Immunoglobulin allotypes in Jewish populations living in Israel and the United States

The ongoing interest in the interrelationships of Jewish populations justifies inclusion of the immunoglobulin allotypes in an ethnohistorical analysis. A total of 2,184 serum specimens obtained from unrelated Israeli Jewish and self-identified Milwaukee, WI, Jewish blood donors were classified as Ashkenazi, Sephardi, Asiatic, or North African and tested for G1m (a, x, z, and f), G3m (b0, b1, b3, b5, g), A2m (1 and 2), and Km (1). Selected sera were also tested for G3m (s, t, c3, c5). The estimated maximum likelihood Gm-Am haplotype frequencies were used in a heterogeneity chi-square analysis. The results indicate that there is less heterogeneity within Jewish populations from Europe, Middle East, and North Africa than in corresponding non-Jewish populations representing the same geographical areas. In order to avoid the hazards of a univariate focus, previously published data were incorporated into two additional analyses: 15 populations with information on 16 genetic loci and 24 populations with information on five genetic loci. Both sets of data were analyzed using principal-components and cluster analysis. In both sets of analyses, with the exception of the Yemenite Jews, Jewish populations grouped together. These analyses support the belief that Jewish populations appear to be derived from a common gene pool, and there has been some genetic drift and minimal gene flow with surrounding populations.     

Evaluation of a DNA pooled-sampling strategy for estimating the RFLP diversity of maize populations

Molecular characterization by means of RFLPs of large sets of populations is presently limited by experimental costs. In order to reduce costs, we have evaluated a method based on the RFLP analysis of balanced bulks of DNA from several individuals. The precision of this approach for estimating allele frequencies within each population was investigated using (i) DNA extracted from controlled bulks of leaf tissues of maize inbred lines, (ii) data obtained from individual analyses of 10 maize populations. Both approaches showed that allele frequencies can generally be estimated with a high precision (coefficients of determination up to 0.99 for some probe-enzyme combinations assayed), relative to the variation in allele frequencies observed among maize populations. Although further efforts are needed to define a set of probe-enzyme combinations that can be routinely image processed, these results, and preliminary results from a 65 maize populations project, suggest that this approach could provide highly informative data for large sets of populations, and at relatively low costs.     

人类免疫球蛋白同种异型G2M（23）因子在中国人群中的分布

应用单克隆抗体酶联免疫吸附吸附抑制实验,对我国３个民族８个群体２１０４份血样进行了免疫球蛋白同种异型Ｇ２ｍ（２３）因子检测。经多元相关和多元回归分析发现,中国人Ｇ２ｍ（２３）基因频率分布呈沿海拔高度和纬度变化的渐变群,据此建立了可预测中国人群Ｇ２Ｍ（２３）基因频率的多元回归方程,本文还讨论了Ｇ２ｍ（２３）基因频率形成渐变群的原因。     

Isoenzymes and migration in the African armyworm Spodoptera exempta (Lepidoptera, Noctuidae)

Techniques for the separation of proteins have proved to be powerful tools in the study of genetic variation. Polymorphisms on protein levels can be used to study the structure of populations. In general, differences in allele frequencies can be found among populations in different parts of the distribution area of a species. If, however, enough gene flow occurs by migration, the whole system can be regarded as one panmictic unit and similar frequencies can be expected in the whole area.
African armyworms are caterpillars of the noctuid moth Spodoptera exempta. They live on all sorts of graminaceous plants on which vast outbreaks can occur. Their economic importance can be considerable since they eat the main human food crops as well as pasture grasses. The occurrence of migration in S. exempta is known but its importance is a main controversial point. Outbreaks move during the year. These outbreaks could be caused by migrating animals or by increasing local populations when conditions are favourable.
The aim of this study has been to determine the relative importance of migration. Allele frequencies have been determined of six alleloenzymes that proved to be genetically polymorphic, an EST, 0-HBDH, ODH, a-GPDH, ME and LDH. Seventeen armyworm samples have been collected at a maximal distance of 2000 km in Kenya, Tanzania and Rhodesia on different food plants during 1975 and 1976.
No heterogeneity among these samples could be detected in the allele frequencies. A comparison with data from relevant literature on insects showed that the lack of heterogeneity cannot be described to inadequacy of the data. The occurrence of extensive migration is concluded to cause the similarity in allele frequencies.     

