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PubMed1994

[Computer technology of the genogeographic study of the gene pool. I. Statistical information from the genogeographic map].

General statistical information that can be derived from an electronic map and listed in its legend is reviewed. Certain map information (extrema, mean and variance of mapped values, the number of initial and mapped values, their statistical distributions) can be used in analysis not only of gene pool, but also of phene pool maps. Another portion of map information, on total gene diversity, heterozygosity, and interpopulation differentiation, is important for consequent detailed analysis of a gene pool. Statistical information that is derived from a genogeographic map aids understanding of the content of a map and is used in comparative quantitative analysis of different regions and various mapped parameters. The possibilities for interpretation of statistical information of genogeographic maps are shown using the human gene pool as an example. Maps of frequencies of ABO-O and Rh-d blood group genes in three hierarchically subordinate gene pools of native inhabitants of Belarus, the Black Sea-Baltic region, and northeast Eurasia are presented for this purpose.

Computer Simulation↗
PubMed2003

Spatial patterns of mitochondrial and nuclear gene pools in chamois (Rupicapra r. rupicapra) from the Eastern Alps.

We have assessed the variability of maternally (mtDNA) and biparentally (allozymes) inherited genes of 443 chamois (Rupicapra r. rupicapra) from 19 regional samples in the Eastern Alps, to estimate the degree and patterns of spatial gene pool differentiation, and their possible causes. Based on a total mtDNA-RFLP approach with 16 hexanucleotide-recognizing restriction endonucleases, we found marked substructuring of the maternal gene pool into four phylogeographic groups. A hierarchical AMOVA revealed that 67.09% of the variance was partitioned among these four mtDNA-phylogroups, whereas only 8.04% were because of partitioning among regional samples within the populations, and 24.86% due to partitioning among individuals within regional samples. We interpreted this spatial pattern of mtDNA variability as a result of immigration of chamois from different Pleistocene refugia surrounding the Alps after the withdrawal of glaciers, rather than from topographic barriers to gene flow, such as Alpine valleys, extended glaciers or woodlands. However, this striking geographical structuring of the maternal genome was not paralleled by allelic variation at 33 allozyme loci, which were used as nuclear DNA markers. Wright's hierarchical F-statistics revealed that only < or =0.45% of the explained allozymic diversity was because of partitioning among the four mtDNA-phylogroups. We conclude that this discordance of spatial patterns of nuclear and mtDNA gene pools results from a phylogeographic background and sex-specific dispersal, with higher levels of philopatry in females.

Animals↗
PubMed2006

[Evaluation of the state of the gene pool of natural populations of vertebrate animals inhabiting the fragmented landscape of Moscow and Moscow district (with special reference to brown frogs)].

A system of urban ecological genetic monitoring has been developed for the first time in Russia and in the world. As a model, two species of brown frogs, Rana arvalis Nilss. and R. temporaria L. (16 populations, seven isozyme loci) were used. An evaluation of the gene pool state in urban frog populations has shown that the diversity in the Moscow frog populations was lower than that in natural populations (up to 80 and 50% in respectively R. anvalis and R. temporaria). Mean heterozygosities per locus were higher in large natural populations than in small urban isolates: in R. arvalis, these values were 0.16 and 0.06; in R. temporaria, 0.34 and 0.18, respectively. The number of polymorphic loci was also higher in natural populations than in the urban ones: 4 versus 2 in R. arvalis and 5 versus 4 in R. temporaria. Using superoxiddismutase as an example, fixation of different alleles of the same locus in different small isolates was shown. The gene pool condition of all but one urban populations of brown frog was evaluated as unsatisfactory, and that of the R. arvalis populations, as critical. These changes of the gene pool are explained mainly by gene drift accompanied by inbreeding, which was caused by human-induced fragmentation of the range and a decrease in population size of the species. The results of this study was employed in the development of the Moscow governmental program on restoration of the gene pools of vanishing animal species on specially protected natural urban territories. The series of works on long-term monitoring and assessment of the state of natural populations of model species in anthropogenic landscapes of Moscow and Moscow district has laid a foundation for a new branch of science, gene urbanology.

Alleles↗
PubMed1999

["Synthetic" maps of the Mari gene pool (from immunobiochemical polymorphism data)].

