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Results for “Genetic Variation”

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PubMed1997

Evolutionary dynamics of genetic variation in Epstein-Barr virus isolates of diverse geographical origins: evidence for immune pressure-independent genetic drift.

The question whether immune pressure exerted by cytotoxic T lymphocytes (CTLs) can influence the long-term evolution of genetically stable viruses such as Epstein-Barr virus (EBV) has generated considerable scientific interest, primarily due to its important implications for the overall biology of the virus. While arguing for a role of CTLs in the evolution of viruses, it is important to differentiate between genetic variation in virus and immune recognition of these variant virus by CTLs. To assess the role of genetic selection in the long-term evolution of EBV, we have analyzed a large panel of type 1 EBV isolates from African, Southeast Asian, Papua-New Guinean (PNG), and Australian Caucasian individuals. Seven different regions of the EBV genome, which include nine CTL epitopes restricted through a range of HLA class I alleles, were sequenced and compared. Although numerous nucleotide changes were identified within these isolates, comparison of synonymous and nonsynonymous substitutions in the CTL epitope indicated that the genetic variation was generated mostly independently of immune selection pressure. Surprisingly, an inverse correlation between genetic variation within certain CTL epitopes and the frequency distribution of HLA alleles that present the CTL epitopes was seen, suggesting that the evolutionary pressures on the CTL epitopes of the virus may be toward their conservation rather than their inactivation. Furthermore, molecular evolutionary genetic analysis of nucleotide sequences revealed that viral isolates from PNG are evolving as a lineage distinct from isolates from African, Southeast Asian, and Australian Caucasian individuals.

Amino Acid Sequence↗

PubMed2006

Public willingness to participate in and public opinions about genetic variation research: a review of the literature.

Scientists are turning to genetic variation research in hopes of addressing persistent racial/ethnic disparities in health. Despite ongoing controversy, the advancement of genetic variation research is likely to produce new knowledge and technologies that will substantially change the ways in which we understand and value health. They also may affect the ways in which individuals and groups organize socially, politically, and economically. Addressing concerns that may exist in different communities is vital to the scientific and ethical advancement of genetic variation research. We review empirical studies of public willingness to participate in and opinions about genetic research with particular attention to differences in consent and opinion by racial/ethnic group membership.

Attitude to Health↗

PubMed1985

Two-dimensional gel studies of genetic variation in the plasma proteins of Amerindians and Japanese.

Genetic variation has been studied in plasma samples from 107 Amerindian children and their parents, and 110 Japanese children and their parents by means of two-dimensional polyacrylamide gel electrophoresis. Twenty-three polypeptides were scored; the identity of nine of these is at present still unknown. Genetic variation was encountered in 11 of these polypeptides. We have previously reported that the index of heterozygosity was 6.2 +/- 0.7% for 20 "randomly selected", silver stained polypeptides scored for genetic variation in Caucasoids (Rosenblum et al. 1983b). For technical reasons only 11 of these 20 polypeptides could be routinely scored in preparations from the Amerindian samples. For these 11 polypeptides, the indices of heterozygosity in the three populations were: Amerindians, 4.5 +/- 0.6%; Japanese, 5.7 +/- 0.7%; Caucasoids, 8.0 +/- 1.1%. Even with these relatively small numbers some striking ethnic differences as regards individual polypeptides are apparent.

Adult↗

PubMed1980

Genetical variation for enzyme activity in a population of Drosophila melanogaster. V. The genetical architecture, as shown by diallel analysis, of alcohol dehydrogenase (ADH) activity.

Fifteen highly inbred lines extracted by sib-mating from the laboratory cage population, "Texas", of Drosophila melanogaster were crossed in a half-diallel mating design. Female progeny were assayed individually for ADH activity at 25 degrees and 35 degrees C and for total protein. At 25 degrees C there was considerable additive genetical variation and the dominance variation was attributable to specific parents and to specific crosses at random in the diallel table. The character total protein also showed considerable additive variation but less dominance variation. Largely independent gene action was shown by the characters ADH activity and total protein. There were strong genotype-environment interactions for heat-stability. At 35 degrees C most of the genetical variation was additive and mainly due to modifier loci. It was concluded that at 25 degrees C dominance was ambidirectional and almost complete. This genetical architecture was compatible with a past history of stabilising selection for ADH activity in the "Texas" population.

