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PubMed2006

Natural selection and population dynamics.

To what extent, and under which circumstances, are population dynamics influenced by concurrent natural selection? Density dependence and environmental stochasticity are generally expected to subsume any selective modulation of population growth rate, but theoretical considerations point to conditions under which selection can have an appreciable impact on population dynamics. By contrast, empirical research has barely scratched the surface of this fundamental question in population biology. Here, we present a diverse body of mostly empirical evidence that demonstrates how selection can influence population dynamics, including studies of small populations, metapopulations, cyclical populations and host-pathogen interactions. We also discuss the utility, in this context, of inferences from molecular genetic data, placing them within the broader framework of quantitative genetics and life-history evolution.

Adaptation, Biological↗
PubMed2002

Genetic management of nonhuman primates.

Genetic management is widely recognized as a critical component of the overall management of captive nonhuman primate colonies which produce animals for biomedical research. In this paper, we review the roles of conservation-oriented genetic management, research-oriented genetic management, genetic management at the level of taxomomic class, genetic management at the level of the population, and quantitative genetic analysis in comprehensive genetic management programs for nonhuman primate colonies. We conclude that genetic management is crucial for maintaining nonhuman primate populations suitable for genetic research on normal and disease-related phenotypes. In addition, for research programs that do not have specific genetic objectives, genetic management is essential to facilitate the selection of samples of well-matched unrelated animals for experimental purposes.

Animals↗
PubMedDate not supplied

[Methods for transcriptome and proteome research: applications for studying the biology of reproduction in cattle].

Improvements of animal health, welfare and product quality are major goals of modern animal breeding. Thus, in addition to the classical production traits, functional traits such as disease resistance, fertility and longevity moved into the center of animal breeder's interests. Due to their low heritability, the improvement of functional traits using conventional approaches of phenotypic testing and quantitative genetics is difficult. A number of studies have been conducted worldwide in various species to map quantitative trait loci (QTLs) and to identify genetic markers for health traits. This has revealed a plethora of chromosome regions which may harbor genes with relevance for animal health. Functional genome research integrates holistic investigations at the level of the genome, at the level of gene activity (transcriptome, proteome) and at various levels of phenotypic expression. The integration of all these levels of information provides the basis for the functional dissection of complex traits. This review provides an overview of the most important strategies for holistic transcriptome and proteome analyses. The successful application of these techniques is exemplified by our studies of bovine reproductive biology.

Animals↗
PubMed2005

Segregation of urine calcium excretion in families ascertained for nephrolithiasis: evidence for a major gene.

BACKGROUND: The quantitative genetics of urine calcium excretion has not been established. It is a trait of interest because hypercalciuria is commonly found in subjects with nephrolithiasis. The aim of this study was to model the segregation of this trait in a sample of French-Canadian families ascertained through a stone former. METHODS: Major gene, polygenic, and mixed models were fit to 24-hour urine calcium excretion from 567 individuals in 221 nuclear families, while simultaneously taking into account gender, age at examination, body mass index (BMI), and the use of thiazide drugs. The nuclear families were extracted from 154 pedigrees, some of which were four generations, with at least two siblings with a history of calcium stones. RESULTS: All the proposed genetic models fit the data significantly better than the null model. The most parsimonious model was the mixed codominant/polygenic model but it was statistically indistinguishable from the single-gene codominant model. In both of these models the heritability attributable to the major gene was estimated to be 0.58. CONCLUSION: Our results suggest that a major gene with a relatively large effect on variation in urine calcium excretion is segregating in French-Canadian families with stone formers. This implies that the power of quantitative trait segregation analysis of urine calcium excretion may be increased in these families, and results indicate that it should be feasible to genetically map the quantitative trait locus.

Adult↗
PubMed1995

Statistical validity for testing associations between genetic markers and quantitative traits in family data.

In genetic analysis it is often of interest to analyze associations between traits of unknown genetic etiology and genetic markers from pedigree data. Statistical methods that assume independence of pedigree members cannot be used because they disregard the statistical dependencies of members in a pedigree. For quantitative traits, a regression model proposed by George and Elston [Genet Epidemiol 4:193-201, 1987] uses an asymptotic likelihood ratio test and incorporates a correlation structure that allows for statistical dependence among the pedigree members. The statistical validity of this test is assessed for finite samples by measuring the discrepancy between the empirical and theoretical chi-square distributions. The variance of the mean of the dependent variable is determined to be related to this discrepancy and can be used to determine whether a pedigree structure is large enough for making valid statistical inferences on the basis of the asymptotic test. A multi-generational pedigree of 200 or so individuals should in many cases be sufficient for valid results when using the asymptotic likelihood ratio test for the association between markers and continuous traits.

