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PubMed2000

[Variability of nucleotide sequences of the mitochondrial DNA cytochrome c gene in dolly varden and taranetz char].

Nucleotide sequence of the 307-bp fragment of the mitochondrial DNA cytochrome b gene was determined in representatives of the three species of the Salvelinus genus, specifically, dolly varden char (S. malma), taranetz char (S. taranetzi), and white-spotted char (S. leucomaenis). These results pointed to a high level of mitochondrial DNA (mtDNA) divergence between white-spotted char and dolly varden char, on the one hand, and taranetz char, on the other (the mean d value was 5.45%). However, the divergence between the dolly varden char and taranetz char was only 0.81%, which is comparable with the level of intraspecific divergence in the dolly varden char (d = 0.87%). It was shown that the dolly varden char mitochondrial gene pool contained DNA lineages differing from the main mtDNA pool at least in the taranetz char-specific mitochondrial lineages. One of these dolly varden char mtDNA lineages was characterized by the presence of the restriction endonuclease MspI-D variant of the cytochrome b gene. This lineage was widely distributed in the Chukotka populations but it was not detected in the Yana River (Okhotsk sea) populations. These findings suggest that dolly varden char has a more ancient evolutionary lineage, diverging from the common ancestor earlier than did taranetz char.

Animals↗

PubMedDate not supplied

A molecular survey of phenylketonuria in Iceland: identification of a founding mutation and evidence of predominant Norse settlement.

Iceland was settled during the late 9th and early 10th centuries AD by Vikings who arrived from Norway and the British Isles. Although it is generally acknowledged that the Vikings brought with them Celtic slaves, the relative contribution of these peoples to the modern Icelandic gene pool has been a matter of considerable discussion. Most population genetic studies using classical markers have indicated a large Irish genetic contribution. We have investigated the molecular basis of phenylketonuria (PKU) in 17 Icelandic patients and found 9 different mutations in the phenylalanine hydroxylase gene. One novel mutation, Y377fsdelT, accounts for more than 40% of the mutant chromosomes. Haplotype data support a common ancestral origin of the mutation, and genealogical examination extending back more than 5 generations shows that this mutation has probably arisen in an isolated part of southern Iceland and was enriched by a founder effect. At least 7 PKU mutations have originated outside iceland. The almost exclusively Scandinavian background of these mutations and the complete absence of common Irish PKU mutations strongly support historical and linguistic evidence of a predominant Scandinavian heritage of the Icelandic people.

DNA Mutational Analysis↗

PubMed2002

Y chromosome evidence for Anglo-Saxon mass migration.

British history contains several periods of major cultural change. It remains controversial as to how much these periods coincided with substantial immigration from continental Europe, even for those that occurred most recently. In this study, we examine genetic data for evidence of male immigration at particular times into Central England and North Wales. To do this, we used 12 biallelic polymorphisms and six microsatellite markers to define high-resolution Y chromosome haplotypes in a sample of 313 males from seven towns located along an east-west transect from East Anglia to North Wales. The Central English towns were genetically very similar, whereas the two North Welsh towns differed significantly both from each other and from the Central English towns. When we compared our data with an additional 177 samples collected in Friesland and Norway, we found that the Central English and Frisian samples were statistically indistinguishable. Using novel population genetic models that incorporate both mass migration and continuous gene flow, we conclude that these striking patterns are best explained by a substantial migration of Anglo-Saxon Y chromosomes into Central England (contributing 50%-100% to the gene pool at that time) but not into North Wales.

Alleles↗

PubMed2002

Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica.

Using amplified fragment length polymorphisms (AFLPs), we analyzed the genetic structure of wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica at different geographical levels to test the hypothesis of asymmetric gene flow and investigate the origin of weedy populations. We showed both by phenetic and admixture population analyses that gene flow is about three- to four-fold higher from domesticated to wild populations than in the reverse direction. This result, combined with other work, points to a displacement of genetic diversity in wild populations due to gene flow from the domesticated populations. The weedy populations appear to be genetically intermediate between domesticated and wild populations, suggesting that they originated by hybridization between wild and domesticated types rather than by escape from cultivation. In addition, the domesticated bean races were genetically similar confirming a single domestication event for the Mesoamerican gene pool. Finally, the genetic diversity of the domesticated bean population showed a lower level of geographic structure in comparison to that of the wild populations.

