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At least 19 recordsLinked to original sources
PubMed2024

Detecting inbreeding depression in structured populations.

Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structures (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients ([Formula: see text]) to quantify the strength of inbreeding depression: allele-sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model (LMM) including a genetic relatedness matrix (GRM) as random effect to account for the nonindependence of observations. We find LMMs give better results in scenarios with population or family structure. Within the LMM, we compare three different GRMs and show that in homogeneous populations, there is little difference among the different [Formula: see text] and GRM for inbreeding depression quantification. However, as soon as a strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if i) the phenotypes are regressed on [Formula: see text] based on a weighted version of the correlation of uniting gametes, giving more weight to common alleles and ii) with the GRM obtained from an allele-sharing relatedness estimator.

Humans↗
PubMed2026

Runs of Homozygosity Predict Inbreeding Depression Across Taxa: A Systematic Review and Meta-Analysis.

Measuring inbreeding via runs of homozygosity (ROH) captures realized autozygosity and can infer inbreeding timing through ROH length. A growing body of literature links the proportion of the genome in ROH (FROH) to fitness outcomes across taxa, yet systematic synthesis has been lacking. Here, we conduct a systematic review and meta-analysis to quantify FROH-fitness associations, identify drivers of variation and derive conservation-relevant recommendations. Narrative synthesis of 44 studies revealed that inbreeding depression operates through multiple interconnected pathways (survival, maternal effects, disease susceptibility, reproduction). Critically, purging cannot be relied upon to eliminate inbreeding depression as substantial fitness costs persist even in historically small populations. Meta-analysis of 62 effect sizes revealed a significant negative association between genomic inbreeding and fitness across taxa (Fisher's z&#x2009;=&#x2009;-0.103, r&#x2009;=&#x2009;-0.10, p&#x2009;<&#x2009;0.0001). Study group, whether wildlife, livestock or humans, explained 22.5% of variance, with wildlife showing strongest effects (6-fold stronger than humans). Survival traits showed the greatest sensitivity to the effects of ROH (r&#x2009;=&#x2009;-0.22). Additionally, ROH detection methodology significantly influenced effect sizes: comprehensive approaches (all ROH lengths) detected stronger depression (r&#x2009;=&#x2009;-0.18) than long-ROH-only analyses (r&#x2009;=&#x2009;-0.08, p&#x2009;=&#x2009;0.008), indicating cumulative genetic load matters. Overall, results indicate significant but variable fitness associations with ROH, with effect magnitude depending on biological context and methodological approach. Comprehensive ROH-based approaches show promise as conservation monitoring tools, but limited wildlife studies, particularly for non-mammalian taxa, highlight an urgent need for standardized protocols and expanded empirical research.

Animals↗
PubMed2026

Genomic inbreeding coefficients and inbreeding depression of semen production traits at genome-wide and chromosomal levels in Japanese Holstein bulls.

We aimed to estimate inbreeding coefficients and the effects of inbreeding depression on semen production traits at both the genome-wide and chromosomal levels. We utilized pedigree data for 19,921 animals, single nucleotide polymorphism (SNP) data on 5700 Japanese Holstein bulls, and 52,193 semen collection records from 775 bulls. We estimated 4 different inbreeding coefficients, namely a pedigree-based coefficient (FPED) and 3 genomic coefficients derived from SNP data. The genomic coefficients consisted of one based on the genomic relationship matrix (FGRM), one based on runs of homozygosity (ROH), and one based on homozygous-by-descent (HBD) segments (FHBD). These genomic coefficients were estimated at both the genome-wide and chromosomal levels. Furthermore, we investigated the effects of these coefficients on semen production traits: semen volume (VOL), sperm concentration (CON), sperm number (NUM), and sperm motility (MOT). In the genome-wide-level analysis, inbreeding coefficients increased markedly in bulls born after 2009, coinciding with the introduction of genomic selection. Significant inbreeding depression of VOL was found. At the chromosomal level, the inbreeding coefficients for most chromosomes showed a similar trend to the genome-wide metrics, although some (e.g., chr10 and chr20) exhibited a more pronounced trend. Suggestive inbreeding effects were detected on specific chromosomes for all traits (chr1 and chr22 for VOL, chr24 and chr29 for CON, chr1, chr12, and chr27 for NUM, chr10 and chr18 for MOT), including the traits that were not significant at the genome-wide level. Our results highlight that chromosomal-level analysis provides information complementary to whole-genome metrics, offering a more detailed perspective for managing inbreeding effects. To mitigate the adverse effects of inbreeding on semen production traits, future breeding programs would benefit from the control of inbreeding effects on high-risk chromosomal regions.

Genomic inbreeding coefficient↗
PubMed1976

Expectations for inbreeding depression on self-fertilization of tetraploids.

