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PubMed1990

Analysis of the inheritance, selection and evolution of growth trajectories.

We present methods for estimating the parameters of inheritance and selection that appear in a quantitative genetic model for the evolution growth trajectories and other "infinite-dimensional" traits that we recently introduced. Two methods for estimating the additive genetic covariance function are developed, a "full" model that fully fits the data and a "reduced" model that generates a smoothed estimate consistent with the sampling errors in the data. By decomposing the covariance function into its eigenvalues and eigenfunctions, it is possible to identify potential evolutionary changes in the population's mean growth trajectory for which there is (and those for which there is not) genetic variation. Algorithms for estimating these quantities, their confidence intervals, and for testing hypotheses about them are developed. These techniques are illustrated by an analysis of early growth in mice. Compatible methods for estimating the selection gradient function acting on growth trajectories in natural or domesticated populations are presented. We show how the estimates for the additive genetic covariance function and the selection gradient function can be used to predict the evolutionary change in a population's mean growth trajectory.

Animals↗
PubMed1993

Effects of multiple retrovirus insertions on quantitative traits of mice.

To assess the potential to generate quantitative genetic variation by insertional mutagenesis in a vertebrate, lines of mice in which many provirus vector inserts segregated at a low initial frequency on an inbred background (insert lines) were subjected to divergent artificial selection on body weight at 6 weeks and responses and heritability estimates compared to control lines lacking inserts. Heritability estimates were more than 1.5 times greater in the insert lines than in the controls, but because the phenotypic variance was substantially higher in the insert lines the genetic variance was about 3 times greater. Realized heritability estimates tended to be lower than heritabilities estimated by an animal model which utilizes information in covariances between all relatives in the data set. A surprisingly large response to selection occurred in the inbred control line. Insert lines were about 20% less fertile than controls. Division of the selection lines into inbred sublines in the later generations of the experiment revealed substantially greater variation among sublines of the insert lines than among the controls. Heritabilities were similar to typical estimates for the trait in outbred populations. In conclusion, there was clear evidence of extra variation deriving from inserts, which has yet to be attributed to individual genes.

Animals↗
PubMed1994

Epistasis can facilitate the evolution of reproductive isolation by peak shifts: a two-locus two-allele model.

The influence of epistasis on the evolution of reproductive isolation by peak shifts is studied in a two-locus two-allele model of a quantitative genetic character under stabilizing selection. Epistasis is introduced by a simple multiplicative term in the function that maps gene effects onto genotypic values. In the model with only additive effects on the trait, the probability of a peak shift and the amount of reproductive isolation are always inversely related, i.e., the higher the peak shift rate, the lower the amount of reproductive isolation caused by the peak shift. With epistatic characters there is no consistent relationship between these two values. Interestingly, there are cases where both transition rates as well as the amount of reproductive isolation are increased relative to the additive model. This effect has two main causes: a shift in the location of the transition point, and the hybrids between the two alternative optimal genotypes have lower average fitness in the epistatic case. A review of the empirical literature shows that the fitness relations resulting in higher peak shift rates and more reproductive isolation are qualitatively the same as those observed for genes causing hybrid inferiority.

Alleles↗
PubMed1994

Analysis of autosomal polygenic variation for the expression of Haldane's rule in flour beetles.

Haldane's rule states that, in interspecific crosses, when hybrid viability or fertility is diminished more in one sex of the hybrids than in the other, the heterogametic sex is more adversely affected. We used quantitative genetic methods to investigate the genetic basis of variation for the expression of the viability aspect of Haldane's rule when Tribolium castaneum males are crossed to Tribolium freemani females. Using a half-sib design, we found significant genetic variance for the expression of Haldane's rule, i.e., variation among T. castaneum sires in the hybrid sex ratios produced by their sons. We also derived 23 independent lineages from the same base population by 8 generations of brother-sister mating. From the same experiments, we also found heritable variation among surviving hybrid males in the incidence of antennal deformities. Upon inbreeding, the variance of both traits (hybrid sex ratio and proportion deformities) increased substantially but the means changed little. Because fitness within T. castaneum lineages declined substantially with inbreeding, we infer that hybrid male viability may have a different genetic basis than viability fitness within species. Deleterious recessive alleles held within species by mutation/selection balance appear not to be a major contributor to hybrid incompatibility.

Animals↗
PubMed1995

Evolutionary endocrinology of juvenile hormone esterase in Gryllus assimilis: direct and correlated responses to selection.

