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A survey of six genetic markers on the populations of Punjab and Rajasthan (India).

190 Punjabis (Hindus and Sikhs) of Chandigarh and 152 Hindus of Jodhpur (Rajasthan) were examined for six genetic markers, four of which (APO C-II, C6, C7 and FXIIIA) were not studied before in Asiatic Indians. For APO C-II and C7 only the common phenotype was found in a total of 229 and 99 subjects, respectively. For the remaining four markers the two samples were pooled since the gene frequency estimates were not significantly different: FXIIIA*2 = 0.205 +/- 0.016; C6*B = 0.366 +/- 0.037; PGM1*2 = 0.247 +/- 0.017; PGD*C = 0.041 +/- 0.008. These data may contribute to evaluate the extent of the Mongoloid genetic admixture into the Caucasoid gene pool of the Punjab and Rajasthan Hindu population.

Apolipoprotein C-II↗

Genetical ESS-models. II. Multi-strategy models and multiple alleles.

The problem of evolutionarily stable strategies (ESS) in sexual populations can be investigated by means of genetical ESS-models which link common sense, phenotypic ESS-models to an underlying genetical system. Thorough results are obtained for multi-strategy models in diploid, panmictic populations on the basis of multi-allelic, one-locus systems. A sexual population will be maintained at a phenotypic ESS if this can possibly be produced by the genotypes currently existing. If there is enough allelic variation, the corresponding gene pool may either be an ESS itself, or belong to an attracting, continuous set of states, which all determine the same evolutionarily stable population. The latter case allows new alleles to enter and spread in the gene pool without disturbing the phenotypic ESS. If a phenotypic ESS cannot be established, ESSs of the genetical model may be found which give rise to stable populations alternatively. Since these depend on the phenotypes determined by the currently existing genotypes, they may be destabilized by the occurrence of new mutations. In this sense, they are less durable than populations maintained at a phenotypic ESS and can be expected to evolve, in the long run, towards a phenotypic ESS.

Alleles↗

Genetic substructure in South African Bantu-speakers: evidence from autosomal DNA and Y-chromosome studies.

The extent of genetic differentiation between seven South African Bantu-speaking groups (Zulu, Xhosa, Tsonga/Shangaan, Southern Sotho, Pedi, Tswana, and Venda) was assessed from coancestry coefficients (F(ST)) estimated from autosomal serogenetic, DNA, and Y-chromosome DNA haplotypes. The overall F(ST) obtained from the autosomal data was 0.002, and that from the Y chromosome data was 0.014. The genetic relationships between groups examined were inferred from their cluster affinities in phylogenetic trees constructed from the genetic distances between them. Both autosomal and Y-chromosome DNA studies reveal that 6 of the 7 South African Bantu-speaking groups cluster according to their linguistic groupings, the exception being the Tsonga, who do not cluster with other Nguni language speakers, but rather with the Venda who live close to them. This suggests that the invading Shangaan-speakers, whose Nguni language was adopted by the Tsonga, did not have a major effect on the Tsonga gene pool, and that gene flow from the Venda into the Tsonga may have been considerable. Genetic distances were found to correlate with geographic distances between the regions where each group's apparent population density is the highest. Linguistic distances were also found to correlate with genetic distances, but linguistic and geographic distances showed no correlation. Together, these results suggest that linguistic and some genetic differentiation took place before the groups (or their forerunners) reached their present-day locations, and that further genetic change occurred after their arrival.

Adult↗

Gene diversity and mode of reproduction in the brooded larvae of the coral Heteroxenia fuscescens.

The soft coral Heteroxenia fuscescens is a common shallow-reef brooding species in the Red Sea. By means of amplified fragment length polymorphism markers, we studied modes of reproduction of planulae (sexual vs. vegetative) and levels of gene diversity of a population residing in the northern Gulf of Eilat, Red Sea. Eighty-nine larvae were collected from 9 mother colonies at 3 locations over a distance of 5 km. Amplifications revealed 221 putative loci, of which 81.4% were polymorphic; gene diversity was 0.29, allowing good identification of individual genotypes. No 2 identical DNA samples were present, so no asexual reproduction of planulae was indicated. The sampled planulae did not exhibit any genetic structure characteristic to a specific location, indicating one large gene pool and extensive gene flow among H. fuscescens specimens inhabiting the northern Gulf of Eilat.

