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At least 19 recordsLinked to original sources
PubMed1992

[Gene pool and gene geography of the USSR population].

Gene pool and gene geography are discussed from the point of view of their conceptual history beginning from the original concept of A.S. Serebrovskiĭ (1928). Difference between the present-day gene geography and gene geography of gene pool is accentuated: the former only represents a portion of the latter. Historical and territorial integrity of the USSR population gene pool, in conjunction with its huge diversity, is the main problem being analysed by various means of computerized genetic cartography. Coupled with the gene frequency mapping, following methods were also used: mapping of average heterozygosity, of interpopulation differentiation, of principal component scores and mapping of geographical trend for each mapped genetic parameter. The work is based on 100 allelic genes and haplotypes from 30 independent loci studied on the average in 225 local populations. Statistical analysis of gene geographical maps is based on 3975 nodes of regular cartographic net for the USSR territory. The wind rose of systematic changes in the USSR gene pool has three main geographic orientations: W-E, SW-NE and S-N. At the same time, there are only two main systematic forces of gene pool evolution: the force of social history with predominant W-E orientation and the force of natural history with predominant S-N orientation of their actions. The heterozygosity level of gene pool declines strictly in accordance with the resultant in the SW-NE direction.

Alleles↗
PubMed1999

[Genogeographic analysis of subdivided population. The Adyge gene pool in the Caucasian gene pool system].

A gene geographic analysis of the indigenous population of the Caucasian historical cultural province was carried out with a set of genetic markers extensively studied in the Adyges (39 alleles of 18 loci): AB0, ACP, C3, FY, GC, GLO, HP, KEL, LEW, MN, MNS, P, PGD, PGM1, RH-C, RH-D, RH-E, and TF. Genetic information on 160 Caucasian populations was used (on average, 65 populations per locus). A synthetic map of the first principal component clearly showed a division into two gene geographic provinces: Northern Caucasus and Transcaucasia. The component significantly differed across the Greater Caucasian Ridge. One of the major regions of extreme values corresponded to the Adyge region. A map of the second component revealed two poles, Northwestern (the Adyges) and Caspian, in gene pool variation of the Caucasian population. The analysis of the maps and the space of principal components showed that the Adyge population is an important component of the Caucasian gene pool. A map of genetic distance from all Caucasian populations to the Adyges showed that the north Caucasian populations (excluding the Ossetes) are the most genetically similar to the Adyges, while Georgians from the Kolkhida Valley and Azerbaijanians from the lowlands near the Caspian Sea and highland steppes are the most genetically remote from the Adyges. The genetic diversity (GST x 10(2)) of the entire Caucasian gene pool was studied. The average diversity of subpopulation within a Caucasian ethnos was GS-E = 0.81, the diversity of ethnoses within a linguistic family was GE-L = 0.83, and the diversity of linguistic families was GL-T = 0.58. The race classification of the Caucasian populations (GS-E = 0.81, GS-R = 0.80, GR-T = 0.76) proved to be more genetically informative than the linguistic one. The major parameters of the Adyges (total diversity HT = 0.364, heterozygosity HS = 0.361, and subpopulation diversity within the ethnos GS-E = 0.69) were similar to those averaged over the entire Caucasian population. A comparison with the same set of genetic markers showed that the interethnic diversity in the Caucasian region was lower than in the other north Eurasian regions (GS-E was 1.24 in the European region, 1.42 in the Ural region, 1.27 in Middle Asia, and 3.85 in Siberia).

Gene Pool↗
PubMed1998

Genome projects and gene pools: new germplasm for plant breeding?

Crop gene pools have adapted to and sustained the demands of agricultural systems for thousands of years. Yet, very little is known about their content, distribution, architecture, or circuitry. The presumably shallow elite gene pools often continue to yield genetic gains while the exotic pools remain mostly untapped, uncharacterized, and underutilized. The concept and content of a crop's gene pools are being changed by advancements in plant science and technology. In the first generation of plant genomics, DNA markers have refined some perceptions of genetic variation by providing a glimpse of a primary source, DNA polymorphism. The markers have provided new and more powerful ways of assessing genetic relationships, diversity, and merit by infusing genetic information for the first time in many scenarios or in a more comprehensive manner for others. As a result, crop gene pools may be supplemented through more rapid and directed methods from a greater variety of sources. Previously limited by the barriers of sexual reproduction, the native gene pools will soon be complemented by another gene pool (transgenes) and perhaps by other native exotic gene pools through comparative analyses of plants' biological repertoire. Plant genomics will be an important force of change for crop improvement. The plant science community and crop gene pools may be united and enriched as never before. Also, the genomes and gene pools, the products of evolution and crop domestication, will be reduced and subjected to the vagaries and potential divisiveness of intellectual property considerations. Let the gains begin.

