Ancestral inbreeding reduces the magnitude of inbreeding depression in Drosophila melanogaster

The influence of natural selection on the magnitude of inbreeding depression is an important issue in conservation biology and the study of evolution. It is generally expected that the magnitude of inbreeding depression in small populations will depend upon the average homozygosity of individuals, as measured by the coefficient of inbreeding (F). However, if deleterious recessive alleles are selectively purged from populations during inbreeding, then inbreeding depression may differ among populations in which individuals have the same inbreeding coefficient. In such cases, the magnitude of inbreeding depression will partly depend on the ancestral inbreeding coefficient (fa), which measures the cumulative proportion of loci that have historically been homozygous and therefore exposed to natural selection. We examined the inbreeding depression that occurred in lineages of Drosophila melanogaster maintained under pedigrees that led to the same inbreeding coefficient (F = 0.375) but different levels of ancestral inbreeding (fa = 0.250 or 0.531). Although inbreeding depression varied substantially among individual lineages, we observed a significant 40% decrease in the median level of inbreeding depression in the treatment with higher ancestral inbreeding. Our results demonstrate that high levels of ancestral inbreeding are associated with greater purging effects, which reduces the inbreeding depression that occurs in isolated populations of small size.     

Exploring the relationship between tychoparthenogenesis and inbreeding depression in the Desert Locust,Schistocerca gregaria

Tychoparthenogenesis, a form of asexual reproduction in which a small proportion of unfertilized eggs can hatch spontaneously, could be an intermediate evolutionary link in the transition from sexual to parthenogenetic reproduction. The lower fitness of tychoparthenogenetic offspring could be due to either developmental constraints or to inbreeding depression in more homozygous individuals. We tested the hypothesis that in populations where inbreeding depression has been purged, tychoparthenogenesis may be less costly. To assess this hypothesis, we compared the impact of inbreeding and parthenogenetic treatments on eight life‐history traits (five measuring inbreeding depression and three measuring inbreeding avoidance) in four laboratory populations of the desert locust, Schistocerca gregaria, with contrasted demographic histories. Overall, we found no clear relationship between the population history (illustrated by the levels of genetic diversity or inbreeding) and inbreeding depression, or between inbreeding depression and parthenogenetic capacity. First, there was a general lack of inbreeding depression in every population, except in two populations for two traits. This pattern could not be explained by the purging of inbreeding load in the studied populations. Second, we observed large differences between populations in their capacity to reproduce through tychoparthenogenesis. Only the oldest laboratory population successfully produced parthenogenetic offspring. However, the level of inbreeding depression did not explain the differences in parthenogenetic success between all studied populations. Differences in development constraints may arise driven by random and selective processes between populations.     

Understanding and predicting the fitness decline of shrunk populations: inbreeding, purging, mutation, and standard selection

The joint consequences of inbreeding, natural selection, and deleterious mutation on mean fitness after population shrinkage are of great importance in evolution and can be critical to the conservation of endangered populations. I present simple analytical equations that predict these consequences, improving and extending a previous heuristic treatment. Purge is defined as the "extra" selection induced by inbreeding, due to the "extra" fitness disadvantage (2d) of homozygotes for (partially) recessive deleterious alleles. Its effect is accounted for by using, instead of the classical inbreeding coefficient f, a purged inbreeding coefficient g that is weighed by the reduction of the frequency of deleterious alleles caused by purging. When the effective size of a large population is reduced to a smaller stable value N (with Nd ≥ 1), the purged inbreeding coefficient after t generations can be predicted as g(t) ≈ [(1 - 1/2N) g(t)(-1) + 1/2N](1 - 2d f(t)(-1)), showing how purging acts upon previously accumulated inbreeding and how its efficiency increases with N. This implies an early fitness decay, followed by some recovery. During this process, the inbreeding depression rate shifts from its ancestral value (δ) to that of the mutation-selection-drift balance corresponding to N (δ*), and standard selection cancels out the inbreeding depression ascribed to δ*. Therefore, purge and inbreeding operate only upon the remaining δ - δ*. The method is applied to the conservation strategy in which family contributions to the breeding pool are equal and is extended to make use of genealogical information. All these predictions are checked using computer simulation.     

