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At least 433 records · Page 24Linked to original sources
PubMed2001

Two-locus identity probabilities and identity disequilibrium in a partially selfing subdivided population.

Measures of association of genes at different loci (linkage disequilibrium) are widely used to determine whether the structure of natural populations is clonal or not, to map genes from population data, or to test for the homogeneity of response of molecular markers to background selection, for example. However, the usual definitions of parameters for gametic associations may not be suitable for all these purposes. In this paper, we derive the recursion equations for one- and two-locus identity probabilities in an infinite island model. We study the role of drift, gene flow, partial selfing and mutation model on the expected association of genes across loci. We define the 'within-subpopulation identity disequilibrium' as the difference between the joint two-locus probability of identity in state and the expected product of one-locus identity probabilities. We evaluate this parameter as a function of recombination rate, effective size, gene flow and selfing rate. Within-subpopulation identity disequilibrium attains maximum values for intermediate immigration rates, whatever the selfing rate. Moreover, identity disequilibrium may be very small, even for high selfing rates. We discuss the implications of these findings for the analysis of data from natural populations.

Alleles↗
PubMed2003

Normal linear models with genetically structured residual variance heterogeneity: a case study.

Normal mixed models with different levels of heterogeneity in the residual variance are fitted to pig litter size data. Exploratory analysis and model assessment is based on examination of various posterior predictive distributions. Comparisons based on Bayes factors and related criteria favour models with a genetically structured residual variance heterogeneity. There is, moreover, strong evidence of a negative correlation between the additive genetic values affecting litter size and those affecting residual variance. The models are also compared according to the purposes for which they might be used, such as prediction of 'future' data, inference about response to selection and ranking candidates for selection. A brief discussion is given of some implications for selection of the genetically structured residual variance model.

Analysis of Variance↗
PubMed1999

First policy then science: why a management unit based solely on genetic criteria cannot work.

In contrast to the goals of the symposium from which this series of papers originated, we argue that attempts to apply unambiguously defined and general management unit criteria based solely on genetic parameters can easily lead to incorrect management decisions. We maintain that conservation genetics is best served by altering the perspective of data analysis so that decision making is optimally facilitated. To do so requires accounting for policy objectives early in the design and execution of the science. This contrasts with typical hypothesis testing approaches to analysing genetic data for determining population structure, which often aspire to objectivity by considering management objectives only after the analysis is complete. The null hypothesis is generally taken as panmixia with a strong predilection towards avoiding false acceptance of the alternative hypothesis (the existence of population structure). We show by example how defining management units using genetic data and standard scientific analyses that do not consider either the specific management objectives or the anthropogenic risks facing the populations being studied can easily result in a management failure by losing local populations. We then use the same example to show how an 'applied' approach driven by specific objectives and knowledge of abundance and mortality results in appropriate analyses and better decisions. Because management objectives stem from public policy, which differs among countries and among species groups, criteria for defining management units must be specific, not general. Therefore, we conclude that the most productive way to define management units is on a case-by-case basis. We also suggest that creating analytical tools designed specifically to address decision making in a management context, rather than re-tooling academic tools designed for other purposes, will increase and improve the use of genetics in conservation.

Animals↗
PubMed2001

Allozyme and microsatellite loci provide discordant estimates of population differentiation in the endangered dusky grouper (Epinephelus marginatus) within the Mediterranean Sea.

The dusky grouper, Epinephelus marginatus, inhabits coastal reefs in the Mediterranean Sea and Atlantic Ocean. A decline in the abundance of this long-lived protogynous hermaphrodite has led to its listing as an endangered species in the Mediterranean, and heightened management concerns regarding its genetic variability and population substructure. To address these concerns, we analysed genetic variation at seven microsatellite and 28 allozyme loci in dusky groupers sampled from seven areas (for microsatellites) and three areas (for allozymes) in the west-central Mediterranean. Levels of genetic variability were higher for microsatellites than for allozymes (mean H(E) = 0.78 and 0.07, respectively), but similar to those observed in other marine fishes with comparable markers. Both microsatellites and allozymes revealed significant genetic differentiation among all areas analysed with each class of marker, but the magnitude of differentiation revealed by allozymes over three locales (F(ST) = 0.214) was greater than that detected with microsatellites over seven areas, or over the three areas shared with the allozyme analysis (F(ST) = 0.018 and approximately 0, respectively). A large proportion of the allozyme differentiation was due to a single locus (ADA*) possibly influenced by selection, but allozyme differentiation over the three areas was still highly significant (F(ST) = 0.06, P < 0.0001), and the 95% confidence intervals for allozyme and microsatellite F(ST) did not overlap when this locus was excluded. There was no evidence of isolation by distance with either class of markers. Our results lead us to conclude that dusky groupers are not panmictic in the Mediterranean Sea and suggest that they should be managed on a local basis. However, more work is needed to elucidate genetic relationships among populations.

