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PubMed2000

Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations.

We describe a novel method for analysis of marker genotype data from admixed populations, based on a hybrid of Bayesian and frequentist approaches in which the posterior distribution is generated by Markov chain simulation and score tests are obtained from the missing-data likelihood. We analysed data on unrelated individuals from eight African-American populations, genotyped at ten marker loci of which two (FY and AT3) are linked (22 cM apart). Linkage between these two loci was detected by testing for association of ancestry conditional on parental admixture. The strength of this association was consistent with European gene flow into the African-American population between five and nine generations ago. To mimic the mapping of an unknown gene in an 'affecteds- only' analysis, a binary trait was constructed from the genotype at the AT3 locus and a score test was shown to detect linkage of this 'trait' with the FY locus. Mis-specification of the ancestry-specific allele frequencies - the probabilities of each allelic state given the ancestry of the allele - was detected at three of the ten marker loci. The methods described here have wide application to the analysis of data from admixed populations, allowing the effects of linkage and population structure (variation of admixture between individuals) to be distinguished. With more markers and a more complex statistical model, genes underlying ethnic differences in disease risk could be mapped by this approach.

Bayes Theorem↗
PubMed1999

Predicting correlated responses in natural populations: changes in JHE activity in the bermuda population of the sand cricket, gryllus firmus

Quantitative genetic methods have been used to examine selection responses in domesticated organisms but there are few cases of their application to predict changes in natural populations: there are, to our knowledge, no cases in which correlated responses to selection have been predicted. In the present paper we use quantitative genetic parameters estimated from a half-sib experiment to predict the changes expected in juvenile hormone esterase (JHE) activity in the Bermuda population of the wing dimorphic cricket, Gryllus firmus. JHE activity is genetically correlated with wing form in this cricket and hence changes in the proportion of macroptery (volant morph) are predicted to bring about a correlated response in JHE activity. The Bermuda population has a higher proportion of macropterous individuals (95%) compared to the stock (35%, originally from Florida) from which the heritabilities and correlations were estimated. The quantitative genetic analysis makes three predictions which were tested both qualitatively and quantitatively. In all cases the null hypothesis that the observed results correspond to those predicted cannot be rejected. As predicted, in the Bermuda population there is: (i) an increase in the population mean JHE activity; (ii) a leftwards shift in the curve relating the probability of microptery (flightless morph) to JHE activity; and (iii) a decrease in the mean JHE activity within each morph.

Journal Article↗
PubMed1991

Intraspecific variation in population gene diversity and effective population size correlates with the mating system in plants.

Published data on allele frequencies at isozyme loci in inbreeding and outbreeding plant species were analyzed to examine intraspecific variation in gene diversity and effective population size (Ne). Compared with outbreeders, inbreeding species showed markedly greater variation among populations in average values of Nei's gene diversity statistic. Effective population size was estimated by assuming that the variation observed at isozyme loci is selectively neutral. Inbreeding species showed greater levels of variation in Ne than did outbreeders, although the upper range of Ne was similar in the two classes of species. The results suggest that there may be considerable genetic variation and potential for evolutionary change in some but not all populations of inbreeders. Moreover, these findings are important with respect to the conservation of genetic resources. In particular, that the amount of intraspecific variation in population genetic diversity and Ne differs between inbreeding and outbreeding species should be taken into account in sampling efforts designed to optimize the diversity of germplasm collections.

Journal Article↗
PubMed1998

Malaria's Eve: evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum.