Journal Article↗
PubMed1997

[Selective structure of a gene pool. I. Feasibility of research].

Possibilities of studying the properties of a selective gene pool structure, a new characteristic of the population genetic structure, are described. The characteristic depends on the type of selection and its effects on individual genes. The selective structure is evaluated by estimating significant differences between the interpopulation variation of i genes (FST(i)) and the average variation of the total gene pool (FST). This allows the role of individual genes in the selective gene pool structure to be determined and a hypothesis on the effect of the selection proposed, thus, providing a possibility of comparing individual genes and gene pools in terms of the effects of the natural selection, the key microevolutionary factor. The authors also describe properties and a reliable estimation of FST(i) and FST, possibilities and factors of estimating a selection-neutral differentiation F(e) from genetic demographical data and the empirical average FST of gene markers (classical, DNA, quasi-genetic), stability of genetic processes and other aspects of using an equality FST = F(e) = 1/[4NeMe + 1], construction of a representative sample of a populations with regard to their hierarchic structure, gene sampling and polymorphism, etc. FST(i) values for gene pools of indigenous populations from various continents and various regions of northeast Eurasia were estimated (> 90 alleles, > 30 loci). For all polymorphic genes (0.05 < or = q < or = 0.95), the average FST x 10(2) was 1.60 in Europe, 8.01 in Asia, 6.63 in Africa, 6.34 in Australia, 11.34 in America, and 6.78 in northeast Eurasia. Regional gene pools of the latter displayed FST of 2.25 in the European part, 2.62 in the Caucasus, 3.55 in the Urals, 2.71 in Central Asia and Kazakhstan, and 8.02 in Siberia and the Russian Far East.

Adaptation, Physiological↗
PubMed2003

Using molecular markers to assess the effect of introgression on quantitative attributes of common bean in the Andean gene pool.

Progress in bean breeding programs requires the exploitation of genetic variation that is present among races or through introgression across gene pools of Phaseolus vulgaris L. Of the two major common bean gene pools, the Andean gene pool seems to have a narrow genetic base, with about 10% of the accessions in the CIAT core collection presenting evidence of introgression. The objective of this study was to quantify the degree of spontaneous introgression in a sample of common bean landraces from the Andean gene pool. The effects of introgression on morphological, economic and nutritional attributes were also investigated. Homogeneity analysis was performed on molecular marker data from 426 Andean-type accessions from the primary centres of origin of the CIAT common bean core collection and two check varieties. Quantitative attribute diversity for 15 traits was studied based on the groups found from the cluster analysis of marker prevalence indices computed for each accession. The two-group summary consisted of one group of 58 accessions (14%) with low prevalence indices and another group of 370 accessions (86%) with high prevalence indices. The smaller group occupied the outlying area of points displayed from homogeneity analysis, yet their geographic origin was widely distributed over the Andean region. This group was regarded as introgressed, since its accessions displayed traits that are associated with the Middle American gene pool: high resistance to Andean disease isolates but low resistance to Middle American disease isolates, low seed weight and high scores for all nutrient elements. Genotypes generated by spontaneous introgression can be helpful for breeders to overcome the difficulties in transferring traits between gene pools.

Breeding↗
PubMed1990

[Ethnogenetics: adaptive structure of the gene pool of the mankind from the data on human polymorphic genetic markers].