Central America↗

PubMedDate not supplied

Further blood genetic studies on Amazonian diversity--data from four Indian groups.

Information related to 31 protein genetic systems was obtained for 307 individuals affiliated with the Cinta Larga, Karitiana, Surui and Kararaô Indians of northern Brazil. In terms of genetic distances the Cinta Larga showed more similarities with the Karitiana (both are Tupi-speaking tribes), while at a more distant level the Surui clustered with the Kararaô. The latter, a Cayapo subgroup, showed a completely different genetic constitution from the other subgroups of this same tribe. Both the Kararaô and Karitiana are small, remnant populations, and their gene pools have presumably been severely affected by random and founder effects. These results were incorporated with those of 25 other Amazonian Indian tribes, and analysis by two multivariate techniques confirmed a previously observed geographical dichotomy, suggesting either that the Amazon river constitutes a barrier to north-south gene flow or that latitudinally different past migrations entered the region from the west.

Alleles↗

PubMed1984

[Role of migration processes in shaping the marriage structure of the Moscow population. I. The age, place of birth and nationality of those entering marriage].

A genetic-demographic study of the dynamics of the Moscow population marriage structure, with respect to the age of marriage, birthplace and nationality of newlyweds has been carried out by means of sample analysis of 1955 and 1980 marriage records; some other demographic and statistic data obtained during several years were also used. The mean age of marriage being practically constant, the proportion of newlyweds younger than 20 in the reproductive part of the Moscow population was shown to be considerably higher at the beginning of the XX century than at present. The number of couples married at the postreproductive age increased in 1980, as compared with 1955. The process of migration contributing to the genetic structure of subsequent Moscow generations has been characterized quantitatively and from the spatio-geographical point of view. High values (0.57 less than m less than 0.86) of the coefficient of migration to Moscow correspond to the period of non-controlled city population growth. As a result of administrative measures for regulation of the city population growth, the value of the coefficient of migration to Moscow decreased considerably by 1980, though still remained at a rather high level (m=0.40). The mean migration distance increased from 230 km, in the beginning of XIX century to 560 km in 1955 and 1100 in 1980. Especially great was the increase of genetic contribution from Eastern and Southern regions of the USSR. The variability of the national composition also increased. These changes in the geography of migration will cause the increasing reproduction of the entire country gene pool in Moscow as a panmixia center that may result in genetic originality of the Moscow population.

Adult↗

PubMed1998

[Position of Russian chicken breeds in the diversity of Eurasian breeds].

Eleven old Russian, four Mediterranean, and nine Asian chicken breeds were compared with the wild species Gallus gallus (red jungle fowl) by 31 discrete morphological characters. The majority of the characters studied show monogenic inheritance. Five large clusters can be detected on a dendrogram constructed on the basis of the morphological characters of the studied breeds. Almost all breeds characterized by their a similar practical use (egg, meat/egg, meat, game, and ornamental) were included in the same cluster independently of their geographical origin. Close morphological and genetic relations of Mediterranean breeds to the wild species Gallus gallus was confirmed. A wide typological diversity of old Russian breeds was shown; five types of breeds were found among them. Russian breeds were joined in the same clusters with similar types of breeds of Mediterranean or Asian origin. However, 10 out of 11 studied Russian breeds were found to be more closely related to Asian breeds. Thus, it may be suggested that the gene pool of old Russian was formed largely under the influence of Asian breeds and, to a lower extent, Mediterranean breeds.

