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PubMed2003

Effects of inbreeding on the genetic diversity of populations.

The study of variability within species is important to all biologists who use genetic markers. Since the discovery of molecular variability among normal individuals, data have been collected from a wide range of organisms, and it is important to understand the major factors affecting diversity levels and patterns. Comparisons of inbreeding and outcrossing populations can contribute to this understanding, and therefore studying plant populations is important, because related species often have different breeding systems. DNA sequence data are now starting to become available from suitable plant and animal populations, to measure and compare variability levels and test predictions.

Evolution, Molecular↗
PubMed2001

Identification of a novel type C porcine endogenous retrovirus: evidence that copy number of endogenous retroviruses increases during host inbreeding.

Different classes of porcine endogenous retroviruses (PERVs), which have the potential to infect humans during xenotransplantation, have been isolated from the pig genome. Because vertebrate genomes may contain numerous endogenous retrovirus sequences, the pig genome was examined for additional endogenous retroviruses, resulting in the isolation of a novel, complete endogenous retrovirus genome, designated PERV-E. The gag, pol and env genes of PERV-E are closely related to those of human endogenous retrovirus (HERV) 4-1, which belongs to the HERV-E family. Results of studies to determine the presence and copy number of PERVs demonstrated that PERV-E and PERV-A/B-like proviruses were present in all genomes tested, but that PERV-C was not found in two of the species examined, including wild boar. Multiple copies of PERVs could be found in each pig genome. Among all of the pig genomes tested, the wild boar genome had the lowest copy number of all PERVs, suggesting that the number of integrations of complete endogenous retroviruses is increased by inbreeding.

Amino Acid Sequence↗
PubMed2003

Test of synergistic interaction between infection and inbreeding in Daphnia magna.

It has been proposed that parasitic infections increase selection against inbred genotypes. We tested this hypothesis experimentally using pairs of selfed and outcrossed sibling lines of the freshwater crustacean Daphnia magna, which can be maintained clonally. We studied the performance of selfed relative to outcrossed sibling clones during repeated pairwise clonal competition in the presence and absence of two species of microsporidian parasites. In 13 of the 14 pairs, the selfed clones did worse than the outcrossed ones in the control treatment, but the presence of either parasite did not result in an overall increase in this difference. Rather, it decreased the performance of the selfed relative to the outcrossed sibling in some pairs and increased it in others. Moreover, the two parasite species did not have the same effect in a given pair. This indicates that, contrary to the hypothesis that parasites generally lead to a decreased performance of inbred genotypes, their effect may depend on the genetic background of the host as well as on the parasite species, and suggests that inbreeding can lead to reduced or increased resistance to parasites. Our findings also indicate that there is variation for specific resistance to different species of parasites in the meta-population from which the hosts for this study were obtained.

Analysis of Variance↗
PubMed2003

Bayesian inference of inbreeding depression in controlled crosses.

This study shows how a Gibbs sampling approach can be used for Bayesian inference of inbreeding depression. The method presented is mainly concerned with organisms that can be both selfed and outcrossed. Tests performed on simulated data with unequal variances and missing observations show that the method works well. Real data from the plant Scabiosa canescens is also analyzed.

Analysis of Variance↗
PubMed2004

Variable queen number in ant colonies: no impact on queen turnover, inbreeding, and population genetic differentiation in the ant Formica selysi.