Animals↗
PubMed2004

Comparison of haplotype inference methods using genotypic data from unrelated individuals.

OBJECTIVE: Haplotypes are gaining popularity in studies of human genetics because they contain more information than does a single gene locus. However, current high-throughput genotyping techniques cannot produce haplotype information. Several statistical methods have recently been proposed to infer haplotypes based on unphased genotypes at several loci. The accuracy, efficiency, and computational time of these methods have been under intense scrutiny. In this report, our aim was to evaluate haplotype inference methods for genotypic data from unrelated individuals. METHODS: We compared the performance of three haplotype inference methods that are currently in use--HAPLOTYPER, hap, and PHASE--by applying them to a large data set from unrelated individuals with known haplotypes. We also applied these methods to coalescent-based simulation studies using both constant size and exponential growth models. The performance of these methods, along with that of the expectation-maximization algorithm, was further compared in the context of an association study. RESULTS: While the algorithm implemented in the software PHASE was found to be the most accurate in both real and simulated data comparisons, all four methods produced good results in the association study.

Algorithms↗
PubMed1980

Genetic drift in a stock of laboratory mice.

Genetic drift in an outbred stock of CFLP mice was monitored for 6 years using genetic polymorphism for glucose phosphate isomerase (GPI) and the shape of the mandible as genetic markers. Statistically significant drift was found in both characters. The cause of this drift was not determined, though it could have arisen as a result of genetic sampling during hysterectomy derivation. The use of inbred strains is recommended on theoretical grounds of long-term genetic constancy is needed.

Animals↗
PubMed2004

VARAN: a web server for variability analysis of DNA microarray experiments.

UNLABELLED: Here, we describe a tool for VARiability Analysis of DNA microarrays experiments (VARAN), a freely available Web server that performs a signal intensity based analysis of the log2 expression ratio variability deduced from DNA microarray data (one or two channels). Two modules are proposed: VARAN generator to compute a sliding windows analysis of the experimental variability (mean and SD) and VARAN analyzer to compare experimental data with an asymptotic variability model previously built with the generator module from control experiments. Both modules provide normalized intensity signals with five possible methods, log ratio values and a list of genes showing significant variations between conditions. AVAILABILITY: http://www.bionet.espci.fr/varan/ SUPPLEMENTARY INFORMATION: http://www.bionet.espci.fr/varan/help.html

Algorithms↗
PubMed2004

Genetic variation in uncoupling protein 3 is associated with dietary intake and body composition in females.

The uncoupling proteins (UCPs) are a family of mitochondrial transport proteins that promote proton leakage across the inner mitochondrial membrane, uncoupling oxidative phosphorylation from adenosine triphosphate (ATP) production and releasing energy as heat. Variation in these genes may disrupt biochemical pathways influencing thermogenesis, energy metabolism, and fuel substrate partitioning and oxidation, which may in turn predispose to obesity. We genotyped polymorphisms in UCP2 and UCP3 in a sample of nondiabetic participants (n = 722) of the San Luis Valley Diabetes Study (SLVDS) and found female-specific associations between UCP3 polymorphisms and measures of dietary intake and body composition. The UCP3-5 variant was statistically significantly associated with total caloric intake (P =.012), fat intake (P =.011), fat mass (P =.004), and lean mass (P =.013), with the C allele corresponding to higher dietary intake and lower fat mass and lean mass. The UCP3p-55 and the UCP3-3 polymorphisms, which were in high linkage disequilibrium (D' = 0.9776), showed similar patterns of association with total caloric intake (P =.031 and P =.042, respectively) and lean mass (P =.035 and P =.059, respectively), with the rare alleles corresponding to higher total intake and lean mass. No statistically significant associations were detected between the outcome variables and polymorphisms in UCP2. Two-way analysis of covariance (ANCOVA), used to evaluate the multi-locus effects and interactions between UCP3-5 and UCP3p-55, showed association with the main effect terms, but no evidence for statistically significant interaction between UCP3-5 and UCP3p-55 in regard to dietary intake. The UCP3-5 polymorphism was the only statistically significant genetic predictor of fat mass. The lean mass model showed no statistically significant association with either UCP3 variant. These results support a role for UCP3 in fuel substrate management and energy metabolism, which may influence body weight regulation.