The contribution to the inbreeding depression from a digenic tetrasomic locus upon self-fertilization involves three genotypic interaction effects which may be thought of as a generalization of the dominance deviation for a diploid locus. It is shown how this contribution may be expressed in terms of these genotypic interaction effects, the gene frequencies and the number of generations of selfing.

Alleles↗
PubMed1975

Population size and selection intensity effects on long-term selection response in mice.

Long-term response to within full-sib family selection for increased postweaning gain was evaluated in lines having different effective population sized (Ne) and selection intensities (i). Line designations were I4(4), I8(2), I16(2), M4(4), M8(2) and M16(2), where I and M indicate selection of the top 50% and 25%, respectively; 4, 8 and 16 represent the number of parental pairs per replicate and number of replicates is given in parentheses. Realized within full-sib family heritabilities (hR-2) in the first phase of selection (0-14 generations) were larger in 16-pair lines than in 4- and 8-pair lines. In the second phase of selection (greater than 14 generations), hR-2 declined significantly (P smaller than .01) in all lines, and only the I16 and M16 lines had hR-2 values significantly (P smaller than .01) greater than zero. Realized genetic correlations involving number born, 12-day litter weight, weaning weight and six-week weight tended to decline in the second phase of selection. The I16, M16 and control (C16) replicates were crossed in all combinations at generation 14. Crosses were then selected within litters for high postweaning gain. The hR-2 values in the crossbred lines were all larger than those in the second selection phase for M16-1. M16-2 and I16-1, but not for I16-2. Within each Ne level, total response was significantly (P smaller than .01) less for I lines compared with M lines. Total response increased as Ne increased, within each level of i. Relatively small differences in realized i values among Ne lines could not account for this result. The difference in total response among the Ne lines at a given selection intensity may be due to inbreeding depression and a combination of interactions involving "drift" and selection. By crossing replicates of the M lines with the C16 control, the effects of inbreeding depression were removed. Inbreeding depression and genetic drift, as defined herein, were equally important in accounting for differences among Ne lines in total response.

Animals↗
PubMed2025

Inbreeding load in finite populations from dominant and overdominant mutations.

Inbreeding depression is a widespread phenomenon that reflects the burden of deleterious effects hidden in heterozygosis in non-inbred populations but exposed in homozygosis in inbred individuals, known as inbreeding load (B). This load can be due to partially or fully recessive deleterious mutations (dominance model) or to heterozygote advantage (overdominance model, where both homozygotes are deleterious relative to the heterozygote). There are many studies addressing the changes in inbreeding load in finite populations assuming the dominance model. However, the contribution of overdominance to inbreeding depression has been focused on infinite-size populations. We carried out computer simulations to investigate the joint impact of dominant and pure overdominant mutations on inbreeding load, both for self-fertilizing populations and for panmictic populations suffering from a drastic bottleneck. We found that the overdominant inbreeding load can be substantially reduced by drift even for symmetrical overdominance, at least when considering mutations of small effect. For panmictic bottlenecked populations, the reduction in inbreeding load under dominance and overdominance loci cannot be easily distinguished. However, while purging depletes inbreeding load from dominant loci, slowing inbreeding depression and leading to partial fitness recovery, for overdominant loci fitness declines monotonically.

Inbreeding↗
PubMed2026

Ex situ reared black-footed ferrets exhibit altered sperm DNA methylation.

Many endangered species rely on ex situ management for survival when external threats exist on the landscape. Yet, ex situ settings pose challenges through space limitation, altered environment, and diet. This can lead to environmentally determined inbreeding depression, where ex situ animals exhibit reduced reproductive fitness compared with their in situ counterparts, despite originating from the same genetic stock. We investigated epigenetic differences as a potential mechanism underlying environmentally determined inbreeding depression in black-footed ferrets (Mustela nigripes), a North American endemic species reliant on ex situ conservation. More specifically, we explored how environmental context may influence sperm DNA methylation in samples collected from 12 ex situ and 5 in situ males. Average sperm DNA methylation was significantly higher in ex situ individuals. We additionally identified more than&#x2009;500 differentially methylated regions between ex situ and in situ sperm samples that were enriched for gene ontology terms pertaining to reproduction and development. Putative genes of interest included NPR2, WEE2, SLC15A1, PDE10A, PIP5K1B, CACNA1E, and CACNA1A, all of which have previously been linked to spermatogenesis, sperm motility, or fertilization in mammals. Results suggest that environmental conditions may alter sperm DNA methylation in black-footed ferrets, with possible links to decreased reproductive success in ex situ settings. These findings provide valuable insights into the molecular mechanisms underlying environmentally determined inbreeding depression in black-footed ferrets and other conservation-reliant species, and can serve as a foundation for future research on improving reproductive health in endangered wildlife.

