differences in relatedness between two samples or for correlating individual relatedness values with another variable.     

Molecular genetic mapping and plant evolutionary biology

With the advent of molecular genetic mapping, it is possible to study the genetic basis of natural heritable variation in new ways. Here, three potential uses of molecular genetic mapping in plant ecology and evolutionary biology are discussed; (1) accurate estimation of genetic parameters, (2) understanding speciation and/or adaptation, and (3) investigating whole genome organization. Basic methods for mapping genes and important mapping strategies are outlined. Recent studies are introduced to illustrate progress so far in applying the new methods in ecological and evolutionary research.     

DIFFERENTIATION AMONG NINE POPULATIONS OF PHLOX. I. ELECTROPHORETIC AND QUANTITATIVE VARIATION

The organization of genetic variation in Phlox drummondii was investigated using both allozyme electrophoresis and quantitative genetics. Variation at five polymorphic enzyme loci was characterized in nine populations, and variation in 16 morphological and life-history characters was examined using an analysis of full- and half-sibs in seven populations. Significant levels of genetic variation were found at enzyme loci and for metric characters. Significant heritabilities were observed for 15 of the 16 characters examined. Genetic differences among populations were revealed both by Nei's genetic distance and by phenotypic differences, summarized by discriminant analysis. Partitioning variance in allozyme frequencies among hierarchical levels of genetic organization indicated that 94% of this variance lay within populations, 4% between populations within varieties, and 2% between varieties. Partitioning phenotypic variance for metric characters indicated that 73% lay within populations, 24% lay between populations within varieties, and 3% lay between varieties. Thus, both electrophoretic and metric characters indicated that despite extensive genetic differentiation among populations, most of the evolutionary potential of the species lies within populations.     

JOINT ALLELIC EFFECTS ON FITNESS AND METRIC TRAITS

Theoretical explanations of empirically observed standing genetic variation, mutation, and selection suggest that many alleles must jointly affect fitness and metric traits. However, there are few direct demonstrations of the nature and extent of these pleiotropic associations. We implemented a mutation accumulation (MA) divergence experimental design in Drosophila serrata to segregate genetic variants for fitness and metric traits. By exploiting naturally occurring MA line extinctions as a measure of line‐level total fitness, manipulating sexual selection, and measuring productivity we were able to demonstrate genetic covariance between fitness and standard metric traits, wing size, and shape. Larger size was associated with lower total fitness and male sexual fitness, but higher productivity. Multivariate wing shape traits, capturing major axes of wing shape variation among MA lines, evolved only in the absence of sexual selection, and to the greatest extent in lines that went extinct, indicating that mutations contributing wing shape variation also typically had deleterious effects on both total fitness and male sexual fitness. This pleiotropic covariance of metric traits with fitness will drive their evolution, and generate the appearance of selection on the metric traits even in the absence of a direct contribution to fitness.     

Softwares and methods for estimating genetic ancestry in human populations

The estimation of genetic ancestry in human populations has important applications in medical genetic studies. Genetic ancestry is used to control for population stratification in genetic association studies, and is used to understand the genetic basis for ethnic differences in disease susceptibility. In this review, we present an overview of genetic ancestry estimation in human disease studies, followed by a review of popular softwares and methods used for this estimation.     

Accurate genetic and environmental covariance estimation with composite likelihood in genome-wide association studies

Genetic and environmental covariances between pairs of complex traits are important quantitative measurements that characterize their shared genetic and environmental architectures. Accurate estimation of genetic and environmental covariances in genome-wide association studies (GWASs) can help us identify common genetic and environmental factors associated with both traits and facilitate the investigation of their causal relationship. Genetic and environmental covariances are often modeled through multivariate linear mixed models. Existing algorithms for covariance estimation include the traditional restricted maximum likelihood (REML) method and the recent method of moments (MoM). Compared to REML, MoM approaches are computationally efficient and require only GWAS summary statistics. However, MoM approaches can be statistically inefficient, often yielding inaccurate covariance estimates. In addition, existing MoM approaches have so far focused on estimating genetic covariance and have largely ignored environmental covariance estimation. Here we introduce a new computational method, GECKO, for estimating both genetic and environmental covariances, that improves the estimation accuracy of MoM while keeping computation in check. GECKO is based on composite likelihood, relies on only summary statistics for scalable computation, provides accurate genetic and environmental covariance estimates across a range of scenarios, and can accommodate SNP annotation stratified covariance estimation. We illustrate the benefits of GECKO through simulations and applications on analyzing 22 traits from five large-scale GWASs. In the real data applications, GECKO identified 50 significant genetic covariances among analyzed trait pairs, resulting in a twofold power gain compared to the previous MoM method LDSC. In addition, GECKO identified 20 significant environmental covariances. The ability of GECKO to estimate environmental covariance in addition to genetic covariance helps us reveal strong positive correlation between the genetic and environmental covariance estimates across trait pairs, suggesting that common pathways may underlie the shared genetic and environmental architectures between traits.     

Maximum likelihood estimation of oncogenetic tree models

We present a new approach for modelling the dependences between genetic changes in human tumours. In solid tumours, data on genetic alterations are usually only available at a single point in time, allowing no direct insight into the sequential order of genetic events. In our approach, genetic tumour development and progression is assumed to follow a probabilistic tree model. We show how maximum likelihood estimation can be used to reconstruct a tree model for the dependences between genetic alterations in a given tumour type. We illustrate the use of the proposed method by applying it to cytogenetic data from 173 cases of clear cell renal cell carcinoma, arriving at a model for the karyotypic evolution of this tumour.