Individual Inbreeding Coefficients Research Articles

Estimation of inbreeding and kinship coefficients via latent identity-by-descent states.

Estimating the individual inbreeding coefficient and pairwise kinship is an important problem in human genetics (e.g. in disease mapping) and in animal and plant genetics (e.g. inbreeding design). Existing methods, such as sample correlation-based genetic relationship matrix, KING, and UKin, are either biased, or not able to estimate inbreeding coefficients, or produce a large proportion of negative estimates that are difficult to interpret. This limitation of existing methods is partly due to failure to explicitly model inbreeding. Since all humans are inbred to various degrees by virtue of shared ancestries, it is prudent to account for inbreeding when inferring kinship between individuals. We present "Kindred," an approach that estimates inbreeding and kinship by modeling latent identity-by-descent states that accounts for all possible allele sharing-including inbreeding-between two individuals. Kindred used non-negative least squares method to fit the model, which not only increases computation efficiency compared to the maximum likelihood method, but also guarantees non-negativity of the kinship estimates. Through simulation, we demonstrate the high accuracy and non-negativity of kinship estimates by Kindred. By selecting a subset of SNPs that are similar in allele frequencies across different continental populations, Kindred can accurately estimate kinship between admixed samples. In addition, we demonstrate that the realized kinship matrix estimated by Kindred is effective in reducing genomic control values via linear mixed model in genome-wide association studies. Finally, we demonstrate that Kindred produces sensible heritability estimates on an Australian height dataset. Kindred is implemented in C with multi-threading. It takes vcf file or stream as input and works seamlessly with bcftools. Kindred is freely available at https://github.com/haplotype/kindred.

Restricted dispersal and inbreeding in a high‐elevation bird across the ‘sky islands’ of the European Alps

AbstractAimHigh‐elevation specialist species are threatened by climate change and habitat loss, and their distributions are becoming increasingly reduced and fragmented. In such a context, dispersal ability is crucial to maintain gene flow among patches of suitable habitat. However, information about dispersal is often lacking for these species, especially for those taxa that are usually considered as good dispersers such as birds. We adopted a landscape genomics approach to investigate dispersal in a climate‐sensitive high‐elevation specialist bird. Our aims were to assess the levels of gene flow within a wide mountain area, and to assess the effects of geographic distance and landscape characteristics on dispersal, by testing the isolation by distance (IBD) hypothesis against the isolation by resistance (IBR) hypothesis.LocationEuropean Alps.Taxon Montifringilla nivalis. MethodsWe sampled individuals from several breeding areas and obtained single nucleotide polymorphism (SNP) data by ddRAD sequencing. We then calculated site‐ and individual level genetic distances and individual inbreeding coefficients. To test IBD versus IBR, we related genetic distances to both geographic distances and different measures of landscape resistance by using maximum likelihood population effects models.ResultsGene flow among breeding areas was partly restricted, and we found support for IBD, indicating that geographic distance limits snowfinch dispersal. Spatial patterns of genetic distances suggested that philopatry strongly contributed to determine the observed IBD. High inbreeding coefficients in several individuals indicated frequent mating among relatives.Main ConclusionsRestricted dispersal and frequent inbreeding within ‘sky island’ systems can also occur in highly mobile species, because their potential ability to cover very large distances can be counteracted by high philopatry levels that are likely related to high dispersal costs. IBD and philopatry will increasingly hinder snowfinch dispersal among suitable areas within the future more restricted and fragmented breeding range, increasing the risks of local extinctions.

Pedigree diversity and implications for genetic selection of Katahdin sheep.

The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (Ne) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the Ne is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current Ne suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term.

Impacts of Population Size and Domestication Process on Genetic Diversity and Genetic Load in Genus Ovis.

In theoretical biology, a prevailing hypothesis posits a profound interconnection between effective population size (Ne), genetic diversity, inbreeding, and genetic load. The domestication and improvement processes are believed to be pivotal in diminishing genetic diversity while elevating levels of inbreeding and increasing genetic load. In this study, we performed a whole genome analysis to quantity genetic diversity, inbreeding, and genetic load across seven wild Ovis species and five domesticated sheep breeds. Our research demonstrates that the genetic load and diversity of species in the genus Ovis have no discernible impact on recent Ne, and three species within the subgenus Pachyceros tend to carry a higher genetic load and lower genetic diversity patterns. The results coincide with these species' dramatic decline in population sizes within the subgenus Pachyceros ~80-250 thousand years ago. European mouflon presented with the lowest Ne, lower genetic diversity, and higher individual inbreeding coefficient but a lower genetic load (missense and LoF). This suggests that the small Ne of European mouflon could reduce harmful mutations compared to other species within the genus Ovis. We showed lower genetic diversity in domesticated sheep than in Asiatic mouflon, but counterintuitive patterns of genetic load, i.e., lower weak genetic load (missense mutation) and no significant difference in strong genetic load (LoF mutation) between domestic sheep and Asiatic mouflon. These findings reveal that the "cost of domestication" during domestication and improvement processes reduced genetic diversity and purified weak genetic load more efficiently than wild species.