Family↗
PubMed2005

Modeling quantitative trait Loci and interpretation of models.

A quantitative genetic model relates the genotypic value of an individual to the alleles at the loci that contribute to the variation in a population in terms of additive, dominance, and epistatic effects. This partition of genetic effects is related to the partition of genetic variance. A number of models have been proposed to describe this relationship: some are based on the orthogonal partition of genetic variance in an equilibrium population. We compare a few representative models and discuss their utility and potential problems for analyzing quantitative trait loci (QTL) in a segregating population. An orthogonal model implies that estimates of the genetic effects are consistent in a full or reduced model in an equilibrium population and are directly related to the partition of the genetic variance in the population. Linkage disequilibrium does not affect the estimation of genetic effects in a full model, but would in a reduced model. Certainly linkage disequilibrium would complicate the detection of QTL and epistasis. Using different models does not influence the detection of QTL and epistasis. However, it does influence the estimation and interpretation of genetic effects.

Gene Frequency↗
PubMed2006

Geographical variation in selection, from phenotypes to molecules.

Molecular technologies now allow researchers to isolate quantitative trait loci (QTLs) and measure patterns of gene sequence variation within chromosomal regions containing important polymorphisms. I develop a simulation model to investigate gene sequence evolution within genomic regions that harbor QTLs. The QTLs influence a trait experiencing geographical variation in selection, which is common in nature and produces obvious differentiation at the phenotypic level. Counter to expectations, the simulations suggest that selection can substantially affect quantitative genetic variation without altering the amount and pattern of molecular variation at sites closely linked to the QTLs. Even with large samples of gene sequences, the likelihood of rejecting neutrality is often low. The exception is situations where strong selection is combined with low migration among demes, conditions that may be common in many plant species. The results have implications for gene sequence surveys and, perhaps more generally, for interpreting the apparently weak connection between levels of molecular and quantitative trait variation within species.

Achillea↗
PubMed2006

A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content.

We have developed a new DH mapping population for oilseed rape, named TNDH, using genetically and phenotypically diverse parental lines. We used the population in the construction of a high stringency genetic linkage map, consisting of 277 loci, for use in quantitative genetic analysis. A proportion of the markers had been used previously in the construction of linkage maps for Brassica species, thus permitting the alignment of maps. The map includes 68 newly developed Sequence Tagged Site (STS) markers targeted to the homologues of defined genes of A. thaliana. The use of these markers permits the alignment of our linkage map with the A. thaliana genome sequence. An additional 74 loci (31 newly developed STS markers and 43 loci defined by SSR and RFLP markers that had previously been used in published linkage maps) were added to the map. These markers increased the resolution of alignment of the newly constructed linkage map with existing Brassica linkage maps and the A. thaliana genome sequence. We conducted field trials with the TNDH population at two sites, and over 2 years, and identified reproducible QTL for seed oil content and erucic acid content. The results provide new insights into the genetic control of seed oil and erucic acid content in oilseed rape, and demonstrate the utility of the linkage map and population.

Brassica napus↗
PubMed1986

The genetics of quantifiable homeostasis: I. The general issues.

Some fundamental issues in developing the quantitative genetics of heritable traits are addressed. Such a trait must be capable of being represented as a quantity. Choice of the metric can be satisfactorily made only in the light of some insight into the nature of the trait and what its revealing characteristics may be. This insight is likely to change as more is known about the process, so the form and detail of the analysis is not static but perhaps continually evolving. Much has been made out of sample means and, at a more sophisticated level, Galton-Fisher theory (the analysis of the first two moments of multivariate Gaussian variates). However, at least some processes seriously violate the assumptions underlying that theory. One such group comprises traits in which the means are unvarying and the genetic message lies in other aspects of the distribution; in these circumstances the standard summary statistics such as heritability, regression, and correlation may be totally uninformative, distracting, or even misleading. This paradox is illustrated by reference to homeostasis, where the Mendelian component lies, not in the mean, but in the degree of laxity of control. Since estimating higher moments is notoriously imprecise, the suggested remedy is the familial and commonsense one of exploring the genetics of the intermediate states and underlying mechanisms and not only that of the resultant ("bottom-line") phenotype. In our chosen problem, the task of relating the outcome to the basic mechanism of inheritance calls for a detailed understanding of the homeostasis involved.

Genetic Diseases, Inborn↗
PubMed2003

Evidence that Egfr contributes to cryptic genetic variation for photoreceptor determination in natural populations of Drosophila melanogaster.