Variation in queen number alters the genetic structure of social insect colonies, which in turn affects patterns of kin-selected conflict and cooperation. Theory suggests that shifts from single- to multiple-queen colonies are often associated with other changes in the breeding system, such as higher queen turnover, more local mating, and restricted dispersal. These changes may restrict gene flow between the two types of colonies and it has been suggested that this might ultimately lead to sympatric speciation. We performed a detailed microsatellite analysis of a large population of the ant Formica selysi, which revealed extensive variation in social structure, with 71 colonies headed by a single queen and 41 by multiple queens. This polymorphism in social structure appeared stable over time, since little change in the number of queens per colony was detected over a five-year period. Apart from queen number, single- and multiple-queen colonies had very similar breeding systems. Queen turnover was absent or very low in both types of colonies. Single- and multiple-queen colonies exhibited very small but significant levels of inbreeding, which indicates a slight deviation from random mating at a local scale and suggests that a small proportion of queens mate with related males. For both types of colonies, there was very little genetic structuring above the level of the nest, with no sign of isolation by distance. These similarities in the breeding systems were associated with a complete lack of genetic differentiation between single- and multiple-queen colonies, which provides no support for the hypothesis that change in queen number leads to restricted gene flow between social forms. Overall, this study suggests that the higher rates of queen turnover, local mating, and population structuring that are often associated with multiple-queen colonies do not appear when single- and multiple-queen colonies still coexist within the same population, but build up over time in populations consisting mostly of multiple-queen colonies.

Animals↗
PubMed2004

No evidence for inbreeding avoidance through postcopulatory mechanisms in the black field cricket, Teleogryllus commodus.

Several studies suggest that females mate multiply so that they can preferentially fertilize eggs with the sperm of genetically more compatible males. Unrelated males are expected to be genetically more compatible with a female than her close relatives. We tested whether black field crickets, Teleogryllus commodus, can bias sperm usage toward unrelated males by comparing egg hatching success of females mated to two of their siblings (SS), two sibling males unrelated to the female (NN) or to one unrelated male and a sibling male (NS or SN). Egg hatching success was highly repeatable. Hatching success varied significantly among females of the three mating types (P = 0.011, n = 245 females). The estimated mean hatching success of 36.8% for SS females was significantly less that the 43.4% of NN females, indicating an effect of inbreeding on hatching success. If females preferentially use the sperm of a less closely related male, the hatching success of NS/SN females should be closer to 43.4% than 36.8%. It was, in fact, only 34.9%. This does not differ significantly from the value expected if the two males contributed an equal amount of sperm that was then used randomly. Although polyandry may confer indirect genetic benefits, our results provide no evidence that female T. commodus gain these benefits by biasing paternity toward genetically more compatible males through postcopulatory mechanisms.

Animals↗
PubMed2005

Inbreeding and kinship in the ant Plagiolepis pygmaea.

In ants the presence of multiple reproductive queens (polygyny) decreases the relatedness among workers and the brood they rear, and subsequently dilutes their inclusive fitness benefits from helping. However, adoption of colony daughters, low male dispersal in conjunction with intranidal (within nest) mating and colony reproduction by budding may preserve local genetic differences, and slow down the erosion of relatedness. Reduced dispersal and intranidal mating may, however, also lead to detrimental effects owing to competition and inbreeding. We studied mating and dispersal patterns, and colony kinship in three populations of the polygynous ant Plagiolepis pygmaea using microsatellite markers. We found that the populations were genetically differentiated, but also a considerable degree of genetic structuring within populations. The genetic viscosity within populations can be attributed to few genetically homogeneous colony networks, which presumably have arisen through colony reproduction by budding. Hence, selection may act at different levels, the individuals, the colonies and colony networks. All populations were also significantly inbred (F=0.265) suggesting high frequencies of intranidal mating and low male dispersal. Consequently the mean regression relatedness among workers was significantly higher (r = 0.529-0.546) than would be expected under the typically reported number (5-35) of queens in nests of the species. Furthermore, new queens were mainly recruited from their natal or a neighbouring related colony. Finally, the effective number of queens coincided with that found upon excavation, suggesting low reproductive skew.

Animals↗
PubMed2006

Postcopulatory inbreeding avoidance by female crickets only revealed by molecular markers.

