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At least 19 recordsLinked to original sources

PubMed2004

Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations.

Current estimators of gene flow come in two methods; those that estimate parameters assuming that the populations investigated are a small random sample of a large number of populations and those that assume that all populations were sampled. Maximum likelihood or Bayesian approaches that estimate the migration rates and population sizes directly using coalescent theory can easily accommodate datasets that contain a population that has no data, a so-called 'ghost' population. This manipulation allows us to explore the effects of missing populations on the estimation of population sizes and migration rates between two specific populations. The biases of the inferred population parameters depend on the magnitude of the migration rate from the unknown populations. The effects on the population sizes are larger than the effects on the migration rates. The more immigrants from the unknown populations that are arriving in the sample populations the larger the estimated population sizes. Taking into account a ghost population improves or at least does not harm the estimation of population sizes. Estimates of the scaled migration rate M (migration rate per generation divided by the mutation rate per generation) are fairly robust as long as migration rates from the unknown populations are not huge. The inclusion of a ghost population does not improve the estimation of the migration rate M; when the migration rates are estimated as the number of immigrants Nm then a ghost population improves the estimates because of its effect on population size estimation. It seems that for 'real world' analyses one should carefully choose which populations to sample, but there is no need to sample every population in the neighbourhood of a population of interest.

Bayes Theorem↗

PubMed2005

[Census population vs. registration population: which population denominator should be used to calculate geographical mortality].

OBJECTIVES: Studies on the geographical differences in mortality tend to use a census population, rather than a registration population, as the denominator of mortality rates in South Korea. However, an administratively determined registration population would be the logical denominator, as the geographical areas for death certificates (numerator) have been determined by the administratively registered residence of the deceased, rather than the actual residence at the time of death. The purpose of this study was to examine the differences in the total number of a district population, and the associated district-specific mortality indicators, when two different measures as a population denominator (census and registration) were used. METHODS: Population denominators were obtained from census and registration population data, and the numbers of deaths (numerators) were calculated from raw death certificate data. Sex- and 5-year age-specific numbers for the populations and deaths were used to compute sex- and age-standardized mortality rates (by direct standardization methods) and standardized mortality ratios (by indirect standardization methods). Bland-Altman tests were used to compare district populations and district-specific mortality indicators according to the two different population denominators. RESULTS: In 1995, 9 of 232 (3.9%) districts were not included in the 95% confidence interval (CI) of the population differences. A total of 8 (3.4%) among 234 districts had large differences between their census and registration populations in 2000, which exceeded the 95% CI of the population differences. Most districts (13 of 17) exceeding the 95% CI were rural. The results of the sex- and age-standardized mortality rates showed 15 (6.5%) and 16 (6.8%) districts in 1995 and 2000, respectively, were not included in the 95% CI of the differences in their rates. In addition, the differences in the standardized mortality ratios using the two different population denominators were significantly greater among 14 districts in 1995 and 11 districts in 2002 than the 95% CI. Geographical variations in the mortality indicators, using a registration population, were greater than when using a census population. CONCLUSION: The use of census population denominators may provide biased geographical mortality indicators. The geographical mortality rates when using registration population denominators are logical, but do not necessarily represent the exact mortality rate of a certain district. The removal of districts with large differences between their census and registration populations or associated mortality indicators should be considered to monitor geographical mortality rates in South Korea.

Censuses↗

PubMed2006

[From population genetics to population genomics of forest trees: integrated population genomics approach].

Early works by Altukhov and his associates on pine and spruce laid the foundation for Russian population genetic studies on tree species with the use of molecular genetic markers. In recent years, these species have become especially popular as nontraditional eukaryotic models for population and evolutionary genomic research. Tree species with large, cross-pollinating native populations, high genetic and phenotypic variation, growing in diverse environments and affected by environmental changes during hundreds of years of their individual development, are an ideal model for studying the molecular genetic basis of adaptation. The great advance in this field is due to the rapid development of population genomics in the last few years. In the broad sense, population genomics is a novel, fast-developing discipline, combining traditional population genetic approaches with the genomic level of analysis. Thousands of genes with known function and sometimes known genomic localization can be simultaneously studied in many individuals. This opens new prospects for obtaining statistical estimates for a great number of genes and segregating elements. Mating system, gene exchange, reproductive population size, population disequilibrium, interaction among populations, and many other traditional problems of population genetics can be now studied using data on variation in many genes. Moreover, population genomic analysis allows one to distinguish factors that affect individual genes, alleles, or nucleotides (such as, for example, natural selection) from factors affecting the entire genome (e.g., demography). This paper presents a brief review of traditional methods of studying genetic variation in forest tree species and introduces a new, integrated population genomics approach. The main stages of the latter are : (1) selection of genes, which are tentatively involved in variation of adaptive traits, by means of a detailed examination of the regulation and the expression of individual genes and genotypes, with subsequent determination of their complete allelic composition by direct nucleotide sequencing; (2) examination of the phenotypic effects of individual alleles by, e.g., association mapping; and (3) determining the frequencies of the selected alleles in natural population for identification of the adaptive variation pattern in the heterogeneous environment. Through decoding the phenotypic effects of individual alleles and identification of adaptive variation patterns at the population level, population genomics in the future will serve as a very helpful, efficient, and economical tool, essential for developing a correct strategy for conserving and increasing forests and other commercially valuable plant and animal species.

