Inbreeding depression and mating-distance dependent offspring fitness in large and small populations of Lychnis flos-cuculi (Caryophyllaceae)

The spatial structure of four Lychnis flos-cuculi populations, varying in size and degree of isolation, was studied by comparing the fitness of offspring resulting from self-pollination and pollinations by neighbouring plants, plants within the same population, and plants from other populations. Selfed offspring had the lowest fitness of the four offspring groups. No significant difference was found between the performance of offspring from pollinations by neighbouring plants and offspring pollinated by plants further apart but within the same population. A lower fitness of offspring from pollinations between neighbours would be expected if these matings, on average, yielded inbred offspring which suffered from inbreeding depression. These results imply that either a tight neighbourhood structuring is not present, or that the inbreeding depression for offspring by neighbours is too low to detect, although these are inbred. Crossings between populations produced offspring with a significantly higher fitness than offspring sired within populations. There were no significant differences in response to inbreeding among the populations, and differences in mean fitness among populations had no clear relation to the population size or degree of isolation. A reduced fitness of small populations due to inbreeding depression or a less severe response to experimental inbreeding due to purging of deleterious alleles is therefore not supported by our results.     

Genetic components of variation in Nemophila menziesii undergoing inbreeding: morphology and flowering time.

The standard approaches to estimation of quantitative genetic parameters and prediction of response to selection on quantitative traits are based on theory derived for populations undergoing random mating. Many studies demonstrate, however, that mating systems in natural populations often involve inbreeding in various degrees (i.e. , self matings and matings between relatives). Here we apply theory developed for estimating quantitative genetic parameters for partially inbreeding populations to a population of Nemophila menziesii recently obtained from nature and experimentally inbred. Two measures of overall plant size and two of floral size expressed highly significant inbreeding depression. Of three dominance components of phenotypic variance that are defined under partial inbreeding, one was found to contribute significantly to phenotypic variance in flower size and flowering time, while the remaining two components contributed only negligibly to variation in each of the five traits considered. Computer simulations investigating selection response under the more complete genetic model for populations undergoing mixed mating indicate that, for parameter values estimated in this study, selection response can be substantially slowed relative to predictions for a random mating population. Moreover, inbreeding depression alone does not generally account for the reduction in selection response.     

Analysis of Inbreeding Depression in Agaricus Bisporus

Inbreeding depression was observed in the commercial button mushroom, Agaricus bisporus, by examining two laboratory populations. The outbred population consisted of 20 compatible pairings, 10 homokaryons with each of the homokaryons Ag1-1 and Ag89-65. The inbred population consisted of 104 backcrosses (among which 52 were expected to be sexually compatible) obtained from the pairings of two progenitor homokaryons, Ag1-1 and Ag89-65, with 52 progeny homokaryons derived from the mating between Ag1-1 and Ag89-65. The eight fitness components examined for these two populations were successful matings as identified by the analysis of restriction fragment length polymorphisms, positive mycelial interaction in these successful matings, heterokaryon growth rate, primordium formation by the successful matings, fertile fruiting body formation, time to first break, average number of fruiting bodies per square foot, and average weight per fruiting body. The outcrossed population showed a significant advantage over the inbred population in three of eight fitness components. Two pairs of traits were significantly correlated. The multiplicative fitness ratio of the inbred to the outcrossed population was 0.18. The relevance of inbreeding depression to the evolution of fungal mating systems and to mushroom breeding is discussed.     

