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PubMed2002

Inbreeding and relatedness coefficients: what do they measure?

This paper reviews and discusses what is known about the relationship between identity in state, allele frequency, inbreeding coefficients, and identity by descent in various uses of these terms. Generic definitions of inbreeding coefficients are given, as ratios of differences of probabilities of identity in state. Then some of their properties are derived from an assumption in terms of differences between distributions of coalescence times of different genes. These inbreeding coefficients give an approximate measurement of how much higher the probability of recent coalescence is for some pair of genes relative to another pair. Such a measure is in general not equivalent to identity by descent; rather, it approximates a ratio of differences of probabilities of identity by descent. These results are contrasted with some other formulas relating identity, allele frequency, and inbreeding coefficients. Additional assumptions are necessary to obtain most of them, and some of these assumptions are not always correct, for example when there is localized dispersal. Therefore, definitions based on such formulas are not always well-formulated. By contrast, the generic definitions are both well-formulated and more broadly applicable.

Gene Frequency↗
PubMed2004

Single-locus complementary sex determination in the inbreeding wasp Euodynerus foraminatus Saussure (Hymenoptera: Vespidae).

The Hymenoptera have arrhenotokous haplodiploidy in which males normally develop from unfertilized eggs and are haploid, while females develop from fertilized eggs and are diploid. Multiple sex determination systems are known to underlie haplodiploidy, and the best understood is single-locus complementary sex determination (sl-CSD) in which sex is determined at a single polymorphic locus. Individuals heterozygous at the sex locus develop as females; individuals that are hemizygous (haploid) or homozygous (diploid) at the sex locus develop as males. sl-CSD can be detected with inbreeding experiments that produce diploid males in predictable proportions as well as sex ratio shifts due to diploid male production. This sex determination system is considered incompatible with inbreeding because the ensuing increase in homozygosity increases the production of diploid males that are inviable or infertile, imposing a high cost on matings between close relatives. However, in the solitary hunting wasp Euodynerus foraminatus, a species suspected of having sl-CSD, inbreeding may be common due to a high incidence of sibling matings at natal nests. In laboratory crosses with E. foraminatus, we find that sex ratios and diploid male production (detected as microsatellite heterozygosity) are consistent with sl-CSD, but not with other sex determination systems. This is the first documented example of sl-CSD in a hymenopteran with an apparent natural history of inbreeding, and thus presents a paradox for our understanding of hymenopteran genetics.

Animals↗
PubMed2000

The evolution of haplodiploidy under inbreeding.

Although haplodiploid organisms tend to be inbred, previous models of the evolution of haplodiploidy have assumed outbred populations. Here a model for the evolution of haplodiploidy is developed which incorporates sib mating, deleterious mutations generated by mutation, and fitness differences between haploids and diploids. Simulations of the model allow an assessment of the effect of inbreeding on the deleterious mutation and maternal transmission theories for the evolution of haplodiploidy. As expected from intuitive arguments, inbreeding favours haplodiploidy under the deleterious mutation hypothesis but disfavours haplodiploidy under the maternal transmission hypothesis. It appears that the effect of inbreeding is greater on the maternal transmission theory, and thus inbreeding may restrict the evolution of haplodiploidy.

Animals↗
PubMed1998

The role of consanguinity and inbreeding as a determinant of spontaneous abortion in Karachi, Pakistan.

The effect of consanguinity and inbreeding on spontaneous abortion is assessed with the help of data from a population-based study conducted in four squatter settlements of Karachi, Pakistan. The analysis is based on 4966 pregnancy records belonging to 873 women. Results of the multivariate analysis show that both consanguinity and inbreeding were independent risk factors for spontaneous abortion despite undertaking control for other biological and socio-demographic factors that could confound the association. The combination of fetal and parental inbreeding led to a greater likelihood of a pregnancy ending in spontaneous abortion than one generation of inbreeding alone.

Abortion, Spontaneous↗
PubMed1996

Age-specific inbreeding depression and components of genetic variance in relation to the evolution of senescence.

Two major theories of the evolution of senescence (mutation accumulation and antagonistic pleiotropy) make different predictions about the relationships between age, inbreeding effects, and the magnitude of genetic variance components of life-history components. We show that, under mutation accumulation, inbreeding decline and three major components of genetic variance are expected to increase with age in randomly mating populations. Under the simplest version of the antagonistic pleiotropy model, no changes in the severity of inbreeding decline, dominance variance, or the genetic variance of chromosomal homozygotes are expected, but additive genetic variance may increase with age. Age-specific survival rates and mating success were measured on virgin males, using lines extracted from a population of Drosophila melanogaster. For both traits, inbreeding decline and several components of genetic variance increase with age. The results are consistent with the mutation accumulation model, but can only be explained by antagonistic pleiotropy if there is a general tendency for an increase with age in the size of allelic effects on these life-history traits.

