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PubMed1998

Different genetic components in the Ethiopian population, identified by mtDNA and Y-chromosome polymorphisms.

Seventy-seven Ethiopians were investigated for mtDNA and Y chromosome-specific variations, in order to (1) define the different maternal and paternal components of the Ethiopian gene pool, (2) infer the origins of these maternal and paternal lineages and estimate their relative contributions, and (3) obtain information about ancient populations living in Ethiopia. The mtDNA was studied for the RFLPs relative to the six classical enzymes (HpaI, BamHI, HaeII, MspI, AvaII, and HincII) that identify the African haplogroup L and the Caucasoid haplogroups I and T. The sample was also examined at restriction sites that define the other Caucasoid haplogroups (H, U, V, W, X, J, and K) and for the simultaneous presence of the DdeI10394 and AluI10397 sites, which defines the Asian haplogroup M. Four polymorphic systems were examined on the Y chromosome: the TaqI/12f2 and the 49a,f RFLPs, the Y Alu polymorphic element (DYS287), and the sY81-A/G (DYS271) polymorphism. For comparison, the last two Y polymorphisms were also examined in 87 Senegalese previously classified for the two TaqI RFLPs. Results from these markers led to the hypothesis that the Ethiopian population (1) experienced Caucasoid gene flow mainly through males, (2) contains African components ascribable to Bantu migrations and to an in situ differentiation process from an ancestral African gene pool, and (3) exhibits some Y-chromosome affinities with the Tsumkwe San (a very ancient African group). Our finding of a high (20%) frequency of the "Asian" DdeI10394AluI10397 (++) mtDNA haplotype in Ethiopia is discussed in terms of the "out of Africa" model.

Black People↗
PubMed2004

[Restriction polymorphism of mitochondrial DNA in Koreans and Mongolians].

Using the data on mitochondrial DNA (mtDNA) restriction polymorphism, the gene pools of Koreans (N = 164) and Mongolians (N = 48) were characterized. It was demonstrated that the gene pools were represented by the common set of mtDNA haplogroups of East Asian origin (M*, M7, M8a, M10, C, D4, G*, G2, A, B*, B5, F1, and N*). In addition to this set, mtDNA haplogroups D5 and Y were identified in Koreans while Mongolians possessed haplogroup Z. Only in Mongolians, a European component with the frequency of 10.4% and represented by the mtDNA types belonging to haplogroups K, U4, and N1, was identified. Phylogenetic and statistical analyses of the data on mtDNA variation in the populations of South Siberia, Central, and East Asia suggested the existence of interpopulation differentiation within these regions, the main role in which was played by the geographical and linguistic factors. Analysis of the pairwise F(ST) distances demonstrated close genetic similarity of Koreans to Northern Chinese, which in turn, were clearly different from Southern Chinese populations. Mongolians occupied an intermediate position between the ethnic groups of South Siberia and Central/East Asia.

DNA, Mitochondrial↗
PubMed1994

The cohort mortality perspective: the emperor's new clothes of epidemiology, an illustration using cancer mortality.

Cohort analysis of cancer mortality in industrialized countries has led to the generally accepted conclusion that these populations have been exposed to increasing levels of carcinogenic influences. Age-specific cancer mortality rates in the United States from 1962 to 1988 were portrayed in both cross-sectional and cohort manners. Both representations are consistent with the Strehler-Mildvan modification of the Gompertz relationship between aging and mortality. These observations suggest that environmental cohort effects are not responsible for rising cancer mortality. The cohort mortality perspective in epidemiology is inherently biased due to the effects of competing mortality. Competing mortality, like environmental exposures, is applied in a cross-sectional manner across multiple birth cohorts. Competing mortality produces selective mortality, or differential survival, within a birth cohort. Differential survival, an underappreciated form of selection bias, alters the gene pool of surviving birth cohort members. Since cross-sectional competing mortality risks vary with age, the gene pool of different birth cohorts is not uniformly altered. Consequently, differences between birth cohorts in age-specific mortality rates with respect to a particular disorder, for example, cancer, do not specifically imply differences in environmental exposures.