Models of geographic distribution of 33 alleles of 10 loci (AB0, TF, GC, PI, HP, AHS, F13B, ACP1, PGM1, GLO1) in the indigenous population of five raions (districts) of Marii El Republic were analyzed by cartographic statistical methods. Based on 33 maps for individual alleles, synthetic maps were constructed; they reflected the general characteristics of the spatial variability of the Mari gene pool. A map of reliability of the synthetic maps was also obtained. This study was the first to use estimates of the reliability of the gene-geographic prognosis for constructing and interpreting the maps of principal components. Synthetic maps of principal components reveal the geography of the main factors that determine the genetic diversity of the Maris. In the map of the first principal component (accounting for 25.5% of the total variation of the Mari gene pool), isolines clearly ran in the latitudinal direction; i.e., the variability exhibited a north-south gradient. The direction of changes reflects the characteristic features of the microevolution of the Mari gene pool, because it differs from the direction of the principal components of in the total Ural gene pool. The second principal component (24.3% of variation) also exhibited a latitudinal gradient in the western part of Marii El. In the eastern part of the republic, isolines drastically change their direction and display a marked west-east gradient. This longitudinal orientation of principal components is characteristic of the Maris in the synthetic maps of the Ural region. Contributions of individual genes in the variation of principal components were analyzed. In proceeding from the geographic space to the space of principal components, it was found that Highland Maris are separated from Meadow Maris not only geographically, but also genetically.

Gene Pool↗
PubMed2002

Markers polymorphic among malting barley ( Hordeum vulgare L.) cultivars of a narrow gene pool associated with key QTLs.

Barley used for malting is a fine-tuned organism, and it requires breeding within narrow gene pools for realistic cultivar enhancement. Significant phenotypic advance within such narrow gene pools has been achieved and the necessary genetic variability for breeding progress has been documented, but it was not well understood. This study was conducted to further characterize detectable genetic variability present within a select set of four closely related malting barley cultivars using three types of molecular markers: RFLP, PCR-RAPD and AFLP. The markers that identified polymorphism among the select malting cultivars tended to link with each other and to map in chromosomal regions associated with quantitative trait loci (QTLs) for agronomic and malting quality traits that differed among the four cultivars. Although RFLPs identified the least amount of polymorphism, the differences detected by the RFLPs best fit the chronology of the cultivars. These results indicate that a large amount of the genetic variability necessary for cultivar improvement may have originally been present in the breeding gene pool, but does not rule out de novo variation. Study of the populations from crosses within this narrow germplasm is needed to further elucidate the basis of the phenotypic variability found among these select barley cultivars.

Journal Article↗
PubMed2001

Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties.

The similarities and differences in the structures of the nifH gene pools of six different soils (Montrond, LCSA-p, Vernon, Dombes, LCSA-c, and Thysse Kaymor) and five soil fractions extracted from LCSA-c were studied. Bacterial DNA was directly extracted from the soils, and a region of the nifH gene was amplified by PCR and analyzed by restriction. Soils were selected on the basis of differences in soil management, plant cover, and major physicochemical properties. Microenvironments differed on the basis of the sizes of the constituent particles and the organic carbon and clay contents. Restriction profiles were subjected to principal-component analysis. We showed that the composition of the diazotrophic communities varied both on a large scale (among soils) and on a microscale (among microenvironments in LCSA-c soil). Soil management seemed to be the major parameter influencing differences in the nifH gene pool structure among soils by controlling inorganic nitrogen content and its variation. However, physicochemical parameters (texture and total C and N contents) were found to correlate with differences among nifH gene pools on a microscale. We hypothesize that the observed nifH genetic structures resulted from the adaptation to fluctuating conditions (cultivated soil, forest soil, coarse fractions) or constant conditions (permanent pasture soil, fine fractions). We attempted to identify a specific band within the profile of the clay fraction by cloning and sequencing it and comparing it with the gene databases. Unexpectedly, the nifH sequences of the dominant bacteria were most similar to sequences of unidentified marine eubacteria.

Bacteria↗
PubMed2005

[Estimating the gene pool condition in natural populations of invertebrates in the fragmented landscape of Moscow and Moscow district with special reference to shrub snail Bradybaena fruticum Müll].

