Are transcriptional responses to inbreeding a functional response to alleviate inbreeding depression?

Previous studies addressing the relationship between gene regulation and inbreeding depression did not allow for discerning the changes that alleviate the depression from those that generate it. We directly addressed this question by analyzing changes in gene expression, using Affymetrix 2.0 arrays in Drosophila melanogaster inbred sublines differing in their magnitudes of inbreeding depression relative to the expression in an outbred control. The total number of arrays analyzed was 27, with 9,133 probe sets showing a significant signal of expression. We found that for those genes differentially expressed between inbred and outbred sublines, most of them showed a pattern of expression consistent with a protective role against inbreeding effects. The observed increase in depression was presumably related to an inability of the genome to do the appropriate expression adjustments. Expression changes detected in our study showed a clear specificity of RNA-splicing and energy derivation functions. Thus, it appears that most of the observed changes in gene expression associated with inbreeding may occur predominantly to alleviate inbreeding depression, i.e., as a protection against the effects of inbreeding.     

Temporal change in inbreeding depression in life‐history traits in captive populations of guppy (Poecilia reticulata): evidence for purging?

Inbreeding depression, which generally affects the fitness of small populations, may be diminished by purging recessive deleterious alleles when inbreeding persists over several generations. Evidence of purging remains rare, especially because of the difficulties of separating the effects of various factors affecting fitness in small populations. We compared the expression of life-history traits in inbred populations of guppy (Poecilia reticulata) with contemporary control populations over 10 generations in captivity. We estimated inbreeding depression as the difference between the two types of populations at each generation. After 10 generations, the inbreeding coefficient reached a maximum value of 0.56 and 0.16 in the inbred and control populations, respectively. Analysing changes in the life-history traits across generations showed that inbreeding depression in clutch size and offspring survival increased during the first four to six generations in the populations from the inbred treatment and subsequently decreased as expected if purging occurred. Inbreeding depression in two other traits was weaker but showed similar changes across generations. The loss of six populations in the inbred treatment indicates that removal of deleterious alleles also occurred by extinction of populations that presumably harboured high genetic load.     

Inbreeding depresses sperm competitiveness,but not fertilization or mating success in male Tribolium castaneum

As populations decline to levels where reproduction among close genetic relatives becomes more probable, subsequent increases in homozygous recessive deleterious expression and/or loss of heterozygote advantage can lead to inbreeding depression. Here, we measure how inbreeding across replicate lines of the flour beetle Tribolium castaneum impacts on male reproductive fitness in the absence or presence of male–male competition. Effects on male evolution from mating pattern were removed by enforcing monogamous mating throughout. After inbreeding across eight generations, we found that male fertility in the absence of competition was unaffected. However, we found significant inbreeding depression of sperm competitiveness: non-inbred males won 57 per cent of fertilizations in competition, while inbred equivalents only sired 42 per cent. We also found that the P₂ ‘offence’ role in sperm competition was significantly more depressed under inbreeding than sperm ‘defence’ (P₁). Mating behaviour did not explain these differences, and there was no difference in the viability of offspring sired by inbred or non-inbred males. Sperm length variation was significantly greater in the ejaculates of inbred males. Our results show that male ability to achieve normal fertilization success was not depressed under strong inbreeding, but that inbreeding depression in these traits occurred when conditions of sperm competition were generated.     

Preference for outbred host plants and positive effects of inbreeding on egg survival in a specialist herbivore

Inbreeding can profoundly affect the interactions of plants with herbivores as well as with the natural enemies of the herbivores. We studied how plant inbreeding affects herbivore oviposition preference, and whether inbreeding of both plants and herbivores alters the probability of predation or parasitism of herbivore eggs. In a laboratory preference test with the specialist herbivore moth Abrostola asclepiadis and inbred and outbred Vincetoxicum hirundinaria plants, we discovered that herbivores preferred to oviposit on outbred plants. A field experiment with inbred and outbred plants that bore inbred or outbred herbivore eggs revealed that the eggs of the outbred herbivores were more likely to be lost by predation, parasitism or plant hypersensitive responses than inbred eggs. This difference did not lead to differences in the realized fecundity as the number of hatched larvae did not differ between inbred and outbred herbivores. Thus, the strength of inbreeding depression in herbivores decreases when their natural enemies are involved. Plant inbreeding did not alter the attraction of natural enemies of the eggs. We conclude that inbreeding can significantly alter the interactions of plants and herbivores at different life-history stages, and that some of these alterations are mediated by the natural enemies of the herbivores.     