Animals↗

Genetic diversity of three lgt loci for biosynthesis of lipooligosaccharide (LOS) in Neisseria species.

Lipooligosaccharide (LOS) is a major virulence factor of the pathogenic Neisseria. Nine lgt genes at three chromosomal loci (lgt-1, 2, 3) encoding the glycosyltransferases responsible for the biosynthesis of LOS oligosaccharide chains were examined in 26 Neisseria meningitidis, 51 Neisseria gonorrhoeae and 18 commensal Neisseria strains. DNA hybridization, PCR and nucleotide sequence data were compared to previously reported lgt genes. Analysis of the genetic organization of the lgt loci revealed that in N. meningitidis, the lgt-1 and lgt-3 loci were hypervariable genomic regions, whereas the lgt-2 locus was conserved. In N. gonorrhoeae, no variability in the composition or organization of the three lgt loci was observed. lgt genes were detected only in some commensal Neisseria species. The genetic organization of the lgt-1 locus was classified into eight types and the lgt-3 locus was classified into four types. Two types of arrangement at lgt-1 (II and IV) and one type of arrangement at lgt-3 (IV) were novel genetic organizations reported in this study. Based on the three lgt loci, 10 LOS genotypes of N. meningitidis were distinguished. Phylogenetic analysis revealed a gene cluster, lgtH, which separated from the homologous genes lgtB and lgtE. The lgtH and lgtE genes were mutually exclusive and were located at the same position in lgt-1. The data demonstrated that pathogenic and commensal Neisseria share a common lgt gene pool and horizontal gene transfer appears to contribute to the genetic diversity of the lgt loci in Neisseria.

Genes, Bacterial↗

Nuclear microsatellites reveal contrasting patterns of genetic structure between western and southeastern European populations of the common ash (Fraxinus excelsior L.).

To determine extant patterns of population genetic structure in common ash and gain insight into postglacial recolonization processes, we applied multilocus-based Bayesian approaches to data from 36 European populations genotyped at five nuclear microsatellite loci. We identified two contrasting patterns in terms of population genetic structure: (1) a large area from the British Isles to Lithuania throughout central Europe constituted effectively a single deme, whereas (2) strong genetic differentiation occurred over short distances in Sweden and southeastern Europe. Concomitant geographical variation was observed in estimates of allelic richness and genetic diversity, which were lowest in populations from southeastern Europe, that is, in regions close to putative ice age refuges, but high in western and central Europe, that is, in more recently recolonized areas. We suggest that in southeastern Europe, restricted postglacial gene flow caused by a rapid expansion of refuge populations in a mountainous topography is responsible for the observed strong genetic structure. In contrast, admixture of previously differentiated gene pools and high gene flow at the onset of postglacial recolonization of western and central Europe would have homogenized the genetic structure and raised the levels of genetic diversity above values in the refuges.

Bayes Theorem↗

Acquisition and rearrangement of sequence motifs in the evolution of bacteriophage tail fibres.

Molecular analysis reveals a surprising sharing of short gene segments among a variety of large double-stranded DNA bacteriophages of enteric bacteria. Ancestral genomes from otherwise unrelated phages, including lambda, Mu, P1, P2 and T4, must have exchanged parts of their tail-fibre genes. Individual genes appear as mosaics with parts derived from a common gene pool. Therefore, horizontal gene transfer emerges as a major factor in the evolution of a specific part of phage genomes. Current concepts of homologous recombination cannot account for the formation of such chimeric genes and the recombinational mechanisms responsible are not known. However, recombination sites for DNA invertases and recombination site-like sequences are present at the boundaries of gene segments conferring the specificity for the host receptor. This, together with the properties of the DNA inversion mechanism, suggests that these site-specific recombination enzymes could be responsible for the exchange of host-range determinants.

Base Sequence↗

Comparing genomes of Helicobacter pylori strains from the high-altitude desert of Ladakh, India.

