Quantitative genetics of speciation: additive and non-additive genetic differentiation between <Emphasis Type="Italic">Drosophila madeirensis</Emphasis> and <Emphasis Type="Italic">Drosophila subobscura</Emphasis>

The role of dominance and epistasis in population divergence has been an issue of much debate ever since the neoDarwinian synthesis. One of the best ways to dissect the several genetic components affecting the genetic architecture of populations is line cross analysis. Here we present a study comparing generation means of several life history-traits in two closely related Drosophila species: Drosophila subobscura, D. madeirensis as well as their F ₁ and F ₂ hybrids. This study aims to determine the relative contributions of additive and non-additive genetic parameters to the differentiation of life-history traits between these two species. The results indicate that both negative dominance and epistatic effects are very important in the differentiation of most traits. We end with considerations about the relevance of these findings for the understanding of the role of non-additive effects in speciation.     

On the Probabilities of Obtaining Negative Estimates of Genetic Variance Components

This paper derives the probabilities of obtaining negative estimates of additive and dominance genetic variances when one uses the traditional weighted least square method for estimating genetic variances as given in MATHER and JINKS (1971). The model considered involves P₁, P₂, F₂, B₁ (Backcross to P₁) and B₂ (Backcross to P₂). The results are derived under the ordinary assumptions as made in the genetic literatures. It is shown that unless the genetic effects are very large and environmental effects small, the probabilities of obtaining negative estimates of additive and dominance variances are in general quite large.     

Analysis of cytoplasmic and maternal effects. II. Genetic models for triploid endosperms

Genetic models for quantitative traits of triploid endosperms are proposed for the analysis of direct gene effects, cytoplasmic effects, and maternal gene effects. The maternal effect is partitioned into maternal additive and dominance components. In the full genetic model, the direct effect is partitioned into direct additive and dominance components and high-order dominance component, which are the cumulative effects of three-allele interactions. If the high-order dominance effects are of no importance, a reduced genetic model can be used. Monte Carlo simulations were conducted in this study for demonstrating unbiasedness of estimated variance and covariance components from the MINQUE (0/1) procedure, which is a minimum norm quadratic unbiased estimation (MINQUE) method setting 0 for all the prior covariances and 1 for all the prior variances. Robustness of estimating variance and covariance components for the genetic models was tested by simulations. Both full and reduced genetic models are shown to be robust for estimating variance and covariance components under several situations of no specific effects. Efficiency of predicting random genetic effects for the genetic models by the MINQUE (0/1) procedure was compared with the best linear unbiased prediction (BLUP). A worked example is given to illustrate the use of the reduced genetic model for kernel growth characteristics in corn (Zea mays L.).     

HERITABILITIES OF DOMINANCE-RELATED TRAITS IN MALE BANK VOLES (CLETHRIONOMYS GLAREOLUS)

A number of studies have shown that in several animal species females prefer dominant males as mating partners, but fewer attempts have been made to measure possible indirect benefits of this choice. One reason for this may be that, even though dominance is a widely used concept, the definition of dominance still remains controversial Furthermore, defining and measuring the heritability of social behaviors is problematic because they are not individual traits but, by definition, involve interactions between at least two individuals. In this study we estimated heritabilities and coefficients of additive genetic variances (CV_A) for male traits that are closely associated with dominance and female mating preferences in bank voles (Clethrionomys glareolus). The heritability values were estimated using father-offspring regression. All heritability estimates were relatively high ranging from 0.531 (urine marking) to 0.767 (preputial glands). The CV_A-values indicated high levels of additive genetic variance especially in the characters most closely related to dominance: the weight of preputial glands and urine marking behavior. All phenotypic correlations among the traits measured were significantly positive and the genetic correlations were of similar magnitude as the corresponding phenotypic counterparts. Even though heritabilities may be lower in the natural environment than under controlled laboratory conditions, our results suggest that characters closely related to dominance may be at least partly genetically determined.     