Hemolymph juvenile hormone esterase (JHE) activity on the third day of the last stadium in the cricket, Gryllus assimilis, exhibited a significant response to selection in each of six replicate lines. Mean realized heritability was 0.26 +/- 0.04. The response was due to changes in whole-organism enzyme activity as well as to changes in the proportion of enzyme allocated to the hemolymph compartment. In vivo juvenile hormone metabolism differed between some lines selected for high vs. low enzyme activity. Only minimal differences were observed between lines with respect to hemolymph protein concentration or whole-cricket activity of juvenile hormone epoxide hydrolase, the other major JH-degrading enzyme. Dramatic correlated responses to selection, equal in magnitude to the direct response, were observed for JHE activity on each of three other days of the last juvenile stadium. In contrast, no correlated responses in JHE activity were observed in adults. This indicates that JHE activities throughout the last stadium will evolve as a highly correlated unit independent of adult activities and the evolution of endocrine mechanisms regulating juvenile development can be decoupled from those controlling adult reproduction. This study represents the first quantitative-genetic analysis of naturally occurring endocrine variation in an insect species.

Age Factors↗
PubMed1996

Association between SSCP haplotypes at the bovine growth hormone gene and milk protein percentage.

The bovine Growth Hormone gene (bGH) is an attractive candidate gene for milk production in cattle. Single-strand conformation polymorphisms at bGH were identified and used to define haplotype configurations at this gene in the Israeli Holstein dairy cattle population (Bos taurus) and in the parent animals of the International Bovine Reference Family Panel (a collection of B. taurus and B. indicus crosses). B. taurus and B. indicus haplotypes at the bGH gene differed qualitatively, confirming the previously proposed long evolutionary separation of these cattle subraces. Only a small number of bGH haplotypes were present in the Israel Holstein population. One of the haplotypes, apparently of B. indicus origin, was found to have a highly significant positive effect on milk protein percentage. This illustrates the utility of the haplotype approach for uncovering candidate gene involvement in quantitative genetic variation in agricultural populations. The strong effect of an indicine haplotype in a taurine background raises the possibility that indicine alleles at other candidate genes may comprise a genetic resource for improvement of taurine populations. It is proposed that haplotype analysis may be a useful adjunct to measures of genetic distance for evaluating rare breeds with respect to gene conservation.

Animals↗
PubMed1996

The evolution of genomic imprinting.

In some mammalian genes, the paternally and maternally derived alleles are expressed differently: this phenomenon is called genomic imprinting. Here we study the evolution of imprinting using multivariate quantitative genetic models to examine the feasibility of the genetic conflict hypothesis. This hypothesis explains the observed imprinting patterns as an evolutionary outcome of the conflict between the paternal and maternal alleles. We consider the expression of a zygotic gene, which codes for an embryonic growth factor affecting the amount of maternal resources obtained through the placenta. We assume that the gene produces the growth factor in two different amounts depending on its parental origin. We show that genomic imprinting evolves easily if females have some probability of multiple partners. This is in conflict with the observation that not all genes controlling placental development are imprinted and that imprinting in some genes is not conserved between mice and humans. We show however that deleterious mutations in the coding region of the gene create selection against imprinting.

Animals↗
PubMed1998

Mapping quantitative trait loci using multiple families of line crosses.

To avoid a loss in statistical power as a result of homozygous individuals being selected as parents of a mapping population, one can use multiple families of line crosses for quantitative trait genetic linkage analysis. Two strategies of combining data are investigated: the fixed-model and the random-model strategies. The fixed-model approach estimates and tests the average effect of gene substitution for each parent, while the random-model approach treats each effect of gene substitution as a random variable and directly estimates and tests the variance of gene substitution. Extensive Monte Carlo simulations verify that the two strategies perform equally well, although the random model is preferable in combining data from a large number of families. Simulations also show that there may be an optimal sampling strategy (number of families vs. number of individuals per family) in which QTL mapping reaches its maximum power and minimum estimation error. Deviation from the optimal strategy reduces the efficiency of the method.

Chromosome Mapping↗
PubMed1998

Epistatic interactions between smell-impaired loci in Drosophila melanogaster.