Genetic population structure in olive fly Bactrocera oleae (Gmelin): gene flow and patterns of geographic differentiation

Four wild Spanish populations of Bactrocera oleae (Gmelin) (Dipt., Tephritidae) were studied by gel electrophoresis, in order to find out their population genetic structure and the relative importance of gene flow in that structure. A great amount of genetic variability was observed. In terms of the pattern of the genetic variability in our populations, the most noticeable characteristics were the similarity of the configuration of allelic frequencies from locality to locality, the existence of exceptions and quantitative differences within that similarity, and the heterogeneity among the variable loci. Gene flow estimated from Wright's method gave a value of Nm = 8.9. However, the F _ST statistic in three of the loci ranged from 0.0451 to 0.0620 indicating a substantial degree of differentiation among populations (P < 0.001). The present observations seem to support the hypothesis that although gene flow could be high ( Nm = 8.9), 'natural' selection, probably due to agricultural practices, may be the major factor responsible for the pattern of the genetic variability observed in B. oleae .     

Distribution of Gene Frequency as a Test of the Theory of the Selective Neutrality of Polymorphisms

The variation in gene frequency among populations or between generations within a population is a result of breeding structure and selection. But breeding structure should affect all loci and alleles in the same way. If there is significant heterogeneity between loci in their apparent inbreeding coefficients F=s_p²/p(1-p), this heterogeneity may be taken as evidence for selection. We have given the statistical properties of F and shown how tests of heterogeneity can be made. Using data from human populations we have shown highly significant heterogeneity in F values for human polymorphic genes over the world, thus demonstrating that a significant fraction of human polymorphisms owe their current gene frequencies to the action of natural selection. We have also applied the method to temporal variation within a population for data on Dacus oleae and have found no significant evidence of selection.     

A program for maximum likelihood estimation and likelihood ratio tests in one-locus ABO-like systems based upon population phenotype data.

Phenotypes in an ABO-like system of a number of genetically-independent persons from a number of populations are supposed to be observed. The program which is written in FORTRAN calculates maximum likelihood estimates of gene frequencies and their standard errors in each population and in the populations taken together. Furthermore the program calculates expected values and likelihood ratio and goodness of fit chi-square tests of Hardy-Weinberg equilibrium. If several subpopulations are pooled together a likelihood ratio test of homogeneity is performed.     

A disequilibrium coefficient approach to Hardy-Weinberg testing

A comparison was made of various tests for Hardy-Weinberg equilibrium, with emphasis on methods for multiple alleles. For an overall test of deviations from equilibrium, the classical chi-square goodness-of-fit test generally performs well, with continuity corrections needed for extreme gene frequencies or extreme departures from equilibrium. For small samples, probability tests are preferable and for multiple alleles these probability tests may be performed on a sample of all possible sets of genotypic frequencies having a fixed set of sample gene frequencies. Numerical work showed that the continuity-corrected chi-square was the most conservative test procedure, and the uncorrected chi-square the least conservative. With multiple alleles, a better appreciation of the nature of departures from equilibrium is given by the use of disequilibrium coefficients, defined for each heterozygote as the difference between observed and expected frequencies. Likelihood-ratio tests can be used to test each of these coefficients individually but a satisfactory procedure is to divide the squared estimate of each coefficient by its estimated variance and regard the ratio as a single-degree-of-freedom chi-square. Numerical studies confirmed the validity of this approach, which has the great advantage of not requiring solutions of nonlinear equations.     

Linkage disequilibria in finite populations

Four-locus recombination frequencies are summarized into two-locus pair frequencies and three-locus frequencies, and further, into two-locus frequencies such that higher-order frequencies are linear functions of lower-order frequencies. Frequencies of gene combinations are defined according to their position on the same or distinct gametes, and linear functions of these provide the measures of linkage disequilibria. These concepts are utilized to derive the transitional behavior of the gene combinations frequencies and the linkage disequilibria in a finite monoecious population with random union of gametes for up to four loci. The transitions of lower-order disequilibria in a higher-order (more loci) setting involve the higher-order disequilibria which must be taken into account in arriving at the final (fixation) frequencies. The methods allow different initial conditions. Since corresponding data functions of the gene combination frequencies provide unbiased estimates of the parameters, estimators follow naturally.     