Epistasis causes outbreeding depression in eucalypt hybrids

The genetic architecture underlying species differentiation is essential for understanding the mechanisms of speciation and post-zygotic reproductive barriers which exist between species. We undertook line-cross analysis of multiple hybrid (F₁, F₂ and backcrosses) and pure-species populations of two diploid eucalypt species from different subseries, Eucalyptus globulus and Eucalyptus nitens, to unravel the genetic architecture of their differentiation. The populations were replicated on two sites and monitored for growth and survival over a 14-year period. The hybrids exhibited severe outbreeding depression which increased with age. Of the composite additive, dominance and epistatic effects estimated, the additive × additive epistatic component was the most important in determining population divergence in both growth and survival. Significant dominance × dominance epistasis was also detected for survival at several ages. While favourable dominance and, in the case of survival, dominance × dominance epistasis could produce novel gene combinations which enhance hybrid fitness, at the population level, these effects were clearly overridden by adverse additive × additive epistasis which appears to be a major driver of overall outbreeding depression in the hybrid populations. The lack of model fit at older ages suggested that even high-order epistatic interactions may potentially have a significant contribution to outbreeding depression in survival. The estimated composite genetic parameters were generally stable across sites. Our results argue that the development of favourable epistasis is a key mechanism underlying the genetic divergence of eucalypt species, and epistasis is an important mechanism underlying the evolution of post-zygotic reproductive barriers.     

DIURNAL PREFERENCE AND SLEEP QUALITY: SAME GENES? A STUDY OF YOUNG ADULT TWINS

The aims of this study were to examine the genetic and environmental influences on diurnal preference and sleep quality, the association between these phenotypes, the genetic and environmental influences on this association, and the magnitude of overlap between these influences. Using a twin design, data on diurnal preference (measured by the Morningness-Eveningness Questionnaire) and sleep quality (measured by the Pittsburgh Sleep Quality Index) were collected from 420 monozygotic twins, 773 dizygotic twins, and 329 siblings (mode age?=?20 yrs, range?=?18–27 yrs) from a population-based twin registry across the UK. Univariate analyses indicated that dominance genetic influence accounted for 52% and non-shared environment 48% of variance in diurnal preference. For sleep quality, additive genetic influence explained 43% and non-shared environment 57% of the variance. The bivariate analysis indicated a significant association between greater eveningness preference and poorer sleep quality (r?=?.27). There was substantial overlap in the additive genetic influences on both phenotypes (rA?=?.57), and overlap in the dominance genetic influences common to both phenotypes was almost absolute (rD = .99). Overlap in non-shared environment was much smaller (rE?=?.02). Additive genetic influence accounted for 2% of the association, dominance genetic influence accounted for 94%, and non-shared environmental influences accounted for the remaining 4%. The substantial overlap in genetic influence between these phenotypes indicates that similar genes are important for diurnal preference and sleep quality. Therefore, those genes already known to influence one phenotype may be possible candidates to explore with regards to the other phenotype. (Author correspondence: ps701nh@gold.ac.uk)     

Apical dominance and the effect of gravity on nutrient distribution

Summary The effect of orientation with resepct to gravity on the accumulation of phosphorus-32 into lateral and leader apices has been investigated in seedling trees of Betula pubescens. In upright, well-branched seedlings, showing only weak apical dominance, basally injected ³²P is distributed more or less equally among the lateral and leader apices. Re-orientation treatments which result in the assumption of strong dominance by a lateral apex also result in a marked accumulation of ³²P into that apex. This effect of orientation on nutrient transport is manifested within two to four days after application of the gravimorphic treatments.The results are discussed in the light of modern concepts of hormone-directed nutrient transport and a working hypothesis for the role of gravity in apical dominance of woody plants is suggested.     

Non-additive genetic effects for fertility traits in Canadian Holstein cattle (Open Access publication )

The effects of additive, dominance, additive by dominance, additive by additive and dominance by dominance genetic effects on age at first service, non-return rates and interval from calving to first service were estimated. Practical considerations of computing additive and dominance relationships using the genomic relationship matrix are discussed. The final strategy utilized several groups of 1000 animals (heifers or cows) in which all animals had a non-zero dominance relationship with at least one other animal in the group. Direct inversion of relationship matrices was possible within the 1000 animal subsets. Estimates of variances were obtained using Bayesian methodology via Gibbs sampling. Estimated non-additive genetic variances were generally as large as or larger than the additive genetic variance in most cases, except for non-return rates and interval from calving to first service for cows. Non-additive genetic effects appear to be of sizeable magnitude for fertility traits and should be included in models intended for estimating additive genetic merit. However, computing additive and dominance relationships for all possible pairs of individuals is very time consuming in populations of more than 200 000 animals.     

