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PubMed1998

Population genetic study of the simultaneously amplified loci HLA DQA1, LDLR, GYPA, HBGG, D7S8, and GC in a German population sample.

A population genetic study of the HLA DQA1 and the "Polymarker" loci LDLR, GYPA, HBG, D7S8, and GC has been performed in a German Caucasian population (Frankfurt am Main area). All loci are in Hardy-Weinberg equilibrium and no unexpected association of loci has been observed. The data of the allele distributions are similar to those of other Caucasian populations. All six loci together have a power of discrimination (PD) of 0.9996 and an exclusion chance in paternity testing of 0.81.

Alleles↗
PubMed2002

[Population genetic study of the Alatyr region of the Republic of Chuvashiia].

Population genetic characteristics were estimated in the Alatyr' raion (administrative district) of the Republic of Chuvashia, which has long been populated by three ethnic groups. The ethnic assortativeness values in the town of Alatyr' and the rural area of the district were 1.17 and 1.21, respectively, for Russians; 1.14 and 4.82, respectively, for Chuvashes; and 1.33 and 2.45, respectively, for Mordovians. Wright's statistics were as follows: Fst = 0.00358, Fit = 0.00178, and Fis = 0.00134. The migration indices were 0.0264 for Alatyr' and 0.0178 for the district. The endogamy indices for the total and the Russian populations of Alatyr' were 0.47 and 0.53, respectively. The parameters of isolation by distance were a = 0.000189 and b = 0.00959 for the urban and a = 0.000318 and b = 0.00919 for the rural area. Schemes of the genetic landscape were constructed. The influence of the polyethnic composition on the genetic structure of the population is discussed.

Emigration and Immigration↗
PubMed2003

Expression of turkey transcription factors and acyl-coenzyme oxidase in different tissues and genetic populations.

Several transcription factors are involved in regulating lipid metabolism in various animal tissues. Peroxisome proliferator-activated receptor (PPAR) gamma and PPARalpha regulate lipogenesis and fatty acid oxidation. Gene fragments for PPARgamma, PPARalpha, and acyl-coenzyme A oxidase (ACO) have been cloned in turkeys, and the sequences of these genes were highly homologous to those of chickens, pigs, and humans. Data showed that turkey PPARgamma and PPARalpha were highly homologous (>97%) with that of the chicken, indicating the genetic relationship between those two species was close. The tissue distribution and genetic effect on mRNA concentrations of PPARgamma, PPARalpha, and ACO in two genetic populations of turkeys [randombred control (RBC2) and growth selected (F line)] was determined. The PPARgamma mRNA was highly expressed in adipose tissue in both populations, but there was no difference between the two populations. The PPARalpha mRNA concentration was high in the liver with less expression in adipose tissue and skeletal muscle. The PPARalpha mRNA concentration was similar between the two genetic populations. The ACO mRNA was expressed in adipose tissue, skeletal muscle, and liver with no difference between the genetic populations. The data suggest that both turkey liver and adipose tissue have considerable capability for fatty acid oxidation and synthesis. Long-term selection for increased 16-wk BW in the F line had no effect on the expression of PPARgamma, PPARalpha, and ACO.

Acyl-CoA Oxidase↗
PubMed2003

Darwin to DNA, molecules to morphology: the end of classical population genetics and the road ahead.

Molecular reductionism has permeated all of biology and because of successive new technical breakthroughs it has succeeded in unraveling the structural details of genes and genomes. The molecular revolution has reached its reductionist limit, i.e., the study of component parts in isolation, and is ready to come full circle through genomics, proteomics, and gene expression studies back to the phenotype and bring evolutionary biology to confront the Darwinian paradigm, the relationship between gene, organism, and environment. Classical experimental population genetics, dealing with genetic polymorphism and estimation of selection coefficients on a gene-by-gene basis, is coming to an end and a new era of interdisciplinary and interactive biology focusing on dynamic relationships among gene, organism, and environment has begun. In the new population genetics, there will be a shift in focus from single genes to gene networks, from gene-structure to gene-regulation, from additivity to epistasis, and from simple phenotypes to gene-interaction networks and the evolution of complex and modular systems.

Animals↗
PubMed1991

Genetic studies of human apolipoproteins. XVII: Population genetics of apolipoprotein polymorphisms in American Samoa.