The genomic diversity of Helicobacter pylori from the vast Indian subcontinent is largely unknown. We compared the genomes of 10 H. pylori strains from Ladakh, North India. Molecular analysis was carried out to identify rearrangements within and outside the cag pathogenicity island (cag PAI) and DNA sequence divergence in candidate genes. Analyses of virulence genes (such as the cag PAI as a whole, cagA, vacA, iceA, oipA, babB, and the plasticity cluster) revealed that H. pylori strains from Ladakh are genetically distinct and possibly less virulent than the isolates from East Asian countries, such as China and Japan. Phylogenetic analyses based on the cagA-glr motifs, enterobacterial repetitive intergenic consensus patterns, repetitive extragenic palindromic signatures, the glmM gene mutations, and several genomic markers representing fluorescent amplified fragment length polymorphisms revealed that Ladakhi strains share features of the Indo-European, as well as the East Asian, gene pools. However, the contribution of genetic features from the Indo-European gene pool was more prominent.

Altitude↗

High level of genetic diversity among spelt germplasm revealed by microsatellite markers.

The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 - proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 +/- 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs.

Alleles↗

Comparison of restriction fragment length polymorphisms of proto-oncogenes in native Hawaiians and other ethnic groups in Hawaii.

The relative genetic diversity of selected proto-oncogenes in the native Hawaiian gene pool was examined by comparing the restriction fragment length polymorphisms of these genes in a group of 23 individuals with at least part Hawaiian ancestry, and in 20 individuals from other ethnic groups. Twenty-one combinations of the proto-oncogenes, c-fms, c-myc, L-myc, c-Ha-ras, and c-Ki-ras, tested with 1 or more of the restriction enzymes Bam HI, Eco RI, Hind III, Pst I, Pvu I and Kpn I were examined. Sixteen of these did not exhibit RFLPs in Hawaiians or in other ethnic groups. Four of the combinations exhibiting RFLPs in native Hawaiians exhibited similar-sized restriction fragments in the other ethnic groups. Only in the case of c-myc digested with Pst I were 5 individuals of Hawaiian ancestry found to have an RFLP which has not been detected in other ethnic groups. These 5 cases exhibited a 13-kb c-myc fragment in addition to the 5.5-kb fragment found in most Hawaiians and always present in other ethnic groups. The presence in Hawaiians of most RFLPs found in other ethnic groups indicates that the genetic diversity of proto-oncogenes in the gene pool of native Hawaiians is not substantially less than that of other ethnic groups.

Blotting, Southern↗

Alien introgression in rice.

Rice (Oryza sativa L.) productivity is affected by several biotic and abiotic stresses. The genetic variability for some of these stresses is limited in the cultivated rice germplasm. Moreover, changes in insect biotypes and disease races are a continuing threat to increased rice production. There is thus an urgent need to broaden the rice gene pool by introgressing genes for such traits from diverse sources. The wild species of Oryza representing AA, BB, CC, BBCC, CCDD, EE, FF, GG and HHJJ genomes are an important reservoir of useful genes. However, low crossability and limited recombination between chromosomes of cultivated and wild species limit the transfer of such genes. AT IRRI, a series of hybrids and monosomic alien addition lines have been produced through embryo rescue following hybridization between rice and several distantly related species. Cytoplasmic male sterility and genes for resistance to grassy stunt virus and bacterial blight have been transferred from A genome wild species into rice. Similarly, genes for resistance to brown planthopper, bacterial blight and blast have also been introgressed across crossability barriers from distanly related species into rice. Some of the introgressed genes have been mapped via linkage to molecular markers. One of the genes Xa-21 introgressed from O. longistaminata has been cloned and physically mapped on chromosome 11 of rice using BAC library and flourescence in-situ hybridization. RFLP analysis revealed introgression from 11 of the 12 chromosomes of C genome species into rice. Introgression has also been obtained from other distant genomes (EE, FF, GG) into rice and in majority of the cases one or two RFLP markers were introgressed. Reciprocal replacement of RFLP alleles of wild species with the alleles of O. sativa indicates alien gene transfer through crossing over. The rapid recovery of recurrent phenotypes in BC2 and BC3 generations from wide crosses is an indication of limited recombination. Further cytogenetic and molecular investigations are required to determine precisely the mechanism of introgression of small chromosome segments from distant genomes in the face of limited homoeologous chromosome pairing. Future research should focus on enhancing recombination between homoeologous chromosomes. Introgression of QTL from wild species should be attempted to increase the yield potential of rice.

Animals↗

[Genetic differentiation between breeds of horses by polymorphic blood protein loci].