Adult↗
PubMed2006

[DNA-technologies application for early detection of caries predisposition].

In the paper the possible use of modern DNA-technologies for estimation of gene pool, dental hard tissue resistance to caries prognosis, hereditary predisposition to the main oral diseases diagnosis are presented. Application potentialities of DNA-markers for multiple testing in population are identified. Today very little information is available concerning Russia gene pool characteristics in genome polymorphism, DNA-markers-allelic gene variants, related to the caries predisposition. These characteristics are needed to solve the problems concerning dental diseases prophylaxis and treatment.

Adolescent↗
PubMed1999

[Restriction polymorphism of the major non-decoding region of mitochondrial DNA in human populations from the Volga-Ural region].

The restriction fragment length polymorphism (RFLP) of the major noncoding region of mitochondrial DNA (mtDNA) was studied in the Bashkir (N = 217), Tatar (N = 57), Chuvash (N = 44), Mari (N = 52), Mordovian (N = 55), Udmurt (N = 62), and Komi (N = 45) populations. Of seven polymorphic AvaII, BamHI, EcoRV, KpnI, and RsaI restriction sites, five were found in Bashkirs and Tatars, and four were found in each of the other populations. In total, 13 mitotypes were detected, and only three of them were common to all populations from the Volga-Ural region. The parameters of gene diversity were calculated with respect to the polymorphic sites and mitotypes. Comparison with published data revealed both Mongoloid and Caucasoid components in the gene pool of the modern populations from the Volga-Ural region. The Mongoloid component was prevalent in the mitochondrial gene pool, which is consistent with historical, anthropological, and ethnographic data.

DNA, Mitochondrial↗
PubMed1995

[Intraspecific genetic diversity: monitoring and principles of conservation].

Genetic differentiation of a species, estimated on average according to the aggregate of allozyme loci, corresponds to a selectively neutral process. Such evolution is traditionally regarded as Markov's chain, in which the genetic dynamics of a population cannot be predicted for more than one generation. According to the concept of population systems, however, intraspecific differentiation can be interpreted as a process with memory, which retains information about the genetic structure of the ancestral population. This memory is maintained due to the organizing effect of gene immigration whose intensity is the higher, the lower the effective size of the local population. The ratio between intra- and inter-population components of gene diversity is maintained at a stable (optimal) level. Consequently, it can be regarded as the basic "reference point" in genetic monitoring of subdivided populations that have evolved under anthropogenic pressure. Such influences, altering established systemic links, distort the balance between differentiation and integration of the species gene pool and lead to adverse effects. Depending on the predominance of the inter- or intra-population component of gene diversity, these influences may be equivalent to outbreeding with an increased segregational load or to inbreeding, respectively. In the first case, the genetic process is adaptive, and, provided the negative influence is terminated in due time, it is possible to restore the genetic structure and normalize reproduction of gene pools in populations. In the second case, the genetic process is maladaptive and leads to degradation of populations. If one knows principles of the systemic organization of a species, it is possible to develop an approach to solving the problem of conservation of biological diversity by organizing non-exhaustive wildlife management.

Adaptation, Biological↗
PubMed2001

Genetic diversity and introgression in the Scottish wildcat.

This paper describes a genetic analysis of wild-living cats in Scotland. Samples from 230 wild-living Scottish cats (including 13 museum skins) and 74 house cats from England and Scotland were surveyed for nine microsatellite loci. Pelage characteristics of the wild-living cats were recorded, and the cats were then grouped into five separate categories depending on the degree to which they conformed to the characteristics attributed to Felis silvestris Schreber, 1775. Allele frequency differences between the morphological groups are greater than those among the three house cat samples. Analysis of genetic distances suggests that more of the differences between individuals can be explained by pelage than geographical proximity, and that pelage and geographical location are not confounded. Ordination of the genetic distances suggests two main groups of wild-living cats, with intermediates, and one group is genetically very similar to the house cats, while the other group contains all cats taxonomically identified as wildcat based on morphology. A genetic mixture analysis gives similar results to the ordination, but also suggests that the genotypes of a substantial number of cats in the wildcat group are drawn from a gene pool with genotypes in approximately equilibrium proportions. We argue that this is evidence that these cats do not have very recent domestic ancestry. However, from the morphological data it is highly likely that this gene pool also contains a contribution from earlier introgression of domestic cat genes.

