Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Gene Pool”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42Linked to original sources
PubMed2006

Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation.

The introduction of culture-independent molecular screening techniques, especially based on 16S rRNA gene sequences, has allowed microbiologists to examine a facet of microbial diversity not necessarily reflected by the results of culturing studies. The bacterial community structure was studied for a pesticide-contaminated site that was subsequently remediated using an efficient degradative strain Arthrobacter protophormiae RKJ100. The efficiency of the bioremediation process was assessed by monitoring the depletion of the pollutant, and the effect of addition of an exogenous strain on the existing soil community structure was determined using molecular techniques. The 16S rRNA gene pool amplified from the soil metagenome was cloned and restriction fragment length polymorphism studies revealed 46 different phylotypes on the basis of similar banding patterns. Sequencing of representative clones of each phylotype showed that the community structure of the pesticide-contaminated soil was mainly constituted by Proteobacteria and Actinomycetes. Terminal restriction fragment length polymorphism analysis showed only nonsignificant changes in community structure during the process of bioremediation. Immobilized cells of strain RKJ100 enhanced pollutant degradation but seemed to have no detectable effects on the existing bacterial community structure.

Arthrobacter↗
PubMed2007

Reduced genetic structure of north Ethiopian cattle revealed by Y-chromosome analysis.

Ethiopia is considered to be a putative migratory corridor for both Near-East Bos taurine and Arabian and Indian B. indicus cattle into East Africa. African pastoralism, which is associated with adaptation to specific habitats and farming systems, has contributed to the composite constitution of Ethiopian cattle. We analyse, for the first time, five Y-chromosome microsatellite markers from seven north Ethiopian cattle populations, using a European Holstein-Friesian population as a reference, to assess the paternal gene pool and to explore the mechanisms behind the genetic structure. Our results reveal that the indicine alleles predominate in the present populations, with only one animal in the Arado carrying the taurine alleles. The north Ethiopian cattle populations with one exception (Abergelle) are characterized by a general low Y-chromosome haplotype diversity, as well as by a reduced interpopulation variance (Phi(ST)=4.0%), which can be a result of strong male-mediated selective sweeps. Population structure revealed by multidimensional-scaling analysis differentiates two populations (Arado and Abergelle) from the rest. Analysis of molecular variance does not lend support to the traditional classification for the populations, which is mainly based on physical characteristics. A network analysis indicates two closely related founding haplotypes accounting for a large proportion (50.0% in Abergelle and 85.0-94.7% in others) of north Ethiopian cattle Y-chromosomes. Our findings point to a common, but limited, paternal origin of the north Ethiopian cattle populations and strong male-mediated gene flow among them. The findings also provide insight into the historical immigration of cattle into East Africa.

Animals↗
PubMed2000

Comparative aspects of high-altitude adaptation in human populations.

The conditions and duration of high-altitude residence differ among high-altitude populations. The Tibetan Plateau is larger, more geographically remote, and appears to have been occupied for a longer period of time than the Andean Altiplano and, certainly, the Rocky Mountain region as judged by archaeological, linguistic, genetic and historical data. In addition, the Tibetan gene pool is less likely to have been constricted by small numbers of initial migrants and/or severe population decline, and to have been less subject to genetic admixture with lowland groups. Comparing Tibetans to other high-altitude residents demonstrates that Tibetans have less intrauterine growth retardation better neonatal oxygenation higher ventilation and hypoxic ventilatory response lower pulmonary arterial pressure and resistance lower hemoglobin concentrations and less susceptibility to CMS These findings are consistent with the conclusion that "adaptation" to high altitude increases with time, considering time in generations of high-altitude exposure. Future research is needed to compare the extent of IUGR and neonatal oxygenation in South American high-altitude residents of Andean vs. European ancestry, controlling for gestational age and other characteristics. Another fruitful line of inquiry is likely to be determining whether persons with CMS or other altitude-associated problems experienced exaggerated hypoxia during prenatal or neonatal life. Finally, the comparison of high-altitude populations with respect to the frequencies of genes involved in oxygen sensing and physiologic response to hypoxia will be useful, once candidate genes have been identified.

