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At least 649 records · Page 36Linked to original sources

PubMed1990

Genetic population structure, clonal phylogeny, and pathogenicity of Salmonella paratyphi B.

Genetic diversity and relationships among 123 strains of Salmonella paratyphi B (serotype 1,4,[5],12:b:[1,2]) were estimated from an assessment of electrophoretically demonstrable allelic variation at 24 chromosomal enzyme gene loci. Fourteen electrophoretic types, marking clones, were distinguished, the phylogeny of the clonal lineages was reconstructed, and biotype and other phenotypic characters were mapped onto this structure. Most d-tartrate-negative strains are members of an abundant, globally distributed clone (Pb 1) that is polymorphic for many biotype characters (including d-tartrate utilization), bacteriophage type, rRNA pattern, and colicin M and phage ES18 sensitivity. This clone is largely responsible for S. paratyphi B enteric fever in humans. In contrast, d-tartrate-positive strains (formerly known as S. java) occurred in all seven of the clonal lineages identified by population genetic analysis, although most d-tartrate-positive isolates belong to only two clones (Pb 3 and Pb 4), which vary in frequency geographically. Monophasic strains represent four closely related clones forming a distinctive phylogenetic lineage. The Kauffmann hypothesis of convergence in serotype among distantly related cell lineages through recombination (via phage transduction or other means) may account for the considerable genotypic diversity among clones of S. paratyphi B. Pb 4, Pb 6, and Pb 7 are more closely allied with clones of S. typhimurium and S. saintpaul than with other clones of S. paratyphi B. Sensitivity or resistance to colicin M and phage ES18 and the electrophoretic pattern of the rRNA, which were incorporated into a recently proposed scheme for the identification of types of S. paratyphi B, individually or in combination fail to mark clones or other meaningful phylogenetic subdivisions.

Colicins↗

PubMed2004

Population genetic structure of Pacific white shrimp (Litopenaeus vannamei) from Mexico to Panama: microsatellite DNA variation.

Genetic variation and population structure of wild white shrimp (Litopenaeus vannamei) from 4 geographic locations from Mexico to Panama were investigated using 5 microsatellite DNA loci. The genetic diversity between populations was indicated by the mean number of alleles per locus and mean observed heterozygosity, which ranged from 7.4 to 8.6 and from 0.241 to 0.388, respectively. Significant departures from Hardy-Weinberg equilibrium were found at most locations at each locus, with the exception Guatemala at Pvan0013, and were caused by high heterozygote deficiencies. Genetic differences between localities were detected by pairwise comparison based on allelic and genotypic frequencies, with the exception of locus Pvan1003. Significant pairwise F (ST) values between locations and total F (ST) showed that the white shrimp population is structured into subpopulations. However, population differentiation does not follow an isolation-by-distance model. Knowledge of the genetic diversity and structure of L.vannamei populations will be of interest for aquaculture and fisheries management to utilize and preserve aquatic biodiversity.

Animals↗

PubMed2006

Identification of management units using population genetic data.

The identification of management units (MUs) is central to the management of natural populations and is crucial for monitoring the effects of human activity upon species abundance. Here, we propose that the identification of MUs from population genetic data should be based upon the amount of genetic divergence at which populations become demographically independent instead of the current criterion that focuses on rejecting panmixia. MU status should only be assigned when the observed estimate of genetic divergence is significantly greater than a predefined threshold value. We emphasize the need for a demographic interpretation of estimates of genetic divergence given that it is often the dispersal rate of individuals that is the parameter of immediate interest to conservationists rather than the historical amount of gene flow.

Animals↗

PubMed2004

[Impacts of malathion on population genetic structure of Oxya chinensis].

Allozyme electrophoresis was employed to compare the difference in mortality among the genotypes at two polymorphic loci of Pgm and Me of grasshopper Oxya chinensis individuals acutely exposed to 1.5g/L malathion which resulted in 56% mortality in 24 hours. The selective lethal effects were observed among the genotypes at Pgm locus but not at Me locus. It is noted that the genotype Pgm-ab experienced the highest mortality (80%), whereas Pgm-bb and Pgm-bc were 49%, lower than the average. The chi(2) tests showed significant difference in morality between Pgm-bb and Pgm-cc. After exposure the allele frequency of Pgm-b showed a notable increase among surviving individuals. The cluster analysis based on Roger's genetic distance indicated that the acute exposure to malathion can cause differentiation in genetic composition at population level in Oxya chinensis. Because malathion is commonly used as the insecticide for grasshopper control, the data obtained in this study suggest that the similar genotype-mortality effects may occur in crop fields.