Animals↗
PubMed2003

Biochemical genetic variability in brown hares (Lepus europaeus) from Greece.

Allozyme variability of 91 brown hares (Lepus europaeus) from seven regions in Greece was compared to existing data of Bulgarian populations to test the hypothesis of the occurrence ofspecific alleles in Greece, likely stemming from an isolated Late Pleistocene refugial population in the southern Balkans. This hypothesis is particularly suggested by some subfossil Late Pleistocene hare remains in Greece and the reported high mtDNA diversity in Greek hares. Allozymic diversity could be higher in Greek hares than in hares from neighboring regions as a result of the accumulation of variants in a long-lasting Pleistocene refugium. Conversely, Greek hares could exhibit reduced genetic diversity because of long-lasting low effective population sizes during the Late Glacial Maximum and a lower chance of postglacial gene flow from other populations into this rather marginal part in the southern Balkans. Horizontal starch gel electrophoresis of proteins from 35 loci revealed three alleles (Es-1(-162), Pep-2(114), Mpi(88)) at low frequencies, which were not found in Bulgarian or any other brown hare population. In contrast, some alleles from the populations from Bulgaria and other regions of Europe were absent in the Greek samples. Population genetic statistics indicated only a slight tendency of increased gene pool diversity in Greek hares, little substructuring in Greek and Bulgarian populations, respectively, as well as an only slightly lower level of gene flow between the two neighboring regions, as compared to the gene flow within each region. The results conform to the hypothesis of a Late Pleistocene refugial population in the southern Balkans, with some few specific nuclear gene pool characteristics, but little effect on the overall genetic differentiation between Greek and Bulgarian hares.

Alleles↗
PubMed2006

Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts.

Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic machinery during infection. To study the prevalence and evolutionary dynamics of this phenomenon, 33 cultured cyanophages of known family and host range and viral DNA from field samples were screened for the presence of two core photosystem reaction center genes, psbA and psbD. Combining this expanded dataset with published data for nine other cyanophages, we found that 88% of the phage genomes contain psbA, and 50% contain both psbA and psbD. The psbA gene was found in all myoviruses and Prochlorococcus podoviruses, but could not be amplified from Prochlorococcus siphoviruses or Synechococcus podoviruses. Nearly all of the phages that encoded both psbA and psbD had broad host ranges. We speculate that the presence or absence of psbA in a phage genome may be determined by the length of the latent period of infection. Whether it also carries psbD may reflect constraints on coupling of viral- and host-encoded PsbA-PsbD in the photosynthetic reaction center across divergent hosts. Phylogenetic clustering patterns of these genes from cultured phages suggest that whole genes have been transferred from host to phage in a discrete number of events over the course of evolution (four for psbA, and two for psbD), followed by horizontal and vertical transfer between cyanophages. Clustering patterns of psbA and psbD from Synechococcus cells were inconsistent with other molecular phylogenetic markers, suggesting genetic exchanges involving Synechococcus lineages. Signatures of intragenic recombination, detected within the cyanophage gene pool as well as between hosts and phages in both directions, support this hypothesis. The analysis of cyanophage psbA and psbD genes from field populations revealed significant sequence diversity, much of which is represented in our cultured isolates. Collectively, these findings show that photosynthesis genes are common in cyanophages and that significant genetic exchanges occur from host to phage, phage to host, and within the phage gene pool. This generates genetic diversity among the phage, which serves as a reservoir for their hosts, and in turn influences photosystem evolution.

Base Composition↗
PubMed2001

Mosaic genes and mosaic chromosomes: intra- and interspecies genomic variation of Streptococcus pneumoniae.

