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Related Individuals (relate + individual)
Selected AbstractsCase-control single-marker and haplotypic association analysis of pedigree dataGENETIC EPIDEMIOLOGY, Issue 2 2005Sharon R. Browning Abstract Related individuals collected for use in linkage studies may be used in case-control linkage disequilibrium analysis, provided one takes into account correlations between individuals due to identity-by-descent (IBD) sharing. We account for these correlations by calculating a weight for each individual. The weights are used in constructing a composite likelihood, which is maximized iteratively to form likelihood ratio tests for single-marker and haplotypic associations. The method scales well with increasing pedigree size and complexity, and is applicable to both autosomal and X chromosomes. We apply the approach to an analysis of association between type 2 diabetes and single-nucleotide polymorphism markers in the PPAR-, gene. Simulated data are used to check validity of the test and examine power. Analysis of related cases has better power than analysis of population-based cases because of the increased frequencies of disease-susceptibility alleles in pedigrees with multiple cases compared to the frequencies of these alleles in population-based cases. Also, utilizing all cases in a pedigree rather than just one per pedigree improves power by increasing the effective sample size. We demonstrate that our method has power at least as great as that of several competing methods, while offering advantages in the ability to handle missing data and perform haplotypic analysis. Genet. Epidemiol. 28:110,122, 2005. © 2004 Wiley-Liss, Inc. [source] Susceptibility of Common and Rare Plant Species to the Genetic Consequences of Habitat FragmentationCONSERVATION BIOLOGY, Issue 3 2007OLIVIER HONNAY diversidad genética; endogamia; fragmentación de hábitat; sistema reproductivo; tamaño poblacional Abstract:,Small plant populations are more prone to extinction due to the loss of genetic variation through random genetic drift, increased selfing, and mating among related individuals. To date, most researchers dealing with genetic erosion in fragmented plant populations have focused on threatened or rare species. We raise the question whether common plant species are as susceptible to habitat fragmentation as rare species. We conducted a formal meta-analysis of habitat fragmentation studies that reported both population size and population genetic diversity. We estimated the overall weighted mean and variance of the correlation coefficients among four different measures of genetic diversity and plant population size. We then tested whether rarity, mating system, and plant longevity are potential moderators of the relationship between population size and genetic diversity. Mean gene diversity, percent polymorphic loci, and allelic richness across studies were positively and highly significantly correlated with population size, whereas no significant relationship was found between population size and the inbreeding coefficient. Genetic diversity of self-compatible species was less affected by decreasing population size than that of obligate outcrossing and self-compatible but mainly outcrossing species. Longevity did not affect the population genetic response to fragmentation. Our most important finding, however, was that common species were as, or more, susceptible to the population genetic consequences of habitat fragmentation than rare species, even when historically or naturally rare species were excluded from the analysis. These results are dramatic in that many more plant species than previously assumed may be vulnerable to genetic erosion and loss of genetic diversity as a result of ongoing fragmentation processes. This implies that many fragmented habitats have become unable to support plant populations that are large enough to maintain a mutation-drift balance and that occupied habitat fragments have become too isolated to allow sufficient gene flow to enable replenishment of lost alleles. Resumen:,Las poblaciones pequeñas de plantas son más propensas a la extinción debido a la pérdida de variación genética por medio de la deriva génica aleatoria, el incremento de autogamia y la reproducción entre individuos emparentados. A la fecha, la mayoría de los investigadores que trabajan con erosión genética en poblaciones fragmentadas de plantas se han enfocado en las especies amenazadas o raras. Cuestionamos si las especies de plantas comunes son tan susceptibles a la fragmentación del hábitat como las especies raras. Realizamos un meta análisis formal de estudios de fragmentación que reportaron tanto tamaño poblacional como diversidad genética. Estimamos la media general ponderada y la varianza de los coeficientes de correlación entre cuatro medidas de diversidad genética y de tamaño poblacional de las plantas. Posteriormente probamos si la rareza, el sistema reproductivo y la longevidad de la planta son moderadores potenciales de la relación entre el tamaño poblacional