We have analyzed DNA sequences from world-wide geographic strains of Plasmodium falciparum and found a complete absence of synonymous DNA polymorphism at 10 gene loci. We hypothesize that all extant world populations of the parasite have recently derived (within several thousand years) from a single ancestral strain. The upper limit of the 95% confidence interval for the time when this most recent common ancestor lived is between 24,500 and 57,500 years ago (depending on different estimates of the nucleotide substitution rate); the actual time is likely to be much more recent. The recent origin of the P. falciparum populations could have resulted from either a demographic sweep (P. falciparum has only recently spread throughout the world from a small geographically confined population) or a selective sweep (one strain favored by natural selection has recently replaced all others). The selective sweep hypothesis requires that populations of P. falciparum be effectively clonal, despite the obligate sexual stage of the parasite life cycle. A demographic sweep that started several thousand years ago is consistent with worldwide climatic changes ensuing the last glaciation, increased anthropophilia of the mosquito vectors, and the spread of agriculture. P. falciparum may have rapidly spread from its African tropical origins to the tropical and subtropical regions of the world only within the last 6,000 years. The recent origin of the world-wide P. falciparum populations may account for its virulence, as the most malignant of human malarial parasites.

Africa↗
PubMed2003

Is elbow breadth a measure of frame size in non-Caucasian populations? A study in low- and high-altitude Central-Asia populations.

UNLABELLED: The concept of frame size has not undergone a thorough evaluation in non-Caucasian populations. Using data from the Central Asia High Altitude Population (CAHAP) study, we tested whether: (1) the relationship between frame size and body composition is different in high-, medium- and low-altitude populations; (2) elbow breadth is a better index of frame size than biacromial and biiliac breadth; and (3) measures of frame size are associated with blood pressure, cholesterol and triglycerides. A number of 334 male subjects aged 33 +/- 10 years (mean +/- standard deviation) were selected from the CAHAP population (n = 384) on the basis of the availability of breadth measurements. The subjects were 85 high-altitude Kirghizs, 105 medium-altitude Kazakhs, 79 low-altitude Kirghizs and 65 low-altitude Uighurs. A detailed anthropometric evaluation and blood pressure, cholesterol and trygliceride measurements were performed on all individuals. Among breadths, elbow had the lowest correlation with arm fat area, thigh fat area, calf fat area and the sum of trunk skinfolds (r < or = 0.196, P < 0.01). Even if elbow breadth did not have the highest correlation with muscularity indexes, its constantly lower association with adiposity indexes shows that it is a better measure of frame size than biacromial breadth and biiliac breadth. The relationship between frame size and body composition did not differ in high-, medium- and low-altitude subjects (P = not significant, analysis of co-variance). Only a weak association was present between breadths, blood pressure, cholesterol and triglycerides (r < or = 0.230, P < 0.01) and it was not influenced by altitude (P = not significant, analysis of co-variance). Elbow breadth was significantly correlated only with diastolic blood pressure (r = 0.121, P < 0.05). IN CONCLUSION: (1) the relationship between frame size and body composition is similar in high- and low-altitude populations; (2) elbow breadth is an index of frame size independent of altitude; and (3) elbow breadth is correlated with diastolic blood pressure, but this correlation is of doubtful biological relevance.

Adult↗
PubMed1999

Temporal trends in the population structure of Bordetella pertussis during 1949-1996 in a highly vaccinated population.

The population structure of Bordetella pertussis in The Netherlands in 5 successive periods, encompassing 1949-1996, was analyzed by DNA typing ("fingerprinting"). In 10 years following the introduction of wide-scale vaccination in 1953, a decrease in genotypic diversity (GD) was observed, suggesting clonal expansion of strains that were adapted to vaccine-induced immunity. In subsequent periods, GD increased to prevaccination levels, probably reflecting a gradual adaptation of the B. pertussis population involving many lineages. In the 1990s, GD decreased again. This decrease coincided with an antigenic shift in the surface protein pertactin. No evidence was found for changes in DNA types or GD in 1996, when a large pertussis epidemic occurred. Thus, gradual changes in the bacterial population previous to 1996 were probably the cause of the 1996 epidemic. The results herein suggest that vaccination has selected for strains that are adapted to a highly vaccinated population. Similar changes may have occurred in other countries, explaining the reemergence of pertussis in vaccinated populations.

Bacterial Vaccines↗
PubMed1983

Population genetics of Drosophila amylase. IV. Selection in laboratory populations maintained on different carbohydrates.