Multiple mating is thought to provide an opportunity for females to avoid the costs of genetic incompatibility by postcopulatory selection of compatible sperm haplotypes. Few studies have tested the genetic incompatibility hypothesis directly. Here we experimentally manipulated the compatibility of females with their mates using the gryllid cricket Teleogryllus oceanicus. We recorded the hatching success of eggs laid by females mated with two nonsibling males, two siblings, or one nonsibling male and one sibling. In contrast with two previous studies on crickets that have adopted this approach, the hatching success of eggs did not differ between females mated with two full siblings and females mated with two unrelated males, indicating that embryo viability was not a cost of inbreeding in this species. We assigned paternity to offspring produced by females mated to both a sibling and a nonsibling male using microsatellite markers. As in previous studies of this species, we were unable to detect any difference in the proportion of offspring sired by the 1st and the 2nd male to mate with a female when females were unrelated to their mates. However, in our experimental matings the proportion of offspring sired by the nonsibling male depended on his sequence position. Paternity was biased toward the nonsibling male when he mated first. Our data show that molecular analyses of paternity are essential to detect subtle mechanisms of postcopulatory sexual selection.

Animals↗
PubMed2006

Founder effects, inbreeding and effective sizes in the Southern cattle tick: the effect of transmission dynamics and implications for pest management.

Since its immigration in the Pacific island of New Caledonia in 1942 (i.e. about 240 tick-generations ago), the cattle tick Boophilus microplus has experienced a remarkable adaptive diversification there. In order to better understand the population factors involved, we have investigated the B. microplus population structure on that main host-species, Bos taurus. This study was based microsatellite loci and confirmed that the island colonization came along with a significant bottleneck. Knowledge on B. microplus biology led us to expect B. microplus populations to be composed of highly inbred lineages irregularly dispatched among the individual hosts belonging to the same herds. Instead, this study evidenced a weak inbreeding level and an absence of genetic differentiation within herds. Complementarily, a significant signal of isolation by distance exhibited that human-traffic of cattle does not promote high tick dispersal within the island. Finally, the tick density was found to be about a few hundreds of reproducing adults per squared kilometre, for a gene dispersal range of about a few hundred metres per tick generation. Results are discussed with regard to the evolution of new adaptive changes.

Animals↗
PubMed2005

The evolution of self-fertilization and inbreeding depression under pollen discounting and pollen limitation.

We model the evolution of plant mating systems under the joint effects of pollen discounting and pollen limitation, using a dynamic model of inbreeding depression, allowing for partial purging of recessive lethal mutations by selfing. Stable mixed mating systems occur for a wide range of parameter values with pollen discounting alone. However, when typical levels of pollen limitation are combined with pollen discounting, stable selfing rates are always high but less than 1 (0.9<s<1 in most cases); in this situation, complete selfing does not evolve because pollen discounting becomes very large at high selfing rates, so that the automatic advantage of selfing changes to a disadvantage. These results suggest that mixed mating systems with high selfing rates can be maintained by selection, whereas mixed mating systems with low to moderate selfing rates are more likely attributable to unavoidable geitonogamous selfing.

Biological Evolution↗
PubMed2005

Family level inbreeding depression and the evolution of plant mating systems.

Variation in the magnitude of inbreeding depression (ID) among families may have important consequences for mating system evolution. Experimental studies have shown that such variation is a common feature of natural plant populations. Unfortunately, the genetic and evolutionary significance of family level estimates remains obscure. Almost any kind of genetic variation will generate differences in ID among families, and as a consequence, a non-zero variance in family level ID is not sufficient to distinguish genetic architectures with wholly different implications for mating system evolution. Quantitative genetic methods provide a means to extract more information from ID experiments. Estimates of quantitative genetic variance components directly inform questions about the genetic basis of ID and should ultimately allow tests of alternative theories of mating system evolution.

Biological Evolution↗
PubMed1976

Inbreeding among some Brahman populations of Tamil Nadu.