The effects of parasitism and inbreeding on the competitive ability in Daphnia magna: evidence for synergistic epistasis

Synergistic epistasis for fitness is often assumed in models of how selection acts on the frequency and distribution of deleterious mutations. Evidence for synergistic epistasis would exist if the logarithm of fitness declines more quickly with number of deleterious mutations, than predicted by a linear decline. This can be studied indirectly by quantifying the effect of different levels of inbreeding on fitness. Here, six sets (different genetic backgrounds) of three increasingly inbred Daphnia magna clones were used to assess their relative fitness according to changes in frequency in a competition experiment against a tester clone. A novelty of the mating procedure was that the inbreeding coefficients (F) of the three clones belonging to each set increased in steps of 0.25 independent of the (unknown) inbreeding coefficient of the common ancestor. The equal increase of the inbreeding coefficients is important, because deviations influence the quantification of inbreeding depression, its variance and the detection of epistasis. In a simple mathematical model we show that when working with a partially inbred population inbreeding depression is underestimated, the variance of fitness is increased, and the detection of epistasis more difficult. Further, to examine whether an interaction between inbreeding and parasitism exists, each inbred clone was tested with and without a microsporidium infection (Octosporea bayeri). We found a nonlinear decrease of the logarithm of fitness across the three levels of inbreeding, indicating synergistic epistasis. The interaction term between parasitism and inbreeding was not significant. Our results suggest that deleterious mutations may be purged effectively once the level of inbreeding is high, but that parasitism seems not to influence this effect.     

Differential inbreeding tolerance in two geographically distinct strains of root voles Microtus oeconomus

Two geographically distinct strains of Microtus oeconomus, each consisting of an inbred (sibling mating) and an outbred treatment group, were bred in the laboratory over three generations to determine the effects of inbreeding on reproductive parameters, growth rates of young and paternal behavior The southern strain (orginating from southern Norway) suffered from depressed reproductive rate (litter size and pregnancy rates) most likely due to inbreeding, while no effects of inbreeding were detected m the northern strain (originating from northern Norway) This result questions previous generalizations about inbreeding tolerance at the species level for Microtus Growth rates and paternal behavior did not differ significantly between inbred and outbred voles in either strain Inbreeding depression rather than inbreeding avoidance is the most likely mechanism behind the depression in reproductive parameters of inbred southern voles This is suggested by the decrease in the proportion of breeding pairs with the number of generations of inbreeding, and by the reduced litter size of inbred compared with outbred pairs Field and laboratory studies have shown that behavioral and demographic traits, possibly related to the degree of inbreeding, differ between the two strains which suggests that inbreeding tolerance might be a life history adaptation     

Inbreeding depression in an insect with maternal care: influences of family interactions,life stage and offspring sex

Although inbreeding is commonly known to depress individual fitness, the severity of inbreeding depression varies considerably across species. Among the factors contributing to this variation, family interactions, life stage and sex of offspring have been proposed, but their joint influence on inbreeding depression remains poorly understood. Here, we demonstrate that these three factors jointly shape inbreeding depression in the European earwig, Forficula auricularia. Using a series of cross‐breeding, split‐clutch and brood size manipulation experiments conducted over two generations, we first showed that sib mating (leading to inbred offspring) did not influence the reproductive success of earwig parents. Second, the presence of tending mothers and the strength of sibling competition (i.e. brood size) did not influence the expression of inbreeding depression in the inbred offspring. By contrast, our results revealed that inbreeding dramatically depressed the reproductive success of inbred adult male offspring, but only had little effect on the reproductive success of inbred adult female offspring. Overall, this study demonstrates limited effects of family interactions on inbreeding depression in this species and emphasizes the importance of disentangling effects of sib mating early and late during development to better understand the evolution of mating systems and population dynamics.     