Two polymorphic systems impinging on alpha-amylase in Drosophila pseudoobscura have been studied in laboratory populations maintained on medium in which the only carbohydrate source was starch (the substrate of amylase) and replicas maintained on medium in which the only carbohydrate source was maltose (the product of amylase). The two polymorphic systems were alleles at the structural gene (Amy) coding for the enzyme (allozymes) and variation in the tissue-specific expression along the adult midgut controlled by several genes. In the seven populations on maltose medium little consistent change was noted in either system. In the seven populations on starch medium, both polymorphisms exhibited selective changes. A midgut pattern of very limited expression of amylase rose in frequency in all starch populations, as did the frequency of the "fast" (1.00) Amy allele. The overall specific amylase activity did not differ between starch-adapted and maltose-adapted flies.--The results, along with previous studies, indicate that when a gene-enzyme system is specifically stressed in laboratory populations, allozymes often exhibit selective differences. Such results make the selectionist hypothesis at least tenable. Furthermore, the fact that both types of polymorphisms responded to selection indicates the role of structural gene vs. gene regulation changes in adaptive evolution is not an either/or question but one of relative roles and interactions.

Alleles↗
PubMedDate not supplied

Gene frequencies in the cat population of Buenos Aires, Argentina, and the possible origin of this population.

The phenotypes of 295 stray cats seen in the capital area of Buenos Aires, Argentina, between March and December of 1989 were recorded. The corresponding mutant allele frequencies were as follows: O = 0.28, a = 0.83, Ta = 0.01; tb = 0.31; d = 0.45; I = 0.40; S = 0.28; W = 0.02. The allele frequencies calculated at the O locus were consistent with those expected for a randomly breeding population according to the formula for the Hardy-Weinberg equilibrium. The analysis of the genetic distances between Buenos Aires and several European cat populations revealed that the Spanish and, especially, those with a proven more ancestral genetic constitution, are the most closely related. When a similar analysis was carried out, including other Latin American cat populations, those of Spanish origin were found to show the highest degree of relatedness. These findings suggest that the Buenos Aires cat population was not genetically structured following the "two-stepping-stone" model and support the hypothesis that differential gene flows play a transcendental role in understanding the genetic composition of domestic cat populations.

Animals↗
PubMed1993

Cancer patterns in three African populations compared with the United States black population.

Cancer incidence rates and patterns in three African populations in the Gambia, Mali and South Africa, have been compared with corresponding data on the Black population in Connecticut, USA. In the African populations, total rates for cancer are much lower than that of US Blacks, even allowing for under-reporting. Chief cancers are those of the oesophagus, liver and cervix. In Mali, stomach cancer is very common. As to trends, among South African Blacks, a population in transition, rates are rising, albeit slowly, of cancers of prosperity--prostate, lung, breast and colon-rectum. Salient questions are: can the number of cancers of underprivilege be lessened, and can cancers linked with rising socioeconomic states be restrained? Discussions of common risk factors, including diet, reproduction, smoking and drinking practices, indicate that for Africans as a whole, continuing poverty will prevent major changes in cancer pattern and rises in occurrence of the disease. However, should prosperity increase for Africans in big cities, rates are ultimately likely to attain those prevailing in the US Black population. Significant avoiding action seems almost impossible.

Black or African American↗
PubMed2004

Microalbuminuria, cardiovascular risk factors and cardiovascular morbidity in a British population: the EPIC-Norfolk population-based study.