Animals↗

PubMed1989

Mitochondrial DNA polymorphisms in Italy. III. Population data from Sicily: a possible quantitation of maternal African ancestry.

mtDNA polymorphisms were studied in a sample of 90 individuals of the Sicilian population using six restriction enzymes: HpaI, BamHI, HaeII, MspI, AvaII and HincII. (1) Three new patterns, for MspI, AvaII and HincII, have been detected. (2) At least two different mutations were found to account for both the AvaII morph 3 and the AvaII morph 9 as in many other Caucasian groups so far examined. (3) Seventeen types were found; of these six are new. The frequency (54.5%) of type 1-2 (2.1.1.1.1.2) is lower than in the rest of Italy whereas those of type 6-2 (2.1.2.1.1.2) (10.0%) and type 18-2 (2.3.1.4.9*.2) (12.2%) lie at the upper level of the Italian range. The 18-derivative, type 57-2 (2.3.1.4.13*.2), which is consistently found in all Italian samples, is present also among Sicilians with an incidence of 2.2%. (4) Of particular interest is that the HpaI-3/AvaII-3 complex, which is unique to groups of African ancestry, was found in Sicily at a frequency of 4.4%. For the first time an estimate of the amount of gene flow from Blacks to the Sicilian gene pool could be obtained.

Africa↗

PubMed1995

Polymerase chain reaction-based assays for the characterisation of plant genetic resources.

Plant genetic resources are an important component of biodiversity and provide the basic genetic variability that allow new and improved cultivars to be developed. Numerous germplasm collections have been established and it is important to established that such collections are representative and accessible to breeders and biotechnologists. Molecular markers provide the best estimate of genetic diversity since they are independent of the confounding effects of environmental factors. Assays based on the polymerase chain reaction (PCR) are considered to meet both the technical and genetical requirements for the characterisation of plant and animal genetic resources. Two main approaches are described, based on anonymous and defined primers. The use of both randomly amplified polymorphic DNA (RAPD) and microsatellites or simple sequence repeats (SSR) for the characterisation of perennial tree species, and distribution of variability within gene pools is reported. The detection of interspecific gene introgression between coffee species with RAPD markers is described together with the use of microsatellites to genotype potato. The use of PCR-based assays will facilitate the evaluation and utilisation of plant genetic resources.

Base Sequence↗

PubMed1976

Evolution of experimental "mutator" populations of Drosophila melanogaster.

The theory of evolution predicts that the rate of adaptation of a population is a function of the amount of genetic variation present in the population. This has been experimentally demonstrated in Drosophila populations in which genetic variability was increased either by mass hybridization of two gene pools, or by X-irradiation.--Mutator genes increase the spontaneous mutation rates of their carriers. We have now studied the effects of a third-chromosome mutator gene, mt, on the rate of adaptation of laboratory populations. Initially, experimental and control populations had similar genetic constitutions except for the presence of absence of the mt gene. The populations were maintained for 20-25 generations by "serial transfer" under conditions of very intense selection.--The number of flies produced per unit time remained constant throughout the experiment in the experimental as well as in the control populations. However, in the mutator-carring populations the average longevity of the flies (and consequently the average population size) gradually decreased. Under the experimental conditions natural selection is unable to counteract completely the increased input of deleterious mutations due to the mt gene.

Animals↗

PubMed2004

Influenza A viruses in feral Canadian ducks: extensive reassortment in nature.

The current dogma of influenza accepts that feral aquatic birds are the reservoir for influenza A viruses. Although the genomic information of human influenza A viruses is increasing, little of this type of data is available for viruses circulating in feral waterfowl. This study presents the genetic characterization of 35 viruses isolated from wild Canadian ducks from 1983 to 2000, as the first attempt at a comprehensive genotypic analysis of influenza viruses isolated from feral ducks. This study demonstrates that influenza virus genes circulating in Canadian ducks have achieved evolutionary stasis. The majority of these duck virus genes are clustered in distinct North American clades; however, some H6 and H9 genes are clustered with those from Eurasian viruses. Genes appeared to reassort in a random fashion. None of the genotypes identified remained present throughout all of the years examined and most PA and PB2 genes that crossed over into swine were clustered in one phylogenetic grouping. Additionally, matrix genes were identified that branch very early in the evolutionary tree. These findings demonstrate the diversity of the influenza virus gene pool in Canadian ducks, and suggest that genes which cluster in specific phylogenetic groupings in the PB2 and PA genes can be used for markers of viruses with the potential for crossing the species barrier. A more comprehensive study of this important reservoir is needed to provide further insight into the genomic composition of viruses that crossover the species barrier, which would be a useful component to pandemic planning.

Animals↗

PubMed2001

Molecular ecology of tetracycline resistance: development and validation of primers for detection of tetracycline resistance genes encoding ribosomal protection proteins.

