Family and population effects on disease resistance in a reptile

Despite its importance in evolutionary biology, studies of the pattern of disease resistance in natural populations are rare. In this paper, we report patterns of infection of a viral eye disease in juvenile Swedish common lizards (Lacerta vivipara). Females were sampled at random from natural populations immediately prior to parturition with equal exposure of pathogens for all lizards once in captivity. No causative agents could be found that linked risk of disease to maternal/interfollicular transfer of pathogens. The results show that a major factor influencing offspring susceptibility is family identity, suggesting heritable variation in pathogen resistance. Our interpopulation comparison provides additional support for a link between genetics and disease resistance. Lizards in northern Sweden were not only more susceptible to the disease but were also more health compromised once infected, with relatively more reduced growth rate and increased mortality than lizards from the south. This scenario suggests that southern lizards have been under selection for resistance to this pathogen, whereas northern lizards have not, or at least not to the same degree. Thus, this study confirms the importance of genetic (family) effects on pathogen resistance with variation in this trait among natural populations.     

Genetic gains from reciprocal recurrent and within-line selection for egg production in the fowl

Summary Selection for survivors percent egg production from first egg to 40 weeks of age was conducted for six generations. Within-line selection (WLS) on the basis of an index of individual records plus sire family and dam family means was compared with reciprocal recurrent selection (RRS) based on sire family selection among cross progeny. Genetically heterogeneous synthetic populations, the Cornell Control and the Purdue Pool strains were used.The responses to WLS (3.84 °) and RRS (2.57 °) were both significantly greater than zero, but were not significantly different from each other. Nevertheless, the responses were proportional to their predicted values (.363 vs. 340). The advantage of WLS was due to the mechanics of selection resulting in slightly greater selection intensity and an increased correlation between the criterion of selection and the trait being improved. On the contrary, the RRS method had a slightly larger realized heritability as would be expected in the presence of non-additive genetic variance. Four of five pure-lines selected under both methods had statistically significant declines in performance due to inbreeding depression effects. All of the results observed are comparable with known genetic theory.Some problems in comparing genetic gains from different selection methods or selection criteria are discussed.Journal Paper No. 4986 of the Purdue University Agricultural Experiment Station. Conducted in cooperation with the Regional Poultry Breeding Laboratory, Project N. C. 89. Supported in part by N. I. H. Grant No. ES00310.     

Genetic variation affecting host-parasite interactions: major-effect quantitative trait loci affect the transmission of sigma virus in Drosophila melanogaster

In natural populations, genetic variation affects resistance to disease. Whether that genetic variation comprises lots of small-effect polymorphisms or a small number of large-effect polymorphisms has implications for adaptation, selection and how genetic variation is maintained in populations. Furthermore, how much genetic variation there is, and the genes that underlie this variation, affects models of co-evolution between parasites and their hosts. We are studying the genetic variation that affects the resistance of Drosophila melanogaster to its natural pathogen — the vertically transmitted sigma virus. We have carried out three separate quantitative trait locus mapping analyses to map gene variants on the second chromosome that cause variation in the rate at which males transmit the infection to their offspring. All three crosses identified a locus in a similar chromosomal location that causes a large drop in the rate at which the virus is transmitted. We also found evidence for an additional smaller-effect quantitative trait locus elsewhere on the chromosome. Our data, together with previous experiments on the sigma virus and parasitoid wasps, indicate that the resistance of D. melanogaster to co-evolved pathogens is controlled by a limited number of major-effect polymorphisms.     

Natal dispersal and personalities in great tits (Parus major)

Dispersal is a major determinant of the dynamics and genetic structure of populations, and its consequences depend not only on average dispersal rates and distances, but also on the characteristics of dispersing and philopatric individuals. We investigated whether natal dispersal correlated with a predisposed behavioural trait: exploratory behaviour in novel environments. Wild great tits were caught in their natural habitat, tested the following morning in the laboratory using an open field test and released at the capture site. Natal dispersal correlated positively with parental and individual exploratory behaviour, using three independent datasets. First, fast-exploring parents had offspring that dispersed furthest. Second, immigrants were faster explorers than locally born birds. Third, post-fledging movements, comprising a major proportion of the variation in natal dispersal distances, were greater for fast females than for slow females. These findings suggest that parental behaviour influenced offspring natal dispersal either via parental behaviour per se (e.g. via post-fledging care) or by affecting the phenotype of their offspring (e.g. via their genes). Because this personality trait has a genetic basis, our results imply that genotypes differ in their dispersal distances. Therefore, the described patterns have profound consequences for the genetic composition of populations.     