Genetic studies in an exotic population of corn (Zea mays L.) grown under two plant densities

Summary Progenies of a Design II [Comstock and Robinson (1948)] using random S ₁ lines from an exotic population of corn (Zea mays L.) were evaluated in a randomized incomplete block design with two replications at two plant-population densities (1 7,222 plants/ha and 68,888 plants/ha) in 1970 and 1971, at Lincoln, Nebraska. Five traits were studied i.e. grain weight, number of ears, days to flower, plant height and ear height.Under both densities the estimates of additive genetic variance were much larger than those of dominance genetic variance for all traits. The ratio of dominance to additive genetic variance estimates was less than 0.5 suggesting that for the majority of loci controlling the traits, partial to complete dominance is likely.The estimates of additive genetic x year interaction variance were high and significantly different from zero under both densities, indicating that estimates of additive genetic variance in this population obtained from experiments conducted in only one year may be seriously biased. The estimates of dominance genetic x year interaction variance were not significant and most of them were negative.Under both densities high genetic inter-relationships were indicated between grain weight and number of ears, days to flower and plant height, days to flower and ear height, and plant height and ear height.Even though there was a large difference between the two densities used in the study, the differences between the estimates of genetic parameters were not significant in all cases.The sample size of S ₁ plants representing each S₀ parent in the crossing nursery used in the present study (11.75) caused a small upward bias in the estimates of additive genetic variance, but it caused an upward bias in the estimates of dominance genetic variance of 6–7% of the total genetic variance.It is suggested that a trait such as grain weight should be expressed on a unit area basis when genetic parameters (except for correlation and the ratio between two values) obtained from experiments with different plant-population densities are to be compared.Published as Paper Number 3542, Journal Series, Nebraska Agricultural Experimental Station. Part of a thesis submitted by the senior author in partial fulfillment of the requirements for the Ph. D. degree.A. I. D. Participant.The work was supported in part by a grant from the Rockefeller Foundation.     

Interpopulation hybridization generates meiotically stable rDNA epigenetic variants in allotetraploid Tragopogon mirus

Uniparental silencing of 35S rRNA genes (rDNA), known as nucleolar dominance (ND), is common in interspecific hybrids. Allotetraploid Tragopogon mirus composed of Tragopogon dubius (d) and Tragopogon porrifolius (p) genomes shows highly variable ND. To examine the molecular basis of such variation, we studied the genetic and epigenetic features of rDNA homeologs in several lines derived from recently and independently formed natural populations. Inbred lines derived from T. mirus with a dominant d‐rDNA homeolog transmitted this expression pattern over generations, which may explain why it is prevalent among natural populations. In contrast, lines derived from the p‐rDNA dominant progenitor were meiotically unstable, frequently switching to co‐dominance. Interpopulation crosses between progenitors displaying reciprocal ND resulted in d‐rDNA dominance, indicating immediate suppression of p‐homeologs in F₁ hybrids. Original p‐rDNA dominance was not restored in later generations, even in those segregants that inherited the corresponding parental rDNA genotype, thus indicating the generation of additional p‐rDNA and d‐rDNA epigenetic variants. Despite preserved intergenic spacer (IGS) structure, they showed altered cytosine methylation and chromatin condensation patterns, and a correlation between expression, hypomethylation of RNA Pol I promoters and chromatin decondensation was apparent. Reversion of such epigenetic variants occurred rarely, resulting in co‐dominance maintained in individuals with distinct genotypes. Generally, interpopulation crosses may generate epialleles that are not present in natural populations, underlying epigenetic dynamics in young allopolyploids. We hypothesize that highly expressed variants with distinct IGS features may induce heritable epigenetic reprogramming of the partner rDNA arrays, harmonizing the expression of thousands of genes in allopolyploids.     

Variable responses of insects to hybrid versus parental sagebrush in common gardens

Both ecological and genetic mechanisms have been proposed to explain patterns of herbivore attack on interspecific plant hybrids, but distinguishing among them can be difficult in natural hybrid zones. We performed a common-garden experiment to evaluate four genetic hypotheses: dominance, additivity, elevated hybrid susceptibility, and elevated hybrid resistance. Censuses and cage experiments were used to compare insect responses to basin big sagebrush (Artemisia tridentata spp. tridentata), mountain big sagebrush (A. t. vaseyana), and their F₂ progeny. After two growing seasons, hybrid shrubs resembled mountain big sagenbrush in size, but were more similar to basin big sagebrush in flower production. Censuses of naturally colonizing insects (the gall midge Rhopalomyia obovata, the bagworm moth Apterona helix, and the aphid Obtusicauda coweni) tended to support the dominance hypothesis: if the insect clearly discriminated between the two parents, its frequency on hybrids closely resembled that on one of the parents. Moreover, colonization of hybrids in all three cases suggested a dominance deviation toward the susceptible parent rather than toward the resistant parent. In contrast to the censuses, cage experiments involving two insects supported the hybrid-susceptibility hypothesis; both survival and growth of the grasshopper Melanoplus sanguinipes and growth of the leaf beetle Trirhabda pilosa were higher on hybrid shrubs than on either parent. Because many secondary compounds have been determined to occur at intermediate concentrations in F₂ shrubs, dominance for susceptibility may indicate that insects respond to plant traits (e.g., oviposition stimulants and deterrents) in a threshold manner. Mechanisms underlying increased hybrid susceptibility are less clear, but our experimental design makes environmental explanations (e.g., the plant-stress hypothesis) unlikely. Although we eliminated several confounding factors, our results agree with the conclusion from natural hybrid zones that insect responses to hybrid plants are likely to be idiosyncratic; even congeneric species did not respond similarly to hybrid and parental plants.     