Alcohol Oxidoreductases↗

PubMed2025

Gut fungi are associated with human genetic variation and disease risk.

Human genetic determinants of the gut mycobiome remain uninvestigated despite decades of research highlighting tripartite relationships between gut bacteria, genetic background, and disease. Here, we present the first genome-wide association study on the number and types of human genetic loci influencing gut fungi relative abundance. We detect 148 fungi-associated variants (FAVs) across 7 chromosomes that statistically associate with 9 fungal taxa. Of these FAVs, several occur in the protein-coding genes PTPRC, ANAPC10, NAV2, and CDH13. Additional FAVs link to tissue-specific gene expression as fungi-associated expression quantitative trait loci. Notably, the relative abundance of gut yeast Kazachstania associates with genetic variation in CDH13 encoding T-cadherin, a protein linked to cardiovascular disease. Kazachstania forms a causal relationship with cardiovascular disease risk in a mendelian two-sample randomization analysis. These findings establish previously unrecognized connections between human genetics, gut fungi, and chronic disease, broadening the paradigm of human-microbe interactions in the gut to the mycobiome.

Humans↗

PubMed1996

Genetic variation in the population of Ibiza (Spain): genetic structure, geography, and language.

A sample of 203 individuals from Ibiza (Balearic Islands, Spain) were tested for blood group and serum protein genetic variation and compared with other circum-Mediterranean populations. Allele frequencies were calculated for the following blood group and serum systems: ABO, Rh, MNSs, P, Lewis, Duffy, Kell, ORM, GC, TF, PI, and HP. The allele frequencies from Ibiza were compared with those from other Balearic Islands (Majorca and Minorca) and with related European and North African groups using an assortment of analytical methods (genetic distances, R matrix analysis, and Mantel tests). R matrix analysis revealed that Ibiza is genetically different from the other Balearic populations and, because of gene flow from Spain, clusters with European groups. The level of genetic microdifferentiation of the Mediterranean populations, measured by RST (average of the R matrix diagonal elements, rii), is 0.028. An examination of the relationship between genetic, geographic, and linguistic distances by Mantel tests revealed that genetic distances are significantly correlated with linguistic distances, whereas the genetic distances are not significantly correlated with geographic distances. The plot of mean per locus heterozygosity versus the genetic distance from the centroid of distribution revealed that all three Balearic Islands have experienced considerable gene flow but that Ibiza has been most affected by the action of stochastic processes.

Blood Group Antigens↗

PubMed2005

Genetic variation for an aphid wing polyphenism is genetically linked to a naturally occurring wing polymorphism.

Many polyphenisms are examples of adaptive phenotypic plasticity where a single genotype produces distinct phenotypes in response to environmental cues. Such alternative phenotypes occur as winged and wingless parthenogenetic females in the pea aphid (Acyrthosiphon pisum). However, the proportion of winged females produced in response to a given environmental cue varies between clonal genotypes. Winged and wingless phenotypes also occur in males of the sexual generation. In contrast to parthenogenetic females, wing production in males is environmentally insensitive and controlled by the sex-linked, biallelic locus, aphicarus (api). Hence, environmental or genetic cues induce development of winged and wingless phenotypes at different stages of the pea aphid life cycle. We have tested whether allelic variation at the api locus explains genetic variation in the propensity to produce winged females. We assayed clones from an F2 cross that were heterozygous or homozygous for alternative api alleles for their propensity to produce winged offspring. We found that clones with different api genotypes differed in their propensity to produce winged offspring. The results indicate genetic linkage of factors controlling the female wing polyphenism and male wing polymorphism. This finding is consistent with the hypothesis that genotype by environment interaction at the api locus explains genetic variation in the environmentally cued wing polyphenism.

Alleles↗

PubMedDate not supplied

Substantial genetic variation in southern African black rhinoceros (Diceros bicornis).

Thirty protein-coding loci of southern African black rhinoceros (Diceros bicornis) from four isolated populations were studied using starch gel electrophoresis and polyacrylamide gel electrophoresis. Gene diversity estimates varied between 0.036 and 0.058, with the Zambezi Valley population having the largest amount of protein variation. These levels are higher than those in other studies of genetic variation in black rhinoceros and are similar to the amount of genetic variation observed for outbred natural populations that are not genetically depauperate. Because the observed levels of genetic variation vastly exceed the expectations for current effective population sizes, the current levels apparently reflect large black rhinoceros populations which have existed until recently. Observed levels of genetic variation within populations are consistent with the expectations when recent demographic events are taken into account.