A statewide survey of four endogamous Brahman populations of Tamil Nadu reveals a low level of inbreeding in three of them. In the fourth population, the Thengalai, the level is higher, but not as high as in other social castes. The Tamil Brahmans rank next to the Telugu and the Kanarese Brahmans in this respect. Uncle-niece marriages also occur as in Telugu-speaking populations, and these exceed in the two Ayyangar populations in comparison to the Ayyar. A decline of first-cousin marriages and an increase of uncle-niece marriages are detected in the first two living generations in each population.

Consanguinity↗
PubMedDate not supplied

Selection against genetic defects in conservation schemes while controlling inbreeding.

We studied different genetic models and evaluation systems to select against a genetic disease with additive, recessive or polygenic inheritance in genetic conservation schemes. When using optimum contribution selection with a restriction on the rate of inbreeding (DeltaF) to select against a disease allele, selection directly on DNA-genotypes is, as expected, the most efficient strategy. Selection for BLUP or segregation analysis breeding value estimates both need 1-2 generations more to halve the frequency of the disease allele, while these methods do not require knowledge of the disease mutation at the DNA level. BLUP and segregation analysis methods were equally efficient when selecting against a disease with single gene or complex polygene inheritance, i.e. knowledge about the mode of inheritance of the disease was not needed for efficient selection against the disease. Smaller schemes or schemes with a more stringent restriction on DeltaF needed more generations to halve the frequency of the disease alleles or the fraction of diseased animals. Optimum contribution selection maintained DeltaF at its predefined level, even when selection of females was at random. It is argued that in the investigated small conservation schemes with selection against a genetic defect, control of DeltaF is very important.

Animals↗
PubMedDate not supplied

Linkage disequilibrium and the genetic distance in livestock populations: the impact of inbreeding.

Genome-wide linkage disequilibrium (LD) is subject to intensive investigation in human and livestock populations since it can potentially reveal aspects of a population history, permit to date them and help in fine-gene mapping. The most commonly used measure of LD between multiallelic loci is the coefficient D'. Data based on D' were recently published in humans, livestock and model animals. However, the properties of this coefficient are not well understood. Its sampling distribution and variance has received recent attention, but its expected behaviour with respect to genetic or physical distance remains unknown. Using stochastic simulations of populations having a finite size, we show that D' fits an exponential function having two parameters of simple biological interpretation: the residual value (rs) towards which D' tends as the genetic distance increases and the distance R at which this value is reached. Properties of this model are evaluated as a function of the inbreeding coefficient (F). It was found that R and rs increase when F increases. The proposed model offers opportunities to better understand the patterns and the origins of LD in different populations and along different chromosomes.

Alleles↗
PubMedDate not supplied

The advantage of factorial mating under selection is uncovered by deterministically predicted rates of inbreeding.

Rates of inbreeding (DeltaF) in selected populations were predicted using the framework of long-term genetic contributions and validated against stochastic simulations. Deterministic predictions decomposed DeltaF into four components due to: finite population size, directional selection, covariance of genetic contribution of mates, and deviation of variance of family size from that expected from a Poisson distribution. Factorial (FM) and hierarchical (HM) mating systems were compared under mass and sib-index selection. Prediction errors were in most cases for DeltaF less than 10% and for rate of gain less than 5%. DelatF was higher with index than mass selection. DeltaF was lower with FM than HM in all cases except random selection. FM reduced the variance of the average breeding value of the mates of an individual. This reduced the impact of the covariance of contributions of mates on DeltaF. Thus, contributions of mates were less correlated with FM than HM, causing smaller deviations of converged contributions from the optimum contributions. With index selection, FM also caused a smaller variance of number of offspring selected from each parent. This reduced variance of family size reduced DeltaF further. FM increases the flexibility in breeding schemes for achieving the optimum genetic contributions.

Animals↗
PubMedDate not supplied

A comparison of two methods for prediction of response and rates of inbreeding in selected populations with the results obtained in two selection experiments.