The estimation of genetic differentiation between 27 horses breeds originated in USSR, based on serum proteins polymorphism (loci Tf, Al, Es) is shown. Genetical variability among aborigine breeds is higher then among cultural ones. The erosion of gene pool of Przewalski's Horse is explained by special history of this population and a few horses in analyzing group. Genetic distances reflect the directions and intensity of breeding. High genetical distances between Przewalski's Horse, Shetland Pony and other horses obtained could be explained by overcoming the "bottle neck" of selections in breeding process. Results of investigation shown that 9 aborigine breeds of USSR are clustered in a special group, differed from foreign horse breeds, because their gene pool was quite unique.

Animals↗

Structural and functional diversity of microbial communities from a lake sediment contaminated with trenbolone, an endocrine-disrupting chemical.

Effects of trenbolone (TBOH), a hormone used in cattle production, on the structure and function of microbial communities in a fresh water sediment from a lake in Southern Germany were studied in a microcosm experiment. The microbial community structure and the total gene pool of the sediment, assessed by 16S rRNA/rDNA and RAPD fingerprint analysis, respectively, were not significantly affected by TBOH. In contrast, the N-acetyl-glucosaminidase activity was almost 50% lower in TBOH treated samples (P<0.05). Also, the substrate utilization potential, measured using the BIOLOG system, was reduced after TBOH treatment. Interestingly, this potential did not recover at the end of the experiment, i.e. 19 days after the addition of the chemical. Repeated application of TBOH did not lead to an additional reduction in the substrate utilization potential. Overall results indicate that microbial community function was more sensitive to TBOH treatment than the community structure and the total gene pool.

Biodegradation, Environmental↗

[Polymorphism of hypervariable segment I of mitochondrial DNA in three ethnic groups of the Volga-Ural region].

A population genetic study of the polymorphism in the first hypervariable segment (HVSI) of mitochondrial DNA control region was carried out for three ethnic populations of the Volga-Ural region, Bashkirs, Russians, and Komi-Permyaks. This analysis showed that most of the mtDNA HVSI haplotypes detected in the populations of Bashkirs, Russians and Komi-Permyaks contained the combinations of nucleotide substitutions detected earlier in Asian, European, and Finno-Ugric populations. These findings are consistent with historical, anthropological, and ethnographical data suggesting the presence of European and Mongoloid components of different geographical descent in the gene pool of the contemporary population of the Volga-Ural region. The data on the genetic structure and the phylogenetic relationships between populations of the Volga-Ural region based on modern molecular genetic methods of mitochondrial genome investigation would be a substantial addition to the already existing information for some other regions of Europe and Asia. These data would provide more complete examination of the development of interethnic diversity of mitochondrial gene pools of contemporary ethnic populations with the purpose of reconstructing the genetic demographic processes that accompanied peopling of the Middle Ural and Volga region.

DNA, Mitochondrial↗

Large intraspecific haplotype variability at the Rph7 locus results from rapid and recent divergence in the barley genome.

To study genome evolution and diversity in barley (Hordeum vulgare), we have sequenced and compared more than 300 kb of sequence spanning the Rph7 leaf rust disease resistance gene in two barley cultivars. Colinearity was restricted to five genic and two intergenic regions representing <35% of the two sequences. In each interval separating the seven conserved regions, the number and type of repetitive elements were completely different between the two homologous sequences, and a single gene was absent in one cultivar. In both cultivars, the nonconserved regions consisted of approximately 53% repetitive sequences mainly represented by long-terminal repeat retrotransposons that have inserted <1 million years ago. PCR-based analysis of intergenic regions at the Rph7 locus and at three other independent loci in 41 H. vulgare lines indicated large haplotype variability in the cultivated barley gene pool. Together, our data indicate rapid and recent divergence at homologous loci in the genome of H. vulgare, possibly providing the molecular mechanism for the generation of high diversity in the barley gene pool. Finally, comparative analysis of the gene composition in barley, wheat (Triticum aestivum), rice (Oryza sativa), and sorghum (Sorghum bicolor) suggested massive gene movements at the Rph7 locus in the Triticeae lineage.

Conserved Sequence↗

Protease inhibitor subtypes in some population groups from Israel.

