Marker-Based Inferences About Epistasis for Genes Influencing Inbreeding Depression (original) (raw)
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Genetical Research, 1997
A deterministic analysis is conducted to examine marginal dominance for two linked viability loci influencing inbreeding depression and its graphical inferences. Four estimators of marginal dominance are derived, assuming a biallelic marker locus completely linked to one of the viability loci, and the biases in expected estimates due to the other deleterious locus are discussed. Three conditions under which apparent partial dominance or underdominance could occur are found, i.e. when two multiplicative, partially recessive loci are linked in coupling phase and when two synergistic, highly overdominant loci are linked in coupling or repulsion phases. Expected frequencies of the three marker genotypes in selfed progeny are derived, considering two linkage phases, two types of marker locus position with respect to the viability loci, and the multiplicative and synergistic fitness models. Segregation ratios are generated for the marker locus linked to either two overdominant or partiall...
The influence of selection and epistasis on inbreeding depression estimates
Journal of Animal Breeding and Genetics, 2001
Inbreeding depression estimates obtained by regression of the individual performance on the inbreeding were studied by stochastic simulation under various genetic models (solely additive, partial dominance, overdominance and epistasis), and mating strategies (random mating versus selection). In all models, inbreeding depression estimates based on the individual pedigree inbreeding coef®cients were compared with estimates based on the true level of autozygosity. For the model with partial dominance and selection, the estimates of inbreeding depression from pedigree information were more negative (lower) than those based on true inbreeding coef®cients whereas, in contrast, they were less negative (higher) for the models with overdominance and selection. The difference in the variation of true and pedigree individual inbreeding coef®cient indicated that biased estimates might occur even in random mating populations. The estimation of inbreeding depression was further complicated when epistatic effects were present. The sign and the magnitude of the inbreeding effect (depression) estimates might be rather heterogeneous if additive by dominance effects are present because they are strongly dependent on the gene frequency. It was also shown that inbreeding depression is possible in models with negative additive by dominance effects. In models with dominance by dominance inheritance it was dif®cult to assess the non-linear relationship between performance and inbreeding, while at the same time, non-linear estimates based on pedigree information were extremely biased. The results obtained indicate that new or additional methodologies are required if reliable conclusions about consequences of inbreeding depression are needed.
Theoretical Population Biology, 1991
We study the evolution of the rate of self-fertilization in response to deleterious mutations at multiple loci. Although partial selting induces associations among loci even in the absence of linkage, associations among mutations at different loci are of a smaller order of magnitude than the mutation rate. Genotypes that carry homozygous lethal mutations in heterozygous form at I loci occur in frequencies of the order ( y) p'. in which T denotes the number of viability loci and n the mutation rate. While associations between mutations at different loci remain small even under inbreeding, each viability locus develops an association with the modifier of the rate of self-fertilization that substantially affects the evolution of the breeding system. Positive associations between enhancers of selting and haplotypes carrying multiple wild-type alleles and positive associations in heterozygosity between the modifier locus and the viability loci promote evolutionary mcreases in the rate of self-fertilization. cl
Inbreeding Depression Doesn't Matter: The Genetic Basis of Mating-System Evolution
Evolution, 1988
Models of mating-system evolution commonly assume that inbreeding depression is independent of the genotype at loci determining the mating system. Because of the association that develops between genotypes at different loci in inbred populations, an individual that is heterozygous at a mating-type locus is more likely to be heterozygous at a fitness locus than is a randomly chosen individual. A modifier model for the evolution of self-fertilization in plants demonstrates that inbreeding depression is not an adequate descriptor ofthe relative fitness ofinbred and outbred progeny. If inbreeding depression is primarily a result of segregation at overdominant loci, intermediate rates of self-fertilization may be favored, even if the inbreeding depression is less than 30%. Indeed, in some cases, mutants that cause some outcrossing can be introduced into completely selfing populations when the inbreeding depression is as little as I%. If inbreeding depression is primarily a result of the expression of recessive lethals in inbred progeny, selfing can evolve in an initially random mating population, even when the inbreeding depression is over 70%.