Variation in inbreeding depression among populations of the seed beetle, Stator limbatus

Inbreeding depression has been documented in many insect species, but the degree to which it varies among traits within populations and among populations within species is poorly understood. We used a single‐generation factorial breeding design to examine variation in inbreeding depression among three populations of the seed‐feeding beetle, Stator limbatus Horn (Coleoptera: Chrysomelidae: Bruchinae), from the southwestern USA. Eggs from sib matings were less likely to develop and hatch, and larval hatch‐to‐adult mortality was higher for offspring of sib matings. Overall, inbreeding resulted in a reduction in the proportion of eggs that produced an adult from >80% for outbred matings in all three populations to an average of only 54% for inbred matings. Of those larvae that survived to adult, inbred beetles took ～1.5 days (>5%) longer to reach adult. The only measured trait not affected by inbreeding was adult body mass. The degree to which inbreeding increased mortality varied among the populations – inbreeding depression was lowest in the population that is most isolated. Although populations of S. limbatus are generally large in nature our results suggest that increased inbreeding associated with population fragmentation can have substantial effects on fitness of S. limbatus.     

Female mating success and risk of pre-reproductive death in a protandrous grasshopper

Numerous studies have assessed the adaptive value of protandry for males in several insect species, considering that male emergence is determined by female availability. However, the possible advantage of the time of emergence for females on their mating success in protandrous insect species has only been explored theoretically. By studying the grasshopper Sphenarium purpurascens we evaluated the hypothesis that late emergence could be adaptive for females. If female maturation occurs when the population density is higher and the sex ratio (males/females) is biased to males, their probability of mating increases. Thus, in this study we estimated (1) the opportunity for mating in females as a function of their sexual maturation time, population density, and sex ratio at the moment they reached sexual maturity. In addition, (2) an analysis incorporating female body size and the total number of female matings was performed. Both analyses support the occurrence of protandry in the studied population. Under the first approach, females with intermediate maturation time had a higher probability of being mated than earlier and late matured females. Thus, it suggests that stabilising selection is acting on female maturation time and this may affect selection on male maturation time. Furthermore, the proportion of mated females increased when the sex ratio was biased to males, and stabilising selection on maturation time was detected also. However, the number of matings of a female depended on her body size. Females with larger body size had more matings than smaller ones at the beginning of the reproductive season. Because selection acts differently on maturation time in males and females of S. purpurascens this result is consistent with a condition for the maintenance of protandry in the population. The present results are discussed in the light of the models for the evolution of protandry.     

Age correlation between mates and average consanguinity in age-structured human populations

When population geneticists wish to determine the genetic consequences of some aspect of mating behavior, it is often necessary to compare observed levels of consanguinity to the level expected when mating is random with respect to the factor being studied. Expectations under random mating are often derived from discrete generation models that ignore age structure. Observed frequencies of consanguineous matings are due to processes that are continuous in time and are affected by variables that are functions of age structure. The extent to which this discrepancy between the models and reality might distort conclusions drawn from comparisons of observed and expected behavior has received insufficient attention. One potential source of error is the tendency for people to choose mates whose ages differ from their own by a certain amount; this tendency influences the frequency of consanguineous matings. Age correlation between mates should therefore also affect average consanguinity between mates and average inbreeding in the population. Expected levels of consanguinity might then differ depending on whether or not age structure has been taken into account. Hajnal developed a model that predicts the frequencies of consanguineous matings in age-structured populations. Hajnal's model is extended here to include relationships that are defined by lineal descent as well as by common ancestry, and to allow calculation of the frequencies of consanguineous matings in the absence of age correlation between mates. The extended model is then used to determine the effect of age correlation between mates on average consanguinity under various sets of conditions. The magnitude of this effect depends on the degree to which the increased frequency of some types of consanguineous matings is offset by the decrease in other types of matings. There is a fairly wide range of conditions under which this compensation is nearly complete and therefore under which the overall effect of age correlation is small. But the size of this effect is sensitive to many factors, especially the distribution of age differences between mates and the variances of ages at maternity and paternity. Under some conditions, age correlation between mates will have a substantial effect on average consanguinity.     

