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PubMed1986

Mitochondrial DNA variability in natural populations of Hawaiian Drosophila. I. Methods and levels of variability in D. silvestris and D. heteroneura populations.

We describe techniques by which mitochondrial DNA (mtDNA) restriction site information can be obtained for up to 16 different restriction endonucleases on individual Hawaiian Drosophila, in particular D. silvestris and D. heteroneura. We have constructed mtDNA restriction site maps for a total of forty-eight wild caught genomes of both species, from seven major collecting sites on the island of Hawaii. Levels of variability are, in general, high in D. silvestris (p of Ewens et al., 1981 = 0.0486) and lower in D. heteroneura (p = 0.0327). Measures of population subdivision using Nei's Gst indicate that about 50-60 per cent of the observed variability is due to interdemic subdivision. In accordance, populations within a species show a much lower level of variability, however some populations harbour individuals that are very divergent from the rest of their conspecifics at the same locality. We review two possible mechanisms that could explain the presence of these divergent individuals, hybridisation and the effects of stochastic branching processes.

Animals↗

PubMed2006

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

N-acetyltransferase 2 (NAT2), an important enzyme in clinical pharmacology, metabolizes antibiotics such as isoniazid and sulfamethoxazole, and catalyzes the transformation of aromatic and heterocyclic amines from the environment and diet into carcinogenic intermediates. Polymorphisms in NAT2 account for variability in the acetylator phenotype and the pharmacokinetics of metabolized drugs. Native Americans, settled in rural areas and large cities of Latin America, are under-represented in pharmacogenetics studies; therefore, we sequenced the coding region of NAT2 in 456 chromosomes from 13 populations from the Americas, and two from Siberia, detecting nine substitutions and 11 haplotypes. Variants *4 (37%), *5B (23%) and *7B (24%) showed high frequencies. Average frequencies of fast, intermediate and slow acetylators across Native Americans were 18, 56 and 25%, respectively. NAT2 intra-population genetic diversity for Native Americans is higher than East Asians and similar to the rest of the world, and NAT2 variants are homogeneously distributed across native populations of the continent.

Acetylation↗

PubMed1998

Bacteriuria in a population sample of women: 24-year follow-up study. Results from the prospective population-based study of women in Gothenburg, Sweden.

The aims of the study were to estimate the prevalence of bacteriuria in a female urban population, to follow up the same population over the years, and to relate bacteriuria to long-term prognosis with respect to mortality and kidney disease. The study was based on a randomly selected population sample comprising 1462 women aged 38-60 years at entrance to the study in 1968-69 with an initial participation rate of 90.1%. Bacteriuria was observed in 3-5%, increasing with age, and most often asymptomatic. Bacteriuria on one occasion meant increased risk of having bacteriuria 6 and 12 years later. The percentages of different types of bacteria and the resistance pattern were similar initially and at follow-up studies after 6 and 12 years. There were no differences in mortality or incidence of severe kidney disease during a 24-year follow-up between those with and those without bacteriuria in the baseline study.

Adult↗

PubMed1999

Molecular genetic analysis of remains of a 2,000-year-old human population in China-and its relevance for the origin of the modern Japanese population.

We extracted DNA from the human remains excavated from the Yixi site ( approximately 2,000 years before the present) in the Shandong peninsula of China and, through PCR amplification, determined nucleotide sequences of their mitochondrial D-loop regions. Nucleotide diversity of the ancient Yixi people was similar to those of modern populations. Modern humans in Asia and the circum-Pacific region are divided into six radiation groups, on the basis of the phylogenetic network constructed by means of 414 mtDNA types from 1, 298 individuals. We compared the ancient Yixi people with the modern Asian and the circum-Pacific populations, using two indices: frequency distribution of the radiation groups and genetic distances among populations. Both revealed that the closest genetic relatedness is between the ancient Yixi people and the modern Taiwan Han Chinese. The Yixi people show closer genetic affinity with Mongolians, mainland Japanese, and Koreans than with Ainu and Ryukyu Japanese and less genetic resemblance with Jomon people and Yayoi people, their predecessors and contemporaries, respectively, in ancient Japan.

