Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “allele frequency changes”

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 145 records · Page 8Linked to original sources
PubMed1975

Linkage disequilibrium causing selection at a neutral locus in pooled Tribolium populations.

The role of linkage disequilibrium with respect to the changes in allele frequencies at a marker locus in newly started polymorphic populations is demonstrated using the marker locus black in Tribolium. The experiments, jointly taken, indicate that the black locus is selectively neutral, or nearly so, under the current experimental conditions. A number of possible mechanisms for selection at the neutral marker locus, i.e. a single linked or non-linked locus and a number of linked and/or non-linked loci through which selection acts, are discussed. On the basis of the experiments some of these models can be excluded, leaving three models for further evaluation: (A) a single linked fitness locus, (B) a number of linked fitness loci and (C) a number of both linked and non-linked fitness loci. The first of these models allows estimation of parameters (recombination fraction and selection coefficients). Models B and C are described in terms of heterozygosity of chromosome pairs. It is argued that in view of the history of a laboratory mutant stock, model C fits best to the experimental results.

Alleles↗
PubMed1994

Sex-linkage of two enzyme loci in Oncorhyncus mykiss (rainbow trout)

We report the first sex-linked loci in Oncorhynchus mykiss (rainbow trout). Previous cytological and breeding experiments have demonstrated an XX/XY sex determining system in this and other salmonid species. Joint segregation data from fathers indicated an average of 8.1 per cent recombination between HEX-2 and the sex determining locus (SEX). The average recombination between HEX-2 and sSOD-1 in fathers was 26.8 per cent. No evidence of non-random segregation of HEX-2 and sSOD-1 was found in mothers; this difference in recombination rates between males and females is concordant with previous studies with rainbow trout and other salmonid species. These results also suggest the possibility that proper chromosomal pairing and segregation in salmonid males does not require a crossover event. Unlike the extreme XX/XY heteromorphy in mammals, functional alleles for HEX-2 and sSOD-1 occur on both the X and Y chromosomes. Significant non-random associations (i.e. gametic disequilibrium) occur between genotypes at HEX-2 and SEX in the hatchery population used for the inheritance study. This gametic disequilibrium has resulted in large changes in allele frequency at HEX-2 from one generation to the next and an excess of heterozygotes in comparison to expected binomial (i.e. Hardy-Weinberg) proportions.

Animals↗
PubMed2004

Microsatellite DNA variation reveals high gene flow and panmictic populations in the Adriatic shared stocks of the European squid and cuttlefish (Cephalopoda).

In the semienclosed Adriatic Sea, the shared stocks of the cephalopods Loligo vulgaris and Sepia officinalis represent important marine fisheries resources exploited by all coastal countries. The improving of knowledge on the demographic features of these shared stocks is internationally relevant for adopting responsible management and conservation of these marine resources. Analyses of microsatellite variation in geographical samples collected from all parts of the Adriatic Sea were performed using arrays of species-specific di-nucleotide and tri-nucleotide loci. In L. vulgaris the level of genetic variability was consistent with that observed in other loliginid species, whereas the S. officinalis stock showed a microsatellite variation markedly lower than that estimated for the Atlantic and Mediterranean populations collected around the Iberian peninsula. The weak spatial genetic differentiation, the discordant results of the genetic divergence estimators and the lack of any geographical cline in the spatial genetic differences suggest the occurrence of single genetically homogeneous populations within the Adriatic stocks of both species, recommending a coordinated management of the squid and cuttlefish by the Adriatic fishing countries. On the contrary, significant differences detected in temporal replicates of S. officinalis might suggest that allelic frequency can change relating to reproductive behaviour.

Animals↗
PubMed1999

Molecular variation in Leymus species and populations.

Icelandic populations of European lymegrass [Leymus arenarius (L.) Hochst.] were examined using amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) of the major ribosomal genes (18S-5.8S-26S rDNA), in comparison with Alaskan populations of its closely related species L. mollis (Trin.) Pilger. The AFLP profiles emerged as two distinct entities, clearly separating the two species, and based on species-specific bands it was simple to distinguish these two morphologically similar species. The rDNA-RFLPs also differentiated the species. Within species, the Icelandic L. arenarius was more homogeneous than the Alaskan L. mollis, and its variation was dispersed over geographically different populations, suggesting a common gene pool. The variation among the Alaskan L. mollis was more extensive and its interrupted pattern may be the result of gene introgression at subspecies level. Within a 40-year-old population of L. mollis established in Iceland from Alaskan material, the molecular profiles separated old and new genotypes. Both AFLP and rDNA revealed the new genotypes to be extremely similar. This rapid change in allele frequency is thought to be the result of adaptation to a new environment.