BACKGROUND: Microalbuminuria is independently associated with increased cardiovascular risk and renal function deterioration in diabetes and hypertension, but the clinical relevance of raised albuminuria in the general population is less certain. We examined the prevalence of microalbuminuria and its relationship to cardiovascular risk factors and cardiovascular morbidity in the UK general population. METHODS: Cross-sectional population-based study of 23,964 individuals, aged 40-79 years recruited in 1993-1997 for the EPIC-Norfolk Study. Smoking status, prevalent physician diagnosed diabetes, hypertension, cardiovascular disease and cancer were derived from a health and lifestyle questionnaire. Albumin-to-creatinine ratios were estimated from random spot urine specimens collected at the survey visit, and using these ratios participants were categorized into normoalbuminuria, microalbuminuria (2.5-25 mg/mmol), and macroalbuminuria. RESULTS: The prevalence of microalbuminuria and macroalbuminuria was 11.8% and 0.9% respectively in the total population and significantly higher in women (14.4%) compared with men (8.9%) (P<0.001). Independent determinants of microalbuminuria were age, sex, systolic blood pressure and current smoking. Microalbuminuria was independently associated with cardiovascular morbidity, after adjusting for known cardiovascular risk factors, with odds ratio (95% confidence interval) for prevalent cardiovascular disease of 1.30 (1.12-1.51) in all men and women. CONCLUSION: Microalbuminuria was present in approximately 12% of this population. It was independently associated with cardiovascular risk factors and prevalent cardiovascular disease. Microalbuminuria may be a useful indicator of high absolute cardiovascular risk in the community but prospective data are needed to establish its independent predictive value for future events.

Adult↗
PubMed2005

Using naturally shed feathers for individual identification, genetic parentage analyses, and population monitoring in an endangered Eastern imperial eagle (Aquila heliaca) population from Kazakhstan.

Genetic analyses on noninvasively collected samples have revolutionized how populations are monitored. Most noninvasive monitoring studies have used hair or scat for individual identification of elusive mammals, but here we utilize naturally shed feathers. The Eastern imperial eagle (EIE) is a species of conservation concern throughout Central Asia and, like most raptors, EIEs are inherently challenging to study because adults are difficult to capture and band using conventional techniques. Over 6 years, we noninvasively collected hundreds of adult feathers and directly sampled EIE chicks at a national nature reserve in Kazakhstan. All samples were genetically sexed and genotyped at a suite of microsatellite loci. Genetically profiled adult feathers identified and monitored the presence of individual eagles over time, enabling us to address a variety of issues related to the biology, demography, and conservation of EIEs. Specifically, we characterized (i) the genetic mating system, (ii) relatedness among mated pairs, (iii) chick sex ratios, and (iv) annual turnover in an adult breeding population. We show that EIEs are genetically monogamous and furthermore, there is no apparent relatedness-based system of mate choice (e.g. inbreeding avoidance). Results indicate that annual adult EIE survivorship (84%) is lower than expected for a long-lived raptor, but initial analyses suggest the current reproductive rate at our study site is sufficient to maintain a stable breeding population. The pristine habitat at our study site supports an EIE population that is probably the most demographically robust in the world; thus, our results caution that populations in marginal habitats may not be self-sustaining.

Animals↗
PubMed2005

Comparison of lifestyle and health among Danish nurses and the Danish female population: is it possible to generalize findings from nurses to the general female population?

AIMS: To generalize findings from a nursing population to the general female population, the aim of this study was to compare lifestyle and health among Danish female nurses with that among Danish women. Furthermore, the aim was to compare lifestyle and health among Danish female nurses with women belonging to the same socio-economic group as nurses. METHODS: Danish females above the age of 44 in 1999 (n = 22,715) were compared with a group of women from the Danish Health and Morbidity Survey conducted in 2000 (n = 4,445). Age standardized risk ratios (SRR) with 95% confidence intervals were calculated to compare the two groups. RESULTS: Nurses smoke less (SRR 0.74, CI: 0.70-0.78) and are more physically active (SRR 2.53, CI: 2.31-2.77) when compared with the general female population. A higher percentage of nurses consume five drinks or more on a weekday compared with the general female population (SRR 2.68, CI: 2.25-3.19). When comparing nurses with women belonging to the same socio-economic group, these differences are also found to be statistically significant, but no differences are found according to overweight/obesity, self-reported health and limitations in daily activities when nurses are compared with women belonging to the same socio-economic group. CONCLUSIONS: In general, Danish nurses have a healthier lifestyle than other Danish women. In future studies, differences and similarities in lifestyle and health between nurses and other women should be considered when generalizing findings from Danish nurses to the Danish female population.