Asian People↗

PubMed1985

The ecological genetics of introduced populations of the giant toad Bufo marinus. II. Effective population size.

The allele frequencies are described at ten polymorphic enzyme loci (of a total of 22 loci sampled) in 15 populations of the neotropical giant toad, Bufo marinus, introduced to Hawaii and Australia in the 1930s. The history of establishment of the ten populations is described and used as a framework for the analysis of allele frequency variances. The variances are used to determine the effective sizes of the populations. The estimates obtained (390 and 346) are reasonably precise, homogeneous between localities and much smaller than estimates of neighborhood size obtained previously using ecological methods. This discrepancy is discussed, and it is concluded that the estimates obtained here using genetic methods are the more reliable.

Animals↗

PubMed1974

The genetic structure of natural populations of Drosophila melanogaster. XII. Linkage disequilibrium in a large local population.

Seven hundred and three second chromosomes were extracted from a Raleigh, North Carolina population of Drosophila melanogaster in 1970. Additionally, four hundred and eighty-nine third chromosomes were extracted from a large cage population founded from the flies in the 1970 Raleigh collection. The alpha glycerol-3-phosphate dehydrogenase-1, malate dehydrogenase-1, alcohol dehydrogenase, and alpha amylase loci were studied from the second chromosomes, and the esterase-6, esterase-C, and octanol dehydrogenase loci were analyzed from the third chromosomes. Inversions, relative viability and fecundity were studied for both classes of chromosomes. The following significant findings were obtained: (1) All loci examined were polymorphic or had at least two alleles at appreciable frequencies. Analysis of the combined data from this experiment with that of Mukai, Mettler and Chigusa (1971) revealed that the frequencies of the genes in the second chromosomes collected in early August were approximately the same over three years. (2) Linkage disequilibria between and among isozyme genes inter se were not detected except in a few cases which can be considered due to non-random sampling. (3) Linkage disequilibria between isozyme genes and polymorphic inversions were detected when the recombination values between the breakage points of the inversions and the genes in question were small. In only a few cases, were second and third order linkage disequilibria including polymorphic inversions detected. (4) Evidence for either variation among genotypes within loci or cumulative effects of heterozygosity was found for viability and fecundity. As a result of these findings, it was tentatively concluded that although selection might be perceptibly operating on some polymorphic isozyme loci, most of the polymorphic isozyme genes are selectively neutral or near-neutral in the populations studied.

Alcohol Oxidoreductases↗

PubMed1979

Mutation rates, population sizes and amounts of electrophoretic variation of enzyme loci in natural populations.

A method is presented for estimating relative mutation rates or relative effective population sizes, under the hypothesis of adaptively neutral allelic variation. This method was applied to seven surveys of electrophoretic variation. It was observed that electrophoretic mutation rates so obtained follow the gamma distribution and, in Drosophila, are positively correlated with the molecular weights of the enzymes subunits. The variance in mutation rate is larger under the step-wise model of electrophoretic mutation than under the infinite-alleles model. Rates for the most variable loci may exceed rates for less variable loci by a factor of 500. For completely invariant loci, this factor may be as high as 4 X 10(4), an observation suggesting that these loci are subject to purifying selection. In contrast to mutation rates, effective population sizes may vary at the most by a factor of ten. These results support the hypothesis that differences in the amount of electrophoretic variability among polymorphic loci may reflect differences in the rate by which electrophoretically detectable variation is generated in population.

Animals↗

PubMed1994

Spline models of biological population dynamics: how to estimate mortality rates for stage structured populations with dimorphic life histories.

Nonparametric spline based models of stage structured population dynamics provide an effective way of decomposing observed population dynamics into birth and death rate processes. Currently available methodology only considers simple life histories in which all individuals pass through the same sequence of stages in the same way. This paper presents techniques for obtaining birth and death rates from structured population time series of organisms with complex life histories. For example, in many species males and females develop at the same rate in early stages, but differently in late stages. The models are motivated by the need to obtain birth and death rates for a pest subject to biocontrol by a parasitoid.

Aging↗

PubMedDate not supplied

Population distribution of alcohol dehydrogenase class I in France: comparison with other populations, and distribution with respect to gender and age. The French Group for Research on Alcohol and Liver.