Inbreeding interferes with the heat-shock response

Inbreeding is typically detrimental to individual fitness, with negative effects being often exaggerated in stressful environments. However, the causal mechanisms underlying inbreeding depression in general and the often increased susceptibility to stress in particular are not well understood. We here test whether inbreeding interferes with the heat-shock response, comprising an important component of the stress response which may therefore underscore sensitivity to stress. To this end we subjected the tropical butterfly Bicyclus anynana to a full-factorial design with three temperatures and three levels of inbreeding, and measured the expression of heat-shock protein (HSP) 70 via qPCR. HSP70 expression increased after exposure to heat as compared with cold or control conditions. Most strikingly, inbreeding strongly interfered with the heat-shock response, with inbred individuals showing a very weak upregulation of HSP70 only. Our results thus indicate that, in our study organism, interference with the heat-shock response may be one mechanism underlying reduced fitness of inbred individuals, especially when exposed to stressful conditions. However, these indications need to be corroborated using a broader range of different temperatures, genes and taxa.     

Inbreeding depression and purging in a haplodiploid: gender-related effects

Compared with diploid species, haplodiploids suffer less inbreeding depression because male haploidy imposes purifying selection on recessive deleterious alleles. However, alleles of genes only expressed in the diploid females are protected in heterozygous individuals. This leads to the prediction that haplodiploids suffer more from inbreeding effects on life-history traits controlled by genes with female-limited expression. To test this, we used a wild population of the haplodiploid mite Tetranychus urticae. First, negative effects of inbreeding were investigated by comparing maturation rate, juvenile survival, oviposition rate and longevity between lines created by three generations of either outbreeding or mother–son inbreeding. Second, purging through inbreeding was investigated by comparing the intensity of inbreeding depression between outbred families with known inbreeding/outbreeding mating histories. Negative effects of inbreeding and evidence for purging were found for the female trait oviposition rate, but not for juvenile survival and longevity. Both male and female maturation rate were negatively affected by inbreeding, most likely due to maternal effects because inbred offspring of outbred mothers was not affected. These results support the hypothesis that, in haplodiploids inbreeding effects and genetic variation due to deleterious recessive alleles may depend on gender.     

The genetic basis and experimental evolution of inbreeding depression in Caenorhabditis elegans

Determining the genetic basis of inbreeding depression is important for understanding the role of selection in the evolution of mixed breeding systems. Here, we investigate how androdioecy (a breeding system characterized by partial selfing and outcrossing) and dioecy (characterized by obligatory outcrossing) influence the experimental evolution of inbreeding depression in Caenorhabditis elegans. We derived inbred lines from ancestral and evolved populations and found that the dioecious lineages underwent more extinction than androdioecious lineages. For both breeding systems, however, there was selection during inbreeding because the diversity patterns of 337 single-nucleotide polymorphisms (SNPs) among surviving inbred lines deviated from neutral expectations. In parallel, we also followed the evolution of embryo to adult viability, which revealed similar starting levels of inbreeding depression in both breeding systems, but also outbreeding depression. Under androdioecy, diversity at a neutral subset of 134 SNPs correlated well with the viability trajectories, showing that the population genetic structure imposed by partial selfing affected the opportunity for different forms of selection. Our findings suggest that the interplay between the disruptions of coevolved sets of loci by outcrossing, the efficient purging of deleterious recessive alleles with selfing and overdominant selection with outcrossing can help explain mixed breeding systems.     