Africa, Southern↗

PubMed1983

Solomon Islander skin pigmentation: ultrastructural differences related to genetic variation in Melanesia.

Genetic differences between Solomon Islander populations are distinguishable on the basis of melanosome packaging in epidermal keratinocytes. By electron microscopic study of skin pigmentation in various Melanesian populations, we have found distinct inter-island differences in the mode of melanosome packaging. Melanosomes are found as singlets in the skin of Bougainville Islanders but are found aggregated in melanosome complexes in Malaita Islanders and Ontong Javanese. This variation in melanosome packaging represents an important biologic difference found between Solomon Islanders and may reflect the genetic diversity existing in the original Melanesian founding population or the genetic diversity existing in the original Melanesian founding population or populations.

Genetic Variation↗

PubMed2005

Temporal patterns of genetic variation across a 9-year-old aerial seed bank of the shrub Banksia hookeriana (Proteaceae).

The pattern of accumulation of genetic variation over time in seed banks is poorly understood. We examined the genetic structure of the aerial seed bank of Banksia hookeriana within a single 15-year-old population in fire-prone southwestern Australia, and compared genetic variation between adults and each year of a 9-year-old seed bank using amplified fragment length polymorphism (AFLP). B. hookeriana is well suited to the study of seed bank dynamics due to the canopy storage of its seeds, and because each annual crop can be identified. A total of 304 seeds from nine crop years and five maternal plants were genotyped, along with 113 plants from the adult population. Genetic variation, as assessed by the proportion of polymorphic markers (P(p)) and Shannon's index (I), increased slightly within the seed bank over time, while gene diversity (H(j)), did not change. P(p), I, and H(j) all indicated that genetic variation within the seed bank quickly approached the maximal level detected. Analysis of molecular variance revealed that less than 4% of variation could be accounted for by variation among seeds produced in different years, whereas there was greater differentiation among maternal plants (12.7%), and among individual seeds produced by different maternal plants (83.4%). With increasing population age, offspring generated each year were slightly more outbred, as indicated by an increase in the mean number of nonmaternal markers per offspring. There were no significant differences for H(j) or I between adults and the seed bank. Viability of seeds decreased with age, such that the viability of 9-year-old seeds was half that of 2-year-old seeds. These results suggest that variable fire frequencies have only limited potential to influence the amount of genetic variation stored within the seed bank of B. hookeriana.

Analysis of Variance↗

PubMed2004

Ecosystem implications of genetic variation in water-use of a dominant riparian tree.

Genetic variation in dominant species can affect plant and ecosystem functions in natural systems through multiple pathways. Our study focuses on how genetic variation in a dominant riparian tree ( Populus fremontii, P. angustifolia and their natural F(1) and backcross hybrids) affects whole-tree water use, and its potential ecosystem implications. Three major patterns were found. First, in a 12-year-old common garden with trees of known genetic makeup, hybrids had elevated daily integrated leaf-specific transpiration ( E(tl); P=0.013) and average canopy conductance ( G(c); P=0.037), with both E(tl) and G(c) approximately 30% higher in hybrid cross types than parental types. Second, delta(13)C values of leaves from these same trees were significantly more negative in hybrids ( P=0.004), and backcross hybrids had significantly more negative values than all other F(1) hybrid and parental types ( P<0.001). Third, in the wild, a similar pattern was found in leaf delta(13)C values where both hybrid cross types had the lowest values ( P<0.001) and backcross hybrids had lower delta(13)C values than any other tree type ( P<0.001). Our findings have two important implications: (1). the existence of a consistent genetic difference in whole-tree physiology suggests that whole-tree gas and water exchange could be another pathway through which genes could affect ecosystems; and (2). such studies are important because they seek to quantify the genetic variation that exists in basic physiological processes-such knowledge could ultimately place ecosystem studies within a genetic framework.

Carbon Isotopes↗

PubMed2002

Genetic variation of apolipoproteins in North Indians.