Alaska↗
PubMed2000

Absence of a genetic bottleneck in a wild rabbit (Oryctolagus cuniculus) population exposed to a severe viral epizootic.

Infectious diseases and their demographic consequences are thought to influence the genetic diversity of populations. In Europe, during the last 50 years, the European rabbit (Oryctolagus cuniculus) has suffered two important viral epizootics: myxomatosis and rabbit viral haemorraghic disease (RVHD). Although mortality rates were very high, the impact of these diseases on genetic diversity has never been assessed directly. The subject of this paper is a wild rabbit population in France, which has been studied since the beginning of the 1980s. The first outbreak of RVHD occurred in 1995 and provoked a demographic crash. The population, sampled for the first time in 1982 and 1994, was sampled again at the end of 1996 to examine the impact of the epizootic on genetic diversity. In spite of the observed high mortality rate ( approximately 90%), analysis of 14 polymorphic loci (allozymes and microsatellites) showed no loss in genetic diversity after the epizootic. Determination of temporal changes in allele frequencies indicated that the population evolved under genetic drift. The temporal method of Waples demonstrated a significant decrease in the effective population size (Ne) correlated with the demographic crash due to the epizootic. However, the population had only been studied for two generations after the epizootic and the remnant population size probably stayed high enough ( approximately 50 individuals) to keep its genetic diversity at the precrash level. These results suggest that, contrary to what is usually thought and in spite of the subsequent high mortality rates, past epizootics (especially myxomatosis) may have had little effect on the genetic diversity of wild rabbit populations in Europe.

Alleles↗
PubMed2003

Census vs. effective population size in chinook salmon: large- and small-scale environmental perturbation effects.

Population viability has often been assessed by census of reproducing adults. Recently this method has been called into question and estimation of the effective population size (Ne) proposed as a complementary method to determine population health. We examined genetic diversity in five populations of chinook salmon (Oncorhynchus tshawytscha) from the upper Fraser River watershed (British Columbia, Canada) at 11 microsatellite loci over 20 years using DNA extracted from archived scale samples. We tested for changes in genetic diversity, calculated the ratio of the number of alleles to the range in allele size to give the statistic M, calculated Ne from the temporal change in allele frequency, used the maximum likelihood method to calculate effective population size (NeM), calculated the harmonic mean of population size, and compared these statistics to annual census estimates. Over the last two decades population size has increased in all five populations of chinook examined; however, Ne calculated for each population was low (81-691) and decreasing over the time interval measured. Values of NeM were low, but substantially higher than Ne calculated using the temporal method. The calculated values for M were generally low (M < 0.70), indicating recent population reductions for all five populations. Large-scale historic barriers to migration and development activities do not appear to account for the low values of Ne; however, available spawning area is positively correlated with Ne. Both Ne and M estimates indicate that these populations are potentially susceptible to inbreeding effects and may lack the ability to respond adaptively to stochastic events. Our findings question the practice of relying exclusively on census estimates for interpreting population health and show the importance of determining genetic diversity within populations.

Animals↗
PubMed2000

Reduced X-linked nucleotide polymorphism in Drosophila simulans.

Population genetic theory predicts that selectively driven changes of allele frequency for both beneficial and deleterious mutants reduce polymorphism at tightly linked sites. All else being equal, these reductions in polymorphism are expected to be greater when recombination rates are lower. Therefore, the empirical observation of a positive correlation between recombination rates and amounts of DNA polymorphism across the Drosophila melanogaster genome can be explained by two very different types of natural selection. Here, we evaluate alternative models of effects of selection on linked sites by comparison of X-linked and autosomal variation. We present polymorphism data from 40 genes distributed across chromosome arms X and 3R of Drosophila simulans, a sibling species of D. melanogaster. We find significantly less silent polymorphism in D. simulans on the X chromosome than on 3R, but no difference between arms for silent divergence between species. This pattern is incompatible with predictions from theoretical studies on the effect of negative selection on linked sites. We propose that some form of positive selection having greater effects on sex chromosomes than on autosomes is the better explanation for the D. simulans data.