Alleles↗

PubMed2003

[Population-genetic structure of Chuvashia (from data on eight DNA loci in the nuclear genome)].

Population-genetic study of indigenous populations representing three ethnic Chuvash group: highland (Cheboksarsk and Morgaush district), lowland (Kanash district) and mid-lowland (Marposad district). Eight polymorphic DNA loci of the nuclear genome (VNTR/PAH, STR/PAH, VNTR/ApoB, VNTR/DAT1, APF, VNTR/eNOS, IVS6aGATT, and KM.19/PstI) were examined in the population of each district. For each of the four population, we estimated the allele and genotype frequency distributions at each polymorphic system, heterozygosities HS and between-population differences FST. In the combined Chuvash sample, HS = 0.464 and FST = 0.006. Loci VNTR(DAT) and VNTR(ApoB) showed highest between-population differentiation (0.009 < or = FST < or = 0.012), and loci IVS6aGATT, APF, VNTR/eNOS, and D7S23 (KM.19), lowest differentiation (0.001 < or = FST < or = 0.003). Analysis of genetic distances revealed somewhat higher genetic similarity between the Cheboksarsk and Morgaush populations belonging to the highland Chuvash group, whereas the highland Chuvash population from the Marposad district, which belong to the mid-lowland group, was more distant from the former populations.

Base Sequence↗

PubMed2000

Variant detection at the delta opioid receptor (OPRD1) locus and population genetics of a novel variant affecting protein sequence.

The three opioid receptor genes, and in particular the mu and delta loci (OPRM1 and OPRD1, respectively), are compelling candidates to influence risk for substance dependence. Previous study of a variant at the OPRD1 locus, T921C, has shown association with opioid dependence. This variant does not alter protein sequence, and could not be directly responsible for a physiologic effect. We sequenced the OPRD1 coding region in six individuals with differing T921C alleles, to identify new common variants more likely to explain the association with phenotype. We identified one novel variant in exon 1, 80T-->G, which predicts a change in amino acid sequence from phenylalanine (80T) to cysteine (80G) (F27C). We present here basic population genetics of this variant, and population genetic data for the T921C variant. We found significant differences in allele frequency between populations, and a maximum frequency of the 80G allele of 9%, in each of two European populations. This variant could contribute to the previously reported association results.

Alleles↗

PubMed1987

Population genetics implications of the premutation hypothesis for the generation of the fragile X mental retardation gene.

The population genetics implications of the premutation hypothesis for the generation of the fragile X mental retardation gene are explored. With some broad assumptions, the consequences of the model are that 50% of mothers of probands carry the premutation; 6.5% of mothers of probands receive the premutation from their mothers, 18.9% from their fathers, and 24.6% as a "new mutation"; the incidence of carriers for the full mutation equals the incidence of affected males, whereas the incidence of carriers for the premutation is 1.35 times the incidence of affected males; assuming mutation rates are equal in eggs and sperm, the mutation rate from normal to premutation alleles is 1.67 X 10(-4); the expected segregation ratio in sibs of probands is 0.44, which corresponds to observed values. In addition, predictions using the premutation hypothesis of the expected segregation ratio in sibs of mothers of probands fits well with the data of Vogel and coworkers.

Female↗

PubMed2004

The molecular population genetics of HIV-1 group O.

HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics and epidemic history of HIV-1 group O from viral gene sequence data and evaluate the effect of variable evolutionary rates and recombination on our estimates. First, model selection tools were used to specify suitable evolutionary and coalescent models for HIV group O. Second, divergence times and population genetic parameters were estimated in a Bayesian framework using Markov chain Monte Carlo sampling, under both strict and relaxed molecular clock methods. Our results date the origin of the group O radiation to around 1920 (1890-1940), a time frame similar to that estimated for HIV-1 group M. However, group O infections, which remain almost wholly restricted to Cameroon, show a slower rate of exponential growth during the twentieth century, explaining their lower current prevalence. To explore the effect of recombination, the Bayesian framework is extended to incorporate multiple unlinked loci. Although recombination can bias estimates of the time to the most recent common ancestor, this effect does not appear to be important for HIV-1 group O. In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome.

Bayes Theorem↗

PubMed1994

Population genetics of fragile X: a multiple allele model with variable risk of CGG repeat expansion.