The in¯uence of selection and epistasis on inbreeding depression estimates
Inbreeding depression estimates obtained by regression of the individual performance on the inbreeding were studied by stochastic simulation under various genetic models (solely additive, partial dominance, overdominance and epistasis), and mating strategies (random mating versus selection). In all models, inbreeding depression estimates based on the individual pedigree inbreeding coef®cients were compared with estimates based on the true level of autozygosity. For the model with partial dominance and selection, the estimates of inbreeding depression from pedigree information were more negative (lower) than those based on true inbreeding coef®cients whereas, in contrast, they were less negative (higher) for the models with overdominance and selection. The difference in the variation of true and pedigree individual inbreeding coef®cient indicated that biased estimates might occur even in random mating populations. The estimation of inbreeding depression was further complicated when epistatic effects were present. The sign and the magnitude of the inbreeding effect (depression) estimates might be rather heterogeneous if additive by dominance effects are present because they are strongly dependent on the gene frequency. It was also shown that inbreeding depression is possible in models with negative additive by dominance effects. In models with dominance by dominance inheritance it was dif®cult to assess the non-linear relationship between performance and inbreeding, while at the same time, non-linear estimates based on pedigree information were extremely biased. The results obtained indicate that new or additional methodologies are required if reliable conclusions about consequences of inbreeding depression are needed.
Heterozygosity-fitness correlations within inbreeding classes: local or genome-wide effects?
Conservation Genetics, 2008
Marker-based studies of inbreeding may lead to an enhanced understanding of inbreeding depression in natural populations, which is a major concern in conservation genetics. Correlations between marker heterozygosity and variation in fitness-associated traits-'heterozygosityfitness correlations' (HFCs)-are of particular importance and have been widely applied in natural populations. In partially inbred populations, HFCs can be driven by selection against inbred individuals and thus reflect inbreeding depression. However, other explanations for HFCs also exist, such as functional effects of the markers per se or that the markers reveal selection on linked fitness genes due to extended linkage disequilibrium (LD) in the population. Accordingly, HFCs do not only arise in partially inbred populations, they may also occur within inbreeding classes such as families, i.e. in situations when there is no variation in the inbreeding coefficient. In this study we focus on the importance of LD for within-family HFCs, thereby aiming at enhancing our general understanding of HFCs. For noncoding markers, within-family HFCs have been proposed to be caused in two ways: either by 'local effects' at linked fitness genes in LD with the markers, or by 'general effects' due to a correlation between proportion of heterozygous markers (H M) and heterozygosity at genome-wide distributed fitness genes (H GW). To evaluate these contrasting hypotheses for within-family HFCs, we analysed simulated data sets of sexually reproducing populations with varying levels of LD. The results confirmed that segregation induces variation in both H M and H GW at a fixed level of inbreeding; as expected, the variation in H M declined with increasing number of markers, whereas the variation in H GW declined with decreasing LD. However, less intuitively, there was no positive correlation between the variation in H M and H GW within inbreeding classes when the local component of H GW was accounted for (i.e. when the part of the chromosome in LD with the markers was excluded). This strongly suggests that within-family HFCs are not caused by general effects. Instead, our results support the idea that HFCs at a known level of inbreeding can be driven by local effects in populations with high to moderate LD. Note however that we define the local component of H GW as the part of the chromosomes in LD with the markers. This implies that when LD is high, the local component will consist of a substantial part of the genome and thus provides a rather 'genome-wide' view. We caution against routinely interpreting positive HFCs as evidence of inbreeding depression and nonsignificant HFCs as lack thereof, especially when few markers are used.