Animals↗
PubMed1988

Adaptation at specific loci. V. Metabolically adjacent enzyme loci may have very distinct experiences of selective pressures.

The polymorphic phosphoglucomutase (PGM) and glucose-6-phosphate dehydrogenase (G6PD) loci have been studied in parallel to experimental work on the phosphoglucose isomerase (PGI) polymorphism in Colias butterflies. PGI, PGM and G6PD are also autosomal in Colias. PGM and G6PD are loosely linked (and represent the first identified autosomal linkage group in Colias); they assort independently from PGI. Recombination occurs in both sexes. Neither PGM nor G6PD shows large, consistent differences in flight capacity through the day among its genotypes, as PGI does. PGM shows some change of allele frequencies, and match to Hardy-Weinberg expectation, with air temperature in middle and latter parts of the season, but not early in the season. G6PD may show some heterozygote excess over Hardy-Weinberg expectation early in the day, but more testing is needed. No evidence for differential survivorship was seen at PGM or G6PD, in contrast to PGI. At the PGM and G6PD loci, male heterozygotes are advantaged in mating with females, but without the evidence of female choice which occurs for PGI. These effects are not correlated among the three loci. There is no assortative mating at G6PD (nor at PGI). There is minor positive assortative mating of PGM heterozygotes, but it is too weak to account for the PGM-genotype-specific male mating advantage. No trends of multilocus genotype frequencies involving PGI are seen. Certain PGM-G6PD two-locus genotypes are over-represented, and others under-represented, in wild adult samples, particularly among males and uniformly among successfully mating males. Our results emphasize that enzyme loci sharing a substrate need not have common experience of the existence or strength of natural selection, and suggest initial food-resource processing and allocation as a possible context for fitness-related effects of the PGM and G6PD polymorphisms.

Animals↗
PubMed1997

Population dynamics inferred from temporal variation at microsatellite loci in the selfing snail Bulinus truncatus.

We analyzed short-term forces acting on the genetics of subdivided populations based on a temporal survey of the microsatellite variability in the hermaphrodite freshwater snail Bulinus truncatus. This species inhabits temporary habitats, has a short generation time and exhibits variable rates of selfing. We studied the variability over three sampling dates in 12 Sahelian populations (1161 individuals). Classical genetic parameters (estimators of Ho, He, f, selfing rate and Fst) showed limited change over time whereas important temporal changes of allelic frequencies were detected for 10 of the ponds studied. These variations are not easily explained by selection, sampling drift and genetic drift alone and may be due to periodic migration. Indeed the habitats occupied by the populations studied are subject to large temporal fluctuations owing to annual cycles of drought and flood. In such ponds our results support a demographic model of population expansions and contractions under which available habitats, after the rainy season, are colonized by individuals originating from a smaller number of refuges (areas that never dry out in the deepest parts of the ponds). In contrast, selfing appeared to be an important force affecting the genetic structure in permanent ponds.

Animals↗
PubMed1997

Historical analysis of genetic variation reveals low effective population size in a northern pike (Esox lucius) population.

Effective population size (Ne) of a natural fish population was estimated from temporal changes in allele frequencies at seven microsatellite loci. Use of a historical collection of fish scales made it possible to increase the precision of estimates by increasing the time interval between samples and to use an equation developed for discrete generations without correcting for demographic parameters. Estimates of Ne for the time intervals 1961-1977 and 1977-1993 were 35 and 72, respectively. For the entire interval, 1961-1993, the estimate of Ne was 48 when based on a weighted mean derived from the above two estimates or 125 when calculated from 1961 and 1993 samples only. Corresponding ratios of effective size to adult census size ranged from 0.03 to 0.14. An Ne of 48 over a 32-year period would imply that this population lost as much as 8% of its heterozygosity in that time. Results suggest the potential for using genetic methods based on microsatellite loci data to compare historical trends in Ne with population dynamic parameters. Such comparisons will help to evaluate the relationship between genetic diversity and long-term persistence of natural populations.