Odor-guided behavior is a polygenic trait determined by the concerted expression of multiple loci. Previously, P-element mutagenesis was used to identify single P[lArB] insertions, in a common isogenic background, with homozygous effects on olfactory behavior. Here, we have crossed 12 lines with these smell impaired (smi) mutations in a half-diallel design (excluding homozygous parental genotypes and reciprocal crosses) to produce all possible 66 doubly heterozygous hybrids with P[lArB] insertions at two distinct locations. The olfactory behavior of the transheterozygous progeny was measured using an assay that quantified the avoidance response to the repellent odorant benzaldehyde. There was significant variation in general combining abilities of avoidance scores among the smi mutants, indicating variation in heterozygous effects. Further, there was significant variation among specific combining abilities of each cross, indicating dependencies of heterozygous effects on the smi locus genotypes, i.e., epistasis. Significant epistatic interactions were identified for nine transheterozygote genotypes, involving 10 of the 12 smi loci. Eight of these loci form an interacting ensemble of genes that modulate expression of the behavioral phenotype. These observations illustrate the power of quantitative genetic analyses to detect subtle phenotypic effects and point to an extensive network of epistatic interactions among genes in the olfactory subgenome.

Animals↗
PubMed1999

Estimation of pairwise relatedness with molecular markers.

Applications of quantitative genetics and conservation genetics often require measures of pairwise relationships between individuals, which, in the absence of known pedigree structure, can be estimated only by use of molecular markers. Here we introduce methods for the joint estimation of the two-gene and four-gene coefficients of relationship from data on codominant molecular markers in randomly mating populations. In a comparison with other published estimators of pairwise relatedness, we find these new "regression" estimators to be computationally simpler and to yield similar or lower sampling variances, particularly when many loci are used or when loci are hypervariable. Two examples are given in which the new estimators are applied to natural populations, one that reveals isolation-by-distance in an annual plant and the other that suggests a genetic basis for a coat color polymorphism in bears.

Animals↗
PubMed2000

Both naturally occurring insertions of transposable elements and intermediate frequency polymorphisms at the achaete-scute complex are associated with variation in bristle number in Drosophila melanogaster.

A restriction enzyme survey of a 110-kb region including the achaete scute complex (ASC) examined 14 polymorphic molecular markers in a sample of 56 naturally occurring chromosomes. Large insertions as a class were associated with a reduction in both sternopleural and abdominal bristle number, supporting deleterious mutation-selection equilibrium models for the maintenance of quantitative genetic variation. Two polymorphic sites were independently associated with variation in bristle number measured in two genetic backgrounds as assessed by a permutation test. A 6-bp deletion near sc alpha is associated with sternopleural bristle number variation in both sexes and a 3.4-kb insertion between sc beta and sc gamma is associated with abdominal bristle number variation in females. Under an additive genetic model, the small deletion polymorphism near sc alpha accounts for 25% of the total X chromosome genetic variation in sternopleural bristle number, and the 3.4 kb insertion accounts for 22% of the total X chromosome variation in female abdominal bristle number. The observation of common polymorphisms associated with variation in bristle number is more parsimoniously explained by models that incorporate balancing selection or assume variants affecting bristle number are neutral, than mutation-selection equilibrium models.

Animals↗
PubMed2001

The evolution of X-linked genomic imprinting.

We develop a quantitative genetic model to investigate the evolution of X-imprinting. The model compares two forces that select for X-imprinting: genomic conflict caused by polygamy and sex-specific selection. Genomic conflict can only explain small reductions in maternal X gene expression and cannot explain silencing of the maternal X. In contrast, sex-specific selection can cause extreme differences in gene expression, in either direction (lowered maternal or paternal gene expression), even to the point of gene silencing of either the maternal or paternal copy. These conclusions assume that the Y chromosome lacks genetic activity. The presence of an active Y homologue makes imprinting resemble the autosomal pattern, with active paternal alleles (X- and Y-linked) and silenced maternal alleles. This outcome is likely to be restricted as Y-linked alleles are subject to the accumulation of deleterious mutations. Experimental evidence concerning X-imprinting in mouse and human is interpreted in the light of these predictions and is shown to be far more easily explained by sex-specific selection.

Alleles↗
PubMed1972

An investigation of the components of Segregation-Distorter systems in Drosophila melanogaster.

The problems of the Segregation-Distorter system are approached and unified in terms of an orthodox quantitative genetic system. It is shown that the SD system involves positive and negative modifier genes of varying strengths, that there is no major Stabiliser gene, and that the Activator gene is not unique. It is further argued that the SD phenomenon is mainly male limited, with "female effects" being of small magnitude.

Age Factors↗
PubMed1996

Sources of covariation among Mini-Mental State Examination scores, education, and cognitive abilities.