Acclimatization↗
PubMed2000

Strong Amerind/white sex bias and a possible Sephardic contribution among the founders of a population in northwest Colombia.

Historical and genetic evidences suggest that the recently founded population of Antioquia (Colombia) is potentially useful for the genetic mapping of complex traits. This population was established in the 16th-17th centuries through the admixture of Amerinds, Europeans, and Africans and grew in relative isolation until the late 19th century. To examine the origin of the founders of Antioquia, we typed 11 markers on the nonrecombining portion of the Y chromosome and four markers on mtDNA in a sample of individuals with confirmed Antioquian ancestry. The polymorphisms on the Y chromosome (five biallelic markers and six microsatellites) allow an approximation to the origin of founder men, and those on mtDNA identify the four major founder Native American lineages. These data indicate that approximately 94% of the Y chromosomes are European, 5% are African, and 1% are Amerind. Y-chromosome data are consistent with an origin of founders predominantly in southern Spain but also suggest that a fraction came from northern Iberia and that some possibly had a Sephardic origin. In stark contrast with the Y-chromosome, approximately 90% of the mtDNA gene pool of Antioquia is Amerind, with the frequency of the four Amerind founder lineages being closest to Native Americans currently living in the area. These results indicate a highly asymmetric pattern of mating in early Antioquia, involving mostly immigrant men and local native women. The discordance of our data with blood-group estimates of admixture suggests that the number of founder men was larger than that of women.

Africa, Northern↗
PubMed2005

Y-chromosome lineages from Portugal, Madeira and Açores record elements of Sephardim and Berber ancestry.

A total of 553 Y-chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Açores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78-83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese sub-populations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum-Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub-clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre-Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub-Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex-related gene flow, most likely mediated by the Atlantic slave trade.

Africa South of the Sahara↗
PubMedDate not supplied

[Ecology and evolution of influenza viruses in Russia (1979-2002)].

The research results on ecology and evolution of influenza A viruses, which has been conducted by the Center of Ecology and Evolution of influenza Viruses of Ivanovsky's Institute of Virology, Russian Academy of Medical Sciences, for more than 30 years, are summarized in the paper. A gene pool of influenza A viruses circulating in Russia's territory was defined. Foci of influenza A viruses were detected in natural biocenosis. Issues conditioned by the population interrelations of influenza viruses, i.e. between the populations of wild and home animals and the populations of people, are also under discussion.

Animals↗
PubMed2001

CTNS mutations in African American patients with cystinosis.

Cystinosis, an autosomal recessive lysosomal storage disorder, is rarely diagnosed in African Americans. The disease results from mutations in the gene CTNS; at least 55 such mutations have been reported. By far the most common is a 57,257-bp deletion of Northern European origin encompassing most of the CTNS gene. We performed mutation analysis on DNA from four African American patients with cystinosis. In one individual with classical, nephropathic cystinosis, we identified a new molecular defect, i.e., a homozygous GT-->CC substitution at the +5 position of IVS 5 of CTNS (IVS 5+5 GT-->CC). The out-of-frame splicing of exon 5 creates a null allele consistent with the patient's severe phenotype. Two patients were heterozygous and one homozygous for the common 57-kb deletion allele, reflecting the admixture of African and Northern European gene pools in North America. The two African Americans heterozygous for the 57-kb deletion were also hemizygous for a 928G-->A change, associated with ocular or nonnephropathic cystinosis. These two individuals are the only known African Americans with ocular cystinosis. We conclude that the diagnosis of cystinosis should be entertained in African Americans with symptoms of the disease, and that mutation analysis for the 57-kb deletion should be considered in this group of patients.

Adolescent↗
PubMed2004

Characterization of admixture in an urban sample from Buenos Aires, Argentina, using uniparentally and biparentally inherited genetic markers.