Variability of individual genetic load: consequences for the detection of inbreeding depression
Genetica, 2012
Inbreeding depression is a key factor affecting the persistence of natural populations, particularly when they are fragmented. In species with mixed mating systems, inbreeding depression can be estimated at the population level by regressing the average progeny fitness by the selfing rate of their mothers. We applied this method using simulated populations to investigate how population genetic parameters can affect the detection power of inbreeding depression. We simulated individual selfing rates and genetic loads from which we computed fitness values. The regression method yielded high statistical power, inbreeding depression being detected as significant (5 % level) in 92 % of the simulations. High individual variation in selfing rate and high mean genetic load led to better detection of inbreeding depression while high among-individual variation in genetic load made it more difficult to detect inbreeding depression. For a constant sampling effort, increasing the number of progenies while decreasing the number of individuals per progeny enhanced the detection power of inbreeding depression. We discuss the implication of among-mother variability of genetic load and selfing rate on inbreeding depression studies.
Selection and inbreeding depression: Effects of inbreeding rate and inbreeding environment
Evolution, 2006
The magnitude of inbreeding depression in small populations may depend on the effectiveness with which natural selection purges deleterious recessive alleles from populations during inbreeding. The effectiveness of this purging process, however, may be influenced by the rate of inbreeding and the environment in which inbreeding occurs. Although some experimental studies have examined these factors individually, no study has examined their joint effect or potential interaction. In the present study, therefore, we performed an experiment in which 180 lineages of Drosophila melanogaster were inbred at slow and fast inbreeding rates within each of three inbreeding environments (benign, high temperature, and competitive). The fitness of all lineages was then measured in a common benign environment. Although slow inbreeding reduced inbreeding depression in lineages inbred under high temperature stress, a similar reduction was not observed with respect to the benign or competitive treatments. Overall, therefore, the effect of inbreeding rate was nonsignificant. The inbreeding environment, in contrast, had a larger and more consistent effect on inbreeding depression. Under both slow and fast rates of inbreeding, inbreeding depression was significantly reduced in lineages inbred in the presence of a competitor D. melanogaster strain. A similar reduction of inbreeding depression occurred in lineages inbred under high temperature stress at a slow inbreeding rate. Overall, our findings show that inbreeding depression is reduced when inbreeding takes place in a stressful environment, possibly due to more effective purging under such conditions.
Journal of dairy science, 1997
The effect of inaccurate estimates of variance and of the location of the quantitative trait locus on the genetic response to marker-assisted selection was studied by simulation of an adult multiple ovulation and embryo transfer nucleus breeding scheme. Two genetic models were simulated for the quantitative trait locus: a total of 10 alleles or 2 distinct alleles per base parent. For both models, the locus explained either 5 or 10% of phenotypic variance. A polygenic component was simulated, and the two genetic components were summed to 35% heritability for a trait measured on females. Overestimation of variance of the quantitative trait locus had minimal effect on genetic gain for marker-assisted selection over the short term, but decreased long-term response. The long-term loss was reduced when variance of the quantitative trait locus was reestimated after four generations of marker-assisted selection. Selection for favorable alleles at a nonexistent quantitative trait locus resul...
Journal of Animal Breeding and Genetics, 2002
Inbreeding depression estimates obtained by regression of the individual performance on the inbreeding were studied by stochastic simulation under various genetic models (solely additive, partial dominance, overdominance and epistasis), and mating strategies (random mating versus selection). In all models, inbreeding depression estimates based on the individual pedigree inbreeding coef®cients were compared with estimates based on the true level of autozygosity. For the model with partial dominance and selection, the estimates of inbreeding depression from pedigree information were more negative (lower) than those based on true inbreeding coef®cients whereas, in contrast, they were less negative (higher) for the models with overdominance and selection. The difference in the variation of true and pedigree individual inbreeding coef®cient indicated that biased estimates might occur even in random mating populations. The estimation of inbreeding depression was further complicated when epistatic effects were present. The sign and the magnitude of the inbreeding effect (depression) estimates might be rather heterogeneous if additive by dominance effects are present because they are strongly dependent on the gene frequency. It was also shown that inbreeding depression is possible in models with negative additive by dominance effects. In models with dominance by dominance inheritance it was dif®cult to assess the non-linear relationship between performance and inbreeding, while at the same time, non-linear estimates based on pedigree information were extremely biased. The results obtained indicate that new or additional methodologies are required if reliable conclusions about consequences of inbreeding depression are needed.