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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↗

PubMed1978

Inbreeding as measured by isonymy, pedigrees, and population size in Törbel, Switzerland.

Törbel provides an interesting test case for the study of the relationship between inbreeding measured by pedigrees and inbreeding measured by isonymy. At the start of this investigation, we were aware that isonymy could introduce biases into the calculation of the inbreeding coefficient in either direction. However, it was expected that in Switzerland, inbreeding from isonymy would be an overestimate due to patrilocal residence and polyphyletic names. One way of dealing with this problem [13] was not to be concerned with the absolute value of inbreeding but only in the difference between estimates. Any bias introduced in the estimate itself disappears in such comparisons, so that a trend of inbreeding can be ascertained correctly. However, it was considered equally important to subject several populations to both a complete pedigree analysis and an isonymic analysis to determine the relationship between estimates of inbreeding. Despite the fact that several authors (Swedlund [18], for example) warned users of isonymy to exercise caution, the careless application of isonymy still persists. In the present study, estimates of inbreeding from isonymy were brought into line with other methods based on pedigree analysis and population size. However, it was possible to do this only in Törbel where pedigree depth was extensive and relatively complete. Similar corrections are possible only when the distribution of mono- and polyphyletic names is known and when migration data are reliable. If the trouble is taken to make these corrections, the same time and effort might as well be spent in pedigree analysis (when fairly complete ascertainment is possible) to achieve the same end result.

Consanguinity↗

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 = -0.103, r = -0.10, p < 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 = -0.22). Additionally, ROH detection methodology significantly influenced effect sizes: comprehensive approaches (all ROH lengths) detected stronger depression (r = -0.18) than long-ROH-only analyses (r = -0.08, p = 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↗

PubMed1975

[Inbreeding in the Samarkand region].

Data on the frequency of inbreeding in some isolated populations of Samarkand region are given. Statistically significant differences were established in the frequency of inbreeding in separate groups and in the general population of the region. Inbreeding marriages were more observed between paralel cousins, occasionally they were made between secon cousins. Strict time dependence of inbreeding frequency was not found, but it was noticed that the level of inbreeding was reduced since 1930 to 1949.

Consanguinity↗

PubMed1975

[Inbreeding in the Samarkand region].

Data on the frequency of inbreeding in some isolated populations of Samarkand region are given. Statistically significant differences were established in the frequency of inbreeding in separate groups and in the general population of the region. Inbreeding marriages were more often observed between paralel cousins, occasionally they were made between second cousins. Strict time dependence of inbreeding frequency was not found, but it was noticed that the level of inbreeding was reduced since 1930 to 1949.

Consanguinity↗

PubMed2026

Genomic diversity, inbreeding, and selection signatures in duroc, landrace, and yorkshire pigs from a long-term closed breeding system.

Duroc (DD), Landrace (LL), and Yorkshire (YY) are among the most widely used commercial pig breeds, having undergone intense long-term selection within closed breeding systems. This study presents a comprehensive genomic analysis of genetic diversity, inbreeding patterns, and selection signatures in DD, LL, and YY populations that have been subject to close breeding for over 15 years. Genomic and pedigree data were available for 1,088 animals (DD = 348, LL = 276, YY = 464), genotyped using the GenoBaits® Porcine 100 K SNP panel. Principal component analysis and genetic diversity metrics revealed distinct population structures among the three breeds. Pairwise genetic differentiation supported this pattern, with DD showing the greatest divergence from LL (0.34 ± 0.24) and YY (0.33 ± 0.24), while LL and YY were more closely related (FST = 0.22 ± 0.19). Linkage disequilibrium (LD) analysis further confirmed these differences, as DD exhibited the highest average r² (0.34), followed by LL (0.28) and YY (0.25). Within-breed genetic diversity metrics, including observed heterozygosity (HO: 0.37 in DD, 0.39 in LL, 0.38 in YY), expected heterozygosity (HE: 0.36 in DD, 0.37 in LL, 0.38 in YY), and minor allele frequency (MAF: 0.27 in DD, 0.28 in LL, 0.29 in YY), indicated greater genetic variability in LL and YY compared to DD. Runs of homozygosity (ROH) analyses revealed different patterns of autozygosity, with DD exhibiting more long ROH indicative of recent inbreeding, while YY harbored a higher number of short ROH, suggestive of more ancient demographic events. ROH-based inbreeding coefficients (FROH) consistently exceeded pedigree-based estimates (FPED) across all breeds, highlighting the presence of recent or unrecorded inbreeding that pedigree data may not fully capture. According to Generation Proxy Selection Mapping (GPSM), 17, 1, and 12 significant SNPs were detected in DD, LL, and YY, respectively. Functional annotation of ROH islands and GPSM-significant loci revealed both breed-specific and overlapping QTLs related to traits such as growth, reproduction, and carcass. In general, the findings of this study contribute to a deeper understanding of the genomic consequences of long-term closed breeding and provide reference information to support consideration of breeding strategies that balance continued selection for productivity with the maintenance of genetic diversity in modern commercial pig populations.

Animals↗

PubMedDate not supplied

Interactions between ageing and inbreeding effects on development of Drosophila melanogaster embryos.