In this study we analyzed a sample of the urban population of La Plata, Argentina, using 17 mtDNA haplogroups, the DYS 199 Y-chromosome polymorphism, and 5 autosomal population-associated alleles (PAAs). The contribution of native American maternal lineages to the population of La Plata was estimated as 45.6%, whereas the paternal contribution was much lower (10.6%), clearly indicating directional mating. Regarding autosomal evidence of admixture, the relative European, native American, and West African genetic contributions to the gene pool of La Plata were estimated to be 67.55% (+/-2.7), 25.9% (+/-4.3), and 6.5% (+/-6.4), respectively. When admixture was calculated at the individual level, we found a low correlation between the ancestral contribution estimated with uniparental lineages and autosomal markers. Most of the individuals from La Plata with a native American mtDNA haplogroup or the DYS199*T native American allele show a genetic contribution at the autosomal level that can be traced primarily to Europe. The results of this study emphasize the need to use both uniparentally and biparentally inherited genetic markers to understand the history of admixed populations.

Argentina↗
PubMed1994

[Genetic polymorphism of the HLA system in Komi and Komi-Permyaks].

High frequencies of HLA-A2, -A3, -A9, -B7, -B13, -Bw35, and -Dw3 antigens were found in Sysolian and Udorian Komi (from Vizinga and Koslan, respectively), as well as in Zyuzdian Komi-Permyaks. In some populations, high frequencies of HLA-A10, -A28, -B21, -B27, and -B40 antigens were also found. Similarity in both gene frequency patterns and heterozygosity level was noted between these populations and the population of more western European regions, as well as Finno-Ugric nations. Frequencies of some alleles, e.g., HLA-B8 -B12, -B16, and -B18, were found to be intermediate between the corresponding estimates for Mongoloids and Caucasoids. The Mongoloid influence on the gene pool is expressed in increased HLA-B27, -B40, -Cw2, -Cw3, and -Cw4 frequencies. The frequencies of HLA-A3, -A28, -B7, -B13, and -B35 antigens are higher, and that of HLA-B5 is lower, than the respective frequencies in both Caucasoids and Mongoloids. This reflects the specificity of the ancestral group, whose peculiarities cannot be attributed exclusively to the results of Caucasoid-Mongoloid intermixing. The high level of genetic differentiation of Komi ethnographic groups (F st = 0.0188 +/- 0.0045) is emphasized. The characteristics of distribution of HLA antigens and haplotypes are explained in terms of the ethnogenesis of the Komi; markers for their constituent ethnic components were found.

Asian People↗
PubMed1991

[DNA analysis and gene diagnosis of cystic fibrosis].

Cystic fibrosis (CF) is the most common autosomal recessive disorder in the Caucasian population, affecting approximately 1 in 2,000 newborns but the actual estimate varies with the geographic location. The incidence of CF in non-Caucasian populations is low. Intensive efforts using genetic linkage information ultimately led to the cloning of the CF gene prior to the identification of the gene product or its function. The gene encodes what is believed to be a transmembrane protein, which has been named the cystic fibrosis transmembrane conductance regulator (CFTR). The CFTR contains two nucleotide-binding folds (NBF) which show homology to numerous transport proteins with the greatest homology to the P-glycoproteins that are encoded by the multiple drug-resistance loci. A three- base deletion resulting in the loss of phenylalanine residue (delta F508) in the tenth exon of the CFTR gene is the mutation occurring on the majority of CF chromosomes. The overall frequency of delta F508 in the present mutant CF gene pool is about 70%, but the study populations are not equally represented: there is marked variation in the population of delta F508 among different geographic populations. Recently, numerous additional, less common mutations have been found. Some mutations occur on 2-5% of the CF chromosomes. Many of these are rare 'private' mutations, occurring in individual families of all racial and ethnic backgrounds. By contrast over 80% of Western European CF mutations have been identified. The highly heterogeneous nature of the remaining CF mutations provides important insights into the structure and function of the protein, but further improvements are needed in DNA-based genetic screening for CF carrier status.