Selective genotyping to detect quantitative trait loci affecting multiple traits: interval mapping analysis

 Segregating quantitative trait loci can be detected via linkage to genetic markers. By selectively genotyping individuals with extreme phenotypes for the quantitative trait, the power per individual genotyped is increased at the expense of the power per individual phenotyped, but linear-model estimates of the quantitative-locus effect will be biased. The properties of single- and multiple-trait maximum-likelihood estimates of quantitative-loci parameters derived from selectively genotyped samples were investigated using Monte-Carlo simulations of backcross populations. All individuals with trait records were included in the analyses. All quantitative-locus parameters and the residual correlation were unbiasedly estimated by multiple-trait maximum-likelihood methodology. With single-trait maximum-likelihood, unbiased estimates for quantitative-locus effect and location, and the residual variance, were obtained for the trait under selection, but biased estimates were derived for a correlated trait that was analyzed separately. When an effect of the QTL was simulated only on the trait under selection, a “ghost” effect was also found for the correlated trait. Furthermore, if an effect was simulated only for the correlated trait, then the statistical power was less than that obtained with a random sample of equal size. With multiple-trait analyses, the power of quantitative-trait locus detection was always greater with selective genotyping. Received: 23 February 1998 / Accepted: 15 May 1998     

INTERACTIVE EFFECTS OF OFFSPRING SIZE AND TIMING OF REPRODUCTION ON OFFSPRING REPRODUCTION: EXPERIMENTAL,MATERNAL, AND QUANTITATIVE GENETIC ASPECTS

We demonstrate that egg size in side-blotched lizards is heritable (parent-offspring regressions) and thus will respond to natural selection. Because our estimate of heritability is derived from free-ranging lizards, it is useful for predicting evolutionary response to selection in wild populations. Moreover, our estimate for the heritability of egg size is not likely to be confounded by nongenetic maternal effects that might arise from egg size per se because we estimate a significant parent-offspring correlation for egg size in the face of dramatic experimental manipulation of yolk volume of the egg. Furthermore, we also demonstrate a significant correlation between egg size of the female parent and clutch size of her offspring. Because this correlation is not related to experimentally induced maternal effects, we suggest that it is indicative of a genetic correlation between egg size and clutch size. We synthesize our results from genetic analyses of the trade-off between egg size and clutch size with previously published experiments that document the mechanistic basis of this trade-off. Experimental manipulation of yolk volume has no effect on offspring reproductive traits such as egg size, clutch size, size at maturity, or oviposition date. However, egg size was related to offspring survival during adult phases of the life history. We partitioned survival of offspring during the adult phase of the life history into (1) survival of offspring from winter emergence to the production of the first clutch (i.e., the vitellogenic phase of the first clutch), and (2) survival of the offspring from the production of the first clutch to the end of the reproductive season. Offspring from the first clutch of the reproductive season in the previous year had higher survival during vitellogenesis of their first clutch if these offspring came from small eggs. We did not observe selection during these prelaying phases of adulthood for offspring from later clutches. However, we did find that later clutch offspring from large eggs had the highest survival over the first season of reproduction. The differences in selection on adult survival arising from maternal effects would reinforce previously documented selection that favors the production of small offspring early in the season and large offspring later in the season—a seasonal shift in maternal provisioning. We also report on a significant parent-offspring correlation in lay date and thus significant heritable variation in lay date. We can rule out the possibility of yolk volume as a confounding maternal effect—experimental manipulation of yolk volume has no effect on lay date of offspring. However, we cannot distinguish between genetic effects (i.e., heritable) and nongenetic maternal effects acting on lay date that arise from the maternal trait lay date per se (or other unidentified maternal traits). Nevertheless, we demonstrate how the timing of female reproduction (e.g., date of oviposition and date of hatching) affect reproductive attributes of offspring. Notably, we find that date of hatching has effects on body size at maturity and fecundity of offspring from later clutches. We did not detect comparable effects of lay date on offspring from the first clutch.     

