Phenotype-associated inbreeding biases estimates of inbreeding depression in a wild bird population

Genetic Parameters of Performance and Conformation Traits of 3-Year-Old Warmblood Sport Horses in the Czech Republic

The aim of this study was to estimate the genetic parameters of a one-day performance test together with the linear type traits of 3-year-old warmblood horses. The study of genetic parameters was based on 5958 tested horses in the period 1998-2021. A total of 22 traits of linear description, three quantitatively measured traits, and one summary mark from the performance test were tested. The model equation included the fixed effect of gender and combination effects of classifier-year of evaluation-place. A single-trait animal model was used for the estimation of heritability and genetic variance, while the two-trait animal model was applied for the estimation of variance and covariance between all traits. The heritability of the overall score of the performance test was 0.25. The range for heritability was between 0.04 and 0.33 for the linear type traits and between 0.46 and 0.57 for the quantitatively measured traits. Genetic correlations were between -0.47 and 0.92. The estimated genetic parameters suggest that the results from the performance test can be incorporated into genetic evaluation in the Czech Republic.

Decomposing phenotypic skew and its effects on the predicted response to strong selection

The major frameworks for predicting evolutionary change assume that a phenotype's underlying genetic and environmental components are normally distributed. However, the predictions of these frameworks may no longer hold if distributions are skewed. Despite this, phenotypic skew has never been decomposed, meaning the fundamental assumptions of quantitative genetics remain untested. Here we demonstrate that the substantial phenotypic skew in the body size of juvenile blue tits (Cyanistes caeruleus) is driven by environmental factors. Although skew had little impact on our predictions of selection response in this case, our results highlight the impact of skew on the estimation of inheritance and selection. Specifically, the nonlinear parent-offspring regressions induced by skew, alongside selective disappearance, can strongly bias estimates of heritability. The ubiquity of skew and strong directional selection on juvenile body size imply that heritability is commonly overestimated, which may in part explain the discrepancy between predicted and observed trait evolution.

How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock

Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13% of a trait’s mean, or 0.59% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates.

Inbreeding depression for kit survival at birth in a rabbit population under long-term selection

Background

Accumulation of detrimental mutations in small populations leads to inbreeding depression of fitness traits and a higher frequency of genetic defects, thus increasing risk of extinction. Our objective was to quantify the magnitude of inbreeding depression for survival at birth, in a closed rabbit population under long-term selection.

Methods

We used an information theory-based approach and multi-model inference to estimate inbreeding depression and its purging with respect to the trait ‘kit survival at birth’ over a 25-year period in a closed population of Pannon White rabbits, by analysing 22,718 kindling records. Generalised linear mixed models based on the logit link function were applied, which take polygenic random effects into account.

Results

Our results indicated that inbreeding depression occurred during the period 1992–1997, based on significant estimates of the z-standardised classical inbreeding coefficient z.F_L (CI_95% − 0.12 to − 0.03) and of the new inbreeding coefficient of the litter z.F_NEWL (CI_95% − 0.13 to − 0.04) as well as a 59.2% reduction in contributing founders. Inbreeding depression disappeared during the periods 1997–2007 and 2007–2017. For the period 1992–1997, the best model resulted in a significantly negative standardised estimate of the new inbreeding coefficient of the litter and a significantly positive standardised estimate of Kalinowski’s ancestral inbreeding coefficient of the litter (CI_95% 0.01 to 0.17), which indicated purging of detrimental load. Kindling season and parity had effects on survival at birth that differed across the three periods of 1992–1997, 1997–2007 and 2007–2017.

Conclusions

Our results support the existence of inbreeding depression and its purging with respect to kit survival at birth in this Pannon White rabbit population. However, we were unable to exclude possible confounding from the effects of parity and potentially other environmental factors during the study period, thus our results need to be extended and confirmed in other populations.

Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load

Inbreeding depression, the deterioration in mean trait value in progeny of related parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant breeding, and conservation biology. The magnitude of inbreeding depression can be quantified by the inbreeding load, typically measured in numbers of lethal equivalents, a population genetic quantity that allows for comparisons between environments, populations or species. However, there is as yet no quantitative assessment of which combinations of statistical models and metrics of inbreeding can yield such estimates. Here, we review statistical models that have been used to estimate inbreeding load and use population genetic simulations to investigate how unbiased estimates can be obtained using genomic and pedigree-based metrics of inbreeding. We use simulated binary viability data (i.e., dead versus alive) as our example, but the concepts apply to any trait that exhibits inbreeding depression. We show that the increasingly popular generalized linear models with logit link do not provide comparable and unbiased population genetic measures of inbreeding load, independent of the metric of inbreeding used. Runs of homozygosity result in unbiased estimates of inbreeding load, whereas inbreeding measured from pedigrees results in slight overestimates. Due to widespread use of models that do not yield unbiased measures of the inbreeding load, some estimates in the literature cannot be compared meaningfully. We surveyed the literature for reliable estimates of the mean inbreeding load from wild vertebrate populations and found an average of 3.5 haploid lethal equivalents for survival to sexual maturity. To obtain comparable estimates, we encourage researchers to use generalized linear models with logarithmic links or maximum-likelihood estimation of the exponential equation, and inbreeding coefficients calculated from runs of homozygosity, provided an assembled reference genome of sufficient quality and enough genetic marker data are available.

Environmental coupling of heritability and selection is rare and of minor evolutionary significance in wild populations

Predicting the rate of adaptation to environmental change in wild populations is important for understanding evolutionary change. However, predictions may be unreliable if the two key variables affecting the rate of evolutionary change-heritability and selection-are both affected by the same environmental variable. To determine how general such an environmentally induced coupling of heritability and selection is, and how this may influence the rate of adaptation, we made use of freely accessible, open data on pedigreed wild populations to answer this question at the broadest possible scale. Using 16 populations from 10 vertebrate species, which provided data on 50 traits (relating to body mass, morphology, physiology, behaviour and life history), we found evidence for an environmentally induced relationship between heritability and selection in only 6 cases, with weak evidence that this resulted in an increase or decrease in the expected selection response. We conclude that such a coupling of heritability and selection is unlikely to strongly affect evolutionary change, even though both heritability and selection are commonly postulated to be dependent on the environment.

Inbreeding, inbreeding depression, and infidelity in a cooperatively breeding bird

Inbreeding depression plays a major role in shaping mating systems: in particular, inbreeding avoidance is often proposed as a mechanism explaining extra-pair reproduction in socially monogamous species. This suggestion relies on assumptions that are rarely comprehensively tested: that inbreeding depression is present, that higher kinship between social partners increases infidelity, and that infidelity reduces the frequency of inbreeding. Here, we test these assumptions using 26 years of data for a cooperatively breeding, socially monogamous bird with high female infidelity, the superb fairy-wren (Malurus cyaneus). Although inbred individuals were rare (∼6% of offspring), we found evidence of inbreeding depression in nestling mass (but not in fledgling survival). Mother-son social pairings resulted in 100% infidelity, but kinship between a social pair did not otherwise predict female infidelity. Nevertheless, extra-pair offspring were less likely to be inbred than within-pair offspring. Finally, the social environment (the number of helpers in a group) did not affect offspring inbreeding coefficients or inbreeding depression levels. In conclusion, despite some agreement with the assumptions that are necessary for inbreeding avoidance to drive infidelity, the apparent scarcity of inbreeding events and the observed levels of inbreeding depression seem insufficient to explain the ubiquitous infidelity in this system, beyond the mother-son mating avoidance.

Genomic analysis reveals depression due to both individual and maternal inbreeding in a free-living mammal population

There is ample evidence for inbreeding depression manifested as a reduction in fitness or fitness-related traits in the focal individual. In many organisms, fitness is not only affected by genes carried by the individual, but also by genes carried by their parents, for example if receiving parental care. While maternal effects have been described in many systems, the extent to which inbreeding affects fitness directly through the focal individual, or indirectly through the inbreeding coefficients of its parents, has rarely been examined jointly. The Soay sheep study population is an excellent system in which to test for both effects, as lambs receive extended maternal care. Here, we tested for both maternal and individual inbreeding depression in three fitness-related traits (birthweight and weight and hindleg length at 4 months of age) and three fitness components (first-year survival, adult annual survival and annual breeding success), using either pedigree-derived inbreeding or genomic estimators calculated using ~37 000 SNP markers. We found evidence for inbreeding depression in 4-month hindleg and weight, first-year survival in males, and annual survival and breeding success in adults. Maternal inbreeding was found to depress both birthweight and 4-month weight. We detected more instances of significant inbreeding depression using genomic estimators than the pedigree, which is partly explained through the increased sample sizes available. In conclusion, our results highlight that cross-generational inbreeding effects warrant further exploration in species with parental care and that modern genomic tools can be used successfully instead of, or alongside, pedigrees in natural populations.