Levels of inbreeding depression over seven generations of selfing in the androdioecious clam shrimp, Eulimnadia texana

Androdioecy (mixtures of males and hermaphrodites) is a rare mating system in both plants and animals. Theory suggests that high levels of inbreeding depression can maintain males in androdioecious populations if hermaphrodites commonly self-fertilize. However, if inbreeding depression (delta) can be 'purged' from selfing populations, maintaining males is more difficult. In the androdioecious clam shrimp, Eulimnadia texana, delta is estimated to be as high as 0.7. Previous work suggests that this high level is maintained in the face of high levels of inbreeding due to an associative overdominance of fitness-related loci with the sex-determining locus. Such associative overdominance would make purging of inbreeding depression difficult to impossible. The current experiment was designed to determine if delta can be purged in these shrimp by tracking fitness across seven generations in selfing and outcrossing treatments. Evidence of purging was found in one of four populations, but the remaining populations demonstrated a consistent pattern of delta across generations. Although the experimental design allowed ample opportunity for purging, the majority of populations were unable to purge their genetic load. Therefore, delta in this species is likely due to associative overdominance caused by deleterious recessive alleles linked to the sex determining locus.     

Experimental evolution of the genetic load and its implications for the genetic basis of inbreeding depression

The degree to which, and rapidity with which, inbreeding depression can be purged from a population has important implications for conservation biology, captive breeding practices, and invasive species biology. The degree and rate of purging also informs us regarding the genetic mechanisms underlying inbreeding depression. We examine the evolution of mean survival and inbreeding depression in survival following serial inbreeding in a seed-feeding beetle, Stator limbatus, which shows substantial inbreeding depression at all stages of development. We created two replicate serially inbred populations perpetuated by full-sib matings and paired with outbred controls. The genetic load for the probability that an egg produces an adult was purged at approximately 0.45-0.50 lethal equivalents/generation, a reduction of more than half after only three generations of sib-mating. After serial inbreeding we outcrossed all beetles then measured (1) larval survival of outcrossed beetles and (2) inbreeding depression. Survival of outcrossed beetles evolved to be higher in the serially inbred populations for all periods of development. Inbreeding depression and the genetic load were significantly lower in the serially inbred than control populations. Inbreeding depression affecting larval survival of S. limbatus is largely due to recessive deleterious alleles of large effect that can be rapidly purged from a population by serial sib-mating. However, the effectiveness of purging varied among the periods of egg/larval survival and likely varies among other unstudied fitness components. This study presents novel results showing rapid and extensive purging of the genetic load, specifically a reduction of as much as 72% in only three generations of sib-mating. However, the high rate of extinction of inbred lines, despite the lines being reared in a benign laboratory environment, indicates that intentional purging of the genetic load of captive endangered species will not be practical due to high rates of subpopulation extinction.     

Selection and inbreeding depression: effects of inbreeding rate and inbreeding environment

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.     

Microsatellite support for active inbreeding in a cichlid fish

In wild animal populations, the degree of inbreeding differs between species and within species between populations. Because mating with kin often results in inbreeding depression, observed inbreeding is usually regarded to be caused by limited outbreeding opportunities due to demographic factors like small population size or population substructuring. However, theory predicts inclusive benefits from mating with kin, and thus part of the observed variation in inbreeding might be due to active inbreeding preferences. Although some recent studies indeed report kin mating preferences, the evidence is still highly ambiguous. Here, we investigate inbreeding in a natural population of the West African cichlid fish Pelvicachromis taeniatus which showed clear kin mating preferences in standardized laboratory experiments but no inbreeding depression. The presented microsatellite analysis reveals that the natural population has, in comparison to two reference populations, a reduced allelic diversity (A = 3) resulting in a low heterozygosity (H_o = 0.167) pointing to a highly inbred population. Furthermore, we found a significant heterozygote deficit not only at population (F_is = 0.116) but also at subpopulation level (F_is = 0.081) suggesting that inbreeding is not only a by-product of population substructuring but possibly a consequence of behavioral kin preferences.     