Adaptation, Physiological↗

PubMed2006

Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population.

The Finnish wolf population (Canis lupus) was sampled during three different periods (1996-1998, 1999-2001 and 2002-2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long-term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period.

Animal Migration↗

PubMed2002

Effective population size and population subdivision in demographically structured populations.

A fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age. This provides a general expression for the probability that a pair of alleles sampled from the population coalesce in the previous time interval. The effective population size is defined as the reciprocal of twice the product of generation time and the coalescence probability. Biologically explicit formulas for effective population size with discrete generations and separate sexes are derived for a variety of different modes of inheritance. The method is also applied to a nuclear gene in a population of partially self-fertilizing hermaphrodites. The effects of population subdivision on a demographically structured population are analyzed, using a matrix of net rates of movement of genes between different local populations. This involves weighting the migration probabilities of individuals of a given age/sex class by the contribution of this class to the leading left eigenvector of the matrix describing the movements of genes between age/sex classes. The effects of sex-specific migration and nonrandom distributions of offspring number on levels of genetic variability and among-population differentiation are described for different modes of inheritance in an island model. Data on DNA sequence variability in human and plant populations are discussed in the light of the results.

Animals↗

PubMed1985

Population bottlenecks and nonequilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck.

A model is presented in which a large population in mutation/drift equilibrium undergoes a severe restriction in size and subsequently remains at the small size. The rate of loss of genetic variability has been studied. Allelic loss occurs more rapidly than loss of genic heterozygosity. Rare alleles are lost especially rapidly. The result is a transient deficiency in the total number of alleles observed in samples taken from the reduced population when compared with the number expected in a sample from a steady-state population having the same observed heterozygosity. Alternatively, the population can be considered to possess excess gene diversity if the number of alleles is used as the statistical estimator of mutation rate. The deficit in allele number arises principally from a lack of those alleles that are expected to appear only once or twice in the sample. The magnitude of the allelic deficiency is less, however, than the excess that an earlier study predicted to follow a rapid population expansion. This suggests that populations that have undergone a single bottleneck event, followed by rapid population growth, should have an apparent excess number of alleles, given the observed level of genic heterozygosity and provided that the bottleneck has not occurred very recently. Conversely, such populations will be deficient for observed heterozygosity if allele number is used as the sufficient statistic for the estimation of 4Nev. Populations that have undergone very recent restrictions in size should show the opposite tendencies.

Alleles↗

PubMedDate not supplied

Population structure and genetic differentiation among the substructured Vysya caste population in comparison to the other populations of Andhra Pradesh, India.

OBJECTIVES: The present paper focuses on the study of the patterns of genetic microdifferentiation among one of the substructured caste populations of Andhra Pradesh, namely Vysya, with reference to 17 other Telugu speaking populations from the same region of India. SUBJECTS AND METHODS: A total of 302 individuals from the three Vysya subgroups (101 of Arya Vysya, 100 from Kalinga Vysya and 101 from Thrivarnika) were typed in 17 blood groups and protein polymorphisms. Nei's gene diversity analysis, as well as neighbour-joining tree and UPGMA cluster diagrams, derived from standard genetic distances, R-matrix analysis and a regression model for investigating the patterns of external gene flow and genetic drift due to isolation under the island model, were done at two levels: (1) considering only the three Vysya populations and (2) considering common loci among 20 populations of Andhra Pradesh. RESULTS: Seven of the 17 systems investigated were found to be monomorphic among all the three Vysya groups. The UPGMA tree and bidimensional scaling of the D(2) distances derived from R-matrix analysis show a very distinct cluster of Vysya populations. Application of the model of regression of average heterozygosity versus the distance of populations from the centroid shows the three Vysya populations placed as clear outliers above the theoretical regression line. CONCLUSIONS: Different approaches employed in this study give support to the hypothesis of different origin and/or demographic story for the three Vysya groups compared with other populations of Andhra Pradesh.

Adult↗

PubMed2006

A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations.