Ageing and brother-sister inbreeding effects were studied simultaneously during the development of Drosophila melanogaster. Egg hatchability and adult emergence were investigated in relation to age of females laying the eggs and the age of the parents of these females. Each couple was followed individually. The effects of parental age varied according to the mating system used. Both hatchability and emergency of inbred eggs were affected by ageing. This indicates that parental constitution can influence early and later stages of development. Control of embryonic and larvo-pupal developments may involve processes perturbed by both ageing and inbreeding. Thus, information related to the genetic control system of development varies with the age of the flies and of their parents and consequently modulates the inbreeding effects. It is postulated that inbreeding and ageing may both involve cytoplasmic-genome interactions implicated in the control of embryogenesis.

Aging↗

PubMed1978

On the evolutionary stability of the female-biased sex ratio in the wood lemming (Myopus schisticolor): the effect of inbreeding.

The evolutionary stability of the female-biased sex ratio observed in the wood lemming (Myopus schisticolor) is discussed. The hypothesis analysed is that the skewed sex ratio is maintained as a result of partial and/or recurrent inbreeding. Fredga et al. (1976, 1977) have suggested that an X-linked mutant gene, X, affects the male-determining action of the Y chromosome, thus converting some XY individuals into females. By a mechanism of selective non-disjunction in the foetal ovary only X-carrying eggs are produced. In particular the stability of that genetic mechanism (or the X chromosome) is analysed by considering the introduction of a "suppressing" sex-linked mutant gene Y. Several deterministic simulation models assuming father-daughter and/or brother-sister matings have been developed and analysed. It is concluded that in the case of extremely strong inbreeding, the hypothesised genetic mechanism may, as a result, be evolutionarily stable. Interpreting field observations on microtine rodents in general it is concluded that only a few species are likely to experience such extreme cases of inbreeding. The wood lemming and the related collared lemming (Dicrostonyx troquatus), another case which seems to have XY-females, are likely to exhibit sufficiently strong inbreeding.

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↗

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 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↗

PubMed1977

The relationship between inbreeding, migration and population density in Norway.

An investigation of the present levels of inbreeding and the proportion of non-migrants (residents in municipality of birth) in rural districts of Norway reveals a relationship between these two characteristics. There is a steady upward trend from 0.39% first- and second-cousin marriages in municipalities with less than 50% non-migrants to 4.3% such consanguineous matings in municipalities where 85% or more of the inhabitants are non-migrants. There is also a significant negative correlation (rs=-0.86, N=18) between inbreeding and population density per square km by county in Norway. In rural districts of Norway maximum inbreeding is observed in sparsley populated areas with maximum proportion of non-migrants, and the ratio of second- to first-cousin marriages ranges between 3.4 and 4.1. A similar high ratio (3.7) is also encountered in densely populated trading and industrial municipalities and in the smaller towns, whereas the semi-urban municipalities and the larger towns have the lowest inbreeding recorded and also a low ratio (1.9). The lowest proportion of non-migrants (39.3%) is recorded in the semi-urban municipalities.

Consanguinity↗

PubMed1977

The inbreeding coefficients of the Hadza.

A systematic tabulation is provided of the frequency of different types of inbreeding in the Hadza. Genealogical information was obtained for 931 individuals, alive and dead. Inbreeding was encountered with 165 individuals. There were 49 different types of inbred genealogy. No attempt was made to calculate an average inbreeding coefficient and the reasons for this are given in the text.

Consanguinity↗

PubMedDate not supplied

Matrimonial distance, inbreeding coefficient and population size: Dhangar data.

Data on the distance between the birthplaces of spouses (matrimonial distance) were collected from 2,260 married individuals belonging to 21 endogamous castes of the Dhangar (shepherd) cast-cluster of Maharashtra, India. The general form of the distribution of matrimonial distances is one which is extremely positively skewed and leptokurtic. The percentage of intra-village marriages generally decreases from the southern areas of Maharashtra to the northern areas of the state, as does the inbreeding coefficient. This situation is in conformity with the socio-cultural norms regulating matrimonial choice in south and north India. An attempt has been made to relate the degree of inbreeding to the mean matrimonial distance and population size. The mean matrimonial distance is more useful in predicting the degree of inbreeding than population size.

Consanguinity↗

PubMed1977

Inbreeding estimation from population data: models, procedures and implications.

Four different estimation procedures for models of population structure are compared. The parameters of the models are shown to be equivalent and, in most cases, easily expressed in terms of the parameters WRIGHT calls "F-statistics." We have estimated the parameters of each of these models with data on nine codominant allele pairs in 47 Yanomama villages, and we find that the different estimators for a given parameter all yield more or less equivalent results. F-statistics are often equated to inbreeding coefficients that are definid as the probability of identity by descent from alleles taken to be unique in some founding population. However, we are led to infer from computer simulation and general historical considerations that all estimates from genotype frequencies greatly underestimate the inbreeding coefficient for alleles in the founding population of American Indians in the western hemisphere. We surmise that in the highly subdivided tribal populations which prevailed until the recent advent of civilization, the probability of identity by descent for homologous alleles was roughly 0.5. We consider some consequences of working with the customary, much lower, estimates--0.005 to 0.01--if, on the time scale of human evolution, these represent only a very recent departure from the inbreeding intensity that prevailed before civilization.

Alleles↗

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↗

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↗