Aging↗
PubMed1976

Inbreeding components of body weight and growth rate in Japanese Quail.

1. The parental inbreeding component of body weight and daily gain was partitioned into paternal and maternal inbreeding components and the latter were found to be the mor important. 2. The contribution of the maternal inbreeding to the depression of characters was more pronounced on 1-d-old chicks, but declined as the chicks grew. 3. The body weight taken near sexual maturity showed a low and non-significant decline. 4. In spite of differences in the body weight of the two populations of Japanese quail the inbreeding components were similar.

Animals↗
PubMed1976

Effects of different rates of inbreeding on the body weight and rate of gain of Japanese quail.

1. The effect of regular full-sib and double first cousin mating on body weight and rate of gain over six generations of Japanese quail was determined. 2. The depression of characters was more pronounced in the full-sib than in the double first cousin mating system, the relative depression due to parental inbreeding and offspring inbreeding depending on the magnitude of parental effect and individual's own genotypic effect on the character. 3. The body weight and rate of gain taken at an early age showed greater depression due to parental inbreeding whereas that taken near sexual maturity was depressed mainly due to individual's own inbreeding.

Animals↗
PubMed2004

Genetic variability and founder effect in the pitcher plant Sarracenia purpurea (Sarraceniaceae) in populations introduced into Switzerland: from inbreeding to invasion.

BACKGROUND AND AIMS: The long-lived and mainly outcrossing species Sarracenia purpurea has been introduced into Switzerland and become invasive. This creates the opportunity to study reactions to founder effect and how a species can circumvent deleterious effects of bottlenecks such as reduced genetic diversity, inbreeding and extinction through mutational meltdown, to emerge as a highly invasive plant. METHODS: A population genetic survey by random amplified polymorphism DNA markers (RAPD) together with historical insights and a field pollination experiment were carried out. KEY RESULTS: At the regional scale, S. purpurea shows low structure (thetast=0.072) due to a recent founder event and important subsequent growth. Nevertheless, multivariate statistical analyses reveal that, because of a bottleneck that shifted allele frequencies, most of the variability is independent among populations. In one population (Tenasses) the species has become invasive and genetic analysis reveals restricted gene flow and family structure (thetast=0.287). Although inbreeding appears to be high (Fis >0.410 from a Bayesian estimation), a field pollination experiment failed to detect significant inbreeding depression upon F1 seed number and seed weight fitness-traits. Furthermore, crosses between unrelated individuals produced F1 seeds with significantly reduced fitness, thus showing local outbreeding depression. CONCLUSIONS: The results suggest that, under restricted gene flow among families, the species may not only have rapidly purged deleterious alleles, but also have undergone some form of selection for inbreeding due to co-adaptation between loci.

Biological Evolution↗
PubMed1982

Estimates of inbreeding in a natural population: a comparison of sampling properties.

The average inbreeding coefficient f of a population can be estimated in several different ways based solely on the genotypic frequencies at a single locus. The means and variances of four different estimates have been compared. While the four estimates are equivalent when there are two alleles, the best estimates when there are three or more alleles are based upon total heterozygosity (Formula: see text) where x and y are the expected and observed number of heterozygotes) and the proportion of alleles that are homozygous (Formula: see text) where k = the number of alleles, aii = the number of AiAi homozygotes, and 2aij = the number of AiAj heterozygotes). Both are minimally based estimates of f and have identical sampling variances when all alleles are equally frequent. However, when alleles have different frequencies, the choice between these two estimates depends on the gene frequencies and the true inbreeding coefficient of a population; f2 is the best estimate when the true average inbreeding coefficient is suspected to be low or f = 0, while f1 is best in populations with large average inbreeding coefficients. Approximate sampling variances of these two estimates are given for any f and any number of alleles with arbitrary gene frequencies; these approximations are accurate for samples as small as n = 100. The chi-square and maximum likelihood estimates of f are not as good for realistic sample sizes.

Alleles↗
PubMed1994

Decline in heterozygosity under full-sib and double first-cousin inbreeding in Drosophila melanogaster.

