Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Inbreeding Depression”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

11 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↗
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↗
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↗
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↗
PubMed2023

Utilizing evolutionary conservation to detect deleterious mutations and improve genomic prediction in cassava.

INTRODUCTION: Cassava (Manihot esculenta) is an annual root crop which provides the major source of calories for over half a billion people around the world. Since its domestication ~10,000 years ago, cassava has been largely clonally propagated through stem cuttings. Minimal sexual recombination has led to an accumulation of deleterious mutations made evident by heavy inbreeding depression. METHODS: To locate and characterize these deleterious mutations, and to measure selection pressure across the cassava genome, we aligned 52 related Euphorbiaceae and other related species representing millions of years of evolution. With single base-pair resolution of genetic conservation, we used protein structure models, amino acid impact, and evolutionary conservation across the Euphorbiaceae to estimate evolutionary constraint. With known deleterious mutations, we aimed to improve genomic evaluations of plant performance through genomic prediction. We first tested this hypothesis through simulation utilizing multi-kernel GBLUP to predict simulated phenotypes across separate populations of cassava. RESULTS: Simulations showed a sizable increase of prediction accuracy when incorporating functional variants in the model when the trait was determined by<100 quantitative trait loci (QTL). Utilizing deleterious mutations and functional weights informed through evolutionary conservation, we saw improvements in genomic prediction accuracy that were dependent on trait and prediction. CONCLUSION: We showed the potential for using evolutionary information to track functional variation across the genome, in order to improve whole genome trait prediction. We anticipate that continued work to improve genotype accuracy and deleterious mutation assessment will lead to improved genomic assessments of cassava clones.

cassava (Manihot esculenta)↗
PubMed2026

Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (Cyprinodon diabolis).

As anthropogenic habitat fragmentation and population decline accelerate globally, growing numbers of species face compounding demographic and genetic threats to long-term survival. Many populations are already forced to persist at chronically small sizes, yet the genomic and fitness consequences of this fate remain poorly understood. Here we leverage the demographic history of the Devils Hole pupfish to investigate how long-term small population size and recent bottlenecks have shaped genetic diversity, genetic load, inbreeding, and fitness through comparative population genomics, historical sequencing, and sampling embryos that died prematurely during development. We find that genetic diversity in Devils Hole pupfish is among the lowest recorded in the wild and that fixed load is high, consistent with thousands of generations of isolation at small population size. Even in the face of this low diversity and high fixed load, we show that inbreeding is still strongly associated with premature embryonic death, which affects up to 25% of offspring in the captive refuge and can be identified in advance based on a characteristic elongated heart tube and reduced heart rate. We discovered a recessive lethal haplotype segregating at ~20% frequency that accounts for 50% of embryonic deaths and contains mutations in MIB1 and MMP16, genes associated with cardiomyopathy and atrial fibrillation. Our findings link genotype, phenotype, and fitness in an iconic endangered species to provide a rare comprehensive view into the evolutionary dynamics and consequences of long-term small effective population size, demonstrating that endangered species remain vulnerable to inbreeding depression despite extremely low genetic diversity.

Journal Article↗