Animals↗
PubMed2000

Monte Carlo evaluation of the likelihood for N(e) from temporally spaced samples.

A population's effective size is an important quantity for conservation and management. The effective size may be estimated from the change of allele frequencies observed in temporally spaced genetic samples taken from the population. Though moment-based estimators exist, recently Williamson and Slatkin demonstrated the advantages of a maximum-likelihood approach that they applied to data on diallelic genetic markers. Their computational methods, however, do not extend to data on multiallelic markers, because in such cases exact evaluation of the likelihood is impossible, requiring an intractable sum over latent variables. We present a Monte Carlo approach to compute the likelihood with data on multiallelic markers. So as to be computationally efficient, our approach relies on an importance-sampling distribution constructed by a forward-backward method. We describe the Monte Carlo formulation and the importance-sampling function and then demonstrate their use on both simulated and real datasets.

Algorithms↗
PubMed2001

Clinal variation for amino acid polymorphisms at the Pgm locus in Drosophila melanogaster.

Clinal variation is common for enzymes in the glycolytic pathway for Drosophila melanogaster and is generally accepted as an adaptive response to different climates. Although the enzyme phosphoglucomutase (PGM) possesses several allozyme polymorphisms, it is unique in that it had been reported to show no clinal variation. Our recent DNA sequence investigation of Pgm found extensive cryptic amino acid polymorphism segregating with the allozyme alleles. In this study, we characterize the geographic variation of Pgm amino acid polymorphisms at the nucleotide level along a latitudinal cline in the eastern United States. A survey of 15 SNPs across the Pgm gene finds significant clinal differentiation for the allozyme polymorphisms as well as for many of the cryptic amino acid polymorphisms. A test of independence shows that pervasive linkage disequilibrium across this gene region can explain many of the amino acid clines. A single Pgm haplotype defined by two amino acid polymorphisms shows the strongest correlation with latitude and the steepest change in allele frequency across the cline. We propose that clinal selection at Pgm may in part explain the extensive amino acid polymorphism at this locus and is consistent with a multilocus response to selection in the glycolytic pathway.

Amino Acids↗
PubMed2003

Selection in a subdivided population with local extinction and recolonization.

In a subdivided population, local extinction and subsequent recolonization affect the fate of alleles. Of particular interest is the interaction of this force with natural selection. The effect of selection can be weakened by this additional source of stochastic change in allele frequency. The behavior of a selected allele in such a population is shown to be equivalent to that of an allele with a different selection coefficient in an unstructured population with a different size. This equivalence allows use of established results for panmictic populations to predict such quantities as fixation probabilities and mean times to fixation. The magnitude of the quantity N(e)s(e), which determines fixation probability, is decreased by extinction and recolonization. Thus deleterious alleles are more likely to fix, and advantageous alleles less likely to do so, in the presence of extinction and recolonization. Computer simulations confirm that the theoretical predictions of both fixation probabilities and mean times to fixation are good approximations.

Alleles↗
PubMed1976

Gene conversion: a hitherto overlooked parameter in population genetics.

Gene conversion causes deviations from the 2:2 segregation of allele pairs in meiosis. Thus, gene conversion is a potential cause for changes of allele frequencies in populations. Equations are derived for the effects of conversion in a large random-mating population. The influence of gene conversion on allele frequencies is compared with that of spontaneous mutation and meiotic drive.

Alleles↗
PubMed1994

Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci.

Genetic divergence and gene flow among closely related populations are difficult to measure because mutation rates of most nuclear loci are so low that new mutations have not had sufficient time to appear and become fixed. Microsatellite loci are repeat arrays of simple sequences that have high mutation rates and are abundant in the eukaryotic genome. Large population samples can be screened for variation by using the polymerase chain reaction and polyacrylamide gel electrophoresis to separate alleles. We analyzed 10 microsatellite loci to quantify genetic differentiation and hybridization in three species of North American wolflike canids. We expected to find a pattern of genetic differentiation by distance to exist among wolflike canid populations, because of the finite dispersal distances of individuals. Moreover, we predicted that, because wolflike canids are highly mobile, hybrid zones may be more extensive and show substantial changes in allele frequency, relative to nonhybridizing populations. We demonstrate that wolves and coyotes do not show a pattern of genetic differentiation by distance. Genetic subdivision in coyotes, as measured by theta and Gst, is not significantly different from zero, reflecting persistent gene flow among newly established populations. However, gray wolves show significant subdivision that may be either due to drift in past Ice Age refugia populations or a result of other causes. Finally, in areas where gray wolves and coyotes hybridize, allele frequencies of gray wolves are affected, but those of coyotes are not. Past hybridization between the two species in the south-central United States may account for the origin of the red wolf.