Dynamics of inbreeding depression due to deleterious mutations in small populations: mutation parameters and inbreeding rate

A multilocus stochastic model is developed to simulate the dynamics of mutational load in small populations of various sizes. Old mutations sampled from a large ancestral population at mutation-selection balance and new mutations arising each generation are considered jointly, using biologically plausible lethal and deleterious mutation parameters. The results show that inbreeding depression and the number of lethal equivalents due to partially recessive mutations can be partly purged from the population by inbreeding, and that this purging mainly involves lethals or detrimentals of large effect. However, fitness decreases continuously with inbreeding, due to increased fixation and homozygosity of mildly deleterious mutants, resulting in extinctions of very small populations with low reproductive rates. No optimum inbreeding rate or population size exists for purging with respect to fitness (viability) changes, but there is an optimum inbreeding rate at a given final level of inbreeding for reducing inbreeding depression or the number of lethal equivalents. The interaction between selection against partially recessive mutations and genetic drift in small populations also influences the rate of decay of neutral variation. Weak selection against mutants relative to genetic drift results in apparent overdominance and thus an increase in effective size (Ne) at neutral loci, and strong selection relative to drift leads to a decrease in Ne due to the increased variance in family size. The simulation results and their implications are discussed in the context of biological conservation and tests for purging.     

Environmental conditions during early life determine the consequences of inbreeding in Agrostemma githago (Caryophyllaceae)

In an inbred population, selection may reduce the frequency of deleterious recessive alleles through a process known as purging. Empirical studies suggest, however, that the efficacy of purging in natural populations is highly variable. This variation may be due, in part, to variation in the expression of inbreeding depression available for selection to act on. This experiment investigates the roles of life stage and early‐life environment in determining the expression of inbreeding depression in Agrostemma githago. Four population‐level crosses (‘self’, ‘within’, ‘near’ and ‘far’) were conducted on 20 maternal plants from a focal population. Siblings were planted into one of three early environmental treatments with varying stress levels. Within the focal population, evidence for purging of deleterious recessive alleles, as well as for variation in the expression of inbreeding depression across the life cycle was examined. In addition, the effect of early environment on the expression of inbreeding depression and the interaction with cross‐type was measured. We find that deleterious recessive alleles have not been effectively purged from our focal population, the expression of inbreeding depression decreases over the course of the life cycle, and a stressful early environment reduces the variance in inbreeding depression expressed later in life, but does not consistently influence the relative fitness of inbred versus outcrossed individuals.     

Simultaneous inbreeding modifies inbreeding depression in a plant–herbivore interaction

Because inbreeding is common in natural populations of plants and their herbivores, herbivore‐induced selection on plants, and vice versa, may be significantly modified by inbreeding and inbreeding depression. In a feeding assay with inbred and outbred lines of both the perennial herb, Vincetoxicum hirundinaria, and its specialist herbivore, Abrostola asclepiadis, we discovered that plant inbreeding increased inbreeding depression in herbivore performance in some populations. The effect of inbreeding on plant resistance varied among plant and herbivore populations. The among‐population variation is likely to be driven by variation in plant secondary compounds across populations. In addition, inbreeding depression in plant resistance was substantial when herbivores were outbred, but diminished when herbivores were inbred. These findings demonstrate that in plant–herbivore interactions expression of inbreeding depression can depend on the level of inbreeding of the interacting species. Furthermore, our results suggest that when herbivores are inbred, herbivore‐induced selection against self‐fertilisation in plants may diminish.     