The mean FST value as a characteristic of gene frequency changes in a random sample of polymorphic genes from population gene pool provides the best indirect estimation of selectively neutral level of genetic variability. The set of test criteria, including chi 2, F and t, can be used in order to compare F1 with F and subdivide gene sample into three subgroups, or classes of genes which are differing from each other by the degree of variation of allelic frequencies. These three classes comprise the adaptive structure of gene pool and consist of the genes which are, respectively, under stabilizing and differentiating selection pressures or neutral ones. Adaptive structures of gene pools of aboriginal human populations at the main 9 geographical regions of the World, taken together, reveal statistically significantly correlation with adaptive structure of the total gene pool of the Mankind. But the correlation is rather small and therefore, the adaptive structure of human gene pool reveals between adaptive structures, the highest is for the USSR and the lowest are for the East-Asiatic and Australian regions. The proportion of neutral to non-neutral genes is about 50% in the average, with the range of variation 40-60% in different regions. But none of the polymorphic genes so far studied reveals constant neutrality in all regional conditions of environment and at different times of evolution history of human gene pool. Its adaptive structure underwent essential transformation from the Palaeolithic till the Postpalaeolithic times, but nevertheless, among the main features of contemporary adaptive structure of human gene pool, those predominate which are of the Palaeolithic origin.

Alleles↗
PubMed1998

[The ecologic component of the geographic variation of the Northern Eurasian gene pool and its archaeological age].

The problem of the relationship between the state of the gene pool and population health was formulated. The subdivision into latitudinal zones, which is a characteristic feature of the northern Eurasian gene pool, was studied. This subdivision was expressed in the geographical distribution of the second principal component (PC2.G) of the total variance of 100 allelic frequencies for 34 polymorphic loci. It was suggested that this distribution of PC2.G resulted from the genetic adaptation of the population to the latitudinal zonality that is characteristic of northern Eurasia. It was also suggested that the latitudinal geographic variation was not inherent in the northern Eurasian gene pool and was younger than its total historical age. The evolutionary age of the principal components of the gene pool was estimated based on the geography of the principal components of the geographic variability of the late Paleolithic material culture, as well as the paleogeography of the Quaternary period. It was demonstrated that the first principal component of the modern gene pool was almost completely formed in the late Pleistocene; hence, its age is at least 16,000-26,000 years. The age of the second principal component (PC2.G) was estimated at less than 12,000-15,000 years; it was mostly formed in Holocene. A hypothesis was advanced that genetic adaptation occurs at the cost of population health, with the cost increasing as the evolutionary age of the genetic adaptation decreases. It was suggested that the latitudinal zonality of gene pool was accompanied by a similar zonality in the geography of morbidity as a cost of genetic adaptation.

Adaptation, Physiological↗
PubMed2001

[The Russian gene pool. Genogeography of serum genetic markers (HP, GC, PI, TF)].

The study continues the series of works on the Russian gene pool. Gene geographic analysis of four serum gene markers best studied in the Russian population (HP, GC, PI, and TF) has been performed. Gene-geographic electronic maps have been constructed for 14 alleles of these loci and their correlations with geographic latitude and longitude. For all maps, statistical characteristics are presented, including the variation range and mean gene frequencies, partial and multiple correlations with latitude and longitude, and parameters of heterozygosity and interpopulation diversity. The maps of five alleles (HP*1, GC*2, GC*1S, PI*M2, and TF*C2) are shown and analyzed in detail. The genetic relief and structural elements of the maps are compared with the ecumenical trends, main variation patterns of these genes in northern Eurasia, and genetic characteristics of the indigenous populations of the Urals and Europe.

Carrier Proteins↗
PubMed2001

[The Russian gene pool. Genogeography of erythrocyte genetic markers (ACP1, PGM1, ESD, GLO1, 6-PGD)].

The study continues the series of works on the Russian gene pool. Gene geographic analysis of five erythrocytic gene markers best studied in the Russian population (ACP1, PGM1, ESD, GLO1, and 6-PGD) has been performed. Gene-geographic electronic maps have been constructed for 13 alleles of these loci and their correlations with geographic latitude and longitude. For all maps, statistical characteristics are presented, including the variation range and mean gene frequencies, partial and multiple correlations with latitude and longitude, and parameters of heterozygosity and interpopulation diversity. The maps of eight alleles (ACP1*A, ACP1*C, PGM1*2+, PGM1*2-, PGM1*1-, ESD*1, GLO1*1, and PGD*C) are shown and analyzed in detail. The genetic relief and structural elements of the maps are compared with the ecumenical trends, main variation patterns of these genes in northern Eurasia, and genetic characteristics of the indigenous populations of the Urals and Europe.