In linkage disequilibrium mapping of genetic variants causally associated with phenotypes, spurious associations can potentially be generated by any of a variety of types of population structure. However, mathematical theory of the production of spurious associations has largely been restricted to population structure models that involve the sampling of individuals from a collection of discrete subpopulations. Here, we introduce a general model of spurious association in structured populations, appropriate whether the population structure involves discrete groups, admixture among such groups, or continuous variation across space. Under the assumptions of the model, we find that a single common principle--applicable to both the discrete and admixed settings as well as to spatial populations--gives a necessary and sufficient condition for the occurrence of spurious associations. Using a mathematical connection between the discrete and admixed cases, we show that in admixed populations, spurious associations are less severe than in corresponding mixtures of discrete subpopulations, especially when the variance of admixture across individuals is small. This observation, together with the results of simulations that examine the relative influences of various model parameters, has important implications for the design and analysis of genetic association studies in structured populations.

Computer Simulation↗

PubMed2006

Variable populations within variable populations: quantifying mitochondrial heteroplasmy in natural populations of the gynodioecious plant Silene vulgaris.

Populations of mitochondria reside within individuals. Among angiosperms, these populations are rarely considered as genetically variable entities and typically are not found to be heteroplasmic in nature, leading to the widespread assumption that plant mitochondrial populations are homoplasmic. However, empirical studies of mitochondrial variation in angiosperms are relatively uncommon due to a paucity of sequence variation. Recent greenhouse studies of Silene vulgaris suggested that heteroplasmy might occur in this species at a level that it is biologically relevant. Here, we use established qualitative methods and a novel quantitative PCR method to study the intraindividual population genetics of mitochondria across two generations in natural populations of S. vulgaris. We show incidences of heteroplasmy for mitochondrial atpA and patterns of inheritance that are suggestive of more widespread heteroplasmy at both atpA and cox1. Further, our results demonstrate that quantitative levels of mitochondrial variation within individuals are high, constituting 26% of the total in one population. These findings are most consistent with a biparental model of mitochondrial inheritance. However, selection within individuals may be instrumental in the maintenance of variation because S. vulgaris is gynodioecious. Male sterility is, in part, regulated by the mitochondrial genome, and strong selection pressures appear to influence the frequency of females in these populations.

Genetic Variation↗

PubMed1975

Attributable risk, population attributable risk, and population attributable fraction of death associated with hypertension in a biracial population.

In 1961, blood pressure was measured in the 40-69-year-old segment of the population of Evans County, Georgia. Mortality was monitored for up to ten years. The relationship found between hypertension and mortality is characterized in this report by four parameters: attributable risk, prevalence, population attributable risk, and population attributable fraction. Attributable risk of death, a measure of the over-all impact of hypertension on those in each race-sex group with hypertension, is high in white males, black males, and black females, and is lowest in white females. Population attributable risk, a measure of the impact of hypertension on each entire race-sex group, is highest in black males and females due to the high prevalence of hypertension in blacks. It is somewhat lower in white males and lowest in white females. The fraction of all deaths attributable to hypertension (population attributable fraction) is highest in black females and lower in the other three groups. The population attributable fraction (ranging from 0.26 to 0.54 for systolic hypertension) is of such magnitude that if the 50% reduction in mortality achieved in the Veteran Administration Cooperative Study could be repeated in the general population, life expectancy after 40 years of age could be substantially increased.

Adult↗

PubMed1984

Population bottlenecks and nonequilibrium models in population genetics. I. Allele numbers when populations evolve from zero variability.

A simple numerical method was developed for the mean number and average age of alleles in a population that was initiated with no genetic variation following a sudden population expansion. The methods are used to examine the question of whether allele numbers are elevated compared with values seen in equilibrium populations having equivalent gene diversity. Excess allele numbers in expanding populations were found to be the rule. This was true whether the population began with zero variation or with low levels of variation in either of two initial distributions (initially an equilibrium allele frequency distribution or initially with loci occurring in only two classes of variation). Although the increase of alleles may persist for only a short time, when compared with the time which is required for approach to final equilibrium, the increase may be long when measured in absolute generation numbers. The pattern of increase in very rare alleles (those present only once in a sample) and the persistence of the original allele were also investigated.

Alleles↗

PubMed1988

Population dynamics of movable genetic elements in Japanese natural populations of Drosophila melanogaster. I. Microevolution of male recombination determinants in experimental populations.