In Caucasians, a genetic polymorphism is known for some alcohol dehydrogenase (ADH) systems (beta and gamma). Knowledge of population frequencies of the beta and gamma hepatic isozyme variants in France is a prerequisite to understanding any role this genetic variation might play in determining the risk of alcohol-related diseases. For the present study, the ADH phenotypes of 115 French Caucasian control subjects, consisting of 64 men and 51 women, were studied. The beta2 subunit was found to have a very low frequency. The relative frequencies of ADH gamma subunits observed in French Caucasians were found to be in good agreement with those already observed in other Caucasian populations. When gender and age were taken into account, a particular group corresponding to young men (age <50 years) was characterized by a manifest discordance with the comparable female population.

Adult↗

PubMed2002

Robust design and the use of auxiliary variables in estimating population size for an open population.

We consider the problem of estimating the population size for an open population where the data are collected over secondary periods within primary periods according to a robust design suggested by Pollock (1982, Journal of Wildlife Management 46, 757-760). A conditional likelihood is used to estimate the parameters associated with a generalized linear model in which the capture probability is assumed to have a logistic form depending on individual covariates. A Horvitz-Thompson-type estimator is used to estimate the population size for each primary period and the survival probabilities between primary periods. The asymptotic properties of the proposed estimators are investigated through simulation and are found to perform well. A data set for such a robust design of a small-mammal capture-recapture study conducted at Dummy Bottom within Browns Park National Wildlife Refuge is analyzed.

Animals↗

PubMed2006

Population prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae in the Netherlands. Should asymptomatic persons be tested during population-based Chlamydia screening also for gonorrhoea or only if chlamydial infection is found?

BACKGROUND: Screening and active case finding for Chlamydia trachomatis (CT) is recommended to prevent reproductive morbidity. However insight in community prevalence of gonococcal infections and co-infections with Neisseria gonorrhoea (NG) is lacking. METHODS: Nested study within a large population-based Chlamydia Screening Pilot among 21.000 persons 15-29 year. All CT-positive (166) and a random sample of 605 CT-negative specimens were as well tested for gonococcal infection. RESULTS: Overall Chlamydia prevalence in the Pilot was 2.0% (95% CI: 1.7-2.3), highest in very urban settings (3.2%; 95% CI: 2.4-4.0) and dependent of several risk factors. Four gonococcal infections were found among 166 participants with CT infection (4/166 = 2.4%; 95% CI: 0.1%-4.7%). All four had several risk factors and reported symptoms. Among 605 CT-negative persons, no infection with NG could be confirmed. CONCLUSION: A low rate of co-infections and a very low community prevalence of gonococcal infections were found in this population based screening programme among young adults in the Netherlands. Population screening for asymptomatic gonococcal infections is not indicated in the Netherlands. Although co-infection with gonorrhoea among CT-positives is dependent on symptoms and well-known algorithms for elevated risks, we advise to test all CT-positives also for NG, whether symptomatic or asymptomatic.

Adolescent↗

PubMed2004

The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs.

Understanding the nature of evolutionary relationships among persons and populations is important for the efficient application of genome science to biomedical research. We have analysed 8,525 autosomal single nucleotide polymorphisms (SNPs) in 84 individuals from four populations: African-American, European-American, Chinese and Japanese. Individual relationships were reconstructed using the allele sharing distance and the neighbour-joining tree making method. Trees show clear clustering according to population, with the root branching from the African-American clade. The African-American cluster is much less star-like than European-American and East Asian clusters, primarily because of admixture. Furthermore, on the East Asian branch, all ten Chinese individuals cluster together and all ten Japanese individuals cluster together. Using positional information, we demonstrate strong correlations between inter-marker distance and both locus-specific FST (the proportion of total variation due to differentiation) levels and branch lengths. Chromosomal maps of the distribution of locus-specific branch lengths were constructed by combining these data with other published SNP markers (total of 33,704 SNPs). These maps clearly illustrate a non-uniform distribution of human genetic substructure, an instructional and useful paradigm for education and research.

Genetics, Population↗

PubMed2026

Mitochondrial genome-derived microsatellites reveal genetic diversity and population structure in Callery pear populations.