Animals↗
PubMed2026

REVIEW: CAUSES AND CONSEQUENCES OF DOING IT WITH ONESELF-SYNTHESIS AND META-ANALYSIS OF NEODERMATAN HERMAPHRODITIC MATING SYSTEMS.

Hermaphroditic mating systems profoundly influence evolution, yet in parasitic flatworms (Neodermata) they remain strikingly understudied. For decades, sweeping claims have oscillated between pervasive selfing and near-universal outcrossing, reflecting a lack of comprehensive synthesis. This review, the first in more than 40 yr, integrates nearly a century of research, from early observational studies to modern genetic analyses, to reveal a far more nuanced picture. Our meta-analysis of population-genetic data shows a sharp departure from the bimodal selfing patterns typical of plants and other hermaphroditic animals: neodermatan parasites are strongly skewed toward outcrossing. We link variation in mating systems to parasite demography and life-history traits, especially in species exhibiting mixed mating or elevated selfing. Current evidence suggests outcrossing is common, but taxonomic and life-history gaps preclude definitive conclusions. Beyond patterns and causes, we explore evolutionary consequences ranging from fitness costs such as inbreeding depression to trait evolution, including delayed selfing, sex allocation, and complex life cycles. Evidence for inbreeding depression is mixed and limited, yet emerging approaches using selfing-rate comparisons offer promising avenues for future research. Notably, demographic constraints, such as infection intensity and life-cycle architecture, often explain mixed mating without invoking selection, challenging classical models. Similarly limited in number, studies on sex allocation indicate that hermaphroditic mating systems can shape reproductive investment, with patterns consistent with local sperm competition in some taxa. By consolidating historical observations with modern genetic insights, this review provides the most comprehensive synthesis of hermaphroditic mating systems in the Neodermata to date. We highlight critical gaps in taxonomic coverage and experimental data and point to future opportunities for integrating genomic approaches with ecological and demographic frameworks. Such integration will be essential to illuminate how mating systems shape parasite evolution and to resolve long-standing questions about the persistence of mixed mating despite theoretical expectations.

Animals↗
PubMed1979

The evolutionary genetics of sexual systems in flowering plants.

Population genetic studies of the evolution of breeding systems in flowering plants are reviewed. The selective advantage of a gene's increasing the selfing rate is stressed. In the evolution of outbreeding mechanisms, some strong disadvantage to selfing must therefore be acting; it is suggested that this disadvantage is inbreeding depression. Populations with no absolute barrier to selfing, and with intermediate levels of self-fertilization, appear to be the most likely starting state for the evolution of outbreeding mechanisms. There is some evidence for inbreeding depression in such populations. The evolution of distyly and dioecy are considered in some detail. An explanation for the existence of supergenes controlling these systems is proposed. The breakdown of distyly and tristyly are also considered. The evolution of recombination rates in selfing and outcrossing species is examined briefly.

Biological Evolution↗
PubMed2025

Conservation Arks: Genomic Erosion and Inbreeding in an Abundant Island Population of Koalas.

The persistence of many threatened species depends on isolated habitat patches such as conservation parks, fenced reserves, and islands. While these 'conservation arks' provide refuge from many contemporary threats, they can also pose risks of genetic diversity loss and inbreeding depression, further exacerbating extinction risk. A pertinent example is the Kangaroo Island koala population in South Australia that originated from a few translocated founding individuals in the 1920s but now sustains a large population with a low prevalence of infectious disease. We investigated the extent and consequences of founder effects on genomic diversity, inbreeding, and adaptive potential in Kangaroo Island koalas by comparing them with mainland Australian&#xa0;populations using high-coverage whole genomes. Our findings support sharp, recent declines in effective population sizes (Ne) in both mainland and Kangaroo Island populations. However, Kangaroo Island koalas had much lower individual and population-level diversity. Together with longer and more numerous runs of homozygosity and an increased proportion of homozygous genetic load, these results support the hypothesis that a severe bottleneck has contributed to inbreeding and maladaptation in Kangaroo Island koalas. While Kangaroo Island has the potential to conserve a viable population of koalas, we recommend genetic rescue to restore diversity and mitigate inbreeding depression in this isolated population. Our results emphasise the need for longitudinal genomic monitoring and genetic management to maintain long-term viability and resilience in potential conservation arks. Understanding the demographic history of such populations will help inform future conservation aimed at preventing genetic erosion and preserving biodiversity.

Animals↗
PubMed1979

The effects of inbreeding and of some genetic polymorphisms on blood pressures, pulse rate and hematocrit in Northeastern Brazil.

The possible role of genetic mechanisms, as revealed by inbreeding depression and pleiotropic effects of the ABO, Es D and CA II loci, on blood pressures, pulse rate and hematocrit, was studied in a sample of 7,642 migrant Brazilian individuals of rural origin. It was not possible to confirm previous claims of the effects of ABO blood groups system and inbreeding on diastolic blood pressure. On the other hand, a significant inbreeding depression on pulse rate of about 1.23 bmp/10% F, among adult individuals, was revealed. The observed significant effects of several markers on hemodynamic variables, due to its number, were attributed to chance.