An adoption/twin design was used to address issues concerning the relationship between education and Mini-Mental State Examination (MMSE) performance. Data on general cognitive abilities, education, and MMSE from 110 identical twin pairs and 177 fraternal pairs aged 50 through 88 were analyzed using multivariate quantitative genetic methods. Genetic influences account for 32% and 19% of the variation in MMSE for men and women, respectively. Furthermore, all of the genetic variation in MMSE is in common with genetic variation for cognitive abilities and education. Finally, correlations between education and MMSE (.21 and .16 for men and women, respectively), which were reduced to near zero when cognitive abilities were partialed out, are primarily attributable to genetic effects for cognitive abilities. These results support the hypothesis that the association between education and MMSE performance predominantly reflects genetically mediated cerebral capacity rather than test bias or health-endangering life styles in less educated individuals.

Cognition↗
PubMed2001

Olfactory functioning and cognitive abilities: a twin study.

A Swedish version of the National Geographic Smell Survey (Wysocki and Gilbert 1989) was completed by 227 twin pairs from the Swedish Adoption/Twin Study of Aging. Twins ranged in age from 45 to 89 years. Quantitative genetic analysis of four measures of olfactory functioning indicated moderate heritability for odor identification and perceived intensity and nonsignificant heritability for odor detection and perceived pleasantness. Bivariate analyses revealed that the relationship between odor identification and measures of verbal ability was primarily genetically mediated. The results provided further support for the hypothesis that odor identification and verbal ability in general tap the same cognitive domain (Larsson 1997).

Aged↗
PubMed2005

Cognitive change in aging: identifying gene-environment correlation and nonshared environment mechanisms.

We describe gene-environment processes that may help account for individual differences in successful aging. Our emphasis is on successful aging in the cognitive domain, wherein individuals come to use a variety of strategies to cope with changes in cognitive capacities. We focus on the role of executive control in particular and define gene-environment correlation and nonshared environmental mechanisms. The quantitative genetic methods used to identify these mechanisms are described, with examples from research in childhood, where such studies are now common. Future work will be most effective if it is guided by life-span development frameworks that address these processes, such as the developmental genotype-->environment theory of Scarr and McCartney and the selection/optimization/compensation theory of Baltes and Baltes.

Aging↗
PubMed2002

Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans.

Epistasis, the interaction between genes, is a topic of current interest in molecular and quantitative genetics. A large amount of research has been devoted to the detection and investigation of epistatic interactions. However, there has been much confusion in the literature over definitions and interpretations of epistasis. In this review, we provide a historical background to the study of epistatic interaction effects and point out the differences between a number of commonly used definitions of epistasis. A brief survey of some methods for detecting epistasis in humans is given. We note that the degree to which statistical tests of epistasis can elucidate underlying biological interactions may be more limited than previously assumed.

Data Interpretation, Statistical↗
PubMed1998

Significant impact of the +93 C/T polymorphism in the apolipoprotein(a) gene on Lp(a) concentrations in Africans but not in Caucasians: confounding effect of linkage disequilibrium.

Lipoprotein(a) [Lp(a)] is a quantitative genetic trait in human plasma associated with atherothrombotic disease. The major determinant of Lp(a) concentration is the apolipoprotein(a) [apo(a)] gene locus. Variation in the number of kringle IV repeats (K-IV VNTR) in apo(a) has a direct effect on Lp(a) concentrations but explains only a fraction of the large intra- and inter-population variance in Lp(a) levels. Effects on Lp(a) of other intragenic polymorphisms including a pentanucleotide repeat (PNRP) in the promoter likely reflect allelic associations with as yet unidentified sequence variation in the apo(a) gene. We have studied a candidate C-->T transition in two European and two African populations. This polymorphism in the 5' region of the apo(a) gene creates an ATG start codon thereby reducing apo(a) translation in vitro by 60%. All samples were also analyzed for the K-IV VNTR and the PNRP to stratify for their effects and to consider allelic associations. Consistent with the in vitro effect the C-->T transition was associated with a significant reduction in Lp(a) levels in both African populations ( P < 0.0056). In Caucasians, however, the effect was not significant. This was explained by linkage disequilibrium of the +93 T with apo(a) alleles of intermediate length (K-24-K-34) and with nine PNRs. In Europeans these alleles are associated with low Lp(a) which makes any potential effect of the +93 T undetectable in the total sample. From our results we conclude (i) that the +93 C/T polymorphism is the second known intragenic apo(a) polymorphism which affects Lp(a) levels directly in vivo ; (ii) that allelic associations may mask the effect of a mutation; and (iii) that heterogeneity of an effect of a mutation across populations does not disprove causality.

Alleles↗