y la diversidad genética. La diversidad genética promedio, el porcentaje de loci polimórficos y la riqueza alélica en los estudios tuvieron una correlación positiva y altamente significativa con el tamaño poblacional, mientras que no encontramos relación significativa entre el tamaño poblacional y el coeficiente de endogamia. La diversidad genética de especies auto compatibles fue menos afectada por la reducción en el tamaño poblacional que la de especies exogámicas obligadas y especies auto compatibles, pero principalmente exogámicas. La longevidad no afectó la respuesta genética de la población a la fragmentación. Sin embargo, nuestro hallazgo más importante fue que las especies comunes fueron tan, o más, susceptibles a las consecuencias genéticas de la fragmentación del hábitat que las especies raras, aun cuando las especies histórica o naturalmente raras fueron excluidas del análisis. Estos resultados son dramáticos porque muchas especies más pueden ser vulnerables a la erosión genética y a la pérdida de diversidad genética como consecuencia de los procesos de fragmentación que lo se asumía previamente. Esto implica que muchos hábitats fragmentados han perdido la capacidad para soportar poblaciones de plantas lo suficientemente grandes para mantener un equilibrio mutación-deriva y que los fragmentos de hábitat ocupados están tan aislados que el flujo génico es insuficiente para permitir la reposición de alelos perdidos. [source] Parental and perinatal factors influencing the development of handedness in captive chimpanzeesDEVELOPMENTAL PSYCHOBIOLOGY, Issue 6 2006William D. Hopkins Abstract It has been proposed that human right handedness is determined by genetic factors associated with the emergence of language, whereas non-human primate handedness is determined by random, non-genetic factors. These different mechanisms account for differences in the distribution of handedness between human and non-human primates. Here we report evidence that genetic factors play a role in the determination of handedness in chimpanzees. We further report that differential rearing has no influence on the expression of handedness in related individuals. Contrary to many theories of the origin of handedness, these results indicate that genetic factors have a significant influence on handedness in chimpanzees. © 2006 Wiley Periodicals, Inc. Dev Psychobiol 48: 428,435, 2006. [source] Assessment of SNP streak statistics using gene drop simulation with linkage disequilibriumGENETIC EPIDEMIOLOGY, Issue 2 2010Alun ThomasArticle first published online: 6 JUL 200 Abstract We describe methods and programs for simulating the genotypes of individuals in a pedigree at large numbers of linked loci when the alleles of the founders are under linkage disequilibrium. Both simulation and estimation of linkage disequilibrium models are shown to be feasible on a genome wide scale. The methods are applied to evaluate the statistical significance of streaks of loci at which sets of related individuals share a common allele. The effects of properly allowing for linkage disequilibrium are shown to be important as they explain many of the large observations. This is illustrated by reanalysis of a previously reported linkage of prostate cancer to chromosome 1p23. Genet. Epidemiol. 34: 119,124, 2010. © 2009 Wiley-Liss, Inc. [source] Testing association in the presence of linkage , a powerful score for binary traitsGENETIC EPIDEMIOLOGY, Issue 6 2007Gudrun Jonasdottir Abstract We present a score for testing association in the presence of linkage for binary traits. The score is robust to varying degrees of linkage, and it is valid under any ascertainment scheme based on trait values as well as under population stratification. The score test is derived from a mixed effects model where population level association is modeled using a fixed effect and where correlation among related individuals is allowed for by using log-gamma random effects. The score, as presented in this paper, does not assume full information about the inheritance pattern in families or parental genotypes. We compare the score to the semi-parametric family-based association test (FBAT), which has won ground because of its flexible and simple form. We show that a random effects formulation of co-inheritance can improve the power substantially. We apply the method to data from the Collaborative Study on the Genetics of Alcoholism. We compare our findings to previously published results. Genet. Epidemiol. 