Alcohol Drinking↗
PubMed2004

Genetic bottlenecks reduce population variation in an experimental RNA virus population.

Genetic bottlenecks are stochastic events that limit genetic variation in a population and result in founding populations that can lead to genetic drift. Evidence of past genetic bottlenecks in numerous biological systems, from mammals to viruses, has been described. In this study, we used an artificial population of Cucumber mosaic virus consisting of 12 restriction enzyme marker-bearing mutants. This population was inoculated onto young leaves of tobacco plants and monitored throughout the course of systemic infection. We show here that the genetic variation in a defined population of an RNA virus is significantly, stochastically, and reproducibly reduced during the systemic infection process, providing clear evidence of a genetic bottleneck.

Cucumovirus↗
PubMed2000

Population based assessment of uveitis in an urban population in southern India.

AIM: To assess the prevalence of active and inactive uveitis unrelated to previous surgery or trauma in an urban population in southern India. METHODS: As part of the Andhra Pradesh Eye Disease Study, 2522 subjects (85.4% of those eligible), a sample representative of the population of Hyderabad city in southern India, underwent interview and detailed dilated eye examination. Presence of sequelae of uveitis without current active inflammation was defined as inactive uveitis. RESULTS: Unequivocal evidence of active or inactive uveitis unrelated to previous surgery or trauma was present in 21 subjects, an age-sex adjusted prevalence of 0.73% (95% confidence interval (CI) 0.44-1.14%). Active uveitis was present in eight subjects, an age-sex adjusted prevalence of 0.37% (95% CI 0. 19-0.70), of which 0.06% was anterior, 0.25% intermediate, and 0.06% posterior. The 0.36% (95% CI 0.17-0.68%) prevalence of inactive uveitis included macular chorioretinitis scars (0.26%), anterior (0. 07%) and previous vasculitis involving the whole eye (0.03%). The prevalence of visual impairment due to uveitis of less than 6/18 in at least one eye was 0.27%, less than 6/60 in at least one eye was 0. 16%, and less than 6/60 in both eyes was 0.03%. CONCLUSION: These population based cross sectional data give an estimate of the prevalence of various types of uveitis in this urban population in India. Active or past uveitis that might need treatment at some stage was present in one of every 140 people in this population.

Acute Disease↗
PubMed1992

Measuring stroke in the population: quality of routine statistics in comparison with a population-based stroke registry.

The validity of routine stroke data (official mortality statistics and hospital discharge registries) and a population-based MONICA stroke registry was assessed in a population of 309,806 25- to 74-year-old people in Sweden. The 'true' number of strokes in the population was estimated by screening for non-stroke diagnoses in death certificates and hospital discharge records and by a period of intensified search for otherwise unrecognized non-hospitalized stroke cases. Applying strict stroke criteria, the proportion of false-positive diagnoses was 10% and false-negative 17% in official mortality statistics. Among patients discharged alive from hospital, there were 32% false-positive and 6% false-negative stroke diagnoses. In the MONICA registry, the proportion of false-negative cases was 6% in fatal cases and 4% in non-fatal cases. Diagnostic information for subtyping stroke improved over time in non-fatal cases but remained essentially unchanged in fatal cases. We conclude that official mortality statistics give a reasonably good estimate of fatal stroke cases in Sweden, whereas hospital discharge records reflect poorly the incidence of stroke in the population. The overall quality of the population-based MONICA registry is good, although 4% of all strokes are missed. The proportion of unspecified stroke is substantial and changes over time; this makes longitudinal studies of stroke subtype difficult.

Adult↗
PubMed2006

Knee complaints vary with age and gender in the adult population. Population-based reference data for the Knee injury and Osteoarthritis Outcome Score (KOOS).