Streptococcus pneumoniae remains a major causative agent of serious human diseases. The worldwide increase of antibiotic resistant strains revealed the importance of horizontal gene transfer in this pathogen, a scenario that results in the modulation of the species-specific gene pool. We investigated genomic variation in 20 S. pneumoniae isolates representing major antibiotic-resistant clones and 10 different capsular serotypes. Variation was scored as decreased hybridization signals visualized on a high-density oligonucleotide array representing 1,968 genes of the type 4 reference strain KNR.7/87. Up to 10% of the genes appeared altered between individual isolates and the reference strain; variability within clones was below 2.1%. Ten gene clusters covering 160 kb account for half of the variable genes. Most of them are associated with transposases and are assumed to be part of a flexible gene pool within the bacterial population; other variable loci include mosaic genes encoding antibiotic resistance determinants and gene clusters related to bacteriocin production. Genomic comparison between S. pneumoniae and commensal Streptococcus mitis and Streptococcus oralis strains indicates distinct antigenic profiles and suggests a smooth transition between these species, supporting the validity of the microarray system as an epidemiological and diagnostic tool.

Alleles↗
PubMed1999

Deep common ancestry of indian and western-Eurasian mitochondrial DNA lineages.

About a fifth of the human gene pool belongs largely either to Indo-European or Dravidic speaking people inhabiting the Indian peninsula. The 'Caucasoid share' in their gene pool is thought to be related predominantly to the Indo-European speakers. A commonly held hypothesis, albeit not the only one, suggests a massive Indo-Aryan invasion to India some 4,000 years ago [1]. Recent limited analysis of maternally inherited mitochondrial DNA (mtDNA) of Indian populations has been interpreted as supporting this concept [2] [3]. Here, this interpretation is questioned. We found an extensive deep late Pleistocene genetic link between contemporary Europeans and Indians, provided by the mtDNA haplogroup U, which encompasses roughly a fifth of mtDNA lineages of both populations. Our estimate for this split is close to the suggested time for the peopling of Asia and the first expansion of anatomically modern humans in Eurasia [4] [5] [6] [7] [8] and likely pre-dates their spread to Europe. Only a small fraction of the 'Caucasoid-specific' mtDNA lineages found in Indian populations can be ascribed to a relatively recent admixture.

Animals↗
PubMed1981

Familial dwarfism with high IR-GH: report of two affected sibs with genetic and epidemiologic considerations.

Two sibs with high serum IR-GH dwarfism, born to first-cousin parents are described. Genetic analysis based upon 25 reported informative kindreds indicates that the condition has an autosomal recessive pattern of inheritance. Population evaluation and epidemiology of the affected subjects suggest that mutation rates of the gene determining the disease in non-Jewish populations could be as rare as 3.2 x 10(-5). However, its prevalence must be exceptionally high among endogamous Oriental Jewish groups derived from a common gene pool in historical times.

Adolescent↗
PubMed2002

[Molecular markers and its clone for salt tolerance gene in wheat].

Genetic and RAPD analysis were studied among [4] individuals in F2 segregated population originating from a cross between wheat cultivator Nongda 85021 (female parent, salt sensitive) and Chadian Red (male parent, salt tolerant). For genetic analysis and chi-square test gave a good fit of 1:2:1 ratio showing that one major gene was controlling the salt tolerant character in Chadian Red. DNA of F2 population was extracted to develop tolerant and sensitive gene pools, respectively, based the BSA (Bulked Segregate Analysis). By RAPD (Randomly Amplified Polymorphic DNAs), 520 random primers were used to amplify the two types of gene pools. Only primer OPZ09 was found to be polymorphic with a fragment of 590 bp in the two parents, F1 and F2 populations. So, the specific fragment OPZ09-590 was, a RAPD marker linked to salt tolerance gene in Chadian Red. By the software JOINMAP (Version 1.4), the recombination was 5.674% and the linking distance was 6.557 cM. OPZ09-590 was extracted from the agarose and mixed with pUCm-T vector, then the vector was transferred into JM109. The clone was determined 591 bp after being sequenced. It indicated that the RAPD marker of salt tolerance gene in Chadian Red was OPZ09-591.

Base Sequence↗
PubMed1991

Population studies in northern Sweden. XVII. Estimates of Finnish and Saamish influence.