Using shrub snail Bradybaena fruticum Müll (20 populations) as a model, we were the first in Russia and in the world to develop a system of urban ecological genetic monitoring of the gene pool of an invertebrate species. The results of isozyme polymorphism studies in shrub snail populations showed a dramatic (up to 70%) reduction in genetic diversity in small isolates from the urbanized environment as compared to large natural populations. In urban populations, genetic diversity parameters were demonstrated to be lower than in natural ones: the mean heterozygosity per locus was reduced up to 0.08 (0.15-0.20 in natural populations); the mean allele number, to 1.9 (2.7 in natural populations); and the number of polymorphic loci, to four, i.e., 2.2-fold (nine in natural populations). In Moscow district, the number of polymorphic loci also decreased to five in the population subjected to anthropogenic pressure. The changes in the population gene pool (as shown by the number of polymorphic loci) were different in Moscow and Moscow district. The percentage of populations with the number of polymorphic loci as low as four to six was 76.9 in Moscow and 23.1% in Moscow district. The gene pool quality of 80% of the urban snail populations was estimated as unsatisfactory, and in half of them, as critical. The main reason for these changes seems to be genetic drift accompanied by inbreeding, caused by fragmentation of the range and reduction in the abundance of populations of the species, due to the anthropogenic pressure. The results of the study were employed in the program of the Moscow government for restoring the gene pools of endangered animals species on the preserved territories of the city.

Animals↗
PubMed1989

Allelic and genotypic composition of ancestral Spanish and colonial Californian gene pools of Avena barbata: evolutionary implications.

Spanish explorers and colonists inadvertently started a massive experiment in evolutionary genetics when they accidentally introduced Avena barbata to California from Spain during the seventeenth and eighteenth centuries. Assays of the Spanish and Californian gene pools of this species for 15 loci show that the present day Spanish gene pool, particularly that of Southwestern Spain, is identical or virtually identical to that of California for five loci and closely similar for nine loci. Despite their similar allelic and single-locus genotypic compositions, the present-day Spanish and Californian gene pools are differently structured on a multilocus genetic basis. Evolutionary implications of these results are discussed.

Alleles↗
PubMed1994

[Computer technology for genetic-geographical study of the gene pool. II. Statistical transformation of maps].

Transformations of computer maps of geographical distribution of gene frequencies using basic mathematical statistical procedures are considered. These transformations are designated as statistical transformation of maps. Two transformation groups are considered: of one map separately and of a group of maps. Transformations possess a value beyond their use as intermediate stages of more complicated cartographical analysis: the resulting maps carry entirely new information on the geography of genes or a gene pool. This article considers three examples of obtaining new genetic profiles using statistical transformation algorithms. These profiles are of: heterozygosity (of HLA-A, B, C loci in northeastern Eurasia); (2) disease risk (Rh-incompatibility of mother and child with simultaneous registration of Rh and ABO blood groups in Eastern Europe); (3) genetic distances (from own mean ethnic values for Belarus' and from mean Russian values for the gene pool of Eastern Europe).

ABO Blood-Group System↗
PubMed1990

[Ethnic genetics: ethnogeographic diversity of the gene pool of human populations around the world].

The study was undertaken to estimate a degree of genetic differentiation in human all-world population at the ethnic level of its structure. The genetic information for this work came from well-known A. Mourant's et al. world-wide survey on human genetic polymorphisms and from regional survey on the same polymorphisms of the USSR peoples. The data were grouped into 9 regional populations studied for 49 alleles and haplotypes belonging to 20 polymorphic loci. Average genetic distances from the all-world human gene pool to each of regional one, and from these to gene pools of ethnic groups within regions were estimated and compared. An unexpected result of this within-between-region comparative analysis is the shortest genetic distance between gene pools of the USSR peoples as a whole on the one hand, and all-world peoples on the other. At the same time, a considerable part of the total human genetic polymorphism is persisted in the USSR region.

Americas↗
PubMed1997

[Computer technology of genogeographic study of the gene pool. IV. Population in the space of principal components].

On the basis of maps of principal components ("synthetic maps"), populations were arranged in the space of principal components. In terms of the applied model, nodes of a dense, uniform grid represented human populations. For each node, the frequency of a given gene was interpolated from these values for all original populations. Principal components were estimated and mapped on the basis of maps for all genes. Each population (grid node) was assigned a marker of an ethnic or some other group of populations and was positioned in the space of principal components according to the values from the original maps. The resultant "ethnic clouds" of populations and "ethnic centroids" of principal components provide some new possibilities for explaining the patterns of changes in gene pools. The maps of reliability of principal components allow the researcher to eliminate the information on populations which is unreliable and turn to the "reliable" space of principal components. The method was tested with the use of the maps of principal components for the gene pool of the East European population. Eastern Slavonic (Russians, Ukrainians, and Belarussians) and western and eastern Finno-Ugrian (Estonians and Mordovians, respectively) ethnic groups were mapped to the space of principal components. The relative positions of the populations of these ethnic groups was analyzed in the spaces of the first and the second, the first and the third, and the second and the third principal components of the East European gene pool.