Indirect genetic effects from ecological interactions in Arabidopsis thaliana

Indirect genetic effects arise when genes expressed in one individual affect the expression of traits in other individuals. The importance of indirect genetic effects has been recognized for a diversity of evolutionary processes including kin selection, sexual selection, community structure and multilevel selection, but data regarding their genetic architecture and prevalence throughout the genome remain scarce, especially for interactions between unrelated individuals. Using a set of 411 Bay-0 x Shahdara Arabidopsis recombinant inbred lines grown with Landsberg neighbours, we examined quantitative trait loci (QTL) having direct and indirect effects on size, developmental, and fitness related traits. Using an interval mapping approach, we identified 15 QTL with direct effects and found that 13 of these QTL had significant indirect effects on trait expression in neighbouring plants. These results suggest widespread pleiotropy, as nearly all direct effect QTL have associated pleiotropic indirect effects. Paradoxically, most indirect effects were of the same sign as direct effects, creating a pattern of nearly universal positive pleiotropy that makes most covariances between direct and indirect effects positive. These results are consistent with a complex genetic basis for intraspecific interactions, but suggest that interactions between neighbouring plants are largely positive, rather than negative as would be expected for competition. In addition to their evolutionary and ecological importance, these pleiotropic relationships between DGE and IGE loci have implications for quantitative genetic studies of natural populations as well as experimental design considerations. Additionally, studies that ignore IGEs may over- or underestimate quantitative genetic parameters, as well as the effect of and variance contributed by QTL.     

Genetic correlation and response to selection in simulated populations

Summary Effects of truncation selection of a primary trait upon genetic correlation with a secondary trait were examined over 30 generations in genetic populations simulated by computer. Populations were 24 males and 24 females mated randomly with replacement; number of offspring was determined by intensity of selection. Each trait was controlled by 48 loci segregating independently, effects were equal at every locus, and gene frequency was arbitrarily set at 0.5 at each locus in the initial generation. All combinations of three genetic correlations, three intensities of selection, and three environmental variances were simulated. Gene action was additive. Genetic correlation was set by number of loci which affected both traits and was measured each generation as the product-moment correlation of genotypic values and estimated by two methods of combining phenotypic covariances between parent and offspring.Genetic correlations in each offspring generation remained consistently near initial correlations for all environmental variances when fraction of offspring saved as parents was as large as one-half. When the fraction of offspring saved was as small as one-fifth, genetic correlations decreased but most rapidly with heritability high and after the 15th generation of selection. Truncation selection caused genetic correlation to decrease in those offspring selected to become parents of the next generation. Amount of reduction depended on heritability of the selected trait rather than on degree of truncation selection. Estimates of genetic correlation from phenotypic covariances between parent and offspring fluctuated markedly from real correlations in the small populations simulated.Michigan Agricultural Experiment Station Journal Article 4836. Part of North Central Regional Project NC-2.     

The role of maternal and paternal effects in the evolution of parental quality by sexual selection

Genetic models of maternal effects and models of mate choice have focused on the evolutionary effects of variation in parental quality. There have been, however, few attempts to combine these into a single model for the evolution of sexually selected traits. We present a quantitative genetic model that considers how male and female parental quality (together or separately) affect the expression of a sexually selected offspring trait. We allow female choice of males based on this parentally affected trait and examine the evolution of mate choice, parental quality and the indicator trait. Our model reveals a number of consequences of maternal and paternal effects. (1) The force of sexual selection owing to adaptive mate choice can displace parental quality from its natural selection optimum. (2) The force of sexual selection can displace female parental quality from its natural selection optimum even when nonadaptive mate choice occurs (e.g. runaway sexual selection), because females of higher parental quality produce more attractive sons and these sons counterbalance the loss in fitness owing to over-investment in each offspring. (3) Maternal and paternal effects can provide a source of genetic variation for offspring traits, allowing evolution by sexual selection even when those traits do not show direct genetic variation (i.e. are not heritable). (4) The correlation between paternal investment and the offspring trait influenced by the parental effects can result in adaptive mate choice and lead to the elaboration of both female preference and the male sexually selected trait. When parental effects exist, sexual selection can drive the evolution of parental quality when investment increases the attractiveness of offspring, leading to the elaboration of indicator traits and higher than expected levels of parental investment.     