Power of tests for QTL detection using replicated progenies derived from a diallel cross

In crop species, most QTL (quantitative trait loci) mapping strategies use segregating populations derived from an initial cross between two lines. However, schemes including more than two parents could also be used. We propose an approach using a high-density restriction fragment length polymorphism (RFLP) map established on six F ₂ populations derived from diallel crosses among four inbred lines and the phenotypic performances of two types of replicated progenies (F ₃ and topcross). The QTL is supposed to be on the marker locus considered. Three linear model tests for the detection of QTL effects (T ₁, T ₂ and T ₃) are described and their power studied for the two types of progeny. T ₁ tests the global genetic effects of the QTL (additivity and dominance) and T ₂ tests only additive effects assuming dominance is absent when it could exist. The models of these two tests assume that the main effects of QTL alleles are constant in different genetic backgrounds. The additive model of test T ₃ considers the six F ₂ populations independently, and T ₃ is the equivalent of the classical mean comparison test if we neglect dominance; it uses only contrasts between the homozygote marker classes. The results show that T ₂ is much more powerful than T ₃. The power of T ₁ and T ₂ depends on the relative sizes of the additive and dominance effects, and their comparison is not easy to establish. Nevertheless, T ₂ seems to be the more powerful in most situations, indicating that it is often more interesting to ignore dominance when testing for a QTL effect. For a given size of genetic effects, the power is affected by the total number of individuals genotyped in F ₂ and the recombination rate between the marker locus and the putative QTL. The approach presented in this paper has some drawbacks but could be easily generalized to other sizes of diallels and different progeny types.     

Host genetic architecture in single and multiple infections

Hosts are often target to multiple simultaneous infections by genetically diverse parasite strains. The interaction among these strains and the interaction of each strain with the host was shown to have profound effects on the evolution of parasite traits. Host factors like genetic architecture of resistance have so far been largely neglected. To see whether genetic architecture differs between different kinds of infections we used joint scaling analysis to compare the genetic components of resistance in the red flour beetle Tribolium castaneum exposed to single and multiple strains of the microsporidian Nosema whitei. Our results indicate that additive, dominance and epistatic components were more important in single infections whereas maternal components play a decisive role in multiple infections. In detail, parameter estimates of additive, dominance and epistatic components correlated positively between single and multiple infections, whereas maternal components correlated negatively. These findings may suggest that specificity of host–parasite interactions are mediated by genetic and especially epistatic components whereas maternal effects constitute a more general form of resistance.     

MALE HYBRID STERILITY IN DROSOPHILA: INTERACTIONS BETWEEN AUTOSOMES AND SEX CHROMOSOMES IN CROSSES OF D. MOJAVENSIS AND D. ARIZONENSIS

By backcrossing hybrids from the cross Drosophila mojavensis female × Drosophila arizonensis male to both parental species we show that several interspecific combinations of autosomes with one or the other sex chromosome (X or Y) result in sperm abnormalities. Two of these incompatibilities will cause the same type of nonreciprocal F₁ male sterility that is observed in this pair of species, but the possibility of an additional incompatibility that would have the same result, e.g., an incompatibility between the mojavensis Y and the arizonensis X chromosomes, cannot be excluded. The incompatibility between the arizonensis Y chromosome and the mojavensis fourth chromosome found to occur for all tested populations of mojavensis race B (Vigneault and Zouros, 1986) is shown also to occur for race A of this species. We further show that a dominance relationship exists between heterospecific homologous autosomes in their interactions with the sex chromosomes and that the direction of the dominance depends on whether the sex chromosome is the X or the Y. The present role of these incompatibilities in preventing gene flow between the two species may be minor, but their genetic basis and mode of action may provide useful insights about the genetic events that have played a significant role in earlier stages of speciation.     