Effects of a single event of close inbreeding on growth and survival in steelhead

For two populations of Alaskan steelhead (Oncorhynchus mykiss) of common ancestry we evaluated effects of inbreeding in second-generation descendants of wild fish by comparing progeny of full-sibling matings to those of non-inbred controls to determine if a single event of close inbreeding has significant effects on survival and growth in captivity or the wild. In captivity, both survival and size were highly variable between inbred and control types within each line and among the five broods during five periods of freshwater culture. However, no consistent patterns of inbreeding enhancement or depression between types within lines across years were evident. In contrast, in the wild marine environment, 34 of 34 pairwise comparisons between inbred and control types in body size of returning adults after 2 or 3 years at liberty in the ocean were consistent with inbreeding depression with significant inbreeding depression varying from 2.9% for female length to 20.0% for female weight. Survival of marked juveniles (smolts) to adults in the wild marine environment was consistently and significantly lower in inbred types for both lines, for an average inbreeding depression of 78.8%. The results underscore the potential problems that can arise from using protective culture technologies, including captive broodstocks, to supplement endangered populations, and they highlight the genetic hazards that can be faced by small wild populations. This study demonstrates that high natural mortality or selection increases the amount of inbreeding depression detected in survival. Inbreeding effects on survival and growth in captivity can be poor indicators of survival and growth in a wild marine environment.     

Evaluation of the genetic trend of milk yield in the multiple ovulation and embryo transfer populations of dairy cows, using stochastic simulation

Stochastic modeling of dairy cattle populations using multiple ovulation and embryo transfer (MOET) was used to compare 15-year genetic responses with an artificial insemination (AI) program. MOET and AI techniques were simulated in four populations, two with 100 breeding females each and two with 400 breeding females. The selection goal was to maximize genetic progress in milk yield. The reduction in genetic variation due to inbreeding and linkage disequilibrium was accounted for in the simulation process. All four MOET breeding schemes studied achieved larger genetic responses than the realized and theoretical genetic gains from the current AI progeny testing populations. Strict restriction against inbred matings slowed genetic progress significantly in the small population but would not be consequential in the larger population. However, allowing inbred matings in the smaller population caused a rapid accumulation of inbreeding. Linkage disequilibrium was as important as inbreeding in reducing genetic variation. Genetic drift variance was much smaller in the larger population.     

Marker densities and the mapping of ancestral junctions

In any partially inbred population, 'junctions' are the loci that form boundaries between segments of ancestral chromosomes. Here we show that the expected number of junctions per Morgan in such a population is linearly related to the inbreeding coefficient of the population, with a maximum in a completely inbred population corresponding to the prediction given by Stam (1980). We further show that high-density marker maps (fully informative markers with average densities of up to 200 per cM) will fail to detect a significant proportion of the junctions present in highly inbred populations. The number of junctions detected is lower than that which would be expected if junctions were distributed randomly along the chromosome, and we show that junctions are not, in fact randomly spaced. This non-random spacing of junctions significantly increases the number of markers that is required to detect 90% of the junctions present on any chromosome: a marker count of at least 12 times the number of junctions present will be needed to detect this proportion.     

On the Theory of Partially Inbreeding Finite Populations. II. Partial Sib Mating

It is assumed that a population has M males in every generation, each of which is permanently mated with c-1 females, and that a proportion beta of matings are between males and their full sisters or half-sisters. Recurrence equations are derived for the inbreeding coefficient of one random individual, coefficients of kinship of random pairs of mates and probabilities of allelic identity when the infinite alleles model holds. If Ft is the inbreeding coefficient at time t and M is large, (1-Ft)/(1-Ft-1)----1-1/(2Ne) as t increases. The effective population number Ne = aM/[1 + (2a-1)FIS], where FIS is the inbreeding coefficient at equilibrium when M is infinite and the constant a depends upon the conditional probabilities of matings between full sibs and the two possible types of half-sibs. When there are M permanent couples, an approximation to the probability that an allele A survives if it is originally present in one AA heterozygote is proportional to FISs1 + (1-FIS)s2, where s1 and s2 are the selective advantages of AA and AA in comparison with AA. The paper concludes with a comparison between the results when there is partial selfing, partial full sib mating (c = 2) and partial sib mating when c is large.     