Sexual selection and individual genetic diversity in a songbird

Here, we report for the first time, to our knowledge, a strong correlation between a measure of individual genetic diversity and song complexity, a sexually selected male trait in sedge warblers, Acrocephalus schoenobaenus. We also find that females prefer to mate with males who will maximize this diversity in individual progeny. The genetic diversity of each offspring is further increased by means of nonrandom fertilization, as we also show that the fertilizing sperm contains a haplotype more genetically distant to that of the egg than expected by chance. These findings suggest that species' mating preferences may be subject to fine tuning aimed at increasing offspring viability through increased genetic diversity. This includes external and internal mechanisms of selection, even within the ejaculate of a single male.     

The population dynamics of two vertically transmitted infections

The transmission of Keystone virus in the mosquito Aedes atlanticus and of Rickettsia rickettsii in the tick Dermacentor andersoni is modeled and analyzed. Both of these infections can be transmitted vertically from an infective parent to newborn offspring as well as horizontally via direct or indirect contacts with infected individuals. The vertical transmission mechanism plays a major role in the maintenance of these infections and its effects are analyzed in detail. This same mechanism can act as a means for controlling the size of the infected host population and an analysis of this effect is also provided. The sensitivity of the threshold parameters and the endemic prevalence rates of the disease to variations in the basic infection transmission components are investigated. The transmission components that are considered include the ability to transmit the pathogen vertically as well as horizontally, the size of the host population, and survival probabilities of the hosts.     

An experimental comparison of selection alternatives to plateaued response

Three alternative selection methods for extending selection limits or breaking response plateaus were compared over ten generations in a replicated model experiment using two unrelated populations of Drosophila melanogaster that no longer responded to purebred selection for high egg number, a heterotic polygenic trait. The three methods were: (1) reciprocal recurrent selection (RRS) with selection within each of the plateaued populations based solely on crossbred performance, (2) a modification of reciprocal recurrent selection (MRRS) with selection within each population based on both purebred and crossbred performance, and (3) purebred selection within a new synthetic population formed by crossing the two plateaued populations.--Conflicting estimates were obtained for heritability of purebred egg number in each of the plateaued populations. The realized heritability values and estimates from diallel analyses indicated an absence of additive genetic variation for both populations; however, estimates from conventional intraclass correlation methods were positive. The diallel analyses revealed significant amounts of nonadditive gene effects for purebred egg number in each population, while the significant gene effects for crossbred egg numbers were additive. Estimates of the genetic correlation between purebred and crossbred egg number were negative (-0.85 +/- 0.68 and -0.32 +/- 0.25) for the two base populations.--All three alternatives to continued purebred selection gave significant responses, with the average gain per generation from MRRS being significantly superior to the other two methods. Observed purebred and crossbred responses under RRS were in agreement with quantitative genetic theory. Such was not the case for MRRS, which suggested the possibility of major gene segregation.--Evidence supporting a negative genetic correlation between purebred and crossbred performance and the possibility of overdominance is presented and discussed.     

Genetic variation in variability: Phenotypic variability of fledging weight and its evolution in a songbird population

Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within‐family variance, which leads to the intriguing situation that within‐family variance can be heritable. For offspring traits, such as birth weight, this implies that within‐family variance in traits can vary among families and can thus be shaped by natural selection. Empirical evidence for this in wild populations is however lacking. We investigated whether within‐family variance in fledging weight is heritable in a wild great tit (Parus major) population and whether these differences are associated with fitness. We found significant evidence for genetic variance in within‐family variance. The genetic coefficient of variation (GCV) was 0.18 and 0.25, when considering fledging weight a parental or offspring trait, respectively. We found a significant quadratic relationship between within‐family variance and fitness: families with low or high within‐family variance had lower fitness than families with intermediate within‐family variance. Our results show that within‐family variance can respond to selection and provides evidence for stabilizing selection on within‐family variance.     