A model of the population genetics of fragile X that incorporates an arbitrarily large number of alleles based on CGG repeat number is presented. The probability of transition from a premutation to a full mutation upon maternal transmission depends on maternal allele size, as suggested by molecular data. Transitions among various sizes of premutation alleles upon both maternal and paternal transmission are also included using empirically determined transition probabilities. Multiple paths to the final full mutation allele are allowed. Algebraic results for equilibrium allele frequencies are presented for an arbitrary number of alleles, and numerical results are presented for the case of 9 alleles. The model predicts large frequencies for alleles near the normal premutation borderline and high mutation probabilities for the first few mutational steps. The model also predicts that the approach to equilibrium allele frequencies is quite slow, and that a premutation allele typically persists for many generations in a given family before the final transition to a full mutation allele. These nonequilibrium effects are sensitive to the transition probability from large normal alleles to small premutation alleles.

Alleles↗

PubMed2001

[Population genetics and medicine].

The paper covers several topics that demonstrate a close relationship between population genetics and medicine. To study isolated populations is an effective tool to detect "new" Mendelian diseases and to map the genes of hereditary diseases. Several new molecular genetic techniques have been developed, which facilitates the procedure of gene mapping. New genetic polymorphisms, such as VNTR, STR, and SNP in particular, have increased the feasibility of searching for genes, which predisposes to common diseases through linkage mapping and association studies. DNA polymorphisms have been shown to be also effective in solving the problems of pharmacological genetics and for detecting genes whose variability is associated with the efficacy of drugs and their side effects.

Chromosome Mapping↗

PubMed1987

[Population genetics study of hemoglobinopathies in Uzbekistan. II. Population dynamics of hemoglobinopathies].

It was shown that on comparing variability of selective neutral genetic marker systems with that of the beta-thalassemia system for the populations of different hierarchical level, the relative importance of selection and genetic drift could be evaluated. The genetic differentiation of the beta-thalassemia gene frequencies in elementary populations (villages) could be solely explained by genetic drift. On the other hand, the differentiation of district populations (the sizes of the populations being 10(6] for beta-thalassemia gene frequencies could be explained by selection forces. This is supported by the fact that the genetic distances and FST values are only significant for the beta-thalassemia gene and not for the neutral genetic systems, when the district populations are compared.

Genetic Markers↗

PubMed1991

Severe combined immunodeficiency among the Navajo. I. Characterization of phenotypes, epidemiology, and population genetics.

Previous studies have identified a high incidence of severe combined immunodeficiency (SCID) among the Navajo Native American population. To determine the incidence and population genetics of this condition, we reviewed the death certificates of all children who died between 1969 and 1982, established the cases that met criteria identified in previously investigated cases, and interviewed the selected children's families. SCID cases were distributed spatially and temporally. Segregation parameter estimates of 0.27-0.38 were obtained from data from 24 interviewed families, suggesting an estimated gene frequency of 2.1% (arguing against a multifactorial inheritance). SCID cases referred to specialty centers lacked T and B cells in their blood, and their serum immunoglobulins ranged from absent to near normal.

Arizona↗

PubMed1991

Germline selection: population genetic aspects of the sexual/asexual life cycle.

Population geneticists make a distinction between sexual and asexual organisms depending on whether individuals inherit genes from one or two parents. When individual genes are considered, this distinction becomes less satisfactory for multicellular sexual organisms. Individual genes pass through numerous asexual mitotic cell divisions in the germline prior to meiosis and sexual recombination. The processes of mitotic mutation, mitotic crossing over, and mitotic gene conversion create genotypic diversity between diploid cells in the germline. Genes expressed in the germline whose products affect cell viability (such as many "housekeeping" enzymes) may be subjected to natural selection acting on this variability resulting in a non-Mendelian output of gametes. Such genes will be governed by the population genetics of the sexual/asexual life cycle rather than the conventional sexual/Mendelian life cycle. A model is developed to investigate some properties of the sexual/asexual life cycle. When appropriate parameter values were included in the model, it was found that mutation rates per locus per gamete may vary by a factor of up to 100 if selection acts in the germline. Sexual/asexual populations appear able to evolve to a genotype of higher fitness despite intervening genotypes of lower fitness, reducing the problems of underdominance and Wright's adaptive landscape encountered by purely sexual populations. As might be expected this ability is chiefly determined by the number of asexual mitotic cell divisions within the germline. The evolutionary consequences of "housekeeping" loci being governed by the dynamics of the sexual/asexual life cycle are considered.

Animals↗

PubMed2005

Molecular evolution and population genetics of circadian clock genes.