Alleles↗
PubMed2005

Estimation of effective population sizes from data on genetic markers.

The effective population size (Ne) is an important parameter in ecology, evolutionary biology and conservation biology. It is, however, notoriously difficult to estimate, mainly because of the highly stochastic nature of the processes of inbreeding and genetic drift for which Ne is usually defined and measured, and because of the many factors (such as time and spatial scales, systematic forces) confounding such processes. Many methods have been developed in the past three decades to estimate the current, past and ancient effective population sizes using different information extracted from some genetic markers in a sample of individuals. This paper reviews the methodologies proposed for estimating Ne from genetic data using information on heterozygosity excess, linkage disequilibrium, temporal changes in allele frequency, and pattern and amount of genetic variation within and between populations. For each methodology, I describe mainly the logic and genetic model on which it is based, the data required and information used, the interpretation of the estimate obtained, some results from applications to simulated or empirical datasets and future developments that are needed.

Evolution, Molecular↗
PubMed1995

Biochemical genetics of a natural population of Escherichia coli: seasonal changes in alleles and haplotypes.

The level of diversity, degree of enzyme polymorphism, effective population size, and the relative roles of drift and selection were examined in a cross-section of a natural Escherichia coli population based on random samples of haplotypes of E. coli isolated from sewage. The population studied contained E. coli strains derived from a human population of approximately 16,000 individuals, as well as from other sources. Three sample sets were taken between May and August. Each set consisted of 100 E. coli clones. Six enzyme loci [GPI (5 alleles), GPD (5 alleles), PGD (10 alleles), ADH (8 alleles), IDH (6 alleles), PGM (6 alleles)] were surveyed electrophoretically for each clone; 159 different haplotypes were obtained and it is likely that all possible combinations are present in the population sampled. The large numbers of different haplotypes observed were distributed as a series of four genetically similar families of clones. The large estimated effective population size (Ne = 10(10)) means that the observed large and highly significant changes in allele frequencies with time are not due to genetic drift. Selection, though not necessarily at the loci studied, is considered the only likely explanation.

Alleles↗
PubMed2026

Quantifying the Evolutionary Potential for Delta Smelt Persistence in a Warming Habitat.

Long-term persistence of managed species will depend, in part, on whether the species harbors the physiological or genetic potential to adjust to warming temperatures, and whether relevant genetic variation is modified by management practices. The critically endangered Delta Smelt (Hypomesus transpacificus) is intensively managed, but little is known about the presence of genetic variation for resistance to elevated temperature. Using a pedigree and whole genome sequencing data, we characterized the genetic basis of CTMax (as a metric of upper thermal tolerance) across control and elevated rearing temperatures, alongside covarying traits (body size and degree of hatchery ancestry). Warmer rearing temperatures increased CTMax through acclimation but also resulted in reduced additive genetic variation for the trait. We observed modest heritability for CTMax at rearing temperatures of 15&#xb0;C and 18&#xb0;C (0.26 and 0.16, respectively), but only a limited number of loci were identified that had consistent effects on CTMax across rearing temperatures. Instead, the genomic basis of thermal tolerance was highly dependent on rearing temperature (i.e., many loci detected with a GxE effect). This temperature-dependent genomic architecture is consistent with our finding that additive genetic variation for CTMax was reduced under warmer rearing conditions, indicating a potential constraint on adaptive evolutionary change. The influence of domestication selection was indicated by changes in allele frequency, and divergence in upper thermal tolerance and plasticity, between low and high hatchery ancestry groups. Minimal overlap between loci associated with domestication and CTMax suggests that these traits possess separate genetic underpinnings. Knowledge of genetic variation supporting ecologically relevant physiological variation may be useful for captive management and may inform supplementation of fish to the wild in an ever-warming environment.

conservation physiology↗