Commonwealth of Independent States↗
PubMed2000

[Microsatellite haplotypes of the Y-chromosome demonstrate the absence of subdivisions and presence of several components in the Tuvinian male gene pool].

The haplotype analysis of seven Y-chromosome microsatellites in three regional populations of Tuvinians revealed high intrapopulation variation in the male gene pool of the modern population of the Tuva Republic. In total, 49 haplotypes were found in 111 individuals; only four haplotypes occurred at a frequency higher than 5%. High genetic diversity (H = 0.935) suggested a high power of discrimination for the Y-chromosome haplotypes. The analysis of molecular variance (AMOVA) and other data did not reveal subdivision of the Tuvinian population with respect to Y-chromosome haplotypes. Most haplotypes found in Tuvinians formed two lines. Line A included approximately 64% of the haplotypes found, line B, approximately 24%. A putative ancestral haplotype of line B was similar to a haplotype most common in modern Caucasoids (Md = 3), whereas a putative ancestral haplotype of line A proved to be distant from the ancestral haplotype of line A and haplotypes common for Caucasoids and Mongoloids. Estimates of the age of the Y-chromosome lines showed that the male gene pool of modern Tuvinians originated in the late Paleolithic or Neolithic period. With two methods, the age of line A was estimated at 3500 or 18,000 years and the age of line B was approximately at 5500 or 15,000 years. Considering the less conservative estimates to be more reliable, line B was assumed to originate from the ancient Caucasoid population of the Tuva region. The more widespread and evolutionarily younger line A was associated with the peopling region by ancient Mongoloid tribes of the Turkic language group in the Hun-Sarmatian period.

Asian People↗
PubMed2003

Distinction between cultivated and wild chicory gene pools using AFLP markers.

The cultivation area of industrial chicory, Cichorium intybus L. cv Sativum, coincides with the natural distribution area of its wild relative, C. intybus L., which could lead to gene flow between wild and cultivated types. The genetic diversity within and between the two types has therefore been studied using AFLP genotyping of samples from 12 wild populations collected in Belgium and ten commercial varieties. The genotyping of 233 individuals allowed the identification of 254 AFLP markers. Similar levels of genetic diversity were observed within wild populations and cultivated varieties, suggesting the absence of any strong bottleneck in the history of the cultivated types. The phylogenetic analysis pointed to a monophyletic origin of cultivated varieties as compared to the local wild populations studied, hence the two types of chicory form two separate gene pools. The genotyping of some individuals sampled in ruderal sites clearly showed that they belong to the cultivated gene pool, which suggests the existence of feral or weedy types. The low differentiation observed among wild populations indicates that gene flow might be important in this species.

Agriculture↗
PubMed2004

The Horizontal Gene Pool: an ESF workshop summary.

The European Science Foundation (ESF) funds a limited number of exploratory workshops each year that enable scientists to meet and develop plans for a program of integrated research which would benefit from a coordinated European effort. In summer 2003, the Standing Committee for Life and Environmental Sciences (LESC) sponsored such a workshop called The Horizontal Gene Pool: The Functional Role of Mobile Genetic Information--How Bacteria Perceive, Sample, and Utilize Genetic Elements in evolution and Local Adaptation. The workshop took place at St. Catherine's College, Oxford, UK. Its purpose was to identify how recent advances in the application of genomics and microbial ecology can be harnessed to determine the genetic mechanisms that underpin the biological role of the horizontal gene pool. Scientific excellence at the workshop was contributed by senior scientists and young investigators from research institutes located in nine European countries.

Bacteria↗
PubMed1992

[Preservation of the plant and animal gene pools in Siberia].

The results of the work on preservation of the gene pools performed at the two experimental bases of the Institute of Cytology and Genetics of the Siberian Division of Academy of Sciences of the USSR are summarized. The collections obtained are represented by a number of aboriginal animal breeds (cattle, sheep, foxes, etc.) and plant variables (300 specimens belong to 113 species of 25 families.

Animals↗
PubMed2001

[Structure of the gene pool of ethnic groups from the Altai-Sayan region from data on mitochondrial polymorphism].