2007. © 2007 Wiley-Liss, Inc. [source] Maximum-likelihood estimation of haplotype frequencies in nuclear familiesGENETIC EPIDEMIOLOGY, Issue 1 2004Tim Becker Abstract The importance of haplotype analysis in the context of association fine mapping of disease genes has grown steadily over the last years. Since experimental methods to determine haplotypes on a large scale are not available, phase has to be inferred statistically. For individual genotype data, several reconstruction techniques and many implementations of the expectation-maximization (EM) algorithm for haplotype frequency estimation exist. Recent research work has shown that incorporating available genotype information of related individuals largely increases the precision of haplotype frequency estimates. We, therefore, implemented a highly flexible program written in C, called FAMHAP, which calculates maximum likelihood estimates (MLEs) of haplotype frequencies from general nuclear families with an arbitrary number of children via the EM-algorithm for up to 20 SNPs. For more loci, we have implemented a locus-iterative mode of the EM-algorithm, which gives reliable approximations of the MLEs for up to 63 SNP loci, or less when multi-allelic markers are incorporated into the analysis. Missing genotypes can be handled as well. The program is able to distinguish cases (haplotypes transmitted to the first affected child of a family) from pseudo-controls (non-transmitted haplotypes with respect to the child). We tested the performance of FAMHAP and the accuracy of the obtained haplotype frequencies on a variety of simulated data sets. The implementation proved to work well when many markers were considered and no significant differences between the estimates obtained with the usual EM-algorithm and those obtained in its locus-iterative mode were observed. We conclude from the simulations that the accuracy of haplotype frequency estimation and reconstruction in nuclear families is very reliable in general and robust against missing genotypes. © 2004 Wiley-Liss, Inc. [source] Estimation of allele frequencies with data on sibshipsGENETIC EPIDEMIOLOGY, Issue 3 2001Karl W. Broman Abstract Allele frequencies are generally estimated with data on a set of unrelated individuals. In genetic studies of late-onset diseases, the founding individuals in pedigrees are often not available, and so one is confronted with the problem of estimating allele frequencies with data on related individuals. We focus on sibpairs and sibships, and compare the efficiency of four methods for estimating allele frequencies in this situation: (1) use the data for one individual from each sibship; (2) use the data for all individuals, ignoring their relationships; (3) use the data for all individuals, taking proper account of their relationships, considering a single marker at a time; and (4) use the data for all individuals, taking proper account of their relationships, considering a set of linked markers simultaneously. We derived the variance of estimator 2, and showed that the estimator is unbiased and provides substantial improvement over method 1. We used computer simulation to study the performance of methods 3 and 4, and showed that method 3 provides some improvement over method 2, while method 4 improves little on method 3. Genet. Epidemiol. 20:307,315, 2001. © 2001 Wiley-Liss, Inc. [source] Parentage analysis in Gabonese colonies of soil-feeding termites belonging to the Cubitermes sp. affinis subarquatus complex of species (Termitidae: Termitinae)INSECT SCIENCE, Issue 2 2010Virginie Roy Abstract,Cubitermes spp. are widely distributed soil-feeding termite species in sub-Saharan Africa which play a fundamental role in soil structure and fertility. A complex of at least four cryptic species (i.e., Cubitermes sp. affinis subarquatus complex of species) has been recently described using molecular markers. In order to investigate the breeding system of these species, five microsatellite markers were used to carry out parentage and relatedness analyses in 15 Gabonese colonies. Monogamy was confirmed as the predominant reproductive organization in Cubitermes spp. (76% of the colonies). Within 30% of these monogamous colonies, a high relatedness between reproductives was shown, suggesting that mating between related individuals occurs. However, Cubitermes colonies can deviate from monogamy. Indeed, parental contributions by at least two related reproductives of the same sex were revealed in four colonies and polyandry was demonstrated in two of them. Infiltration of reproductives in the colony is the most plausible explanation for such cases of polygamy in Cubitermes spp. [source] The evolution of cooperation and altruism , a general framework and a classification of modelsJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2006L. LEHMANN Abstract One of the enduring puzzles in biology and the social sciences is the origin and persistence of intraspecific cooperation and altruism in humans and other species. Hundreds of theoretical models have been proposed and there is much confusion about the relationship between these models. To clarify the situation, we developed a synthetic conceptual framework that delineates the conditions necessary for the evolution of altruism and cooperation. We show that at least one of the four following conditions needs to be fulfilled: direct benefits to the focal individual performing a cooperative act; direct or indirect information allowing a better than random guess about whether a given individual will behave cooperatively in repeated reciprocal interactions; preferential interactions between related