Environment-dependent inbreeding depression: its ecological and evolutionary significance

Inbreeding depression is a major evolutionary and ecological force that influences population dynamics and the evolution of inbreeding-avoidance traits such as mating systems and dispersal. There is now compelling evidence that inbreeding depression is environment-dependent. Here, we discuss ecological and evolutionary consequences of environment-dependent inbreeding depression. The environmental dependence of inbreeding depression may be caused by environment-dependent phenotypic expression, environment-dependent dominance, and environment-dependent natural selection. The existence of environment-dependent inbreeding depression challenges classical models of inbreeding as caused by unconditionally deleterious alleles, and suggests that balancing selection may shape inbreeding depression in natural populations; loci associated with inbreeding depression in some environments may even contribute to adaptation to others. Environment-dependent inbreeding depression also has important, often neglected, ecological and evolutionary consequences: it can influence the demography of marginal or colonizing populations and alter adaptive optima of mating systems, dispersal, and their associated traits. Incorporating the environmental dependence of inbreeding depression into theoretical models and empirical studies is necessary for understanding the genetic and ecological basis of inbreeding depression and its consequences in natural populations.     

Recent approaches into the genetic basis of inbreeding depression in plants

Predictions for the evolution of mating systems and genetic load vary, depending on the genetic basis of inbreeding depression (dominance versus overdominance, epistasis and the relative frequencies of genes of large and small effect). A distinction between the dominance and overdominance hypotheses is that deleterious recessive mutations should be purged in inbreeding populations. Comparative studies of populations differing in their level of inbreeding and experimental approaches that allow selection among inbred lines support this prediction. More direct biometric approaches provide strong support for the importance of partly recessive deleterious alleles. Investigators using molecular markers to study quantitative trait loci (QTL) often find support for overdominance, though pseudo-overdominance (deleterious alleles linked in repulsion) may bias this perception. QTL and biometric studies of inbred lines often find evidence for epistasis, which may also contribute to the perception of overdominance, though this may be because of the divergent lines initially crossed in QTL studies. Studies of marker segregation distortion commonly uncover genes of major effect on viability, but these have only minor contributions to inbreeding depression. Although considerable progress has been made in understanding the genetic basis of inbreeding depression, we feel that all three aspects merit more study in natural plant populations.     

Mate choice for optimal (k)inbreeding

Mating between related individuals results in inbreeding depression, and this has been thought to select against incestuous matings. However, theory predicts that inbreeding can also be adaptive if it increases the representation of genes identical by descent in future generations. Here, I recapitulate the theory of inclusive fitness benefits of incest, and extend the existing theory by deriving the stable level of inbreeding in populations practicing mate choice for optimal inbreeding. The parsimonious assumptions of the model are that selection maximizes inclusive fitness, and that inbreeding depression is a linear function of homozygosity of offspring. The stable level of inbreeding that maximizes inclusive fitness, and is expected to evolve by natural selection, is shown to be less than previous theory suggests. For wide range of realistic inbreeding depression strengths, mating with intermediately related individuals maximizes inclusive fitness. The predicted preference for intermediately related individuals as reproductive partners is in qualitative agreement with empirical evidence from mate choice experiments and reproductive patterns in nature.     

Royal dynasties as human inbreeding laboratories: the Habsburgs

The European royal dynasties of the Early Modern Age provide a useful framework for human inbreeding research. In this article, consanguineous marriage, inbreeding depression and the purging of deleterious alleles within a consanguineous population are investigated in the Habsburgs, a royal dynasty with a long history of consanguinity over generations. Genealogical information from a number of historical sources was used to compute kinship and inbreeding coefficients for the Habsburgs. The marriages contracted by the Habsburgs from 1450 to 1750 presented an extremely high mean kinship (0.0628±0.009), which was the result of the matrimonial policy conducted by the dynasty to establish political alliances through marriage. A strong inbreeding depression for both infant and child survival was detected in the progeny of 71 Habsburg marriages in the period 1450–1800. The inbreeding load for child survival experienced a pronounced decrease from 3.98±0.87 in the period 1450–1600 to 0.93±0.62 in the period 1600–1800, but temporal changes in the inbreeding depression for infant survival were not detected. Such a reduction of inbreeding depression for child survival in a relatively small number of generations could be caused by elimination of deleterious alleles of a large effect according with predictions from purging models. The differential purging of the infant and child inbreeding loads suggest that the genetic basis of inbreeding depression was probably very different for infant and child survival in the Habsburg lineage. Our findings provide empirical support that human inbreeding depression for some fitness components might be purged by selection within consanguineous populations.     

