The authors evaluated the relevant literature related to purging, which is the interaction between selection and inbreeding in which the population may eliminate its inbreeding load at least partially. According to the relevant literature, the inbreeding load and the process of purging were evaluated via pedigree methods based on ancestral inbreeding, the inbreeding–purging model, and expressed opportunity of purging, along with genomic methods. Most ancestral inbreeding-related studies were performed in zoos, where only a small proportion of the studied populations show signs of purging. The inbreeding–purging model was developed with Drosophila, and it was used to evaluate different zoo ungulates and Pannon white rabbits. Purging was detected in both studies. The expressed opportunity of purging was applied in Jersey cattle and Pannon white rabbits. In the Jersey cattle, it had an effect of 12.6% for fitness, while in the Pannon white rabbits, the inbreeding load was between 40% and 80% of its original value. The genomic studies also signalled purging, but they also made it clear that, contrary to the detected purging, the evaluated populations still suffered from inbreeding depression. Therefore, especially for domesticated animals, it can be concluded that deliberate inbreeding with the purpose of generating purging is not advocated.

Authors evaluated the relevant literature related to the purging which is the interaction between selection and inbreeding where the population may get rid of its inbreeding load at least partially. The backroad of the relevant theory was given and the available methods were described both based on the conventional quantitative genetic approach (based on genealogy data) and based on the latest genomic methods. The different parameters necessary for signalling purging (highlighting those inbreeding coefficients which are not yet been widely known in animal and veterinary science) were presented together with the relevant results of the literature. The available statistical methods together with the softwares and R packages to calculate various inbreeding coefficients and to determine inbreeding depression and purging were provided. The main results of the different approaches obtained in laboratory ZOO and domesticated populations (lethal equivalents, ancestral inbreeding, Inbreeding-Purging Model, genomic approaches) were summarized and presented. Application possibilities and future prospective of purging was also discussed.

In conserving the genetic diversity of domestic animal breeds, strategies that emphasise between-breed diversity may not be optimal, as they neglect within-breed variation. The aim of the present study was to assess the extent of population subdivision in three Mangalica pig breeds and the contribution of migration to their substructure. Wright’s F_ST coefficient was calculated based on genealogical data with breeding animals born between 1981 and 2023, with three colour variants (Blonde, Swallow-Belly and Red). These Wright’s F_ST coefficients were analysed using multidimensional scaling to reveal the population substructure. The average F_ST coefficient was 0.04 for the Blonde breed and 0.047 for the Swallow-Belly and Red Mangalica breeds, while these parameters were lower in the active herds at 0.03 and 0.04, respectively. The migration of individuals between herds was 61.63% for the Blonde breed and 75.53% and 63.64% for the Swallow-Belly and Red Magalica breeds, respectively. No population substructure was observed in any of the Mangalica breeds, which can be explained by the extensive migration between herds.

In a closed population with a limited population size, mating of related animals is unavoidable. In this study, the genealogy data of a synthetic maternal rabbit breed called Pannon Ka were used to calculate different inbreeding coefficients. The evaluated animals were born between 1995 and 2020, and the pedigree consisted of 5819 animals that originated from 4205 rabbit does and from 1314 rabbit bucks. The pedigree was further extended with 16,013 dummy progeny records in order to calculate litter inbreeding coefficients. Besides the conventional Wright inbreeding coefficients, the so-called ancestral and new inbreeding coefficients were also calculated using the gene dropping method. By the end of the evaluated period, the litter inbreeding increased to almost 11 and 60% for Wright and Ballou inbreeding, while the Kalinowski and the Kalinowski new inbreeding coefficients were 9.25 and 16.67%, respectively. Correlation coefficients were calculated for the does and for the litters. Finally, the effects of pedigree length and completeness were also taken into account using the complete generation equivalents in a partial correlation analysis. Based on the results, it could be seen that the different ancestral inbreeding coefficients had high correlation. Similarly, the conventional Wright inbreeding coefficients showed strong correlation with the new inbreeding coefficients. On the contrary, the correlation between ancestral and new inbreeding coefficients was low. Taking the complete generation equivalent into account did not give unambiguous results. It could be concluded that the different inbreeding coefficients are based on different concepts, and they are clearly different population parameters.

In preserving genetic diversity among domestic animal breeds, the strategies emphasizing be-tween-breed diversity may be not optimal by neglecting within-breed variation. The present study aimed to assess the extent of the population subdivision of Mangalica pigs and the contri-bution of migration intensity to their substructure. Genealogy analysis was performed for breeding animals born between 1981 and 2023 examining three colour variations (Blonde, Swal-low-Belly, and Red). The fixation index (FST) was calculated and evaluated by Multidimensional Scaling and Clustering to expose the population substructure. The average FST is 0.04 for the Blonde and 0.05 for the Swallow-Belly and the Red while in the active herds, these parameters are smaller being 0.03 and 0.04, respectively. The migration of individuals affected 61.63% of the Blonde, 75.53% of the Swallow-Belly, and 63.64% of the Red breed herds. No population sub-structure was found in any Mangalica breed which can be explained by the extensive within breed migration among the herds.

Background: Pedigree-based inference remains central to animal breeding and to conservation, evolutionary, and human-isolate research. However, existing pedigree software offers no integrated support for X-linked analysis, limited partial-decomposition functionality, no standardised pedigree-quality framework, and limited scalability to industry-sized pedigrees. Results: We developed PedXylo, which extends previously published gene-dropping software for ancestral and partial inbreeding analysis into a comprehensive pedigree-analysis platform with integrated pedigree management, quality assessment, and effective-population-size estimation. PedXylo computes classical (F), Kalinowski’s new (F _N ), and ancestral (F _aB , F _aK , AHC) inbreeding coefficients on both autosomes and the X chromosome and provides ancestor-resolved (partial) decomposition of all five coefficient families in both inheritance modes, a combination not currently available in any other tool. Pedigree quality is summarised through complete (CGE) and discrete (DGE) generation equivalents alongside two new metrics: the asymmetrical pedigree equivalents (cAPE and mAPE) and the pedigree tree imbalance (PTI). cAPE and mAPE were only weakly correlated with CGE in the European bison reference population, indicating that they capture information not represented by depth-based metrics alone. Per-individual rates of inbreeding (ΔF and ΔF _X ) and effective population sizes are estimated for both autosomes and the X chromosome. We illustrate these analyses using the Habsburg lineage and a long-term captive European bison pedigree and demonstrate scalability on a 23.2-million-individual Holstein pedigree analysed in approximately 18 h on a single 40-thread workstation. Conclusions: PedXylo provides a unified, scalable framework for pedigree-based inference suitable for routine application in animal breeding and applicable to wide use in conservation, evolutionary, and human-isolate research. By integrating sex-linked analysis, partial decomposition of ancestral coefficients, and new pedigree-quality metrics, it enables hypotheses that could not previously be tested with available pedigree software. The software is freely available with documentation and worked examples.