Alleles↗
PubMed1999

Using genetic analyses to clarify the distinction between depressive and anxious symptoms in children.

Self-report measures of depression and anxiety in children are highly correlated and distinguishing between shared and independent factors in their etiologies is therefore problematic. The aim of this article was to test whether less correlated measures of depression and anxiety could be produced and, if so, what genetic and environmental factors would account for the variance in these symptoms. Second-order factor analysis of the items from two standardized self-report questionnaires of depression and anxiety collected from 395 pairs of same-sex twins aged 8 to 16 years resulted in purer dimensions of depression and anxiety. Behavioral genetic analyses confirmed the distinction between these two dimensions, and bivariate analyses revealed that the association between the two was primarily accounted for by shared genetic factors.

Adolescent↗
PubMed2004

Evaluation of body condition score measured throughout lactation as an indicator of fertility in dairy cattle.

Body condition score (BCS) records of primiparous Holstein cows were analyzed both as a single measure per animal and as repeated measures per sire of cow. The former resulted in a single, average, genetic evaluation for each sire, and the latter resulted in separate genetic evaluations per day of lactation. Repeated measure analysis yielded genetic correlations of less than unity between days of lactation, suggesting that BCS may not be the same trait across lactation. Differences between daily genetic evaluations on d 10 or 30 and subsequent daily evaluations were used to assess BCS change at different stages of lactation. Genetic evaluations for BCS level or change were used to estimate genetic correlations between BCS measures and fertility traits in order to assess the capacity of BCS to predict fertility. Genetic correlation estimates with calving interval and non-return rate were consistently higher for daily BCS than single measure BCS evaluations, but results were not always statistically different. Genetic correlations between BCS change and fertility traits were not significantly different from zero. The product of the accuracy of BCS evaluations with their genetic correlation with the UK fertility index, comprising calving interval and non-return rate, was consistently higher for daily than for single BCS evaluations, by 28 to 53%. This product is associated with the conceptual correlated response in fertility from BCS selection and was highest for early (d 10 to 75) evaluations.

Analysis of Variance↗
PubMed1993

Knowledge of genetics among residents in obstetrics and gynecology.

A supervised genetics examination was administered to 76 obstetrics and gynecology (ob/gyn) residents from 15 different institutions in the Philadelphia area. The questions were specifically designed to be applicable to obstetrical practice. Overall, the mean score was 69% (range 32%-88%). Using the nonparametric Mann-Whitney rank sum test, we found that the 25 residents from institutions with an obstetrics-gynecology-genetics (OGG) program, coordinated by an obstetrician/gynecologist board certified in clinical genetics, had statistically significant higher scores than the remaining 51 residents from institutions without an OGG program (77% vs. 65%, respectively; P < .001). This study demonstrates that knowledge of genetics among residents in ob/gyn is deficient, especially among residents at institutions without OGG programs. Special efforts should be made to provide genetics education to these individuals. We propose that more obstetricians be encouraged to pursue postgraduate training in genetics in light of the rapid development of medical genetics; its application to prenatal screening, diagnosis, and counseling; the anticipated utilization of genetics services; and the need for educational initiatives geared toward ob/gyn patients.

Genetics↗
PubMedDate not supplied

A bivariate genetic analysis of cerebral white matter hyperintensities and cognitive performance in elderly male twins.

White matter hyperintensities (WMHs) are frequently observed on MRI scans of elderly nondemented people and have been associated in the past with cognitive impairment and physical dysfunction. Individual differences in the prevalence and severity of WMHs have been documented and more recently we reported on the significant contribution of genetic influences to this variability. The objective of the present study was to further investigate, in the context of a behavioral genetic paradigm, the nature of the association between WMHs and cognitive and physical function. MRI brain scans and a battery of neuropsychological and physical function tests were given to 142 male-male twin pairs [72 monozygotic (MZ) and 70 dizygotic (DZ)], participants in the 4th exam of the NHLBI Twin Study. Biometric genetic modeling was used to estimate the genetic and/or environmental covariation between WMHs and cognitive and physical summary scores. The phenotypic association between WMHs and cognitive function in this sample of twins was modest but statistically significant. Genetic analyses of cognitive and physical function summary scores found that 55% to 70% of the observed variability was due to genetic influences. A further decomposition of the phenotypic association between WMHs and cognitive function found that 70% to 100% of the phenotypic covariation was due to common genetic effects. Similar results explained the association between WMHs and performance on two physical function tests. We conclude from these analyses that common genetic influences explain to a large extent previously observed phenotypic associations between large amounts of WMHs and poor cognitive and physical function in the elderly.

Aged↗