Cystic Fibrosis↗
PubMed2000

Single-strand conformational polymorphism and sequence polymorphism of Mhc-DRB in Latxa and Karrantzar sheep: implications for Caprinae phylogeny.

Single-strand conformational polymorphism analysis and DNA sequencing were used to characterize Mhc-DRB second exon variability in the Latxa and Karrantzar breeds of sheep. The presence of more than two sequences in some animals indicates that alleles of two different loci have been amplified. Six new alleles were identified by sequencing. The allele frequency distribution of the DRB1 gene is striking, with two alleles accounting for half of the gene pool in both breeds under study. The most frequent allele in both breeds was the same (named DRB1*0702), with some specific amino acids: Tyr in position 31 and Thr in 51. A species variability analysis was also performed including the entire set of sheep DRB exon 2 sequences. Based on the patchwork patterns of different alleles, interallelic recombination appears to be playing a significant role in the generation of allelic diversity at this locus in sheep. The phylogenetic tree of all known Caprinae DRB sequences shows that certain alleles from one species are more closely related to those from other species than they are to each other. Allele DRB1*0702 merits special attention due to its high similarity to the Mufflon allele. As this is the most frequent in both breeds analyzed, one can hypothesize that in sheep, both Mufflon and Argali have had different influences depending on the sheep breed under study and that the relationship between domestic sheep and Mufflon is greater than previously thought. The data generated in this study can serve as a basis for developing a typing assay for the sheep DRB genes in the Latxa and Karrantzar populations.

Alleles↗
PubMed1988

Genetic studies of human apolipoproteins. VII. Population distribution of polymorphisms of apolipoproteins A-I, A-II, A-IV, C-II, E, and H in Nigeria.

Genetic variation at various human apolipoprotein gene loci plays a vital role in modulating lipid metabolism. However, information regarding genetic variation at apolipoprotein loci is scanty, and the available data are largely restricted to Caucasian populations. Using recently developed isoelectric focusing-immunoblotting techniques, we have screened a large number of serum samples from Nigerian blacks to investigate structural variation at six apolipoprotein loci: A-I, A-II, A-IV, C-II, E, and H. With the exception of a single example of a putative APO A-I variant, the APO A-I and A-II loci were found to be monomorphic. Several new variants have been identified at the APO A-IV locus, which are apparently restricted to the black gene pool. By comparison with Caucasians, in whom APO C-II is invariant, four allelic variants have been identified in the Nigerians at the APO C-II structural locus. A common three-allele polymorphism has been observed for APO E, with a striking high frequency of the APO E*4 allele. In addition to three common alleles, the APO H locus is characterized by having an allele marker unique to blacks. The mean heterozygosity at these apolipoprotein loci is higher in Nigerian blacks as compared with the Caucasians.

Alleles↗
PubMed2006

Drought-adaptive traits derived from wheat wild relatives and landraces.

Exotic parents are being used to increase allelic diversity in bread wheat breeding through (i) interspecific hybridization of the ancestral genomes to produce so-called synthetic derived (SYN-DER) wheat, and (ii) crossing with landrace accessions, originating in abiotically stressed environments, that have become isolated from mainstream gene pools. Evaluation of the inherent genetic diversity encompassed by drought-adapted landraces compared with checks using DNA fingerprinting confirmed that some landraces were not only distant from checks but also showed significant diversity among each other. Improvement in performance of SYN-DER lines compared with recurrent parents was not associated with a larger overall investment in root dry weight, but rather an increased partitioning of root mass to deeper soil profiles (between 60 cm and 120 cm) and increased ability to extract moisture from those depths. The best Mexican landraces showed superior ability in terms of water extraction from soil depth, as well as increased concentration of soluble carbohydrates in the stem shortly after anthesis. Although it can be argued that inferring theoretical yield gains from the over-expression of any of these traits is questionable, since compensatory mechanisms may be at work, the fact remains that mechanistic or genetic linkages among physiological traits remain largely un-established. In the meantime, trait information is being used to make strategic crosses based on the theoretical combination of useful stress-adaptive traits with the possibility of realizing additive gene action in selected progeny. Candidates for crossing with elite check cultivars include landraces identified that showed relatively high biomass under drought combined with favourable expression of physiological traits such as stem carbohydrates, water extraction characteristics, and transpiration efficiency.