individuals; and genetic correlation between genes coding for altruism and phenotypic traits that can be identified. When one or more of these conditions are met, altruism or cooperation can evolve if the cost-to-benefit ratio of altruistic and cooperative acts is greater than a threshold value. The cost-to-benefit ratio can be altered by coercion, punishment and policing which therefore act as mechanisms facilitating the evolution of altruism and cooperation. All the models proposed so far are explicitly or implicitly built on these general principles, allowing us to classify them into four general categories. [source] Fine-scale natal homing and localized movement as shaped by sex and spawning habitat in Chinook salmon: insights from spatial autocorrelation analysis of individual genotypesMOLECULAR ECOLOGY, Issue 14 2006H. M. NEVILLE Abstract Natal homing is a hallmark of the life history of salmonid fishes, but the spatial scale of homing within local, naturally reproducing salmon populations is still poorly understood. Accurate homing (paired with restricted movement) should lead to the existence of fine-scale genetic structuring due to the spatial clustering of related individuals on spawning grounds. Thus, we explored the spatial resolution of natal homing using genetic associations among individual Chinook salmon (Oncorhynchus tshawytscha) in an interconnected stream network. We also investigated the relationship between genetic patterns and two factors hypothesized to influence natal homing and localized movements at finer scales in this species, localized patterns in the distribution of spawning gravels and sex. Spatial autocorrelation analyses showed that spawning locations in both sub-basins of our study site were spatially clumped, but the upper sub-basin generally had a larger spatial extent and continuity of redd locations than the lower sub-basin, where the distribution of redds and associated habitat conditions were more patchy. Male genotypes were not autocorrelated at any spatial scale in either sub-basin. Female genotypes showed significant spatial autocorrelation and genetic patterns for females varied in the direction predicted between the two sub-basins, with much stronger autocorrelation in the sub-basin with less continuity in spawning gravels. The patterns observed here support predictions about differential constraints and breeding tactics between the two sexes and the potential for fine-scale habitat structure to influence the precision of natal homing and localized movements of individual Chinook salmon on their breeding grounds. [source] Detecting dyads of related individuals in large collections of DNA-profiles by controlling the false discovery rateMOLECULAR ECOLOGY RESOURCES, Issue 4 2010H. J. SKAUG Abstract The search for pairs (dyads) of related individuals in large databases of DNA-profiles has become an increasingly important inference tool in ecology. However, the many, partly dependent, pairwise comparisons introduce statistical issues. We show that the false discovery rate (FDR) procedure is well suited to control for the proportion of false positives, i.e. dyads consisting of unrelated individuals, which under normal circumstances would have been labelled as related individuals. We verify the behaviour of the standard FDR procedure by simulation, demonstrating that the FDR procedure works satisfactory in spite of the many dependent pairwise comparisons involved in an exhaustive database screening. A computer program that implements this method is available online. In addition, we propose to implement a second stage in the procedure, in which additional independent genetic markers are used to identify the false positives. We demonstrate the application of the approach in an analysis of a DNA database consisting of 3300 individual minke whales (Balaenoptera acutorostrata) each typed at ten microsatellite loci. Applying the standard procedure with an FDR of 50% led to the identification of 74 putative dyads of 1st- or 2nd-order relatives. However, introducing the second step, which involved additional genotypes at 15 microsatellite loci, revealed that only 21 of the putative dyads can be claimed with high certainty to be true dyads. [source] Characterization of microsatellite loci in the subsocial spider Stegodyphus lineatus (Araneae: Eresidae)MOLECULAR ECOLOGY RESOURCES, Issue 1 2009T. BILDE Abstract Stegodyphus lineatus spiders live in groups consisting of closely related individuals. There appears to be no discrimination against related individuals as mates but females mate multiply, despite the fact that matings are shown to carry a cost. We have developed eight polymorphic dinucleotide microsatellite markers that allow us to assess levels of heterozygosity and relatedness among individuals of this species. These molecular markers are likely to prove highly effective tools for estimating levels of inbreeding and thus allow us to test hypotheses about the relationships between social structure, mating strategies and inbreeding avoidance. [source] | ||||||||||