Carboxylesterase↗
PubMed1998

[Selective structure of the gene pool. IV. Estimation from the selection intensity index Rs].

A new approach for investigating the selective structure of the gene pool reflecting the type and intensity of selection is proposed. Selection pressure is estimated on the basis of interpopulation gene diversity with the use of the selection intensity index: RS(i) = NeS(i) = 1/4(1/FST(i)-1/Fe). Distributions of RS(i) in gene pools of indigenous populations from all continents and five subregions of the northeastern Eurasia were examined. It was shown that, of all theoretical distributions, only beta-distributions provide a good approximation of RS(i) estimates. Based on the confidence intervals of RS obtained from beta-distributions, genes can be grouped into the three following classes according to their selective structure: LOWER DIFF, NEUTRAL, and SUPER DIFF. These classes, respectively, include genes subjected mainly to stabilizing selection (RS(i) > 0; LOWER DIFF), genes subjected mainly to differentiating selection (RS(i) < 0; SUPER DIFF), and arbitrarily selectively neutral genes (RS(i) approximately 0; NEUTRAL). Simulation of gene pool sampling (10(6) samples from 50 markers for each gene pool) allowed us to characterize the selective structure by determining markers that fall into the same selective class irrespective of the variant for the sampling process. The selective structure of gene pools from six continents (Europe, Asia, Africa, Australia, America, and southeastern Eurasia) and five subregions of northeastern Eurasia was characterized. It was shown that approximately one-third of genes is subjected to selection irrespective of the hierarchical level of the region. In gene pools of Europe, northeastern Eurasia, and European and Ural subregions, the proportion of genes under stabilizing selection was higher, the proportion of selectively neutral genes, lower. Debatable issues of tests for selective neutrality based on heterogeneity of interpopulation gene diversity are considered. These issues include the effect on FST of the hierarchical population structure, sample size, number of subpopulations, and other factors that shift estimates of gene selective values.

Gene Pool↗
PubMed1998

[Selective structure of the gene pool. II. Standard method using F(ST) statistics].

A new approach to the description of the selective structure of the gene pool that is determined by the type and intensity of selection for individual genes is suggested. Selective pressure is defined based on the heterogeneity of the interpopulation diversity index FST. It is assumed that a significant difference between the estimated heterogeneity for the ith gene FST(i) and the selectively neutral interpopulation differentiation of the gene pool (Fe) indicate an effect of selection on the ith gene. In order to reveal such significant differences, empirical FST(i) distributions for the human gene pools of all parts of the world and five subregions of northeastern Eurasia were approximated by different theoretical distributions. It was demonstrated that only beta-distributions yielded a good approximation of the empirical FST(i) estimations in all studied gene pools. Based on the beta-approximations, confidence intervals for FST were calculated. These intervals allowed the genes to be divided into three classes of selective structure. Class NEUTRAL comprised genes that were assumed to be selectively neutral (FST(i) approximately equal to Fe); classes LOWER DIFF and SUPER DIFF comprised selectively important genes with significantly decreased (FST(i) < Fe) and increased (FST(i) > Fe) differentiation, respectively. Positions of 80 immunologically important biochemical markers were determined in the selective structure of the gene pools of six regions of the world: Europe, Asia, Africa, Australia, America, and northwestern Eurasia. The suggested method of estimating selective structure can be used if FST = Fe, where Fe is a selectively neutral variation of genes. Fe = 4NeMe + 1)-1; the main conditions for the use of this method are the following assumptions: (1) the genetic process is stationary and (2) the effective population size (Ne), the migration rate (Me), and the selection rate (S) are constant in time and space. If these conditions are not met, a correction (numeric resampling) is required.

Gene Pool↗
PubMed1998

[Interpopulation diversity of the gene pool: beta distribution of Wright's F(ST) statistics].