Selection programmes are mainly concerned with increasing genetic gain. However, short-term progress should not be obtained at the expense of the within-population genetic variability. Different prediction models for the evolution within a small population of the genetic mean of a selected trait, its genetic variance and its inbreeding have been developed but have mainly been validated through Monte Carlo simulation studies. The purpose of this study was to compare theoretical predictions to experimental results. Two deterministic methods were considered, both grounded on a polygenic additive model. Differences between theoretical predictions and experimental results arise from differences between the true and the assumed genetic model, and from mathematical simplifications applied in the prediction methods. Two sets of experimental lines of chickens were used in this study: the Dutch lines undergoing true truncation mass selection, the other lines (French) undergoing mass selection with a restriction on the representation of the different families. This study confirmed, on an experimental basis, that modelling is an efficient approach to make useful predictions of the evolution of selected populations although the basic assumptions considered in the models (polygenic additive model, normality of the distribution, base population at the equilibrium, etc.) are not met in reality. The two deterministic methods compared yielded results that were close to those observed in real data, especially when the selection scheme followed the rules of strict mass selection: for instance, both predictions overestimated the genetic gain in the French experiment, whereas both predictions were close to the observed values in the Dutch experiment.

Animals↗
PubMed2005

The effects of dominance, regular inbreeding and sampling design on Q(ST), an estimator of population differentiation for quantitative traits.

To test whether quantitative traits are under directional or homogenizing selection, it is common practice to compare population differentiation estimates at molecular markers (F(ST)) and quantitative traits (Q(ST)). If the trait is neutral and its determinism is additive, then theory predicts that Q(ST) = F(ST), while Q(ST) > F(ST) is predicted under directional selection for different local optima, and Q(ST) < F(ST) is predicted under homogenizing selection. However, nonadditive effects can alter these predictions. Here, we investigate the influence of dominance on the relation between Q(ST) and F(ST) for neutral traits. Using analytical results and computer simulations, we show that dominance generally deflates Q(ST) relative to F(ST). Under inbreeding, the effect of dominance vanishes, and we show that for selfing species, a better estimate of Q(ST) is obtained from selfed families than from half-sib families. We also compare several sampling designs and find that it is always best to sample many populations (>20) with few families (five) rather than few populations with many families. Provided that estimates of Q(ST) are derived from individuals originating from many populations, we conclude that the pattern Q(ST) > F(ST), and hence the inference of directional selection for different local optima, is robust to the effect of nonadditive gene actions.

Analysis of Variance↗
PubMed2005

Low genetic variation and inbreeding depression in small isolated populations of the Japanese rosy bitterling, Rhodeus ocellatus kurumeus.

The Japanese rosy bitterling, Rhodeus ocellatus kurumeus, has been affected not only by the invasion of another subspecies, R. o. ocellatus, from China, but also by habitat fragmentation. In this study, the effects of habitat fragmentation on the fitness of R. o. kurumeus were investigated. Owing to exclusion by R. o. ocellatus, R. o. kurumeus in Honshu and Shikoku has disappeared entirely, except for small populations in isolated man-made ponds in Osaka and Kagawa. In Kyushu it still occupies open water systems, into which R. o. ocellatus has only recently invaded. Meristic and genetic data show that the diversity of R. o. kurumeus is significantly lower in the isolated Osaka and Kagawa populations than the non-isolated Fukuoka population. The Osaka population is inferior to the Fukuoka population in terms of viability and growth. The viability of reciprocal inter-population hybrids between the Osaka and Fukuoka populations was, however, as high as that of the Fukuoka population. In addition to the high scores of band sharing index (BSI) in RAPD-PCR analysis, acceptance of transplanted scales among individuals, irrespective of natal pond, indicates that the Osaka population forms a highly inbred line. These results suggest that low genetic variation is associated with inbreeding depression in the small isolated Osaka populations. Consequently, the management of ponds, including the free movement of individuals, in addition to measures to prevent the invasion of R. o. ocellatus, is necessary for the conservation of R. o. kurumeus.

Animals↗