Phylogenetic analysis of tetracycline resistance genes encoding the ribosomal protection proteins (RPPs) revealed the monophyletic origin of these genes. The most deeply branching class, exemplified by tet and otrA, consisted of genes from the antibiotic-producing organisms Streptomyces rimosus and Streptomyces lividans. With a high degree of confidence, the corresponding genes of the other seven classes (Tet M, Tet S, Tet O, Tet W, Tet Q, Tet T, and TetB P) formed phylogenetically distinct separate clusters. Based on this phylogenetic analysis, a set of PCR primers for detection, retrieval, and sequence analysis of the corresponding gene fragments from a variety of bacterial and environmental sources was developed and characterized. A pair of degenerate primers targeted all tetracycline resistance genes encoding RPPs except otrA and tet, and seven other primer pairs were designed to target the specific classes. The primers were used to detect the circulation of these genes in the rumina of cows, in swine feed and feces, and in swine fecal streptococci. Classes Tet O and Tet W were found in the intestinal contents of both animals, while Tet M was confined to pigs and Tet Q was confined to the rumen. The tet(O) and tet(W) genes circulating in the microbiota of the rumen and the gastrointestinal tract of pigs were identical despite the differences in animal hosts and antibiotic use regimens. Swine fecal streptococci uniformly possessed the tet(O) gene, and 22% of them also carried tet(M). This population could be considered one of the main reservoirs of these two resistance genes in the pig gastrointestinal tract. All classes of RPPs except Tet T and TetB P were found in the commercial components of swine feed. This is the first demonstration of the applicability of molecular ecology techniques to estimation of the gene pool and the flux of antibiotic resistance genes in production animals.

Animal Feed↗

PubMed2004

Synthesis and cytological characterization of trigeneric hybrids of durum wheat with and without Ph1.

Wild grasses in the tribe Triticeae, some in the primary or secondary gene pool of wheat, are excellent reservoirs of genes for superior agronomic traits, including resistance to various diseases. Thus, the diploid wheatgrasses Thinopyrum bessarabicum (Savul. and Rayss) A. Love (2n = 2x = 14; JJ genome) and Lophopyrum elongatum (Host) A. Love (2n = 2x = 14; EE genome) are important sources of genes for disease resistance, e.g., Fusarium head blight resistance that may be transferred to wheat. By crossing fertile amphidiploids (2n = 4x = 28; JJEE) developed from F1 hybrids of the 2 diploid species with appropriate genetic stocks of durum wheat, we synthesized trigeneric hybrids (2n = 4x = 28; ABJE) incorporating both the J and E genomes of the grass species with the durum genomes A and B. Trigeneric hybrids with and without the homoeologous-pairing suppressor gene, Ph1, were produced. In the absence of Ph1, the chances of genetic recombination between chromosomes of the 2 useful grass genomes (JE) and those of the durum genomes (AB) would be enhanced. Meiotic chromosome pairing was studied using both conventional staining and fluorescent genomic in situ hybridization (fl-GISH). As expected, the Ph1-intergeneric hybrids showed low chromosome pairing (23.86% of the complement), whereas the trigenerics with ph1b (49.49%) and those with their chromosome 5B replaced by 5D (49.09%) showed much higher pairing. The absence of Ph1 allowed pairing and, hence, genetic recombination between homoeologous chromosomes. Fl-GISH analysis afforded an excellent tool for studying the specificity of chromosome pairing: wheat with grass, wheat with wheat, or grass with grass. In the trigeneric hybrids that lacked chromosome 5B, and hence lacked the Ph1 gene, the wheat-grass pairing was elevated, i.e., 2.6 chiasmata per cell, a welcome feature from the breeding standpoint. Using Langdon 5D(5B) disomic substitution for making trigeneric hybrids should promote homoeologous pairing between durum and grass chromosomes and hence accelerate alien gene transfer into the durum genomes.

Alleles↗

PubMed1983

[Genetic factors linked to the HLA system conferring increased susceptibility to acute lymphoblastic leukemia in children].