The distribution of FST(i) estimates were studied in representative samples of ith genes for the gene pools of the major human populations, including the populations of Europe, Asia, Africa, Australia, America, North-eastern Eurasia, and five subregions of the latter. An average of 80 FST(i) estimates were analyzed for each sample of marker genes with a level of polymorphism (q) from 0.05 to 0.95. For each gene pool, the empirical distributions of FST(i) estimates were approximated by the main types of theoretical distributions--the normal, chi 2, Weibull, gamma, and beta distributions. In all gene pools, only beta distributions were good approximations of the empirical FST(i) distributions. The parameters of the beta distributions are reported in this study. It was demonstrated that the characteristics of beta distributions for all major gene pools studied could be interpolated to the smaller constituent gene pools. since the use of the traditional parametric tests starts from an assumption of normal distribution, they are inapplicable to analysis of FST statistics. Therefore, the obtained parameters of beta distributions should be used. These parameters allow the confidence intervals of the average FST values to be determined and permit correct comparison between the characteristics of both individual genes and gene pools to be performed.

Africa↗
PubMed1998

[East European gene pool and diseases in the rural population of European Russia].

New data on the association of the state of health and the disease incidence with the gene pool were obtained in the East European population. The second principal component (PC2.G, 11.4% of the total variance) of the geographic variation in the gene pool (100 alleles of 34 loci) showed a distinct latitudinal dependence corresponding to the natural zonality of Eastern Europe. This was also characteristic of the first principal component (PC1.M, 75.6% of the total variance) of the geographic variation in the disease incidence (i.e., the number of all new cases diagnosed in out-patient clinics per year) in the rural population. The disease incidence decreased from the south-southeast to the north-northwest in European Russia. The coefficient of the geographic pairwise correlation between PC2.G and PC1.M was r = 0.945; their specific correlation remained high (r = 0.864), even after a correction for the effects of age composition and heterozygosity. Thus, an insignificant variation in the gene pool was shown to significantly affect the geographic distribution of disease incidence in the East European population of Russia (eta 2 = 0.892). A correlation of mapped geographic distributions of PC1.M and PC2.G in the modern population with those of the principal components of the geographic variation of the late Paleolithic material culture in Eastern Europe was analyzed. The origin of the latitudinal zonality of the modern gene pool was dated back to the late Pleistocene-early Holocene. A conclusion was made that diseases that affected reproduction and lethality in the Paleolithic population still represent a mechanism of the gene pool's adaptation to the natural zonality of the environment. The latitudinal zonality of disease incidence, which was characteristic of the ancient population, is conserved in the today's population, owing to the gene pool.

Adolescent↗
PubMed2005

Evidence of a large novel gene pool associated with prokaryotic genomic islands.

Microbial genes that are "novel" (no detectable homologs in other species) have become of increasing interest as environmental sampling suggests that there are many more such novel genes in yet-to-be-cultured microorganisms. By analyzing known microbial genomic islands and prophages, we developed criteria for systematic identification of putative genomic islands (clusters of genes of probable horizontal origin in a prokaryotic genome) in 63 prokaryotic genomes, and then characterized the distribution of novel genes and other features. All but a few of the genomes examined contained significantly higher proportions of novel genes in their predicted genomic islands compared with the rest of their genome (Paired t test = 4.43E-14 to 1.27E-18, depending on method). Moreover, the reverse observation (i.e., higher proportions of novel genes outside of islands) never reached statistical significance in any organism examined. We show that this higher proportion of novel genes in predicted genomic islands is not due to less accurate gene prediction in genomic island regions, but likely reflects a genuine increase in novel genes in these regions for both bacteria and archaea. This represents the first comprehensive analysis of novel genes in prokaryotic genomic islands and provides clues regarding the origin of novel genes. Our collective results imply that there are different gene pools associated with recently horizontally transmitted genomic regions versus regions that are primarily vertically inherited. Moreover, there are more novel genes within the gene pool associated with genomic islands. Since genomic islands are frequently associated with a particular microbial adaptation, such as antibiotic resistance, pathogen virulence, or metal resistance, this suggests that microbes may have access to a larger "arsenal" of novel genes for adaptation than previously thought.

Bacteriophages↗
PubMed1998

[Selective structure of the gene pool. III. Technology of determination from F(ST)-statistics using numerical resampling].