A simple method to account for natural selection when predicting inbreeding depression

It has been widely appreciated that natural selection opposes the progress of inbreeding in small populations, thus limiting the actual inbreeding depression for fitness traits. However, no method to account for the consequences of this process has been given so far. I give a simple and intuitive method to predict inbreeding depression, taking into account the increase in selection efficiency against recessive alleles during inbreeding. It is based on the use of a “purged inbreeding coefficient” g_t that accounts for the reduction of the probability of the deleterious homozygotes caused by the excess d of detrimental effect for deleterious alleles in the homozygous condition over its additive expectation. It is shown that the effect of purging can be important even for relatively small populations. For between-loci variable deleterious effects, accurate predictions can be obtained using the effective homozygous deleterious excess d_e, which can be estimated experimentally and is robust against variation of the ancestral effective population size. The method can be extended to any trait and it is used to predict the evolution of the mean viability or fecundity in a conservation program with equal or random family contributions.     

Severe inbreeding depression in collared flycatchers (Ficedula albicollis)

The causes and magnitude of inbreeding depression are of considerable importance for a wide range of issues in evolutionary and conservation biology, but we have only a limited understanding of inbreeding depression in natural populations. Here, we present a study of inbreeding in a large wild population of collared flycatchers (Ficedula albicollis). Inbreeding was rare, to the extent that we detected only 1.04% of 2139 matings over 18 years that resulted in offspring with a non-zero inbreeding coefficient, f > 0. When it did occur, inbreeding caused a significant reduction in the egg-hatching rate, in fledgling skeletal size and in post-fledging juvenile survival, with the number of offspring being recruited to the breeding population from a nest of f = 0.25 being reduced by 94% relative to a non-inbred nest. A maximum-likelihood estimate of the number of lethal equivalents per gamete was very high at B = 7.47, indicating a substantial genetic load in this population. There was also a non-significant tendency for inbreeding depression to increase with the strength of selection on a trait. The probability of mating between close relatives (f = 0.25) increased throughout the breeding season, possibly reflecting increased costs of inbreeding avoidance. Our results illustrate how severe inbreeding depression and considerable genetic load may exist in natural populations, but detecting them may require extensive long-term datasets.     

Detecting purging of inbreeding depression by a slow rate of inbreeding for various traits: the impact of environmental and experimental conditions

Inbreeding depression (ID) has since long been recognized as a significant factor in evolutionary biology. It is mainly the consequence of (partially) recessive deleterious mutations maintained by mutation-selection balance in large random mating populations. When population size is reduced, recessive alleles are increasingly found in homozygous condition due to drift and inbreeding and become more prone to selection. Particularly at slow rates of drift and inbreeding, selection will be more effective in purging such alleles, thereby reducing the amount of ID. Here we test assumptions of the efficiency of purging in relation to the inbreeding rate and the experimental conditions for four traits in D. melanogaster. We investigated the magnitude of ID for lines that were inbred to a similar level, F ≈ 0.50, reached either by three generations of full-sib mating (fast inbreeding), or by 12 consecutive generations with a small population size (slow inbreeding). This was done on two different food media. We observed significant ID for egg-to-adult viability and heat shock mortality, but only for egg-to-adult viability a significant part of the expressed inbreeding depression was effectively purged under slow inbreeding. For other traits like developmental time and starvation resistance, however, adaptation to the experimental and environmental conditions during inbreeding might affect the likelihood of purging to occur or being detected. We discuss factors that can affect the efficiency of purging and why empirical evidence for purging may be ambiguous.Subject terms: Evolutionary genetics, Inbreeding     