Callery pear (Pyrus calleryana Decne.; PC) possesses many desirable characteristics valued in managed landscapes. This has driven the release of numerous cultivars, including both hybrids and selections derived from native populations. The extensive planting of PC cultivars in managed areas has contributed to the widespread occurrence of invasive individuals across a broad range of habitats in the eastern United States (US). Self-incompatibility, tolerance to various environmental conditions, pathogen and pest resistance, intraspecific hybridization among the cultivars, possible interspecific hybridization with other Pyrus species, and seed dispersal by various vertebrates have contributed to the spread and persistence of PC across diverse environments. Because effective and environmentally appropriate management options remain limited, improved understanding of PC genetics may help inform management strategies. Previous studies have characterized PC diversity using nuclear genomic short sequence repeats (gSSRs), however, neither a mitochondrial genome resource nor mitochondrial short sequence repeats (mtSSRs) have been developed for this purpose. Here, we assembled a mitochondrial genome of 485,892 bp and used five mtSSRs to characterize mitochondrial diversity and population structure among accessions from the species' native range in Asia (n = 72), southeastern US escapees (SNesc; n = 90), Tennessee escapees (TNesc; n = 90), and US-released commercial cultivars (UScult; n = 69 representing 14 unique cultivars). We found a high genetic diversity (He = 0.728) and evidence of genetic structure in PC. In distance-based and multivariate analyses, UScult occupied an intermediate position between the Asian populations and the US escapees. The observed mitochondrial diversity among samples assigned to PC cultivars is consistent with a complex genetic landscape and may reflect distinct maternal lineages, cultivar-labeling or record-keeping discrepancies, and/or technical variation. This study underscores the need for broader genomic investigations using authenticated cultivar reference material and high-resolution nuclear markers to resolve cultivar ancestry, validate true-to-name identity, and inform species management.

Genetic Variation↗

PubMed2004

Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations.

We present a Bayesian statistical inference approach for simultaneously estimating mutation rate, population sizes, and migration rates in an island-structured population, using temporal and spatial sequence data. Markov chain Monte Carlo is used to collect samples from the posterior probability distribution. We demonstrate that this chain implementation successfully reaches equilibrium and recovers truth for simulated data. A real HIV DNA sequence data set with two demes, semen and blood, is used as an example to demonstrate the method by fitting asymmetric migration rates and different population sizes. This data set exhibits a bimodal joint posterior distribution, with modes favoring different preferred migration directions. This full data set was subsequently split temporally for further analysis. Qualitative behavior of one subset was similar to the bimodal distribution observed with the full data set. The temporally split data showed significant differences in the posterior distributions and estimates of parameter values over time.

Biological Evolution↗

PubMed2005

Characteristics of population with normal serum creatinine impaired renal function and: the validation of a MDRD formula in a healthy general population.

BACKGROUND AND AIMS: Glomerular filtration rate (GFR) provides the most accurate estimation of renal function. This study investigated the clinical characteristics of patients with impaired renal function having a normal serum creatinine level. We also validated whether the new Modification of Diet in Renal Disease (MDRD) formula can be applied in a healthy general population. MATERIAL AND METHODS: A total 393 participants who had serum creatinine concentration below 132.6 micromol/L without underlying diseases were randomly selected on an address basis in Ansan City. According to the level of GFR, they were divided into 3 groups and we analyzed their clinical characteristics. In 75 subjects, who were randomly selected 25 cases in each group based on GFR estimated by Cockcroft-Gault (C-G) formula, true GFR was measured using the 99mTc-DTPA renal clearance method. RESULTS: A total 393 (male: 106, female: 287) participants were as follows: GFR < 60 ml/min/1.73 m2; 4% (n = 25); 60 < or = GFR < 90 ml/min/1.73 m2; 26.2% (n = 103); GFR > or = 90 ml/min/1.73 m2; 67.4% (n = 265). In the group of decreased GFR, the mean age was older (67.4+/-10.7 vs. 48.7+/-12.8 vs. 39.4+/-8.2 years, p < 0.001), the gender was male (90.33+/-28.77 vs. 110.55+/-31.64, p < 0.001), and amount of proteinuria more increased (0.61 (0.56) vs. 0.33 (0.34) vs. 0.38 (0.33) gm/day, p = 0.007). The accuracy and precision of each formula were assessed by the difference in GFR measured by the 99mTc-DTPA renal clearance method--estimated GFR by each formula (deltaGFR), and the coefficient of determination (r2) of different predictive equations. The results were as follows: deltaGFR = -14.78+/-46.03, r2 = 0.79 (24-hour urinary creatinine clearance), deltaGFR=-16.79+/-57.32, r2 = 0.66 (100/serum creatinine), deltaGFR = 9.54+/-39.18, r2 = 0.87 (C-G formula), deltaGFR = -12.30+/-54.31, r2 = 0.66 (AASK formula), deltaGFR = 8.70+/-37.62, r2 = 0.79 (MDRD formula). Multiple linear regression analysis and logistic regression analysis showed that age, serum creatinine, total cholesterol and 24-hour urinary protein excretion were independently related to GFR and associated with a significant increase in the risk of decrement of GFR. CONCLUSIONS: From these results, a more accurate assessment of renal function should be required in a population characterized by older age, male gender and more proteinuria. The MDRD study formula and Cockcroft-Gault formula have greater accuracy and precision with true GFR, and this equation can be applied in subjects with healthy general population.