Variation in human apolipoprotein genes is a major source of phenotypic differences in human lipid metabolism. Data regarding genetic variation at apolipoprotein loci in various populations are only beginning to accumulate, and they suggest that different populations vary widely in distribution of apolipoprotein alleles. Using isoelectric focusing-immunoblotting techniques, we screened 67 serum samples from self-identified Samoan residents of American Samoa to investigate structural variation at six apolipoprotein loci: A-I, A-II, A-IV, C-II, E, and H. The APO A-I, A-II, and C-II loci were found to be monomorphic by isoelectrical focusing. In Samoans, the common three-allele polymorphism was observed for APO E, with no striking differences in frequencies from Caucasian populations. The three common alleles of the APO H locus also were identified; however, frequencies of the less common alleles (APO H*I and APO H*3) were different from those observed elsewhere for Caucasians.

Adult↗
PubMed2005

Lessons from European population genetic databases: comparing the law in Estonia, Iceland, Sweden and the United Kingdom.

The advent of large-scale, population genetic databases (PGDs) in several countries around the world marks a significant development in human DNA banking and genetic research. The European countries that have led the way in the development of PGDs are Iceland, Sweden, Estonia and the U.K. In legal terms, the emergence of PGDs has been far from straightforward as such projects pose a range of difficult and complex issues for the law to address. This article canvasses the current law in Iceland, Estonia, Sweden and the U.K. on four fundamental issues of principle pertaining to PGDs, in order to illustrate the difficulties that have emerged around PGDs, highlight key areas of legal concern, and shed light on possible ways forward. It compares and contrasts the differing legal positions and lawmakers' responses to date in these four European countries that have established PGDs or are seeking to do so. The four fundamental issues examined are: (1) consent, especially for secondary research purposes; (2) ownership of biological samples, data and databases; (3) the rights of certain third parties to gain access to, and to use, PGD biological samples and data; and (4) benefit sharing, including the provision of feedback and genetic counselling to participants. This analysis may offer some guidance for policymakers in other jurisdictions where PGDs have been proposed or are being established.

Databases, Genetic↗
PubMed1977

A population genetic study of the Kota in the Nilgiri Hills, South India.

A population genetic study among the Kota of the Nilgiri Hills, South India, involved tests for abnormal haemoglobins, 5 red cell antigen systems, 4 serum protein and 13 red cell enzymes systems. Twelve systems are invariant in the Kota. The most distinctive characteristics are extremely low frequency of the A1 gene and complete absence of A2 in the ABO system, r(cde) in the Rh system, LDH cal-1 among the enzyme systems as well as absence of abnormal haemoglobins. A comparison of gene frequencies in those systems, which show variation, suggests that the Kota are more similar to the Toda than to any other tribal or caste population of the area. Genetic distance as well principal component analysis also reveals that the Toda and Kota are close to each other, in agreement with tradition.

Blood Group Antigens↗
PubMed2001

Absence of population genetic differentiation in the New Zealand greenshell mussel Perna canaliculus (Gmelin 1791) as assessed by allozyme variation.

Genetic variation in the endemic New Zealand greenshell mussel, Perna canaliculus (Gmelin 1791), was examined using starch-gel electrophoresis at seven protein-coding loci (Idh; Acon-1; Acon-2; Gpd; Pgi; Pgm; Pgd) in 35 populations (N=1038 mussels). For all loci and all populations, Fisher's exact tests indicated highly significant departures from Hardy-Weinberg equilibrium (HWE), but this overall result was caused by significant heterozygote deficiencies at only two loci (Pgm and Pgd), and in only three northern populations (Kuaotunu, Te Haumi and Days Bay). Allelic and genotypic differentiation between population pairs at individual loci and across all loci were nonsignificant, and genotypic disequilibrium at each locus pair was also nonsignificant for all populations. Genetic variation in all populations was high (mean heterozygosity, 0.210+/-0.113), while Nei's D among populations was very low (0.002+/-0.002). Low population subdivision (θ=-0.001+/-0.002) and high levels of gene flow (Nm(p)=10.18; Nm(θ)=infinity) also indicated that the single panmictic unit model best explains population genetic homogeneity in P. canaliculus over a north-south distance >2000 km. Lack of genetic subdivision in this species is discussed in light of two previous allozyme studies, with differing results: one suggested that a north-south division exists between greenshell mussel stocks, and the other suggested that population structure in this species can be explained through isolation by distance model modified by local hydrology.