Optimised parent selection and minimum inbreeding mating in small aquaculture breeding schemes: a simulation study

The effectiveness of low cost breeding scheme designs for small aquaculture breeding programmes were assessed for their ability to achieve genetic gain while managing inbreeding using stochastic simulation. Individuals with trait data were simulated over 15 generations with selection on a single trait. Combinations of selection methods, mating strategies and genetic evaluation options were evaluated with and without the presence of common environmental effects. An Optimal Parent Selection (OPS) method using semi-definite programming was compared with a truncation selection (TS) method. OPS constrains the rate of inbreeding while maximising genetic gain. For either selection method, mating pairs were assigned from the selected parents by either random mating (RM) or Minimum Inbreeding Mating (MIM), which used integer programming to determine mating pairs. Offspring were simulated for each mating pair with equal numbers of offspring per pair and these offspring were the candidates for selection of parents of the next generation. Inbreeding and genetic gain for each generation were averaged over 25 replicates. Combined OPS and MIM led to a similar level of genetic gain to TS and RM, but inbreeding levels were around 75% lower than TS and RM after 15 generations. Results demonstrate that it would be possible to manage inbreeding over 15 generations within small breeding programmes comprised of 30 to 40 males and 30 to 40 females with the use of OPS and MIM. Selection on breeding values computed using Best Linear Unbiased Prediction (BLUP) with all individuals genotyped to obtain pedigree information resulted in an 11% increase in genetic merit and a 90% increase in the average inbreeding coefficient of progeny after 15 generations compared with selection on raw phenotype. Genetic evaluation strategies using BLUP wherein elite individuals by raw phenotype are genotyped to obtain parentage along with a range of different samples of remaining individuals did not increase genetic progress in comparison to selection on raw phenotype. When common environmental effects on full-sib families were simulated, performance of small breeding scheme designs was little affected. This was because the majority of selection must anyway be applied within family due to inbreeding constraints.     

Egg size evolution and energetic constraints on population dynamics.

We use population models that are based on dynamic energy budget models for individuals in order to study the evolution of offspring size and its relationship to the evolution of population dynamics. We show the existence of alternative evolutionarily stable strategies for offspring investment strategy resulting from a trade off between offspring number and time-to-maturity. The model predicts egg energy in Daphnia magna well, and suggests that the observed egg energy in D. magna is the result of selection for minimal egg investment constrained by minimum viable egg energy, combined with selection for a juvenile energy reserve. The selection for minimal egg size pushes populations toward chaotic dynamics. However, the minimum viable egg size combined with low efficiency of conversion of energy to new biomass is sufficient to keep population dynamics out of chaos.     

Prediction of breeding values for group-recorded traits including genomic information and an individually recorded correlated trait

Records on groups of individuals could be valuable for predicting breeding values when a trait is difficult or costly to measure on single individuals, such as feed intake and egg production. Adding genomic information has shown improvement in the accuracy of genetic evaluation of quantitative traits with individual records. Here, we investigated the value of genomic information for traits with group records. Besides, we investigated the improvement in accuracy of genetic evaluation for group-recorded traits when including information on a correlated trait with individual records. The study was based on a simulated pig population, including three scenarios of group structure and size. The results showed that both the genomic information and a correlated trait increased the accuracy of estimated breeding values (EBVs) for traits with group records. The accuracies of EBV obtained from group records with a size 24 were much lower than those with a size 12. Random assignment of animals to pens led to lower accuracy due to the weaker relationship between individuals within each group. It suggests that group records are valuable for genetic evaluation of a trait that is difficult to record on individuals, and the accuracy of genetic evaluation can be considerably increased using genomic information. Moreover, the genetic evaluation for a trait with group records can be greatly improved using a bivariate model, including correlated traits that are recorded individually. For efficient use of group records in genetic evaluation, relatively small group size and close relationships between individuals within one group are recommended.Subject terms: Genetic markers, Animal breeding     