This article discusses a number of common methodologies used in the field of population genetics and evolution and reviews their application within circadian rhythm research. We examine the basic principles behind phylogenetic analysis and how these can be used to illuminate clock gene evolution. We then discuss genetic variation between and within species and show how neutrality tests can reveal the signatures of selection or drift on clock genes. These tests are particularly important for moving beyond "just so" stories when discussing the evolution of clock phenotypes, and we provide relevant circadian examples. We also focus on methods that can be used to study genetic variation, such as quantitative trait loci analysis. We discuss the various bootstrapping or resampling techniques that can be applied to generate confidence intervals in the various methodologies and then examine the use of interspecific transformation studies, which can, and have, provide some useful insights, not only into clock gene evolution in particular, but "behavioral" gene evolution in general. Finally, we assess gene/protein alignments and protein structure predictions and their implicit evolutionary bases.

Animals↗

PubMed1996

A population genetic study of the evolution of SINEs. II. Sequence evolution under the master copy model.

A transient population genetic model of SINE (short interspersed repetitive element) evolution assuming the master copy model is theoretically investigated. Means and variances of consensus frequency of nucleotides, nucleotide homozygosity, and the number of shared differences that are considered to have caused by mutations occurring in the master copy lineages are computed. All quantities investigated are shown to be monotone functions of the duration of the expansion period. Thus, they can be used to estimate the expansion period although their sampling variances are generally large. Using the theoretical results, the Sb subfamily of human Alu sequences is analyzed. First, the expansion period is estimated from the observed mean and variance of homozygosity. The expansion period is shown to be short compared to the time since the end of the expansion of the subfamily. However, the observed number of the shared differences is more than twice that expected under the master copy model with the estimated expansion period. Alternative models including that with multiple master copy loci to explain this observation are discussed.

Animals↗

PubMed2003

Population genetic structure in a human-disturbed environment: a case study in the land snail Helix aspersa (Gastropoda: Pulmonata).

Local patterns of genetic variation were analysed in the land snail Helix aspersa for 32 populations sampled within a patchy agricultural landscape: the polders of the Bay of Mont-Saint-Michel (France). This investigation examined the allele frequencies at four enzymatic markers and five microsatellite loci through the genotyping of 580 individuals. A strongly significant population genetic substructuring (mean F(ST)=0.088, P<0.001) was found at the scale of the whole polders area (3050 ha) and both categories of markers displayed a similar magnitude of spatial genetic differentiation. We did not find any obvious effects of habitat fragmentation on the distribution of genetic variability. Despite the reality of habitat patchiness and environmental instability (related to farming practices), an isolation by distance process was clearly depicted, although selective pressures cannot be ruled out for one enzymatic locus. Overall, genetic drift, along with occasional long-distance episodes of gene flow, was presumably the most likely evolutionary force that shaped the observed pattern of genetic variation.

Alleles↗

PubMed1984

Line-of-descent and genealogical processes, and their applications in population genetics models.

A variety of results for genealogical and line-of-descent processes that arise in connection with the theory of some classical selectively neutral population genetics models are reviewed. While some new results and derivations are included, the principle aim is to demonstrate the central importance and simplicity of genealogical Markov chains in this theory. Considerable attention is given to "diffusion time scale" approximations of such genealogical processes. A wide variety of results pertinent to (diffusion approximations of) the classical multiallele single-locus Wright-Fisher model and its relatives are simplified and unified by this approach. Other examples where such genealogical processes play an explicit role, such as the infinite sites and infinite alleles models, are discussed.

Alleles↗

PubMed2001

Characterization of AFLP markers in damselflies: prevalence of codominant markers and implications for population genetic applications.

Amplified fragment length polymorphism (AFLP) analysis is becoming increasingly popular as a method for generating molecular markers for population genetic applications. For practical considerations, it is generally assumed in population studies that AFLPs segregate as dominant markers, i.e., that present and absent are the only possible states of a given locus. We tested the assumption of dominance in natural populations of the damselfly Nehalennia irene (Hagen) (Odonata: Coenagrionidae). Electro-blotted AFLP products from 21 samples were probed with individual markers. Eleven markers were analyzed, of which two were monomorphic and nine were polymorphic. Only two of the polymorphic markers behaved in a strictly dominant manner. The remaining seven polymorphic markers displayed various degrees of codominance, with 2-10 visible alleles in the sample. Of the three markers displaying the highest degree of variability, two contained microsatellite repeat tracts. Our results suggest that the assumption of dominance is unfounded. As a result, AFLP analysis may be unsuitable for estimating several important population genetic parameters, including genetic diversity.

Alleles↗