Adult↗

PubMed1989

Risk factors for coronary heart disease in a self-referred population compared with a general population.

Screening programmes for community coronary heart disease risk factors aim to identify persons who are at a high risk of the development of coronary heart disease by screening the population for the prevalence of smoking, obesity, high blood pressure and high blood cholesterol concentrations. The effectiveness of such screening programmes is dependent on a number of factors. The characteristics of individuals who attend such screening programmes voluntarily, and the prevalence of abnormal coronary heart disease risk factors that is detected, give a strong indication of the population reach and the potential benefits of the preventive strategy. In this study, persons who attended a self-referred risk-factor screening programme for coronary heart disease were compared with a random sample of the Australian urban population. A disproportionately high number of older persons and of women presented for the self-referred screening programme while smokers were underrepresented. In general, the risk-factor levels of those in the older age-groups who attended the screening programme were lower than were the corresponding measurements that were found in the random sample; the opposite was true for those in the younger age-groups. These results suggest that coronary heart disease risk-factor screening programmes in the community appeal more to those in the health-conscious older age-groups and to women. For heart disease prevention programmes to be more effective, it will be necessary to design screening programmes to attract more men, those in younger age-groups and smokers.

Adolescent↗

PubMed1999

[Population-based study of antibodies to certain potential infectious triggers of spondylarthropathies: a study of Ugro-Finnish population of Russia].

A study was made of antibodies to some enterobacteria--potential triggers of spondyloarthropathies in population of mordva characterized by higher frequency of HLA-B27. 141 and 148 plasm samples were taken from erzya and moksha subpopulations, respectively. Enzyme immunoassay has detected specific antibodies IgA, IgM, IgG to Salmonella, Yersinia, Campylobacter and Klebsiella. Specific immune response in the mordva population appeared to depend on gender, age and nationality but not HLA-B27. In the study population the role of Klebsiella infection in development of ankylosing spondylarthritis was not confirmed though the number of the patients was not sufficient to reject this suggestion.

Antibodies, Viral↗

PubMed2000

[Prevalence and intensity of smoking among adult urban population of Tiumen': data of population mail questionnaire survey].

AIM: To estimate prevalence and intensity of smoking among adult Tyumen citizens by mail questionnaire survey. MATERIALS AND METHODS: A representative sample of adult population of Tyumen (central district) was randomly selected using the list of the electors. The questioning covered a total of 3200 citizens (8 groups per 400 age- and sex-matched subjects). The response reached 71.5%. Smoking in the population was studied in three aspects: prevalence, intensity and passive smoking. RESULTS: Overall prevalence of smoking was not great (28.8%), but smoking was frequent in women, especially young, was intensive in males of all the age groups. The number of smokers who had quit smoking was small. Passive smoking at jobs was prevalent. CONCLUSION: The data of the survey indicate difficulties of social adaptation for the studied population who fall under risk to develop cardiovascular diseases.

Adult↗