Inheritance of HLA antigens in 55 families of patients with ALL was analyzed. Significantly increased sharing of DR antigens was observed among the parents of the affected children (p = 0.003). A similar increase was noted in the sharing of HLA-B antigens (p = 0.02). The observed number of DR homozygotes among the patients was twice the expected value in families where the parents shared a B and a DR antigen. Segregation analysis of the shared antigens disclosed significant prevalence of heterozygotes among the healthy siblings, which suggested the occurrence of gametic selection in such families. This study indicates that mating of certain shared alleles of the HLA system (especially of the DR locus) is associated with a risk for the offspring to develop ALL in childhood. Restricted heterogeneity of the parental HLA gene pool favours the expression of linked recessive genes and, presumably, of those involved in susceptibility to ALL.

Child↗

PubMed1987

Genetic structure and differentiation of human populations.

The concepts of genetic constitution and genetic structure are defined in terms of arrays of gene frequencies, the array and distribution of genotypes, and the distribution of probable ancestral contributions to the gene pool. These concepts can, however, be differentiated. Examples of their application to human populations, to illustrate their descriptive, analytical and epidemiological uses, show that the two concepts help to resolve different types of problems.

Alleles↗

PubMed1994

EcoRI, RsaI, and MspI RFLPs of the COL1A2 gene (type I collagen) in the Cayapa, a Native American population of Ecuador.

EcoRI, RsaI, and MspI RFLPs of the COL1A2 gene were analyzed, using the polymerase chain reaction technique, for the first time in a native American population: the Cayapa of Ecuador. These polymorphisms recently turned out to be good anthropological markers, both at the allele and at the haplotype frequency level. These data underline the well-known genetic affinity between the Cayapa and Asian populations. Moreover, our data on DNA polymorphisms agree with the indication of extremely low, if any, gene flow into the Cayapa gene pool from the neighboring black community, as already suggested not only by cultural data but also by protein polymorphisms.

Alleles↗

PubMed2005

The peopling of modern Bosnia-Herzegovina: Y-chromosome haplogroups in the three main ethnic groups.

The variation at 28 Y-chromosome biallelic markers was analysed in 256 males (90 Croats, 81 Serbs and 85 Bosniacs) from Bosnia-Herzegovina. An important shared feature between the three ethnic groups is the high frequency of the "Palaeolithic" European-specific haplogroup (Hg) I, a likely signature of a Balkan population re-expansion after the Last Glacial Maximum. This haplogroup is almost completely represented by the sub-haplogroup I-P37 whose frequency is, however, higher in the Croats (approximately 71%) than in Bosniacs (approximately 44%) and Serbs (approximately 31%). Other rather frequent haplogroups are E (approximately 15%) and J (approximately 7%), which are considered to have arrived from the Middle East in Neolithic and post-Neolithic times, and R-M17 (approximately 14%), which probably marked several arrivals, at different times, from eastern Eurasia. Hg E, almost exclusively represented by its subclade E-M78, is more common in the Serbs (approximately 20%) than in Bosniacs (approximately 13%) and Croats (approximately 9%), and Hg J, observed in only one Croat, encompasses approximately 9% of the Serbs and approximately 12% of the Bosniacs, where it shows its highest diversification. By contrast, Hg R-M17 displays similar frequencies in all three groups. On the whole, the three main groups of Bosnia-Herzegovina, in spite of some quantitative differences, share a large fraction of the same ancient gene pool distinctive for the Balkan area.

Bosnia and Herzegovina↗

PubMed2001

Diversity arrays: a solid state technology for sequence information independent genotyping.

Here we present the successful application of the microarray technology platform to the analysis of DNA polymorphisms. Using the rice genome as a model, we demonstrate the potential of a high-throughput genome analysis method called Diversity Array Technology, DArT'. In the format presented here the technology is assaying for the presence (or amount) of a specific DNA fragment in a representation derived from the total genomic DNA of an organism or a population of organisms. Two different approaches are presented: the first involves contrasting two representations on a single array while the second involves contrasting a representation with a reference DNA fragment common to all elements of the array. The Diversity Panels created using this method allow genetic fingerprinting of any organism or group of organisms belonging to the gene pool from which the panel was developed. Diversity Arrays enable rapid and economical application of a highly parallel, solid-state genotyping technology to any genome or complex genomic mixtures.

Blotting, Southern↗