Genetic variation at three apolipoprotein loci (APOA4, APOH, and APOE) has been examined in nine endogamous populations of Punjab, North India. The overall pattern of allele frequency variation at different loci is compatible with that of European populations, but observed microvariation differentiates the populations according to their position in the Indian caste structure. The most common allele at the APOA4 locus was APOA4*1 with a narrow frequency range (89%-92%). APOH*2 allele frequency was highest in these populations (0.852-0.914). APOE*E4 allele frequency was relatively low (6%-10%) in the North Indian populations compared to its frequency in many European populations. The anthropological usage of these polymorphisms was evaluated using multivariate analyses. Genetic distance analysis and principal correspondence analysis showed that the North Indian populations are closest to Europeans, followed by Chinese and African populations. Overall, this study highlights the usefulness of apolipoproteins as genetic markers for clinical, population, and anthropological studies.

Adult↗

PubMedDate not supplied

The impact of human genetic variation on HIV disease in the era of HAART.

Human genetic variation may directly or indirectly influence response to modern antiretroviral therapies for HIV. It is already known that some immunogenetic and other human genetic variations affect the natural history of HIV disease progression where individuals are untreated, but less information is available as to whether these differences are still relevant in the context of HAART. Antiretroviral therapy adds additional opportunities for human genetic contributions to affect variable prognosis--in particular for those genes which influence pharmacokinetics and/or adverse events. To date, the majority of studies investigating the influence of human genetic variation on HIV disease and treatment outcome have focused on single nucleotide polymorphisms or a small number of polymorphisms within a single gene. Reports to date have generally described small effect sizes, and have often been contradictory. Thus, while simple genetic markers relevant to HIV disease or treatment response have indeed been identified (e.g. CCR5delta32 in the context of untreated HIV disease, or HLA-B*5701 allele on the abacavir hypersensitivity reaction in the context of HAART), it is more likely that HIV disease and treatment outcomes are influenced by a multitude of interacting genotypes and phenotypes, a hypothesis that will become increasingly possible to investigate as improvements in molecular and computational technologies are made.

Antiretroviral Therapy, Highly Active↗

PubMed2005

Genetic variation at nine short tandem repeat loci among islanders of the eastern Adriatic coast of Croatia.

We have analyzed the extent of genetic variation at nine autosomal short tandem repeat loci (D3S1358, VWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820) among six populations from Croatia: five distributed in the islands of the eastern Adriatic coast and one from the mainland. The purpose is to investigate the usefulness of these loci in detecting regional genetic differentiation in the studied populations. Significant heterogeneity among the island and mainland populations is revealed in the distributions of allele frequencies; however, the absolute magnitude of the coefficient of gene differentiation is small but significant. The summary measures of genetic variation, namely, heterozygosity, number of alleles, and allele size variance, do not indicate reduced genetic variation in the island populations compared to the mainland population. In contrast to the two measures of genetic variation, allele size variance and within-locus heterozygosity, the imbalance index (beta) indicates evidence of recent expansion of population sizes in all islands and in the mainland. High mutation rates of the studied loci together with local drift effects are likely explanations for interisland genetic variation and the observed lack of reduced genetic diversity among the island populations.

Alleles↗

PubMed1979

Genetic variation in prenatal survival and litter size.

The nature of genetic variation in litter size and its components was examined using results of long term selection and of crossing selected lines of mice. Selection for small and for large litters produced strains with mean litter size of approximately 6 and 15, respectively. The large litter size line showed a period of renewed response after 45 generations of selection, following a period of 15 generations with no response. The relative contribution of genotype of the dam and of the embryo to prenatal survival was examined using results of selection, crossing and embryo transfer. Genotype of female carrying the litter was responsible for most of the observed differences. Genes for poor survival expressed by the embryo were present in some strains, but accounted for less variation than did maternal genotype. Information from the selected lines and from crosses among them provided evidence for dominance of genes affecting fertility and prenatal survival and additivity of genes affecting ovulation rate and body weight. The information was used to suggest a model for more effective exploitation of heterosis using breeds or strains of animals of known performance for different components. The extent of genetic variation for prenatal survival suggests that natural selection in this species may not always be for maximum survival. It is suggested that the ability to reduce litter size after conception, in response to nutritional or other stress, may at times be of selective advantage, contributing to maintenance of genetic variation in survival rate.