Drawing inferences about the coancestry coefficient

The coancestry coefficient, also known as the population structure parameter, is of great interest in population genetics. It can be thought of as the intraclass correlation of pairs of alleles within populations and it can serve as a measure of genetic distance between populations. For a general class of evolutionary models it determines the distribution of allele frequencies among populations. Under more restrictive models it can be regarded as the probability of identity by descent of any pair of alleles at a locus within a random mating population. In this paper we review estimation procedures that use the method of moments or are maximum likelihood under the assumption of normally distributed allele frequencies. We then consider the problem of testing hypotheses about this parameter. In addition to parametric and non-parametric bootstrap tests we present an asymptotically-distributed chi-square test. This test reduces to the contingency-table test for equal sample sizes across populations. Our new test appears to be more powerful than previous tests, especially for loci with multiple alleles. We apply our methods to HapMap SNP data to confirm that the coancestry coefficient for humans is strictly positive.     

Studies of chromosome structure polymorphism in Asia Minor and Persian populations of Drosophila subobscura Coll

Summary By means of the male sample method samples of D. subobscura from the north and south coast of Asia Minor and from the south coast of the Caspian Sea were examined with regard to the gene arrangements contained in them. The samples were judged by the following three criteria: (1) the number of different gene arrangements present, (2) the frequencies in which these gene arrangements occur, and (3) the rate of zygotic combinations.The samples from Asia Minor were found to be highly polymorphic. In this respect, they are comparable with other samples from the northern border of the Mediterranean region.The Persian populations are poor as regards number of gene arrangements. Commonly, some gene arrangements are highly frequent and, accordingly, high rates of homozygous combinations dominate. Presumably, these are marginal populations.Comparisons between samples from the north and south coast of Asia Minor confirm the findings from other parts of the species' range. As a rule, the frequencies of various gene arrangements vary according to the latitude in which they occur. Since climate and vegetation are also largely correlated with latitude, it is assumed that this is due to adaptive reaction to ecological factors.Comparing populations from the Western and Eastern Mediterranean region, similar differences were recorded. Some gene arrangements seem to be confined to either the western or eastern part of the area, and other gene arrangements differ in frequency. Since the ecological conditions in these areas appear to be comparable, such differences might be due to the history of the formation and dispersal of gene arrangements.In general, the frequencies of the gene arrangements in the chromosomes A, U, E and O are most equal along the northern margin of the Mediterranean area and, correspondingly, the frequencies of the heterokaryotypes are highest. It may be assumed that many heterokaryotypes reach their highest degree of heterotic supremacy in this area, and/or that the different homokaryotypes are uniform with respect to adaptive values. The reasoning rests on the additional assumption that in this area the biological conditions are the least extreme, or, in other words, that D. subobscura is best adapted to this environment. As it is, the region appears to lie geographically near the center of the species' range. In the I-chromosome the most equal frequencies of gene arrangements along with the highest frequency of the heterokaryotypes are to be found in Central Europe.On the other hand, in various populations lying supposedly at the borders of the species' range, the frequencies of gene arrangements of at least some chromosomes are strongly unequal and, accordingly, the frequencies of the homokaryotypes are high.In populations where the polymorphism is high, the character of the polymorphism varies slightly from chromosome to chromosome. In the O-chromosome usually one gene arrangement is abundant, while a large number of others are rare; two gene arrangements tend to dominate in the I- and U-chromosome, whereas in the E-chromosome several gene arrangements are apt to share similar frequencies.     

Interaction between Natural Selection for Heterozygotes and Directional Selection

Significant correlations between allelic frequencies and environmental variables in a number of insect species have been demonstrated by multivariate techniques. Since many environmental variables show a strong relationship to geographic location and since gene flow between populations can also produce patterns of gene frequencies which are related to the geographic location, both selection and gene-flow hypotheses are consistent with the observed correlations. The genetic variables can be corrected for geographic location and so for linear gene-flow patterns. If, after correction, the genetic variables still show significant correlations with similarly corrected environmental variables, then these correlations are consistent with hypotheses of selection but not of gene flow. The data of Johnson and Schaffer (1973) have been reanalyzed using the method of canonical correlation after correction for geographical location by means of multiple regression. Five of the nine loci studied exhibit significant canonical correlations. These results, under the assumption of linear gene flow, support hypotheses of selective action of environmental variables in the genotype-environment relationships observed.     