The North-Swedish population is a mixture of Finnish, Saamish and Central-Swedish ethnic groups. We have studied the Finnish and Saamish admixture by means of genetic markers in 23 North-Swedish subpopulations. The Finnish influence was estimated using the transferrin genes B0-1, DCHI and C3 and the enzyme gene SOD1*2, and markers for Saamish influence were the blood group gene ABO*A2, the serum group gene GC*1F and the enzyme gene 6PGD*C. In the subpopulations the Finnish influence (admixture) varied between 0 and 84% and the Saamish influence between 0 and 34%. The Saamish influence was strongest in the western and northern parts of the area. In the northern part of the area, between 1/4 and 1/3 of the gene pool of the present-day population may be Saamish in origin. The Finnish influence was strongest in the northern and northeastern parts of the area. In the subpopulations along the Finnish border, between 60 and 80% of the gene pool may be Finnish in origin. Significant correlations were found between the Saamish marker genes and between the Finnish marker genes. Due to geographical overlapping of Finnish and Saamish influence, significant correlations were also found between Finnish and Saamish marker genes. The geographical pictures of Saamish and Finnish influence in northern Sweden showed a fair agreement with the expectations derived from historical knowledge. Although a substantial part of the genetic heterogeneity of the North-Swedish population is ethnic in origin, it is obvious that founder effect and genetic drift also have played an important role.

Ethnicity↗
PubMed2004

[Intraspecific structure and reproductive relationships between Elymus mutabilis and E. transbaicalensis (Poaceae) in southern Siberia from the viewpoint of taxonomical genetics].

The relationships between StH-genomic species Elymus mutabilis (Drob.) Tzvel. and E. transbaicalensis (Nevski) Tzvel. were examined using biosystematic and biochemical (SDS electrophoresis of endosperm proteins) methods. The results showed the following. (1) There is interspecific morphological discreteness that permits assigning most individuals from the wild to a definite species. However, self-fertile intermediate individuals of introgressive origin were found. (2) Both taxa exhibited marked specificity of electrophoretic characteristics of endosperm proteins. (3) The species form two separate recombination gene pools (RGPs). Thus, E. mutabilis and E. transbaicalensis should be regarded as two distinct species. Nevertheless, there is some genetic exchange and unidirectional gene flow between the RGPs, especially in secondary (successive) habitats where mixed populations are observed. Two RGPs form the single introgressive gene pool (IGP), which includes other StH-genomic species of Northern Eurasia.

Electrophoresis, Polyacrylamide Gel↗
PubMed1997

Collaborative study to assess the suitability of a proposed working reagent for human parvovirus B19 DNA detection in plasma pools by gene amplification techniques. B19 Collaborative Study Group.

BACKGROUND AND OBJECTIVES: A collaborative study was done to examine the sensitivity and specificity of assays for the detection of human parvovirus B19 DNA in plasma pools by PCR techniques and to establish a working reagent for B19 DNA testing of plasma pools. MATERIALS AND METHODS: Duplicate samples consisting of a tenfold dilution series of a positive cryosupernatant diluted in B19 DNA-negative cryosupernatant were sent to 17 laboratories. RESULTS: The sensitivity of the assays varied: 2 laboratories were able to detect the 10(-7) dilution while 1 laboratory failed to detect B19 DNA in any samples. In addition, 5 laboratories obtained false-positive results. CONCLUSIONS: In general, laboratories using assays optimised for rapid detection of B19 DNA in serum samples did not perform well, indicating that such rapid methods are not adequate for examination of plasma pools. The 10(-6) dilution was detected by approximately half the laboratories and could be used as the working reagent.

DNA, Viral↗
PubMed2003

Development and characterization of a pooled Haemophilus influenzae genomic library for the evaluation of gene expression changes associated with mucosal biofilm formation in otitis media.