The quantitative genetics of indirect genetic effects: a selective review of modelling issues

Indirect genetic effects (IGE) occur when the genotype of an individual affects the phenotypic trait value of another conspecific individual. IGEs can have profound effects on both the magnitude and the direction of response to selection. Models of inheritance and response to selection in traits subject to IGEs have been developed within two frameworks; a trait-based framework in which IGEs are specified as a direct consequence of individual trait values, and a variance-component framework in which phenotypic variance is decomposed into a direct and an indirect additive genetic component. This work is a selective review of the quantitative genetics of traits affected by IGEs, with a focus on modelling, estimation and interpretation issues. It includes a discussion on variance-component vs trait-based models of IGEs, a review of issues related to the estimation of IGEs from field data, including the estimation of the interaction coefficient Ψ (psi), and a discussion on the relevance of IGEs for response to selection in cases where the strength of interaction varies among pairs of individuals. An investigation of the trait-based model shows that the interaction coefficient Ψ may deviate considerably from the corresponding regression coefficient when feedback occurs. The increasing research effort devoted to IGEs suggests that they are a widespread phenomenon, probably particularly in natural populations and plants. Further work in this field should considerably broaden our understanding of the quantitative genetics of inheritance and response to selection in relation to the social organisation of populations.     

Genome-wide association analysis and genetic architecture of egg weight and egg uniformity in layer chickens

The pioneering work by Professor Soller et al., among others, on the use of genetic markers to analyze quantitative traits has provided opportunities to discover their genetic architecture in livestock by identifying quantitative trait loci (QTL). The recent availability of high-density single nucleotide polymorphism (SNP) panels has advanced such studies by capitalizing on population-wide linkage disequilibrium at positions across the genome. In this study, genomic prediction model Bayes-B was used to identify genomic regions associated with the mean and standard deviation of egg weight at three ages in a commercial brown egg layer line. A total of 24,425 segregating SNPs were evaluated simultaneously using over 2900 genotyped individuals or families. The corresponding phenotypic records were represented as individual measurements or family means from full-sib progeny. A novel approach using the posterior distribution of window variances from the Monte Carlo Markov Chain samples was used to describe genetic architecture and to make statistical inferences about regions with the largest effects. A QTL region on chromosome 4 was found to explain a large proportion of the genetic variance for the mean (30%) and standard deviation (up to 16%) of the weight of eggs laid at specific ages. Additional regions with smaller effects on chromosomes 2, 5, 6, 8, 20, 23, 28 and Z showed suggestive associations with mean egg weight and a region on chromosome 13 with the standard deviation of egg weight at 26-28 weeks of age. The genetic architecture of the analyzed traits was characterized by a limited number of genes or genomic regions with large effects and many regions with small polygenic effects. The region on chromosome 4 can be used to improve both the mean and standard deviation of egg weight by marker-assisted selection.     

The genetic basis of male fertility in relation to haplodiploid reproduction in Leptopilina clavipes (Hymenoptera: Figitidae)

Traits under relaxed selection are expected to become reduced or disappear completely, a process called vestigialization. In parthenogenetic populations, traits historically involved in sexual reproduction are no longer under selection and potentially subject to such reduction. In Leptopilina clavipes, thelytokous (parthenogenetic) populations are infected by Wolbachia bacteria. Arrhenotokous populations do not harbor Wolbachia. When antibiotics are applied to infected females, they are cured from their infection and males arise. Such males are capable of producing offspring with uninfected females, but with lower fertilization success than sexual males. This can be attributed to the lack of selection on male fertility in thelytokous lines. In this study we used this variation in L. clavipes male fertility to determine the genetic basis of this trait. Males from cured thelytokous populations were crossed to females from uninfected populations. Using AFLP markers, a genetic linkage map was generated, consisting of five linkage groups and spanning a total distance of 219.9 cM. A single QTL of large effect (explaining 46.5% of the phenotypic variance) was identified for male fertility, which we call male fertility factor (mff). We discuss possible mechanisms underlying the effect of mff, as well as mechanisms involved in vestigialization of traits involved in sexual reproduction.