Adaptation, Physiological↗
PubMed2006

Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA.

BACKGROUND: India is a country with enormous social and cultural diversity due to its positioning on the crossroads of many historic and pre-historic human migrations. The hierarchical caste system in the Hindu society dominates the social structure of the Indian populations. The origin of the caste system in India is a matter of debate with many linguists and anthropologists suggesting that it began with the arrival of Indo-European speakers from Central Asia about 3500 years ago. Previous genetic studies based on Indian populations failed to achieve a consensus in this regard. We analysed the Y-chromosome and mitochondrial DNA of three tribal populations of southern India, compared the results with available data from the Indian subcontinent and tried to reconstruct the evolutionary history of Indian caste and tribal populations. RESULTS: No significant difference was observed in the mitochondrial DNA between Indian tribal and caste populations, except for the presence of a higher frequency of west Eurasian-specific haplogroups in the higher castes, mostly in the north western part of India. On the other hand, the study of the Indian Y lineages revealed distinct distribution patterns among caste and tribal populations. The paternal lineages of Indian lower castes showed significantly closer affinity to the tribal populations than to the upper castes. The frequencies of deep-rooted Y haplogroups such as M89, M52, and M95 were higher in the lower castes and tribes, compared to the upper castes. CONCLUSION: The present study suggests that the vast majority (> 98%) of the Indian maternal gene pool, consisting of Indio-European and Dravidian speakers, is genetically more or less uniform. Invasions after the late Pleistocene settlement might have been mostly male-mediated. However, Y-SNP data provides compelling genetic evidence for a tribal origin of the lower caste populations in the subcontinent. Lower caste groups might have originated with the hierarchical divisions that arose within the tribal groups with the spread of Neolithic agriculturalists, much earlier than the arrival of Aryan speakers. The Indo-Europeans established themselves as upper castes among this already developed caste-like class structure within the tribes.

Chromosomes, Human, Y↗
PubMed1983

[Role of recessive lethal genes in spontaneous embryonal lethality in random-bred rat and mouse populations in Cuba].

Spontaneous embryonic lethality and the recessive lethal gene frequency in the gene pool of noninbred mice and rats of the bioteria of the National Research Center of the Cuba Republic Academy of Sciences were investigated. It was established that the level of spontaneous embryonic lethality among mice increased greatly as compared to that in 1977 and was 40% (versus 20% in 1977). Of this number, 30% falls within the postimplantation period. In noninbred rats, these values constituted 21.4 and 8.1%, respectively. High embryonic lethality among noninbred mice may be determined by genetic causes and the influence of ecological factors. The frequency of recessive lethals among noninbred mice was 28%, that among rats 20.8%. It is characteristic that in both categories, recessive lethals became apparent only in the postimplantation period of embryogenesis.

Animals↗
PubMed2005

Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations.

Genetic affinities between aboriginal Taiwanese and populations from Oceania and Southeast Asia have previously been explored through analyses of mitochondrial DNA (mtDNA), Y chromosomal DNA, and human leukocyte antigen loci. Recent genetic studies have supported the "slow boat" and "entangled bank" models according to which the Polynesian migration can be seen as an expansion from Melanesia without any major direct genetic thread leading back to its initiation from Taiwan. We assessed mtDNA variation in 640 individuals from nine tribes of the central mountain ranges and east coast regions of Taiwan. In contrast to the Han populations, the tribes showed a low frequency of haplogroups D4 and G, and an absence of haplogroups A, C, Z, M9, and M10. Also, more than 85% of the maternal lineages were nested within haplogroups B4, B5a, F1a, F3b, E, and M7. Although indicating a common origin of the populations of insular Southeast Asia and Oceania, most mtDNA lineages in Taiwanese aboriginal populations are grouped separately from those found in China and the Taiwan general (Han) population, suggesting a prevalence in the Taiwanese aboriginal gene pool of its initial late Pleistocene settlers. Interestingly, from complete mtDNA sequencing information, most B4a lineages were associated with three coding region substitutions, defining a new subclade, B4a1a, that endorses the origin of Polynesian migration from Taiwan. Coalescence times of B4a1a were 13.2 +/- 3.8 thousand years (or 9.3 +/- 2.5 thousand years in Papuans and Polynesians). Considering the lack of a common specific Y chromosomal element shared by the Taiwanese aboriginals and Polynesians, the mtDNA evidence provided here is also consistent with the suggestion that the proto-Oceanic societies would have been mainly matrilocal.