UNLABELLED: Haemophilus influenzae is one of the most important respiratory pathogens of man. It has been etiologically associated with otitis media, otorrhea, and chronic obstructive pulmonary disease. Identification of new genomic elements will provide novel targets to fight chronic infections caused by this organism. OBJECTIVE: The new paradigm that chronic infections are caused by bacterial biofilms prompted us to study the relationship between bacterial pathogenicity, biofilm formation and bacterial communal cooperation. To do this, it is essential to determine the virulence gene sets that are involved in the above processes and whether they are present in every bacterial cell or distributed in a "communal gene-pool", the distributed genome hypothesis (DGH). We designed, constructed and characterized a highly redundant genomic DNA library comprised of the genomes of ten low passage clinical isolates of H. influenzae carrying large numbers of genes that are not present in the laboratory strains of H. influenzae. METHODS: Genomic DNA fragments of the ten clinical strains were hydro-dynamically sheared to produce a mean fragment size of 1.5-2.5 kb. The ten sheared DNAs were than pooled and used in the construction of a genomic library with 76800 clones. RESULTS: Our restriction endonuclease and sequence analyses of 800 clones demonstrate that 75% of the clones carry an insert larger than 0.5 kb. The library has an approximately 1.5 kb average insert size, and therefore, better than 4.5x redundancy for each of the genomes of the ten clinical isolates. Our sequencing effort ( approximately 1 million nucleotides to date) reveals that a high percentage of genes (75 clones, 11% of the 686 sequenced clones) present in this library are not represented in the genome of the reference strain H. influenzae Rd. CONCLUSIONS: The library, based on the above results, has a better than 4.5x coverage for each of the ten constituent genomes. On the basis of our preliminary sequencing data ( approximately 1 million nucleotides) the library lacks of highly repeated sequences, therefore, the expected genome coverage (4.5x) is not degraded. Using the prevalence of non-Rd like sequences (11%) detected during characterization of the genomic library, we estimated that the library contains DNA sequences equivalent to approximately 2 million bp, which are not represented in the reference genome of the H. influenzae Rd strain and that is greater in size than the genome of this reference strain, providing ample targets for innovative drug design.

Base Sequence↗
PubMed1997

Genetic and ecological data on the Anisakis simplex complex, with evidence for a new species (Nematoda, Ascaridoidea, Anisakidae).

Isozyme analysis at 24 loci was carried out on anisakid nematodes of the Anisakis simplex complex, recovered from various intermediate/paratenic (squid, fish) and definitive (marine mammals) hosts from various parts of the world. A number of samples were found to belong to A. simplex sensu stricto and Anisakis pegreffii, widely extending the geographic ranges and the number of hosts of these 2 species. In addition, a new distinct gene pool was detected, showing different alleles with respect to A. simplex s. str and A. pegreffii at 5 diagnostic loci (99% level). Samples with this gene pool were assigned to a new species, provisionally labeled A. simplex C. Reproductive isolation between A. simplex C and the other 2 Anisakis species was directly assessed by the lack of hybrid and recombinant genotypes in mixed samples from sympatric areas, i.e., Pacific Canada for A. simplex C+A. simplex s. str., South Africa and New Zealand for A. simplex C+A. pegreffii, even when such samples were recovered from the same individual host. Similar levels of genetic divergence were observed among the three species (DNei from 0.36 to 0.45). At the intraspecific level, Canadian Pacific and Austral populations of A. simplex C were found to be genetically rather differentiated from one another (average DNei = 0.08), contrasting with the remarkable genetic homogeneity detected within both A. simplex s. str. and A. pegreffii (average DNei about 0.01). Accordingly, a lower amount of gene flow was estimated within A. simplex C (Nm = 1.6) than within the other 2 species (Nm = 5.4 and 17.7, respectively). Anisakis simplex C showed the highest average values of genetic variability with respect to both A. simplex s. str. and A. pegreffii, e.g., expected mean heterozygosity. Hr = 0.23, 0.16, and 0.11, respectively, in the 3 species. Data on geographic distribution and hosts of the 3 members so far detected in the A. simplex complex are given. Their ecological niche is markedly differentiated, with a low proportion of hosts shared. Intermediate and definitive hosts of A. simplex s. str. and A. pegreffii appear to belong to distinct food webs, benthodemersal, and pelagic, respectively; this would lead to different transmission pathways for the parasites.

Animals↗