Journal Article↗
PubMed2005

Models of the population genetics of transposable elements.

Although transposable elements (TEs) have been found in all organisms in which they have been looked for, the ways in which they invade genomes and populations are still a matter of debate. By extending the classical models of population genetics, several approaches have been developed to account for the dynamics of TEs, especially in Drosophila melanogaster . While the formalism of these models is based on simplifications, they enable us to understand better how TEs invade genomes, as a result of multiple evolutionary forces including duplication, deletion, self-regulation, natural selection and genetic drift. The aim of this paper is to review the assumptions and the predictions of these different models by highlighting the importance of the specific characteristics of both the TEs and the hosts, and the host/TE relationships. Then, perspectives in this domain will be discussed.

Animals↗
PubMed1996

Human population genetics of the VNTR locus D1S80 in the north-eastern Poland.

Population genetic studies within VNTR locus D1S80 were carried out on a population sample from the north-eastern Poland. DNA extraction was performed using the Chelex method. DNA amplification was followed by high-resolution PAGE and silver staining (AMP-FLP technique). In 116 unrelated individuals 20 alleles were observed. The D1S80 locus demonstrated a heterozygosity of 0.85. Comparison of the observable allele frequencies with population data from other Caucasian populations revealed no significant differences.

Alleles↗
PubMed2005

The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome.

RNA viruses are characterized by high genetic variability resulting in rapid adaptation to new or resistant hosts. Research for plant RNA virus genetic structure and its variability has been relatively scarce compared to abundant research done for human and animal RNA viruses. Here, we utilized a molecular population genetic framework to characterize the evolution of a highly pathogenic plant RNA virus [Tomato spotted wilt virus (TSWV), Tospovirus, Bunyaviridae]. Data from genes encoding five viral proteins were used for phylogenetic analysis, and for estimation of population parameters, subpopulation differentiation, recombination, divergence between Tospovirus species, and selective constraints on the TSWV genome. Our analysis has defined the geographical structure of TSWV, attributed possibly to founder effects. Also, we identify positive selection favouring divergence between Tospovirus species. At the species level, purifying selection has acted to preserve protein function, although certain amino acids appear to be under positive selection. This analysis provides demonstration of population structuring and species-wide population expansions in a multisegmented plant RNA virus, using sequence-based molecular population genetic analyses. It also identifies specific amino acid sites subject to selection within Bunyaviridae and estimates the level of genetic heterogeneity of a highly pathogenic plant RNA virus. The study of the variability of TSWV populations lays the foundation in the development of strategies for the control of other viral diseases in floral crops.

Base Sequence↗
PubMed2004

Comparisons of amplified fragment length polymorphism (AFLP), microsatellite, and isoenzyme markers: population genetics of Aedes aegypti (Diptera: Culicidae) from Phnom Penh (Cambodia).

Aedes aegypti is the main vector of dengue viruses responsible for dengue hemorrhagic fever, which has become a major public health concern in tropical countries. Because vaccines are still under development, dengue prevention depends entirely on vector control. Knowledge of gene dispersal patterns is required to develop efficient vector control strategies. Here we report the use of amplified fragment length polymorphism (AFLP) to infer the genetic structure of Ae. aegypti populations at a local levels (Phnom Penh, Cambodia). The amount of variation and patterns of gene flow detected are compared with those obtained with two other more widely used markers, isoenzymes and microsatellites. The pattern of differentiation depicted by AFLP data were confirmed by comparison of the Fst values of the three markers. Even though Fst values estimated with AFLP markers are three- to fivefold higher than those estimated with isoenzymes or microsatellites, these different markers reveal the same population structure. This technique is useful for population genetic studies of Ae. aegypti and is especially advantageous when few individuals specimens are available because of the ability to AFLP to simultaneously amplify large numbers of polymorphic DNA fragments.

Aedes↗
PubMed2001

[Analyses of population genetic structure by using dominant markers].