Using the data on mitochondrial DNA (mtDNA) polymorphism, genetic structures of the four Turkic-speaking ethnic groups of Altai-Sayan highlands, Southern Altaians (Altai-Kizhi), Khakassians, Shorians, and Sojots, were described. Mitochondrial gene pools of the populations examined were characterized by different ratios between Mongoloid (M*, C, D, E, G, A, B, and F) and Caucasoid (H, U, T, J, and K) mtDNA lineages. All the populations studied had a strongly pronounced Mongoloid component, the frequency of which was 88.2% in Sojots, 75.9% in Khakassians, 67.4% in Altaians, and 64.3% in Shorians. Maximum frequency of the Caucasoid component (35.7%) was observed in Shorians. Phylogenetic and statistical analyses of the mtDNA group frequency distribution patterns in the gene pools of the ethnic populations of Altai-Sayan highlands and the adjacent territories showed that the populations of the region fell into three groups. The first group included Khakassians, Tuvinians and Altaians, the second group consisted of Sojots, Buryats, and Mongols, while the third group was composed of Uigurs, Kazakhs, and Kyrgyzes. The isolated position of Shorians among the populations examined can be explained by their different anthropological composition and their presumptive relatedness to Finno-Ugric populations of Siberia.

DNA, Mitochondrial↗
PubMed2004

[Structure of the gene pool of eastern Ukrainians from Y-chromosome haplogroups].

Y chromosomes from representative sample of Eastern Ukrainians (94 individuals) were analyzed for composition and frequencies of haplogroups, defined by 11 biallelic loci located in non-recombining part of the chromosome (SRY1532, YAP, 92R7, DYF155S2, 12f2, Tat, M9, M17, M25, M89, and M56). In the Ukrainian gene, pool six haplogroups were revealed: E, F (including G and I), J, N3, P, and R1a1. These haplogroups were earlier detected in a study of Y-chromosome diversity on the territory of Europe as a whole. The major haplogroup in the Ukrainian gene pool, haplogroup R1a1 (earlier designated HG3), accounted for about 44% of all Y chromosomes in the sample examined. This haplogroup is thought to mark the migration patterns of the early Indo-Europeans and is associated with the distribution of the Kurgan archaeological culture. The second major haplogroup is haplogroup F (21.3%), which is a combination of the lineages differing by the time of appearance. Haplogroup P found with the frequency of 9.6%, represents the genetic contribution of the population originating from the ancient autochthonous population of Europe. Haplogroups J and E (11.7 and 4.2%, respectively) mark the migration patterns of the Middle-Eastern agriculturists during the Neolithic. The presence of the N3 lineage (9.6%) is likely explained by a contribution of the assimilated Finno-Ugric tribes. The data on the composition and frequencies of Y-chromosome haplogroups in the sample studied substantially supplement the existing picture of the male lineage distribution in the Eastern Slav population.

Base Sequence↗
PubMed2006

Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers.

Common bean (Phaseolus vulgaris L.) cultivars are distinguished morphologically, agronomically and ecologically into specific races within each of the two gene pools found for the species (Andean and Mesoamerican). The objective of this study was to describe the race structure of the Mesoamerican gene pool using microsatellite markers. A total of 60 genotypes previously described as pertaining to specific Mesoamerican races as well as two Andean control genotypes were analyzed with 52 markers. A total of 267 bands were generated with an average of 5.1 alleles per marker and 0.297 heterozygosity across all microsatellites. Correspondence analysis identified two major groups equivalent to the Mesoamerica race and a group containing both Durango and Jalisco race genotypes. Two outlying individuals were classified as potentially of the Guatemala race although this race does not have a defined structure and previously classified members of this race were classified with other races. Population structure analysis with K = 1-4 agreed with this classification. The genetic diversity based on Nei's index for the entire set of genotypes was 0.468 while this was highest for the Durango-Jalisco group (0.414), intermediate for race Mesoamerica (0.340) and low for race Guatemala (0.262). Genetic differentiation (G (ST)) between the Mesoamerican races was 0.27 while genetic distance and identity showed race Durango and Jalisco individuals to be closely related with high gene flow (N (m)) both between these two races (1.67) and between races Durango and Mesoamerica (1.58). Observed heterozygosity was low in all the races as would be expected for an inbreeding species. The analysis with microsatellite markers identified subgroups, which agreed well with commercial class divisions, and seed size was the main distinguishing factor between the two major groups identified.

Genes, Plant↗