Inbreeding – lessons from animal breeding, evolutionary biology and conservation genetics

QTL mapping of inbreeding-related cold sensitivity and conditional lethality in Drosophila melanogaster

Inbreeding depression is a central theme within genetics, and is of specific interest for researchers within evolutionary and conservation genetics and animal and plant breeding. Inbreeding effects are thought to be caused by the joint expression of conditional and unconditional deleterious alleles. Whenever the expression of deleterious alleles is conditional, this can result in extreme environmental sensitivity in certain inbred lineages. Analysis of conditional lethal effects can reveal some of the loci that are sensitive to inbreeding. We performed a QTL (quantitative trait locus) mapping study of inbreeding-related and conditionally expressed lethality in Drosophila melanogaster. The lethal effect was triggered by exposure to a cold shock. We used a North Carolina crossing Design 3 to establish the mapping population, as well as to estimate the average dominance ratio and heritability. We found two QTL on the major autosomes carrying recessive lethals that caused male mortality, one of which also affected female mortality. More detailed study of these loci will provide information on the mechanistic basis and environmental sensitivity of inbreeding depression.

Role of inbreeding depression and purging in captive breeding and restoration programmes

Inbreeding depression is a major force affecting the evolution and viability of small populations in captive breeding and restoration programmes. Populations that experience small sizes may be less susceptible to future inbreeding depression because they have been purged of deleterious recessive alleles. We review issues related to purging, as they apply to the management of small populations, and discuss an experiment we conducted examining purging in populations of mosquitofish (Gambusia affinis). Purging is an important process in many small populations, but the literature contains a diversity of responses to purging both within and among studies. With the exception that slow inbreeding results in more purging and less threat to population viability, there seem to be few consistent trends that aid in prediction of how a purging event will affect a population. In our examination of purging on population viability in mosquitofish, single or multiple bottlenecks do not appear to have resulted in any purging of the influence of genetic load on population growth. Rather, serial bottlenecks resulted in a marked decline in population growth and an increase in extinction. Our results, taken together with those of reviewed studies, suggest that in small populations there is great uncertainty regarding the success of any single purging event in eliminating inbreeding depression, together with the high likelihood that purging will depress population viability through the fixation of deleterious alleles. In management of captive breeding and restoration programmes, the common practice of avoiding inbreeding and small population sizes should be followed whenever possible.

Analysis of inbreeding depression in the first litter size of mice in a long-term selection experiment with respect to the age of the inbreeding

An understanding of inbreeding and inbreeding depression are important in evolutionary biology, conservation genetics, and animal breeding. A new method was developed to detect departures from the classical model of inbreeding; in particular, it investigated differences between the effects of inbreeding in recent generations from that in the more distant past. The method was applied in a long-term selection experiment on first-litter size in mice. The total pedigree included 74,630 animals with approximately 30,000 phenotypic records. The experiment comprised several different lines. The highest inbreeding coefficients (F) within a line ranged from 0.22 to 0.64, and the average effective population size (N(e)) was 58.1. The analysis divided F into two parts, corresponding to the inbreeding occurring in recent generations ('new') and that which preceded it ('old'). The analysis was repeated for different definitions of 'old' and 'new', depending on length of the 'new' period. In 15 of these tests, 'new' inbreeding was estimated to cause greater depression than 'old'. The estimated depression ranged from -11.53 to -0.79 for the 'new' inbreeding and from -5.22 to 15.51 for 'old'. The difference was significant, the 'new' period included at least 25 generations of inbreeding. Since there were only small differences in N(e) between lines, and near constant N(e) within lines, the effect of 'new' and 'old' cannot be attributed to the effects of 'fast' versus 'slow' inbreeding. It was concluded that this departure from the classical model, which predicts no distinction between this 'old and 'new' inbreeding, must implicate natural selection and purging in influencing the magnitude of depression.

Inbreeding avoidance through non-random mating in sticklebacks

Negative effects of inbreeding are well documented in a wide range of animal taxa. Hatching success and survival of inbred offspring is reduced in many species and inbred progeny are often less attractive to potential mates. Thus, individuals should avoid mating with close kin. However, experimental evidence for inbreeding avoidance through non-random mating in vertebrates is scarce. Here, we show that gravid female three-spined sticklebacks (Gasterosteus aculeatus) when given the choice between a courting familiar brother and a courting unfamiliar non-sib prefer to mate with the non-sib and thus avoid the disadvantages of incest. We controlled for differences in males' body size and red intensity of nuptial coloration. Thus, females adjust their courting behaviour to the risk of inbreeding.

Effects of genome-wide heterozygosity on a range of biomedically relevant human quantitative traits

The dramatic changes in human population structure over the last 200 years have resulted in significant levels of outbreeding, which, in turn, is predicted to lead to increased levels of individual genetic diversity (genome-wide heterozygosity, h). To investigate possible effects of these large demographic changes on global health, we studied the effect of h, measured as relative heterozygosity, h(R), on 15 disease-related traits in four groups of individuals with widely differing ancestral histories (ranging from outbred to inbred) from the Dalmatian islands in Croatia. Higher levels of h(R), estimated using 1184 STR/indel markers, were found in the outbred group (P < 0.0001) and were associated with lower blood pressure (BP) and total/LDL cholesterol (P = 0.01 and 0.01, respectively) after controlling for other factors, with BP showing a strong sex effect (males P > 0.5 and females P = 0.002). These findings, if replicated, suggest that h(R) be considered as a genetic risk factor in genetic epidemiological studies on common disease traits. They are consistent with the well-known effects of heterosis (hybrid vigour) described when outcrossing animals and plants. Outbreeding resulting from urbanization and migration from traditional population subgroups may be leading to increasing h(R) and may have beneficial effects on a range of traits associated with human health and disease. Other traits, such as age at menarche, IQ and lifespan, which have been changing during the decades of urbanization, may also have been influenced by demographic factors.

Genome-wide analysis on inbreeding effects on gene expression in Drosophila melanogaster

The deleterious consequences of inbreeding, especially in the form of inbreeding depression, are well known. However, little is known about how inbreeding affects genome-wide gene expression. Here, we show that inbreeding changes transcription levels for a number of genes. Gene expression profiles of Drosophila melanogaster lines inbred to F approximately = 0.67 at different rates changed relative to those of noninbred lines, but the rate of inbreeding did not significantly affect gene expression patterns. Genes being differentially expressed with inbreeding are disproportionately involved in metabolism and stress responses, suggesting that inbreeding acts like an environmental stress factor.