One objective of quantitative genetics is to identify the nucleotide variants within genes that contribute to phenotypic variation and susceptibility [1]. In an evolutionary context, this means characterizing the molecular polymorphisms that modify the penetrance and expressivity of perturbed traits. A survey of association between 267 SNPs in almost 11 kb of the D. melanogaster Egfr and the degree of eye roughening due to a gain-of-function Egfr(E1) allele crossed into 210 isogenic wild-type lines provides evidence that a handful of synonymous substitutions supply cryptic variation for photoreceptor determination. Ten sites exceed Bonferroni threshold for association in two sets of crosses to different Egfr(E1) backgrounds including a particularly significant cluster of sites in tight linkage disequilibrium toward the 3' end of the coding region. Epistatic interaction of this cluster with one other site enhances the expressivity of this haplotype. Replication of the strongest associations with an independent sample of 302 phenotypically extreme individuals derived from 1000 crosses of Egfr(E1) to freshly trapped males was achieved using modified case-control and transmission-disequilibrium tests. A tendency for the rarer alleles to have more disrupted eye development suggests that mutation-selection balance is a possible mechanism contributing to maintaining cryptic variation for Egfr.

Alleles↗
PubMed2006

Genetic analysis of agricultural traits in rice related to phosphorus efficiency.

Relative tillering ability, available spike, biomass, and grain yield of P1, P2, F1, and F(2,3) were used to study the genetic development of rice related to phosphorus efficiency with a quantitative genetic model. The results indicated that under a low-P condition, the relative tillering ability and the relative available spike were apt to the additivity-dominance-epistasis model with two couples of major genes, between which additive, dominant and epistatic effects existed, and with multi-gene modifications. Their maximum major gene effect mostly indicated additivity, but sub-maximum major gene effect mostly indicated dominance. Relative biomass and grain yield were apt to the additivity-dominance-epistasis and multi-genes model. The heritabilities of the major genes were 60.08% and 37.70%, and those of the multi-genes were 32.15% and 58.9%, respectively. This meant that the heritabilities of the relative tillering ability, the relative available spike, and the relative biomass were high, so they were ideal indexes for rice breeding tolerating to low-P stress; whereas, the heritability of the relative grain yield was low, which meant that the grain yield was easily affected by the environment.

Biomass↗
PubMed2005

The evolution of genetic architecture. I. Diversification of genetic backgrounds by genetic drift.

The genetic architecture of a phenotype plays a critical role in determining phenotypic evolution through its effects on patterns of genetic variation. Genetic architecture is often considered to be constant in evolutionary quantitative genetic models. However, genetic architecture may be variable and itself evolve when there are dominance and epistatic interactions among alleles at the same and different loci, respectively. The evolution of genetic architecture by genetic drift is examined here by testing the breeding value of four standard inbred mouse strains mated across a set of 26 related recombinant quasi-inbred (RqI) lines generated from the intercross of the Large (LG/J) and Small (SM/J) inbred mouse strains. Phenotypes of interest include age-specific body weights, growth, and adult body composition. If the genetic architecture of these traits has differentiated by genetic drift during the production of the RqI strains, we should observe interactions between tester strain and RqI strain. The breeding values of the tester strains will change relative to one another depending on which RqI strain they are crossed to. The study included an average of 15.1 offspring per cross, over a total of 100 different crosses. Multivariate and univariate analyses of variance indicate that there is strongly significant interaction for all traits. Interaction is more pronounced in males than in females and accounted for an average of about 40% of the explained variation in males and 30% in females. These results indicate that the genetic architecture of these traits has differentiated by genetic drift in the RqI strains since their isolation from a common founder population. Further analysis indicates that this differentiation results in changes in the order of tester strain effects so that common patterns of selection in these differentiated populations could result in the fixation of different alleles.

Animals↗
PubMed2000

The quantitative and molecular genetics of human intelligence.

General cognitive ability or g as measured by IQ tests has been the most intensively studied trait in human behaviour genetics. Although there has been much debate about how best to describe and measure intelligence, this is addressed elsewhere in this volume and here I will assume that there is utility in the concept of general intelligence and review the data showing that, whatever it is, g is familial and influenced by genes. Next, I will briefly describe some of the main quantitative genetics models that have been used in trying to tease out the genetic and environmental sources of variation. Finally, I will outline current molecular genetic research aiming to locate and identify genes influencing human intelligence and try to predict the directions in which such research will lead.

Adolescent↗
PubMed1999

The genetic analysis of age-dependent traits: modeling the character process.