A comparison of male and female responses to inbreeding in Cucurbita pepo subsp. texana (Cucurbitaceae)

Accurate estimates of inbreeding depression are necessary in order to predict the evolutionary dynamics of a population, but many studies estimate inbreeding depression based solely on components of female function such as fruit set, seed set, and seed quality. Because total fitness is achieved through both male and female functions in hermaphroditic plants, estimates of both male and female fitness are needed to estimate accurately the magnitude of inbreeding depression. Seedlings of a wild gourd, Cucurbita pepo subsp. texana, with coefficients of inbreeding of 0 and 0.75 were planted in an experimental garden, and several components of male and female fitness were measured over the course of the growing season. Fitness in inbred plants was confounded by both maternal and genetic inbreeding effects. Inbred individuals produced significantly fewer fruits than outcrossed individuals, and percentage germination of seeds from inbred individuals was significantly lower than seeds from outcrossed individuals. Inbred plants also produced significantly fewer staminate flowers and marginally fewer and smaller pollen grains per flower. Pollen from inbred plants also grew significantly more slowly in vitro than pollen from outcrossed plants. Multiplicative estimates of inbreeding depression revealed inbreeding depression for both male and female functions in wild gourd, but inbreeding depression through female function was stronger than inbreeding depression through male function.     

Inbreeding depression of female fecundity by genetic factors retained in natural populations of a male-haploid social mite (Acari: Tetranychidae)

We previously determined that certain recessive genes decrease female fecundity in a haplo-diploid spider mite, Stigmaeopsis miscanthi (Saito). However, whether the depression was caused by the breakdown of heterosis or the expression of deleterious genes retained in a population could not be determined, because we had started our inbreeding experiment from a mixture of two isolated populations. In order to answer this basic question, inbreeding effects on survival and fecundity were measured for eight small populations occurring far from the two initial populations. There was little depression of immature survival of inbred lineages in all populations. On the other hand, in two inbred lineages, both originating from the smallest populations, female oviposition decreased significantly with the increase of Wrights f-value, showing that mildly deleterious genes are actually retained even in natural populations of haplo-diploid organisms.     

Inbreeding depression of female fecundity by genetic factors retained in natural populations of a male-haploid social mite (Acari: Tetranychidae)

We previously determined that certain recessive genes decrease female fecundity in a haplo-diploid spider mite, Stigmaeopsis miscanthi (Saito). However, whether the depression was caused by the breakdown of heterosis or the expression of deleterious genes retained in a population could not be determined, because we had started our inbreeding experiment from a mixture of two isolated populations. In order to answer this basic question, inbreeding effects on survival and fecundity were measured for eight small populations occurring far from the two initial populations. There was little depression of immature survival of inbred lineages in all populations. On the other hand, in two inbred lineages, both originating from the smallest populations, female oviposition decreased significantly with the increase of Wrights f-value, showing that mildly deleterious genes are actually retained even in natural populations of haplo-diploid organisms.     

Efficiency of selection, as measured by single nucleotide polymorphism variation, is dependent on inbreeding rate in Drosophila melanogaster

It is often hypothesized that slow inbreeding causes less inbreeding depression than fast inbreeding at the same absolute level of inbreeding. Possible explanations for this phenomenon include the more efficient purging of deleterious alleles and more efficient selection for heterozygote individuals during slow, when compared with fast, inbreeding. We studied the impact of inbreeding rate on the loss of heterozygosity and on morphological traits in Drosophila melanogaster. We analysed five noninbred control lines, 10 fast inbred lines and 10 slow inbred lines; the inbred lines all had an expected inbreeding coefficient of approximately 0.25. Forty single nucleotide polymorphisms in DNA coding regions were genotyped, and we measured the size and shape of wings and counted the number of sternopleural bristles on the genotyped individuals. We found a significantly higher level of genetic variation in the slow inbred lines than in the fast inbred lines. This higher genetic variation was resulting from a large contribution from a few loci and a smaller effect from several loci. We attributed the increased heterozygosity in the slow inbred lines to the favouring of heterozygous individuals over homozygous individuals by natural selection, either by associative over‐dominance or balancing selection, or a combination of both. Furthermore, we found a significant polynomial correlation between genetic variance and wing size and shape in the fast inbred lines. This was caused by a greater number of homozygous individuals among the fast inbred lines with small, narrow wings, which indicated inbreeding depression. Our results demonstrated that the same amount of inbreeding can have different effects on genetic variance depending on the inbreeding rate, with slow inbreeding leading to higher genetic variance than fast inbreeding. These results increase our understanding of the genetic basis of the common observation that slow inbred lines express less inbreeding depression than fast inbred lines. In addition, this has more general implications for the importance of selection in maintaining genetic variation.