Reduced population size can induce quick evolution of inbreeding depression in the invasive ladybird <Emphasis Type="Italic">Harmonia axyridis</Emphasis>

Understanding biological invasion is currently one of the main scientific challenges for ecologists. The introduction process is crucial for the success of an invasion, especially when it involves a demographic bottleneck. A small introduced population is expected to face a higher risk of extinction before the first stage of invasion is complete if inbreeding depression, caused by the expression of deleterious alleles, is important. Changes in mating regimes or in population size can induce the evolution of deleterious allele frequencies, either by selection or by drift, possibly resulting in the purging or the fixation of such alleles within the population. The harlequin ladybird Harmonia axyridis became invasive on several continents following a scenario including at least one event of demographic bottleneck. Although native populations suffered from severe inbreeding depression, it was greatly reduced in invasive ones suggesting that deleterious alleles were purged during the invasion process. In this study, we performed an experiment designed to manipulate the effective population size of H. axyridis across successive generations to mimic contrasting introduction events. We used the measurement of two fitness-related phenotypic traits in order to test (1) if inbreeding depression can evolve at the time-scale of an invasion; and (2) if the changes in inbreeding depression following a bottleneck in laboratory conditions are compatible with the purging of deleterious alleles observed in this species. We found that two generations of very low population size are enough to induce a substantial change in inbreeding depression. Although the genetic changes mostly consisted in fixation of deleterious alleles, purging did also occur, sometimes simultaneously with fixation.     

Purging of inbreeding depression and fitness decline in bottlenecked populations of Drosophila melanogaster

Drastic reductions in population size, or bottlenecks, are thought to significantly erode genetic variability and reduce fitness. However, it has been suggested that a population can be purged of the genetic load responsible for reduced fitness when subjected to bottlenecks. To investigate this phenomenon, we put a number of Drosophila melanogaster isofemale lines known to differ in inbreeding depression through four ‘founder‐flush’ bottleneck cycles with flush sizes of 5 or 100 pairs and assayed for relative fitness (single‐pair productivity) after each cycle. Following the founder‐flush phase, the isofemale lines, with a large flush size and a history of inbreeding depression, recovered most of the fitness lost from early inbreeding, consistent with purging. The same isofemale lines, with a small flush size, did not regain fitness, consistent with the greater effect of genetic drift in these isofemale lines. On the other hand, the isofemale lines that did not show initial inbreeding depression declined in fitness after repeated bottlenecks, independent of the flush size. These results suggest that the nature of genetic variation in fitness may greatly influence the way in which populations respond to bottlenecks and that stochastic processes play an important role. Consequently, an attempt intentionally to purge a population of detrimental variation through inbreeding appears to be a risky strategy, particularly in the genetic management of endangered species.     

On the expected relationship between inbreeding,fitness, and extinction

We assessed the expected relationship between the level and the cost of inbreeding, measured either in terms of fitness, inbreeding depression or probability of extinction. First, we show that the assumption of frequent, slightly deleterious mutations do agree with observations and experiments, on the contrary to the assumption of few, moderately deleterious mutations. For the same inbreeding coefficient, populations can greatly differ in fitness according to the following: (i) population size; larger populations show higher fitness (ii) the history of population size; in a population that recovers after a bottleneck, higher inbreeding can lead to higher fitness and (iii) population demography; population growth rate and carrying capacity determine the relationship between inbreeding and extinction. With regards to the relationship between inbreeding depression and inbreeding coefficient, the population size that minimizes inbreeding depression depends on the level of inbreeding: inbreeding depression can even decrease when population size increases. It is therefore clear that to infer the costs of inbreeding, one must know both the history of inbreeding (e.g. past bottlenecks) and population demography.