Blood Pressure↗
PubMed1992

Optimal effective population size for the global population of black and white dairy cattle.

The replacement of other black and white cattle strains by the North American Holstein breed, which itself is dominated by a small number of elite sires, has reduced the genetic diversity of the global population. Intense selection on a global basis leads to rapid genetic improvement but reduces effective population size. The optimal global effective population size was chosen to maximize the net present value of all future benefits from the breeding program. Two separate discount rates were used to reflect concerns about the long-term costs of small effective population size. This led to a higher optimal number of bull-sires than in past analyses. The optimum was sensitive to the magnitude of inbreeding depression and to the discount rates, but not to the variance caused by new mutations and the size of the world population. The genetic correlation between the breeding objectives of different AI studs controls the extent to which they all select the same sires of sons and, hence, affects the global effective population size. The prediction is made that different countries will select partially different sires, but genetically isolated strains will not reemerge. A better global breeding program is likely when selection of sires takes account of inbreeding depression and small genotype by environment interactions.

Animals↗
PubMed2024

Questioning inbreeding: Could outbreeding affect productivity in the North African catfish in Thailand?

The North African catfish (Clarias gariepinus) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding.

Animals↗
PubMed1992

Parents suppress reproduction and stimulate dispersal in opposite-sex juvenile white-footed mice.

Juvenile dispersal is sex-biased in many mammals and birds: one sex often disperses more often or farther than the other. Two hypotheses are generally presented for sex-biased dispersal. The first holds that juvenile dispersal reduces reproductive and/or resource competition between parents and same-sexed offspring. If so, presence of a parent on the natal home range should both promote dispersal of same-sex offspring and suppress reproduction of those that remain. The second is that juvenile dispersal reduces matings between parents and offspring, thus decreasing the likelihood of inbreeding depression. If so, presence of a parent should favour dispersal and reproductive suppression of offspring of the opposite sex. Here I present evidence that juvenile dispersal in white-footed mice, Peromyscus leucopus, is due to inbreeding avoidance. When population density was high, experimental removal of one parent delayed dispersal of opposite-sexed offspring and only the presence of the parents of opposite sex suppressed juvenile reproduction.

Animals↗
PubMed1992

Classical and mixed-model analysis of an index selection experiment for fecundity in Drosophila melanogaster.

A comparison of three family indices to increase number of pupas from 3-d lay in Drosophila melanogaster is reported. The three indices were Id, based exclusively on dam's information; Ihd, based additionally on dam's full-sibs' and half-sibs' information; and Ihs, which also included the sire's full-sibs' and half-sibs' records. Three lines, D, HD, and HS, were selected, each according to one of the three indices: Id, Ihd, or Ihs. Each line consisted of 10 sires and 60 dams. Each dam contributed one male offspring and three female offspring. Seven generations of selection were performed in a two-replicate experiment. The expected advance of Ihs and Ihd over Id in the seventh generation was .38 and .15 phenotypic standard deviations, respectively. The experiment was analyzed in terms of both classical ordinary least squares (OLS) and mixed-model methodology (MMM). The phenotypic trends in the first replicate were 4.06 +/- 1.74, 1.42 +/- 1.76, and .26 +/- 1.94 pupas per generation for Lines D, HD, and HS, respectively, and in the second replicate 8.52 +/- 2.40, 6.16 +/- 3.21, and 4.21 +/- 2.60, respectively. The genetic trends in the first replicate were 2.18 +/- .61, 1.08 +/- .67, and .24 +/- .68 pupas per generation and, in the second replicate, 2.51 +/- .60, .16 +/- .61, and .05 +/- .64 for Lines D, HD, and HS, respectively. Despite theoretical expectations, the Id index was consistently better than the more complex indices. Several explanations for these results are possible: 1) smaller than expected selection differential, 2) inbreeding depression, and 3) incorrect heritability used to construct the indices.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of Variance↗
PubMed1979

Inbreeding and copulatory behavior in house mice: a further consideration.

Comparisons were made of the copulatory behavior of randomly bred (one population: WRL) and inbred wild (five strains: PAA, ab, ac, ad, and PAE) male house mice. All inbred and randomly bred stocks were derived from a single foundation population. The inbred males tended to have shorter latencies to the first mount and intromission, longer latencies to ejaculation, and more preejaculatory mounts and thrusts than randomly bred males. All these effects parallel those observed in a previous study in which a wild population was compared with various domestic inbred strains. If inbreeding depression is related to adaptive significance, these data suggest that, although rapid initiation of copulation in a novel environment may not be adaptive, it may be adaptive for mice to ejaculate rapidly once copulation is initiated.

Adaptation, Psychological↗