The effects of inbreeding on heterozygosities and reproductive fitness were determined by carrying out full-sib and double first-cousin inbreeding in Drosophila melanogaster populations for up to 18 generations. Parents were scored each generation for five or six polymorphic enzyme loci, and progeny numbers per pair were recorded. Inbreeding depression, in the form of significant reductions in progeny numbers and significant extinction of lines, was observed. Heterozygosity decreased at a significantly slower rate than predicted, being about 80% of expected. The full-sib and double first-cousin treatments showed similar disagreement with expectations over comparable ranges of inbreeding. Natural selection was shown to favor heterozygotes in the inbred lines. Associative overdominance was the most probable explanation for the slower than expected decline in heterozygosity.

Alleles↗
PubMed1998

Mutant alleles of small effect are primarily responsible for the loss of fitness with slow inbreeding in Drosophila melanogaster.

Multilocus simulation is used to identify genetic models that can account for the observed rates of inbreeding and fitness decline in laboratory populations of Drosophila melanogaster. The experimental populations were maintained under crowded conditions for approximately 200 generations at a harmonic mean population size of Nh approximately 65-70. With a simulated population size of N = 50, and a mean selective disadvantage of homozygotes at individual loci approximately 1-2% or less, it is demonstrated that the mean effective population size over a 200-generation period may be considerably greater than N, with a ratio matching the experimental estimate of Ne/Nh approximately 1.4. The buildup of associative overdominance at electrophoretic marker loci is largely responsible for the stability of gene frequencies and the observed reduction in the rate of inbreeding, with apparent selection coefficients in favor of the heterozygote at neutral marker loci increasing rapidly over the first N generations of inbreeding to values approximately 5-10%. The observed decline in fitness under competitive conditions in populations of size approximately 50 in D. melanogaster therefore primarily results from mutant alleles with mean effects on fitness as homozygotes of sm < or = 0.02. Models with deleterious recessive mutants at the background loci require that the mean selection coefficient against heterozygotes is at most hsm approximately 0.002, with a minimum mutation rate for a single Drosophila autosome 100 cM in length estimated to be in the range 0.05-0.25, assuming an exponential distribution of s. A typical chromosome would be expected to carry at least 100-200 such mutant alleles contributing to the decline in competitive fitness with slow inbreeding.

Adaptation, Physiological↗
PubMed1999

Improving the efficiency of artificial selection: more selection pressure with less inbreeding.

The use of population genetic variability in present-day selection schemes can be improved to reduce inbreeding rate and inbreeding depression without impairing genetic progress. We performed an experiment with Drosophila melanogaster to test mate selection, an optimizing method that uses linear programming to maximize the selection differential applied while at the same time respecting a restriction on the increase in inbreeding expected in the next generation. Previous studies about mate selection used computer simulation on simple additive genetic models, and no experiment with a real character in a real population had been carried out. After six selection generations, the optimized lines showed an increase in cumulated phenotypic selection differential of 10.76%, and at the same time, a reduction of 19.91 and 60.47% in inbreeding coefficient mean and variance, respectively. The increased selection pressure would bring greater selection response, and in fact, the observed change in the selected trait was on average 31.03% greater in the optimized lines. These improvements in the selection scheme were not made at the expense of the long-term expectations of genetic variability in the population, as these expectations were very similar for both mate selection and conventionally selected lines in our experiment.

Animals↗
PubMedDate not supplied

Inbreeding, microsatellite heterozygosity, and morphological traits in Lipizzan horses.

While the negative effects of inbreeding and reduced heterozygosity on fecundity and survival are well established, only a few investigations have been carried out concerning their influence on morphological traits. This topic is of particular interest for a small and closed population such as the Lipizzan horse. Thus, 27 morphological traits were measured in 360 Lipizzan mares and were regressed on the individual inbreeding coefficients, as well as on the individual heterozygosity and mean squared distances (mean d(2)) between microsatellite alleles within an individual. Both individual heterozygosity and mean d(2) were based on 17 microsatellite loci dispersed over 14 chromosomes. The results obtained by multivariate analysis reveal significant effects of stud (P <.0001), age at measurement (P <.0001), and mean d(2) (P =.0143). In univariate analyses, significant associations were obtained between length of pastern-hindlimbs and inbreeding coefficient (P <.01), length of cannons-hindlimb and mean d(2) (P <.01), and length of neck and mean d(2) (P <.001). After adjustment of single-test P values for multiple tests (Hochberg's step-up Bonferroni method), only the association of the length of neck and mean d(2) remained significant (P =.0213). Thus, no overall large effects of inbreeding, microsatellite heterozygosity, and mean d(2) on morphological traits were observed in the Lipizzan horse.

Animals↗
PubMed1976

Inbreeding and canine mammary cancer: a retrospective study.