The extension of classical quantitative genetics to deal with function-valued characters (also called infinite-dimensional characters) such as growth curves, mortality curves, and reaction norms, was begun by Kirkpatrick and co-workers. In this theory, the analogs of variance components for single traits are covariance functions for function-valued traits. In the approach presented here, we employ a variety of parametric models for covariance functions that have a number of desirable properties: the functions (1) are positive definite, (2) can be estimated using procedures like those currently used for single traits, (3) have a small number of parameters, and (4) allow simple hypotheses to be easily tested. The methods are illustrated using data from a large experiment that examined the effects of spontaneous mutations on age-specific mortality rates in Drosophila melanogaster. Our methods are shown to work better than a standard multivariate analysis, which assumes the character value at each age is a distinct character. Advantages over existing methods that model covariance functions as a series of orthogonal polynomials are discussed.

Aging↗
PubMed2003

Directional selection has shaped the oral jaws of Lake Malawi cichlid fishes.

East African cichlid fishes represent one of the most striking examples of rapid and convergent evolutionary radiation among vertebrates. Models of ecological speciation would suggest that functional divergence in feeding morphology has contributed to the origin and maintenance of cichlid species diversity. However, definitive evidence for the action of natural selection has been missing. Here we use quantitative genetics to identify regions of the cichlid genome responsible for functionally important shape differences in the oral jaw apparatus. The consistent direction of effects for individual quantitative trait loci suggest that cichlid jaws and teeth evolved in response to strong, divergent selection. Moreover, several chromosomal regions contain a disproportionate number of quantitative trait loci, indicating a prominent role for pleiotropy or genetic linkage in the divergence of this character complex. Of particular interest are genomic intervals with concerted effects on both the length and height of the lower jaw. Coordinated changes in this area of the oral jaw apparatus are predicted to have direct consequences for the speed and strength of jaw movement. Taken together, our results imply that the rapid and replicative nature of cichlid trophic evolution is the result of directional selection on chromosomal packages that encode functionally linked aspects of the craniofacial skeleton.

Animals↗
PubMed2005

A genetic interpretation of the variation in inbreeding depression.

Inbreeding depression is expected to play an important but complicated role in evolution. If we are to understand the evolution of inbreeding depression (i.e., purging), we need quantitative genetic interpretations of its variation. We introduce an experimental design in which sires are mated to multiple dams, some of which are unrelated to the sire but others are genetically related owing to an arbitrary number of prior generations of selfing or sib-mating. In this way we introduce the concept of "inbreeding depression effect variance," a parameter more relevant to selection and the purging of inbreeding depression than previous measures. We develop an approach for interpreting the genetic basis of the variation in inbreeding depression by: (1) predicting the variation in inbreeding depression given arbitrary initial genetic variance and (2) estimating genetic variance components given half-sib covariances estimated by our experimental design. As quantitative predictions of selection depend upon understanding genetic variation, our approach reveals the important difference between how inbreeding depression is measured experimentally and how it is viewed by selection.

Analysis of Variance↗
PubMed2003

Diagnostic tools in linkage analysis for quantitative traits.

Diagnostic methods are key components in any good statistical analysis. Because of the similarities between the variance components approach and regression analysis with respect to the normality assumption, when performing quantitative genetic linkage analysis using variance component methods, one must check the normality assumption of the quantitative trait and outliers. Thus, the main purposes of this paper are to describe methods for testing the normality assumption, to describe various diagnostic methods for identifying outliers, and to discuss the issues that may arise when outliers are present when using variance components models in quantitative trait linkage analysis. Data from the Rochester Family Heart Study are used to illustrate the various diagnostic methods and related issues.

Coronary Artery Disease↗
PubMed2002

Genetic drift and gene flow in a prehistoric population of the Azapa valley and coast, Chile.

The present paper studies the evolutionary process operating on prehistoric groups from the Azapa valley and coast (northern Chile). The sample consists of 237 crania from the Archaic Late, Early Intermediate, Middle, Late Intermediate, and Late periods. Six metric variables were used, which were transformed to eliminate the special environmental component and to increase the proportion of genetic variance. Population structure was assessed using a method based on quantitative genetic theory, which predicts a lineal relationship between average within-group phenotypic variance and group distance to the population centroid. Results indicate that 17.5% of the total variance accounts for special environmental variance. An excess in extraregional genetic flow is observed in the population corresponding to the Early Intermediate period in the valley. A reduced differentiation is observed between Archaic and Early Intermediate coastal groups, as well as between the latter and the inhabitants of the valley in the same period. Genetic differences between both areas increased substantially since the Middle period. Evidence indicates that long-range gene flow was lower on the coast than in the valley, the lowest estimated Fst being 0.0199 for the total population (coast and valley), 0.0111 for the coastal population, and 0.0057 for the valley. Results are discussed in terms of regional archeological and ethnohistorical evidence, and a microevolutionary model is presented to account for the biological history of the population.

Anthropology↗