Animals↗

PubMed1988

Population amalgamation and genetic variation: observations on artificially agglomerated tribal populations of Central and South America.

The interpretation of data on genetic variation with regard to the relative roles of different evolutionary factors that produce and maintain genetic variation depends critically on our assumptions concerning effective population size and the level of migration between neighboring populations. In humans, recent population growth and movements of specific ethnic groups across wide geographic areas mean that any theory based on assumptions of constant population size and absence of substructure is generally untenable. We examine the effects of population subdivision on the pattern of protein genetic variation in a total sample drawn from an artificial agglomerate of 12 tribal populations of Central and South America, analyzing the pooled sample as though it were a single population. Several striking findings emerge. (1) Mean heterozygosity is not sensitive to agglomeration, but the number of different alleles (allele count) is inflated, relative to neutral mutation/drift/equilibrium expectation. (2) The inflation is most serious for rare alleles, especially those which originally occurred as tribally restricted "private" polymorphisms. (3) The degree of inflation is an increasing function of both the number of populations encompassed by the sample and of the genetic divergence among them. (4) Treating an agglomerated population as though it were a panmictic unit of long standing can lead to serious biases in estimates of mutation rates, selection pressures, and effective population sizes. Current DNA studies indicate the presence of numerous genetic variants in human populations. The findings and conclusions of this paper are all fully applicable to the study of genetic variation at the DNA level as well.

Alleles↗

PubMed2004

AFLP analysis of Cynodon dactylon (L.) Pers. var. dactylon genetic variation.

Cynodon dactylon (L.) Pers. var. dactylon (common bermudagrass) is geographically widely distributed between about lat 45 degrees N and lat 45 degrees S, penetrating to about lat 53 degrees N in Europe. The extensive variation of morphological and adaptive characteristics of the taxon is substantially documented, but information is lacking on DNA molecular variation in geographically disparate forms. Accordingly, this study was conducted to assess molecular genetic variation and genetic relatedness among 28 C. dactylon var. dactylon accessions originating from 11 countries on 4 continents (Africa, Asia, Australia, and Europe). A fluorescence-labeled amplified fragment length polymorphism (AFLP) DNA profiling method was used to detect the genetic diversity and relatedness. On the basis of 443 polymorphic AFLP fragments from 8 primer combinations, the accessions were grouped into clusters and subclusters associating with their geographic origins. Genetic similarity coefficients (SC) for the 28 accessions ranged from 0.53 to 0.98. Accessions originating from Africa, Australia, Asia, and Europe formed major groupings as indicated by cluster and principal coordinate analysis. Accessions from Australia and Asia, though separately clustered, were relatively closely related and most distantly related to accessions of European origin. African accessions formed two distant clusters and had the greatest variation in genetic relatedness relative to accessions from other geographic regions. Sampling the full extent of genetic variation in C. dactylon var. dactylon would require extensive germplasm collection in the major geographic regions of its distributional range.

Cynodon↗

PubMedDate not supplied

Genetic variation and inferences about perceived taste intensity in mice and men.

The study of genetic variation in taste produces parallels between mice and men. In mice, genetic variation across strains has been documented with psychophysical and anatomical measures as well as with recordings from whole nerves. In humans, the variation has been documented with psychophysical and anatomical measures. Whole-nerve recordings from animals and psychophysical ratings of perceived intensities from human subjects have a similar logical limitation: absolute comparisons across individuals require a standard stimulus that can be assumed equally intense to all. Comparisons across whole-nerve recordings are aided by single-fiber recordings. Comparisons across psychophysical ratings of perceived intensity have been aided by recent advances in methodology; these advances now reveal that the magnitude of genetic variation in human subjects is larger than previously suspected. In females, hormones further contribute to variation in taste. There is evidence that the ability to taste (particularly bitter) cycles with hormones in women of child-bearing age, rises to a maximum early in pregnancy and declines after menopause. Taste affects food preferences, which in turn affect dietary behavior and thus disease risks. Valid assessment of taste variation now permits measurement of the impact of taste variation on health. Advances in psychophysical methodology were essential to understanding genetic variation in taste. In turn, the association of perceived taste intensities with tongue anatomy now provides a new tool for psychophysics. The ability of a psychophysical scale to provide across-subject comparisons can be assessed through its ability to show the fungiform papillae density-taste association.

Animals↗