Using clonal replicates to explore genetic variation in a perennial plant species

Summary An experimental design is presented for estimating genetic parameters using a family structure with clonally replicated individuals. This experimental design provides a technique to quantify genetic variation in a population, with partial separation of additive, dominance and epistatic gene action. Our method is offered as an alternative to techniques for estimating epistatic gene action that require several generations and/or inbreeding. Such methods are not particularly useful for long-lived perennials with long generation cycles. An example of the analysis is given with a forest tree species, Populus deltoides Bartr., and parameter estimates are presented for traits measured over 8 years.     

Male dominance linked to size and age,but not to 'good genes' in brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>)

Background  

Males that are successful in intra-sexual competition are often assumed to be of superior quality. In the mating system of most salmonid species, intensive dominance fights are common and the winners monopolise most mates and sire most offspring. We drew a random sample of mature male brown trout (Salmo trutta) from two wild populations and determined their dominance hierarchy or traits linked to dominance. The fish were then stripped and their sperm was used for in vitro fertilisations in two full-factorial breeding designs. We recorded embryo viability until hatching in both experiments, and juvenile survival during 20 months after release into a natural streamlet in the second experiment. Since offspring of brown trout get only genes from their fathers, we used offspring survival as a quality measure to test (i) whether males differ in their genetic quality, and if so, (ii) whether dominance or traits linked to dominance reveal 'good genes'.     

Different competitive outcomes among four species of cladocerans under different alga combinations of colonial <Emphasis Type="Italic">Microcystis</Emphasis> spp. and green alga <Emphasis Type="Italic">Scenedesmus obliquus</Emphasis>

Cyanobacteria blooms (especially Microcystis spp.) are thought to alter dominance of large-sized daphnids into small-sized metazoan zooplankton. However, several field investigations show different phenomena. Laboratory experiments were conducted based on the hypothesis that different Microcystis spp. concentrations would influence competitive outcomes using two algal combinations of different concentrations and four species of cladocerans. In the algal combination of 50 mg l⁻¹ colonial Microcystis spp. + 1 mg l⁻¹ Scenedesmus obliquus (fresh weight), Daphnia carinata was absent during the experiment in competition with other cladocerans. Decreasing colonial Microcystis spp. concentration (10 mg l⁻¹) resulted in a shift from dominance by small-sized cladocerans to dominance by D. carinata. No significant effects of different concentrations of colonial Microcystis spp. on competitive outcomes were shown among three small-sized cladocerans. These results support the idea that cyanobacteria concentration affects the dominance status of large-bodied daphnid.     

Plant strategies and secondary succession on Brittany heathlands after severe fire

Abstract. Plant succession on heathlands subjected to major fire disturbance and humus burn in 1976 was studied over twelve years following burning. Life history strategies of principal heathland species are described with reference to concepts outlined by Grime (1979) and Whittaker & Goodman (1979). Heathlands and closely related communities are characterised by dominance of speciestolerant of physical stress (‘S’ strategists) whereas species which colonise disturbed sites are closer to rude-rals (‘R’ strategists). After severe burning three main successional patterns were identified. They depend on water and nutrient availability relative to temporal population dynamics. Recovery of heathland is often retarded due to monospecific dominance, e.g. of Polytrichum commune, Molinia caerulea and Betula pubescens. These patterns of secondary succession illustrate the inhibition model advanced by Connell & Slatyer (1977).     

Establishing Causality between Population Genetic Alterations and Environmental Contamination in Aquatic Organisms

Contaminant-induced alterations in genetic diversity or allele/genotype frequencies can occur via genetic bottlenecks, selection, or increased mutation rate, and may affect population growth, sustainability, and adaptability. Determination of causality of genetic effects requires demonstration of some or all of the following criteria: (1) Strength of association: use of multiple reference and contaminated populations, and demonstration of effects that cannot otherwise be explained by evolutionary theory; (2) Consistency of association: effects corroborated by other studies, in other species, or with multiple genetic markers; (3) Specificity of association: concordance of genetic effects with exposure/effect bioindicators, genotypedependant fitness and biomarkers, and consideration of confounding factors; (4) Temporality of effects: use of phylogenetics and analysis of genetic diversity using different methodologies to differentiate historical vs. recent events; (5) Biological gradients: sampling sites that are known to have differing levels of contamination; (6) Experimental evidence: exposure of small populations to contaminants in laboratories, mesocosms, or in situ cages, or measurement of genotype-dependant biomarkers; (7) Biological plausibility: existence of contaminants at levels great enough to affect fitness, recruitment, or mutation rates, or a demonstrated mechanism for selection. Application of these criteria to population genetic studies is illustrated by case studies involving RAPD analysis of mosquitofish populations.