BACKGROUND: Self-reported knee complaints may vary with age and gender. Reference data from the adult population would help to better interpret the outcome of interventions due to knee complaints. The objectives of the present study were to describe the variation of self-reported knee pain, function and quality of life with age and gender in the adult population and to establish population-based reference data for the Knee injury and Osteoarthritis Outcome Score (KOOS). METHODS: Population-based cohort retrieved from the national population register. The knee-specific Knee injury and Osteoarthritis Outcome Score (KOOS) was mailed to 840 subjects aged 18-84 yrs. RESULTS: 68% response rate. Women in the age group 55-74 reported more knee-related complaints in all the KOOS subscales than age-matched men. The differences were significant for the subscales Pain (p = 0.027), Symptoms (p = 0.003) and ADL function (p = 0.046). In men, worse ADL and Sport and Recreation function was seen in the oldest age group 75-84 years compared to the younger age groups (p < 0.030). In women, worse Pain (p < 0.007), ADL (p < 0.030), Sport and Recreation (p < 0.001) and QOL (p < 0.002) were seen already in the age group 55-74 compared to the younger age groups. CONCLUSION: We found pain and other symptoms, physical function, and knee-related quality of life to vary with age and gender implying the use of age- and gender matched reference values for improved understanding of the outcome after interventions due to knee injury and knee OA.

Adolescent↗
PubMed2004

Quality of life in patients with colorectal cancer 1 year after diagnosis compared with the general population: a population-based study.

PURPOSE: Quality of life (QOL) has become an important outcome measure for patients with cancer, but long-term results from population-based studies are rare. The objective of our study was to identify specific limitations of QOL in survivors of colorectal cancer in comparison with men and women from the general population 1 year after diagnosis when acute treatment effects are expected to have declined. PATIENTS AND METHODS: QOL was assessed 1 year after diagnosis in a population-based cohort of 439 patients with colorectal cancer from Saarland (Germany) using the EORTC-QLC30 questionnaire. Specific functional and symptom QOL scores were compared with published reference data from the general population. RESULTS: Of 439 patients, 378 of them survived the first year after tumor diagnosis (86.1%). Of these, 309 returned the questionnaire (response rate, 81.7%). Compared with the general population, colorectal cancer patients scored their physical, role, cognitive, and global health functioning only slightly worse. More severe limitations were observed for the emotional and social functioning scales and for the symptom subscales of fatigue, dyspnea, insomnia, constipation, diarrhea, and financial difficulties. The differences regarding functional and symptom scores were predominantly found in younger age groups whereas older cancer patients and controls rated their health and QOL similarly. CONCLUSION: Deficits in emotional and social functioning and specific limitations like fatigue, dyspnea, insomnia, constipation, diarrhea, and financial difficulties are main factors hampering the QOL among colorectal cancer patients and seem to affect predominantly younger patients.

Adaptation, Psychological↗
PubMed2024

Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia.

The genetic identification of evolutionary significant units and information on their connectivity can be used to design effective management and conservation plans for species of concern. Despite having high dispersal capacity, several seabird species show population structure due to both abiotic and biotic barriers to gene flow. The Kelp Gull is the most abundant species of gull in the southern hemisphere. In Argentina it reproduces in both marine and freshwater environments, with more than 100,000 breeding pairs following a metapopulation dynamic across 140 colonies in the Atlantic coast of Patagonia. However, little is known about the demography and connectivity of inland populations. We aim to provide information on the connectivity of the largest freshwater colonies (those from Nahuel Huapi Lake) with the closest Pacific and Atlantic populations to evaluate if these freshwater colonies are receiving immigrants from the larger coastal populations. We sampled three geographic regions (Nahuel Huapi Lake and the Atlantic and Pacific coasts) and employed a reduced-representation genomic approach to genotype individuals for single-nucleotide polymorphisms (SNPs). Using clustering and phylogenetic analyses we found three genetic groups, each corresponding to one of our sampled regions. Individuals from marine environments are more closely related to each other than to those from Nahuel Huapi Lake, indicating that the latter population constitutes the first freshwater Kelp Gull colony to be identified as an evolutionary significant unit in Patagonia.

Humans↗