The selection pressure on the ith gene was determined on the basis of the heterogeneity of interpopulation diversity FST(i), assumpting that the significant deviation of FST(i) (observed differentiation of the ith gene) from Fe (selectively neutral differentiation) indicates selection. A selectively neutral variation Fe was estimated from the mean FST, averaged over the total set of genes. Since the validity of the equation FST approximately Fe = (4NeMe + 1)-1 depends on the fulfillment of conditions of the theoretical model as well as on organization of sampling of genes and subpopulations rather than on statistical parameters of the gene sample, an additional correction by boot-strapping is suggested. Simulation of sampling of the gene pool using numerical resampling (10(6) samples from each of the 50 markers) allowed us to characterize the selective structure of the gene pool. This structure consists of the following: one class of selectively neutral genes, NEUTRAL (FST(i) approximately Fe); and two classes of selective genes, LOWER DIFF (FST(i) < Fe) and SUPER DIFF (FST(i) > Fe). Interclass regions N-LOWER and N-SUPER between the classes of neutral and selective genes were defined with the use of bootstrapping. The hypothesis on the presence or absence of selection cannot be formulated with regard to the genes included in the interclass regions. A general trend for all gene pools of the world was revealed: the ratio between the boundary values of selective classes and Fe is constant. On the basis of this, a rapid and simple technique for estimating selective values of genes was developed. The positions of more than 80 immunobiochemical gene markers in the selective structure of six gene pools of the world (Europe, Asia, Africa, Australia, America, and northeastern Eurasia) are presented. The selective structure of five subregions of northeastern Eurasia (Caucasus, Europe, Ural, Siberia, and Central Asia) are characterized as well.

Data Interpretation, Statistical↗
PubMed2003

Comparing the dehalogenase gene pool in cultivated alpha-halocarboxylic acid-degrading bacteria with the environmental metagene pool.

Culture-dependent and culture-independent approaches were used to determine the relationship between the dehalogenase gene pool in bacteria enriched and isolated on 2,2-dichloropropionic acid (22DCPA) and the environmental metagene pool (the collective gene pool of both the culturable and uncultured microbes) from which they were isolated. The dehalogenases in the pure-cultures isolates, which were able to degrade 22DCPA, were similar to previously described group I and II dehalogenases. Significantly, the majority of the dehalogenases isolated from activated sludge by degenerate PCR with primers specific for alpha-halocarboxylic acid dehalogenases were not closely related to the dehalogenases in any isolate. Furthermore, the dehalogenases found in the pure cultures predominated in the enrichments but were a minor component of the community used to inoculate the batch cultures. Phylogenetic analysis of the dehalogenase sequences isolated by degenerate PCR showed that the diversity of the group II deh gene was greater than that of the group I deh gene. Direct plating of the activated sludge onto minimal media supplemented with 22DCPA resulted in biomass and DNA from which dehalogenases were amplified. Analysis of the sequences revealed that they were much more closely related to the sequences found in the community used to start the enrichments. However, no pure cultures were obtained with this isolation method, and thus no pure cultures were available for identification. In this study we examined the link between genes found in pure cultures with the metagene pool from which they were isolated. The results show that there is a large bias introduced by culturing, not just in the bacteria isolated but also the degradative genes that they contain. Moreover, our findings serve as a caveat for studies involving the culturing of pure cultures of bacteria and conclusions which are drawn from analysis of these organisms.

Bacteria↗
PubMed2005

[The population gene pool of Yakutia: cartographic analysis based on the polymorphism of immune and biochemical markers].

The gene pool of the indigenous population of Sakha Republic (Yakutia) has been studied within the borders of this republic coinciding with the main area of Yakuts, which was formed by the end of the 19th century and have remained stable until the present time. Maps of the geographic variation of the integrated characteristics of the Yakut gene pool, including the principal components, parameters of genetic diversity, and genetic distances from the "average" Yakut population are presented. It has been demonstrated that ethnographers' reports on intense internal assimilation in modem Yakutia agree with genetic data. The stratification of the Yakut gene pool reflected in the maps of two principal components corresponds to the observed general (H(T)) and interpopulation (FST) gene diversities.

Biomarkers↗