Quantitative trait mapping in a diallel cross of recombinant inbred lines

A recombinant inbred intercross (RIX) is created by generating diallel F₁ progeny from one or more panels of recombinant inbred (RI) strains. This design was originally introduced to extend the power of small RI panels for the confirmation of quantitative trait loci (QTL) provisionally detected in a parental RI set. For example, the set of 13 C × B (C57BL/6ByJ × BALB/cByJ) RI strains can, in principle, be supplemented with 156 isogenic F₁s. We describe and test a method of analysis, based on a linear mixed model, that accounts for the correlation structure of RIX populations. This model suggests a novel permutation algorithm that is needed to obtain appropriate threshold values for genome-wide scans of an RIX population. Despite the combinational multiplication of unique genotypes that can be generated using an RIX design, the effective sample size of the RIX population is limited by the number of progenitor RI genomes that are combined. When using small RI panels such as the C × B there appears to be only modest advantage of the RIX design when compared with the original RI panel for detecting QTLs with additive effects. The RIX, however, does have an inherent ability to detect dominance effects, and, unlike RI strains, the RIX progeny are genetically reproducible but are not fully inbred, providing somewhat more natural genetic context. We suggest a breeding strategy, the balanced partial RIX, that balances the advantage of RI and RIX designs. This involves the use of a partial RIX population derived from a large RI panel in which the available information is maximized by minimizing correlations among RIX progeny.     

Effects of inbreeding on coastal Douglas fir growth and yield in operational plantations: a model-based approach

In advanced generation seed orchards, tradeoffs exist between genetic gain obtained by selecting the best related individuals for seed orchard populations, and potential losses due to subsequent inbreeding between these individuals. Although inbreeding depression for growth rate is strong in most forest tree species at the individual tree level, the effect of a small proportion of inbreds in seed lots on final stand yield may be less important. The effects of inbreeding on wood production of mature stands cannot be assessed empirically in the short term, thus such effects were simulated for coastal Douglas fir [Pseudotsuga menziesii var. menziesii (Mirb.) Franco] using an individual-tree growth and yield model TASS (Tree and Stand Simulator). The simulations were based on seed set, nursery culling rates, and 10-year-old field test performance for trees resulting from crosses between unrelated individuals and for inbred trees produced through mating between half-sibs, full-sibs, parents and offspring and self-pollination. Results indicate that inclusion of a small proportion of related clones in seed orchards will have relatively low impacts on stand yields due to low probability of related individuals mating, lower probability of producing acceptable seedlings from related matings than from unrelated matings, and a greater probability of competition-induced mortality for slower growing inbred individuals than for outcrossed trees. Thus, competition reduces the losses expected due to inbreeding depression at harvest, particularly on better sites with higher planting densities and longer rotations. Slightly higher breeding values for related clones than unrelated clones would offset or exceed the effects of inbreeding resulting from related matings. Concerns regarding the maintenance of genetic diversity are more likely to limit inclusion of related clones in orchards than inbreeding depression for final stand yield.Communicated by O. Savolainen     

Inferred Paternity and Male Reproductive Success in a Killer Whale (Orcinus orca) Population

We used data from 78 individuals at 26 microsatellite loci to infer parental and sibling relationships within a community of fish-eating ("resident") eastern North Pacific killer whales (Orcinus orca). Paternity analysis involving 15 mother/calf pairs and 8 potential fathers and whole-pedigree analysis of the entire sample produced consistent results. The variance in male reproductive success was greater than expected by chance and similar to that of other aquatic mammals. Although the number of confirmed paternities was small, reproductive success appeared to increase with male age and size. We found no evidence that males from outside this small population sired any of the sampled individuals. In contrast to previous results in a different population, many offspring were the result of matings within the same "pod" (long-term social group). Despite this pattern of breeding within social groups, we found no evidence of offspring produced by matings between close relatives, and the average internal relatedness of individuals was significantly less than expected if mating were random. The population's estimated effective size was <30 or about 1/3 of the current census size. Patterns of allele frequency variation were consistent with a population bottleneck.     