Asian People↗
PubMed2005

Genetic components in contemporary Faroe Islands Cattle as revealed by microsatellite analysis.

The gene pool of indigenous Faroe Islands Cattle is strongly affected by crossing with Norwegian Red. In this study, the genetic structure in 191 animals representing five North European cattle breeds (Faroe Islands, Icelandic, Blacksided Troender, Western Fjord and Norwegian Red) and the genetic admixture in the contemporary Faroe Islands Cattle at the population and individual level were evaluated using 20 polymorphic microsatellite loci. Only 6.7% of the total genetic variation could be attributed to the differences amongst the breeds. The factorial correspondence analysis based on all allele frequencies could hardly reveal a divergence between Faroe Islands Cattle and Norwegian Red. In addition, a Neighbor-Net tree constructed to examine the allocation of individuals of Faroe Islands Cattle and Norwegian Red provided a detailed interrelationship network for all the 72 animals. An estimation of the population admixture proportion showed a strong genetic contribution by Norwegian Red (47.3%) in the contemporary Faroe Islands Cattle. On the other hand, individual admixture analysis demonstrated that only seven of the individual Faroe Islands Cattle analysed, which also showed more traditional colour patterns, could be assigned to the Faroe Islands Cattle cluster, probably representing the breed's remaining purebred animals. Strategies for preserving the original native genes in Faroe Islands Cattle should be considered in order to prevent the breed from becoming extinct and to strengthen the breed's capability in future breeding programmes.

Animals↗
PubMed2005

Amount of introgression in flycatcher hybrid zones reflects regional differences in pre and post-zygotic barriers to gene exchange.

Introgression is the incorporation of alleles from one species or semispecies into the gene pool of another through hybridization and backcrossing. The rate at which this occurs depends on the frequency of hybridization and the fitness of hybrids and backcrosses compared to 'pure' individuals. The collared flycatcher (Ficedula albicollis) and the pied flycatcher (F. hypoleuca) co-exist and hybridize at low to moderate frequencies in a clinal hybrid zone in Central Europe and on the islands of Gotland and Oland off the Swedish east coast. Data on hatching success suggest that hybrids are less fertile in Central Europe compared to on the islands. Direct fitness estimates using molecular markers to infer paternity are consistent with the demographic data. Applying a tag-array-based minisequencing assay to genotype interspecific substitutions and single nucleotide polymorphisms we demonstrate that the amount of introgression from the pied to the collared flycatcher is higher in the two island populations (Gotland and Oland) than in two geographically distinct areas from the Central European hybrid zone (Czech Republic and Hungary). In all areas the amount of introgression from collared to pied flycatchers is very low or seemingly absent. The different patterns of introgression are consistent with regional differences in rates of hybridization and fitness of hybrids. We suggest that barriers to gene exchange may have been partly broken down on the islands due to asymmetric gene flow from allopatry. Alternatively, or in addition, more pronounced reinforcement of prezygotic isolation in Central Europe might have increased post-zygotic isolation through hitchhiking, since genes affecting pre and post-zygotic isolation are both sex-linked in these birds. One of our genetic markers appears to introgress from pied to collared flycatchers at a much higher rate than the other markers. We discuss the possibility that the introgressed marker may be linked to a gene which is under positive selection in the novel genetic background.

Animals↗