Dominant markers tend to under-estimate the amount of genetic diversity relative to codominant systems when applying in population genetics. In order to compare various existing methods for analysis of genetic structure, RAPD markers were used to detect genetic variability of 5 populations of Oryza granulata from China. The results indicated that both Shannon index of diversity and Nei gene diversity were superior to percentage of polymorphic bands (PPB) because the latter lacked of ability to describe frequency difference of polymorphic bands. Mantel test showed significant relation (r > 0.95, t > t0.01) among matrice of 17 different genetic similarities, which indicated that all of them could be used in analysis of genetic relations of individuals of Oryza granulata. Both AMOVA analysis based on phi st distance and analysis of Nei's distance showed consistent results in defining relationship among the 5 populations, and Lynch-Milligan pruning should be used to improve the estimation of population parameters. All of AMOVA, Gst and Shannon diversity analyses obtained similar results with majority of genetic variation occurring between Yunnan and Hainan, and low levels of genetic diversity resided within regions and populations.

Genetic Markers↗
PubMed2000

A population genetics model for multiple quantitative traits exhibiting pleiotropy and epistasis.

We study a population genetics model of an organism with a genome of L(tot)loci that determine the values of T quantitative traits. Each trait is controlled by a subset of L loci assigned randomly from the genome. There is an optimum value for each trait, and stabilizing selection acts on the phenotype as a whole to maintain actual trait values close to their optima. The model contains pleiotropic effects (loci can affect more than one trait) and epistasis in fitness. We use adaptive walk simulations to find high-fitness genotypes and to study the way these genotypes are distributed in sequence space. We then simulate the evolution of haploid and diploid populations on these fitness landscapes and show that the genotypes of populations are able to drift through sequence space despite stabilizing selection on the phenotype. We study the way the rate of drift and the extent of the accessible region of sequence space is affected by mutation rate, selection strength, population size, recombination rate, and the parameters L and T that control the landscape shape. There are three regimes of the model. If LT< >L(tot), there are many small peaks that can be spread over a wide region of sequence space. Compensatory neutral mutations are important in the population dynamics in this case.

Animals↗
PubMedDate not supplied

Population genetic and family studies on aldehyde dehydrogenase deficiency and alcohol sensitivity.

Population genetic studies on the prevalence of aldehyde dehydrogenase isozyme I (ALDH I) deficiency in various Caucasian, Oriental, African, and American Indian subjects were carried out using hair roots as peripheral source of the enzyme activity. While a very high percentage of Orientals with Mongoloid origin were found deficient in ALDH I activity, no deficiency was detected in Caucasian and African populations. Native American Indians showed a relatively low incidence of ALDH I deficiency. A genetic model based on the phenotype determination using antisera against purified human liver ALDH I is proposed. Pedigree analysis of Japanese families suggests an autosomal codominant mode of inheritance.

Aldehyde Dehydrogenase↗
PubMed1983

[Use of methods of 2-dimensional electrophoresis in population genetics].

The review of literature on application of the methods of two-dimensional electrophoresis according to O'Farrel, in population genetics and in some adjacent fields of biology, is presented. Resolution capacities of both conventional and two-dimensional electrophoresis are briefly characterized. Data on application of two-dimensional electrophoresis methods for evaluation the degree of inter- and intraspecific variability, for detection and characterization of mutations, as well as for analysis of molecular mechanisms of inborn pathology are reviewed.

Alleles↗
PubMed2003

Population genetic structure and cladistic analysis of Trypanosoma brucei isolates.

Using a novel multilocus DNA marker analysis method, we studied the population genetic structure of Trypansoma brucei stocks and derived clones isolated from animal and rhodesiense sleeping sickness patients during a national sleeping sickness control program in Mukono district, Uganda. We then performed a cladistic analysis to trace relationships and evolution, using stocks and clones recovered from geographically and temporally matched hosts, including inter-strain comparisons with T. b. gambiense stocks and clones. Our results show that while there was close genetic relatedness among parasite populations from the same geographical region, micro-heterogeneities exist between different stocks. Data are presented that indicate that not every human sleeping sickness focus may be associated with a particular human-infective trypanosome strain responsible for long-term stability of the reference focus. We provide evidence of genetic sub-structuring among type 1 T. b. gambiense stocks, which has potentially important implications for molecular epidemiology of T. brucei.

Animals↗