The transition to social inbred mating systems in spiders: role of inbreeding tolerance in a subsocial predecessor

The social spiders are unusual among cooperatively breeding animals in being highly inbred. In contrast, most other social organisms are outbred owing to inbreeding avoidance mechanisms. The social spiders appear to originate from solitary subsocial ancestors, implying a transition from outbreeding to inbreeding mating systems. Such a transition may be constrained by inbreeding avoidance tactics or fitness loss due to inbreeding depression. We examined whether the mating system of a subsocial spider, in a genus with three social congeners, is likely to facilitate or hinder the transition to inbreeding social systems. Populations of subsocial Stegodyphus lineatus are substructured and spiders occur in patches, which may consist of kin groups. We investigated whether male mating dispersal prevents matings within kin groups in natural populations. Approximately half of the marked males that were recovered made short moves (< 5m) and mated within their natal patch. This potential for inbreeding was counterbalanced by a relatively high proportion of immigrant males. In mating experiments, we tested whether inbreeding actually results in lower offspring fitness. Two levels of inbreeding were tested: full sibling versus non-sib matings and matings of individuals within and between naturally occurring patches of spiders. Neither full siblings nor patch mates were discriminated against as mates. Sibling matings had no effect on direct fitness traits such as fecundity, hatching success, time to hatching and survival of the offspring, but negatively affected offspring growth rates and adult body size of both males and females. Neither direct nor indirect fitness measures differed significantly between within patch and between-patch pairs. We tested the relatedness between patch mates and nonpatch mates using DNA fingerprinting (TE-AFLP). Kinship explained 30% of the genetic variation among patches, confirming that patches are often composed of kin. Overall, we found limited male dispersal, lack of kin discrimination, and tolerance to low levels of inbreeding. These results suggest a history of inbreeding which may reduce the frequency of deleterious recessive alleles in the population and promote the evolution of inbreeding tolerance. It is likely that the lack of inbreeding avoidance in subsocial predecessors has facilitated the transition to regular inbreeding social systems.     

Confidence Intervals in Qtl Mapping by Bootstrapping

The determination of empirical confidence intervals for the location of quantitative trait loci (QTLs) was investigated using simulation. Empirical confidence intervals were calculated using a bootstrap resampling method for a backcross population derived from inbred lines. Sample sizes were either 200 or 500 individuals, and the QTL explained 1, 5, or 10% of the phenotypic variance. The method worked well in that the proportion of empirical confidence intervals that contained the simulated QTL was close to expectation. In general, the confidence intervals were slightly conservatively biased. Correlations between the test statistic and the width of the confidence interval were strongly negative, so that the stronger the evidence for a QTL segregating, the smaller the empirical confidence interval for its location. The size of the average confidence interval depended heavily on the population size and the effect of the QTL. Marker spacing had only a small effect on the average empirical confidence interval. The LOD drop-off method to calculate empirical support intervals gave confidence intervals that generally were too small, in particular if confidence intervals were calculated only for samples above a certain significance threshold. The bootstrap method is easy to implement and is useful in the analysis of experimental data.     

Inbreeding depression in a critically endangered carnivore

Harmful effects arising from matings between relatives (inbreeding) is a long‐standing observation that is well founded in theory. Empirical evidence for inbreeding depression in natural populations is however rare because of the challenges of assembling pedigrees supplemented with fitness traits. We examined the occurrence of inbreeding and subsequent inbreeding depression using a unique data set containing a genetically verified pedigree with individual fitness traits for a critically endangered arctic fox (Vulpes lagopus) population. The study covered nine years and was comprised of 33 litters with a total of 205 individuals. We recorded that the present population was founded by only five individuals. Over the study period, the population exhibited a tenfold increase in average inbreeding coefficient with a final level corresponding to half‐sib matings. Inbreeding mainly occurred between cousins, but we also observed two cases of full‐sib matings. The pedigree data demonstrated clear evidence of inbreeding depression on traditional fitness traits where inbred individuals displayed reduced survival and reproduction. Fitness traits were however differently affected by the fluctuating resource abundande. Inbred individuals born at low‐quality years displayed reduced first‐year survival, while inbred individuals born at high‐quality years were less likely to reproduce. The documentation of inbreeding depression in fundamental fitness traits suggests that inbreeding depression can limit population recovery. Introducing new genetic material to promote a genetic rescue effect may thus be necessary for population long‐term persistence.     