Using files of the Animal Neoplasm Registry (ANR) in Alameda and Contra Costa Counties, California, we conducted a retrospective study to compare the degree of inbreeding in the ancestry of purebred dogs with mammary and other cancers, and of those without tumors. Wright's coefficients of inbreeding, calculated for all animals in the three groups, ranged from 0.000 to 0.535. The median inbreeding coefficients of the mammary cancer and comparison groups (consisting of other cancers) were approximately twice that of the nonneoplastic group, but neither difference was statistically significant. Dogs with mammary adenocarcinoma and mixed mammary cancer had similar degrees of inbreeding.

Animals↗
PubMed2004

Do female great reed warblers seek extra-pair fertilizations to avoid inbreeding?

Females of many species mate with several males. According to a recent hypothesis, female promiscuity serves to avoid inbreeding. We tested this hypothesis in a polygynous bird, the great reed warbler (Acrocephalus arundinaceus), in which extra-pair fertilization, inbreeding and inbreeding depression occur. However, the extra-pair males and social males did not differ in relatedness to the promiscuous females, nor did the least related males sire most of the females' chicks. Thus, contrary to recent findings in some insects, birds and reptiles, we found no evidence for inbreeding avoidance among the promiscuous females. Instead, female great reed warblers may seek other potential benefits when cuckolding, such as good gene effects at particular functional genes.

Animals↗
PubMed2005

Severe inbreeding depression in a wild wolf (Canis lupus) population.

The difficulty of obtaining pedigrees for wild populations has hampered the possibility of demonstrating inbreeding depression in nature. In a small, naturally restored, wild population of grey wolves in Scandinavia, founded in 1983, we constructed a pedigree for 24 of the 28 breeding pairs established in the period 1983-2002. Ancestry for the breeding animals was determined through a combination of field data (snow tracking and radio telemetry) and DNA microsatellite analysis. The population was founded by only three individuals. The inbreeding coefficient F varied between 0.00 and 0.41 for wolves born during the study period. The number of surviving pups per litter during their first winter after birth was strongly correlated with inbreeding coefficients of pups (R2=0.39, p<0.001). This inbreeding depression was recalculated to match standard estimates of lethal equivalents (2B), corresponding to 6.04 (2.58-9.48, 95% CI) litter-size-reducing equivalents in this wolf population.

Animals↗
PubMed1998

Inbreeding, fluctuating asymmetry, and ejaculate quality in an endangered ungulate.

An ever-increasing number of species are suffering marked reductions in population size as a consequence of human activities. To understand the impact of these changes it is essential to assess how small population size affects individual fitness and the viability of populations. This issue acquires special relevance among endangered species in which numbers have decreased to such an extent that captive breeding must be established with a few founders. A major risk associated with small population size is inbreeding depression. The effects of inbreeding upon male reproductive traits are the subject of an ongoing controversy, since the evidence linking lack of genetic variability and poor ejaculate quality at the population level has been criticized recently by several authors. We report that among Gazella cuvieri males, inbreeding coefficient shows a strong inverse relationship with ejaculate quality. Furthermore, the degree of fluctuating asymmetry is positively related to the coefficient of inbreeding and negatively related to the proportion of normal sperm, suggesting that it is a reliable indicator of genetic stress and of ejaculate quality.

Animals↗
PubMed2005

Inbreeding uncovers fundamental differences in the genetic load affecting male and female fertility in a butterfly.

Inbreeding depression is most pronounced for traits closely associated with fitness. The traditional explanation is that natural selection eliminates deleterious mutations with additive or dominant effects more effectively than recessive mutations, leading to directional dominance for traits subject to strong directional selection. Here we report the unexpected finding that, in the butterfly Bicyclus anynana, male sterility contributes disproportionately to inbreeding depression for fitness (complete sterility in about half the sons from brother-sister matings), while female fertility is insensitive to inbreeding. The contrast between the sexes for functionally equivalent traits is inconsistent with standard selection arguments, and suggests that trait-specific developmental properties and cryptic selection play crucial roles in shaping genetic architecture. There is evidence that spermatogenesis is less developmentally stable than oogenesis, though the unusually high male fertility load in B. anynana additionally suggests the operation of complex selection maintaining male sterility recessives. Analysis of the precise causes of inbreeding depression will be needed to generate a model that reliably explains variation in directional dominance and reconciles the gap between observed and expected genetic loads carried by populations. This challenging evolutionary puzzle should stimulate work on the occurrence and causes of sex differences in fertility load.

Animals↗