Five natural populations of D. melanogaster in Japan were surveyed for male recombination frequency in terms of the quantities of the mean and variance after crossing with cn bw females. The experimental condition enabled P-M system hybrid dysgenesis to take place. The means were not so different from one another, but there was a vast variation in the variances between them. Using one of these populations, two additional experimental populations were started, and the male recombination frequencies were monitored for 30 generations. Both the means and variances decreased in value at 25 degrees C. The regression line was Y = -0.000030X + 0.001706 on generation for the mean values, and was Y = -0.000098X + 0.005068 for the standard deviations in the cage population. There was no correlation between the means or the standard deviations and the copy numbers of the members of P element family as a whole. The experimental results indicate that the complete P transposable elements still retained in population were decreased in frequency and replaced by its degenerative nonautonomous forms.

Analysis of Variance↗

PubMed1985

Population bottlenecks and nonequilibrium models in population genetics. III. Genic homozygosity in populations which experience periodic bottlenecks.

The amount of variability in a population that experiences repeated restrictions in population size has been calculated. The restrictions in size occur cyclically with a fixed cycle length. Analytical formulas for describing the gene identity at any specific time in the expanded and restricted phases of the cycle, and for the average and second moment of the gene identity, have been derived. It is shown that the level of genetic diversity depends critically on the two parameters that account for the population size, mutation rate and the time of duration for each of the two phases in the cycle. If one or both of these composite parameters are small, the gene diversity will be much reduced, and population gene diversity will then be predictable from knowledge of the harmonic mean population size over the entire cycle. If these parameters take on intermediate values, diversity changes constantly during the cycle, fluctuating steadily from a high to a low value and back again. If these parameters are large, gene diversity will fluctuate rapidly between extreme values and will stay at the extremes for long periods of time.

Gene Frequency↗

PubMed1981

[Population genetics of the population in the European north of the RSFSR. V. An evaluation of the virtual size of the population by computer simulation of marriage and migration processes].

The paper deals with the effect of assortative matings on some parameters of population structure. To solve this problem, two rural populations near Archangelsk (river Peosa region) were used. Some genetic and demographic characteristics of these populations were described in previous publications. A comparison between random matches through a random number generator and true marriages was made by computer estimation of the spouses kinship coefficients. Significant avoidance of first and second cousins marriages in real populations was discovered. As a consequence of this avoidance of consanguinity, the effective breeding size of villages is increased twofold. Similar results were obtained by estimation os isonymy.

Computers↗

PubMed2002

Population data of five genetic markers in the Turkish population: comparison with four American population groups.

In this study, the phenotype and allele frequencies of five enzyme systems were determined in a total of 611 unrelated Turkish individuals and analyzed by using the exact and the chi 2 test. The following five red cell enzymes were identified by cellulose acetate electrophoresis: phosphoglucomutase (PGM), adenosine deaminase (ADA), phosphoglucose isomerase (PGI), adenylate kinase (AK), and 6-phosphogluconate dehydrogenase (6-PGD). The ADA, PGM and AK enzymes were found to be polymorphic in the Turkish population. The results of the statistical analysis showed, that the phenotype frequencies of the five enzyme under study are in Hardy-Weinberg equilibrium. Statistical analysis was performed in order to examine whether there are significant differences in the phenotype frequencies between the Turkish population and four American population groups. This analysis showed, that there are some statistically significant differences between the Turkish and the other groups. Moreover, the observed phenotype and allele frequencies were compared with those obtained in other population groups of Turkey.

Adenosine Deaminase↗

PubMed2006

Perfect simulation from nonneutral population genetic models: variable population size and population subdivision.

We show how the idea of monotone coupling from the past can produce simple algorithms for simulating samples at a nonneutral locus under a range of demographic models. We specifically consider a biallelic locus and either a general variable population size mode or a general migration model for population subdivision. We investigate the effect of demography on the efficacy of selection and the effect of selection on genetic divergence between populations.

Algorithms↗

PubMed1989

[Population density as a regulation factor of genetic structure and size of animal populations. Phenotypic variability of reaction to increase in density in Drosophila populations].

The presence of considerable level of phenotypic variability for the nature of fertility change in conditions of imago density increase has been shown in Drosophila natural populations. Genetic peculiarities of insects play the main role in its determination. The genotype groups sensitive and stable to density increase exist in the populations. The former have relatively high fertility at low density and low fertility at overcrowding. The latter are of contrary nature of fertility at given density conditions.

Analysis of Variance↗

PubMed1988

[Comparative studies of the population structure of a Kurd village population of Southeast Turkey. II. Morphologic differentiation within the population].

A small scale village society from southern Turkey has been investigated by demographic, social and anthropological criteria. An internal differentiation of the population on the basis of demographic and social data could be verified for morphological features, too. This is shown clearly by a differentiation of the population into two family complexes. The consequences for the interpretation of metrical random sample surveys in typological investigations are discussed.

Adult↗