Effects of Partial Inbreeding on Fixation Rates and Variation of Mutant Genes

Diffusion methods were used to investigate the fixation probability, average time until fixation and extinction, and cumulative heterozygosity and genetic variance for single mutant genes in finite populations with partial inbreeding. The critical parameters in the approximation are the coefficient of inbreeding due to nonrandom mating (F) and the effective population size (Ne), which also depends on F and the variance of family size. For large Ns, the fixation probability (u) is u = 2(Ne/N)s (F + h - Fh), where N is the population census, s is the coefficient of selection of the mutant homozygote and h is the coefficient of dominance. For Poisson family size (independent Poisson distributions of selfed and nonselfed offspring with partial selfing, and independent Poisson distributions of male and female numbers with partial sib mating), Ne = N/(1 + F), and the time until fixation is approximately equal to Ne/N times the time to fixation with random mating, but this relation does not hold, however, for other distributions of family size. The cumulative nonadditive variance until fixation or loss for dominant genes is reduced with increasing F while for recessive genes it is increased with intermediate values of F. The average time until extinction of deleterious mutations is reduced by increasing F. This reduction, when expressed as a proportion, is approximately independent of the initial gene frequency as well as the selective disadvantage if this is large.     

Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust

The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n=409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods—resampling, selective genotyping, and selective phenotyping—to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping. Electronic Supplementary Material Supplementary material is available for this article at     

Combined effects of host quality and local mate competition on sex allocation inLariophagus distinguendus

Summary Many parasitoid wasps are known to adjust sex ratio in response to either local mate competition (LMC) or host quality. Nevertheless, few studies have investigated the combined effects of these two factors on sex allocation. The sex allocation pattern inLariophagus distinguendus, a parasitoid of granary weevil larvae, is contrasted to the expectations of Werren's (1984) model combining LMC and host quality. Several predictions of the model are confirmed, but others are not. Sex ratio on both large and small hosts declines with proportion of small hosts attacked in a manner consistent with the model. However, when only one host size is parasitized, sex ratio is not independent of that host size, as predicted by the model. Various possibilities for the deviation between expected and observed are discussed. A partial LMC/host quality model is developed which allows for some matings outside the natal patch, and predictions of this model conform more closely to the pattern observed inL. distinguendus. Finally, the application of parasitoid studies to basic questions in evolutionary ecology is briefly discussed.     

Inbreeding depression in development,survival, and reproduction in the adzuki bean beetle (<Emphasis Type="Italic">Callosobruchus chinensis</Emphasis>)

Inbreeding depression of an aspect of fitness is observed in many insects, but the traits that are of importance for inbreeding depression of fitness remain poorly understood. Here the magnitude of inbreeding depression of fitness-related traits in the development and adult stages was measured in a captive population of the adzuki bean beetle, Callosobruchus chinensis (Coleoptera: Bruchidae). Beetles produced by full-sib matings had 8% lower survival in the development stage than did beetles produced by unrelated matings. Although inbred and outbred offspring did not differ in body size after emergence, inbred offspring took 2–3% longer to develop to emergence. This indicates inbreeding depression of growth rate. At the adult stage, inbreeding had no significant effect on longevity, however lifetime offspring production was reduced by 11%. Thus, the magnitude of inbreeding depression was relatively large for offspring production. This suggests inbreeding depression of fitness manifests, to a particularly significant extent, in reduced productivity. This study shows the C. chinensis population, which has been in captivity for more than 100 generations, harbors genetic loads.