Results of protease inhibitor (PI) subtyping on polyacrylamide gel isoelectrofocusing of 599 Israeli non-Jews and 1,393 Israeli Jews are recorded. A discriminant analysis (DS) was performed on frequency data of the 5 PI alleles (M1, M2, M3, S and Z) with data of Europeans, Israeli non-Jews and Israeli Jews. A higher percentage of correct classification was obtained when Jews were treated as a separate population group rather than when distributed in their areas of origin. This suggests a greater resemblance, in the PI system, of the studied Jewish groups to each other than of the European Jews to Europeans and of the studied mediterranean Jews to Middle Eastern non-Jews. A cluster analysis disclosed distance relationships in a similar direction. PI allele distribution, in the studied Jewish samples, has the following characteristics: Jews share with Middle Eastern non-Jews an absence of PIZ, which is present in Europeans. Mediterranean Jews have higher frequencies than Ashkenazi Jews, of PIS alleles, which are absent in Middle Eastern non-Jews. European Jews are closer to the Europeans than Middle Eastern Jews in their PIM allele frequencies. An original common gene pool of Jews with Middle Eastern non-Jews is postulated, of which the Sephardic (Spanish) and Middle Eastern Jews differ, now, in having PIS, and European Jews differ in having slightly lower PIM3 and PIM2 and higher PIM1 frequencies. A possibility of admixture and selection, affecting different alleles in different Jewish communities at different times, is suggested to have contributed to the present-day deviations from the supposed original gene pool.

Gene Frequency↗

[Hereditary biochemical diversity in the processes of evolution and individual development].

Results of long-term studies of Russian authors on regularities of expression of hereditary biochemical diversity in evolution and development are reviewed. Primary attention is given to the concepts of genetic monomorphism and genetic stability of population systems, principles of adaptive gene pool structure and optimum genetic diversity, historical and conservation genetics, the concept of the multilevel gene expression, and temporal regulation of ontogenetic functioning of gene clusters coding for enzymes. A universal genetic approach to the problems of evolution and ontogeny is proposed. A population is regarded as a superorganism whose key property is the hierarchic structure of its genetic stability from the stability of monomorphic genes via stability of polymorphic gene frequencies in a multilevel population system to the stability of the total amount of gene diversity in this system. A multicellular organism is also regarded as a developing hierarchical system of populations of cells and genes interacting in a nonrandom fashion. This maintains stability of metabolic processes and is expressed in consistent correlations between monogenic and polygenic morphophysiological characters. Properties of both organisms are determined by the adaptive heterozygosity optimum, the disturbance of which has negative consequences for both individuals and populations. On the basis of these results and the concept on the common nature of evolutionary and ontogenetic processes, the following conclusions are drawn: genetic processes can be either favorable or adverse for developing organisms and populations; the state of genetic processes can be determined by analysis of gene diversity and their deviations from the optimum, taking into account the adaptive gene pool structure; and negative hazardous consequences of extreme external effects at both the individual and population levels can be detected by methods of biochemical genetics in specially planned monitoring programs. Knowledge of normal processes of realization of hereditary information in evolution of populations and in ontogeny opens up new perspectives in detection of unfavorable processes and their correction. This approach proved promising both for preventive and clinical medicine and for exploitation and artificial reproduction of biological resources.

Adaptation, Physiological↗

[Genetic analysis of the South Altaian population of the Mendur-Sokkon village, Altai Republic].

This study was a continuation of complex research on the gene pool of indigenous Siberian populations conducted at the Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences. In the population of South Altaians from the Mendur-Sokkon village, Ust'-Kanskii raion, Altai Republic, polymorphism for the following genetic markers was studied: blood groups ABO, MNSs, Rhesus, Kell, Duffy, and P; erythrocyte acid phosphatase (AcP); phosphoglucomutase 1 (PGM1); haptoglobin (Hp); and transferrin (Tf). The genetic position of South Altaians relative to the populations of the European part of Russia, Siberia, and the Urals was estimated. It was demonstrated that the gene pool of the South Altaian population of Mendur-Sokkon possessed both Caucasoid and Mongoloid genetic characteristics, with the latter prevailing. Genetically, this population is most closely related to Mongols and Nentsis. The genetic distance between South and North Altaians was large; this agreed with earlier genetic data and confirmed anthropological and ethnographic evidence indicating that these two groups had different backgrounds and were at different stages of ethnogenesis.

Adolescent↗