An unbiased estimator of gene diversity in samples containing related individuals

Gene diversity is sometimes estimated from samples that contain inbred or related individuals. If inbred or related individuals are included in a sample, then the standard estimator for gene diversity produces a downward bias caused by an inflation of the variance of estimated allele frequencies. We develop an unbiased estimator for gene diversity that relies on kinship coefficients for pairs of individuals with known relationship and that reduces to the standard estimator when all individuals are noninbred and unrelated. Applying our estimator to data simulated based on allele frequencies observed for microsatellite loci in human populations, we find that the new estimator performs favorably compared with the standard estimator in terms of bias and similarly in terms of mean squared error. For human population-genetic data, we find that a close linear relationship previously seen between gene diversity and distance from East Africa is preserved when adjusting for the inclusion of close relatives.     

An analysis of the ABO gene frequencies in Turkey

Regional ABO gene frequencies were estimated. The heterogeneity in these frequencies among regions were analysed statistically. The populations of the southeast Anatolia and east Black Sea regions and of the eastern part of the Aegean region were found to be responsible for the heterogeneity among the regions of Turkey. The results were interpreted in relation to the history of Turkey.     

Regional heterogeneity and gene flow maintain variance in a quantitative trait within populations of lodgepole pine

Genetic variation is of fundamental importance to biological evolution, yet we still know very little about how it is maintained in nature. Because many species inhabit heterogeneous environments and have pronounced local adaptations, gene flow between differently adapted populations may be a persistent source of genetic variation within populations. If this migration-selection balance is biologically important then there should be strong correlations between genetic variance within populations and the amount of heterogeneity in the environment surrounding them. Here, we use data from a long-term study of 142 populations of lodgepole pine (Pinus contorta) to compare levels of genetic variation in growth response with measures of climatic heterogeneity in the surrounding region. We find that regional heterogeneity explains at least 20% of the variation in genetic variance, suggesting that gene flow and heterogeneous selection may play an important role in maintaining the high levels of genetic variation found within natural populations.     

Population Genetics of Euphydryas Butterflies. I. Genetic Variation and the Neutrality Hypothesis

Twenty-one populations of the checkerspot butterfly, Euphydryas editha, and ten populations of Euphydryas chalcedona were sampled for genetic variation at eight polymorphic enzyme loci. Both species possessed loci that were highly variable from population to population and loci that were virtually identical across all populations sampled. Our data indicate that the neutrality hypothesis is untenable for the loci studied, and therefore selection is indicated as the major factor responsible for producing these patterns. Thorough ecological work allowed gene flow to be ruled out (in almost all instances) as a factor maintaining similar gene frequencies across populations. The Lewontin-Krakauer test indicated magnitudes of heterogeneity among standardized variances of gene frequencies inconsistent with the neutrality hypothesis. The question of whether or not to correct this statistic for sample size is discussed. Observed equitability of gene frequencies of multiple allelic loci was found to be greater than that predicted under the neutrality hypothesis. Genetic differentiation persisting through two generations was found between the one pair of populations known to exchange significant numbers of individuals per generation. Two matrices of genetic distance between populations, based on the eight loci sampled, were found to be significantly correlated with a matrix of environmental distance, based on measures of fourteen environmental parameters. Correlations between gene frequencies and environmental parameters, results of multiple regression analysis, and results of principle component analysis showed strong patterns of association and of "explained" variation. The correlation analyses suggest which factors might be further investigated as proximate selective agents.     

The HLA system in Italy

4,902 Italians were typed for HLA-A antigens, 4,721 for HLA-B and 1,503 for HLA-C. The samples, which were composed of unrelated, healthy individuals born in Italy, were used for estimating HLA-A, HLA-B and HLA-C gene frequencies with the maximum-likelihood method. Different Italian regions showed significant differences in the HLA alleles, providing further evidence for the genetic heterogeneity of the Italian population. HLA gene frequencies place continental Italy and Sicily in a position which is similar to that of other Mediterranean populations, whereas the genetic isolation of Sardinia is quite evident. The most significant linkage disequilibrium values found in the Italian population (except for Sardinia) were in agreement with those observed in other Caucasian populations. The difference between Northern and Southern Italy and between continental Italy and Sardinia was emphasized by the linkage disequilibrium values and by the principal-component analysis as well.