A homozygosity-based investigation of the South African feral Tankwa goat population

The Tankwa goat is a known feral goat landrace that originated in the Karoo region of South Africa. These goats are able to thrive with no managerial intervention, and prosper in the harsh, arid conditions that characterizes their natural habitat. This study aimed to use a ROH-approach to describe the Tankwa goat in terms of autozygosity and to identify possible signatures of selection. Genome-wide SNP data for 360 Tankwa goats were used to calculate diversity statistics, detect runs of homozygosity and estimate individual genetic inbreeding coefficients. SNP genotypes of 48 Angora and 40 Dairy individuals were compared using the FST approach to detect signatures of selection. Relatively low minor allele frequency (0.249), and high linkage disequilibrium (r2 = 0.469) levels were estimated for the Tankwa population, with moderate levels of heterozygosity (HE = 0.368; HO = 0.367). The results for both the detected runs of homozygosity and inbreeding estimate, indicates an ancient origin of inbreeding for the Tankwa goats with low levels of autozygosity. Signatures of selection were identified in 50 SNPs, of which 0.1% was considered significant. A total of 49 genes were identified that may possibly be significant in various biological pathways. Three of these genes, namely GJB2, GJB6 and GJA3 on CHI12, were previously associated with adaptation to heat and drought resistance in other breeds. Genes GJB2 and GJB6 are known to be linked to the sensory perception of sound, while GJA3 and OPA3 are linked to visual perception. These genes could play an important role in the survival of an individual existing in a harsh environment in terms of foraging and evading predators. Understanding the genetic background of these genes, as well as the metabolic pathways that they control, could assist in further investigating production efficiency of domesticated species in a climate change environment.

Iterative Level-0: A new and fast algorithm to traverse mating networks calculating the inbreeding and relationship coefficients

In population medical genetics, the study of autosomal recessive disorders in highly endogamous populations is a major topic where calculating the inbreeding and relationship coefficients on mating networks is crucial. However, a challenge arises when dealing with large and complex mating networks, making their traversal difficult during the calculation process. For this calculation, we propose using Iterative Level-0 (IL0) as a new and faster algorithm that traverses mating networks more efficiently. The purpose of this work is to explain in detail the IL0 algorithm and prove its superiority by comparing it with two algorithms based on the best-known algorithms in the area: Depth First Search (DFS) and Breadth First Search (BFS). A Cytoscape application has been developed to calculate the inbreeding and relationship coefficients of individuals composing any mating network. In this application, the IL0 proposal together with DFS-based and BFS-based algorithms have been implemented. Any user can access this freely available Cytoscape application (https://apps.cytoscape.org/apps/inbreeding) that allows the comparison between the IL0 proposal and the best-known algorithms (based on DFS and BFS). In addition, a diverse set of mating networks has been collected in terms of complexity (number of edges) and species (humans, primates, and dogs) for the experiments. The runtime obtained by the IL0, DFS-based, and BFS-based algorithms when calculating the inbreeding and relationship coefficients proved the improvement of IL0. In fact, a speedup study reflected that the IL0 algorithm is 7.60 to 127.50 times faster than DFS-based and BFS-based algorithms. Moreover, a scalability study found that the growth of the IL0 runtime has a linear dependence on the number of edges of the mating network, while the DFS-based and BFS-based runtimes have a quadratic dependence. Therefore, the IL0 algorithm can solve the problem of calculating the inbreeding and relationship coefficients many times faster (up to 127.50) than the two algorithms based on the famous DFS and BFS. Furthermore, our results demonstrate that IL0 scales much better as the complexity of mating networks increases.

Conservation Genetics of Clinch Dace Chrosomus sp. cf. saylori

Clinch Dace (Chrosomus sp. cf. saylori) is a newly recognized and yet-undescribed species of minnow with a restricted and fragmented distribution in the upper Tennessee River basin in southwestern Virginia, USA. We collected Clinch Dace from seven streams and observed variations at nine selectively neutral microsatellite DNA loci to infer population genetic processes and identify units for conservation management. Bayesian cluster analysis showed that three of the seven surveyed populations were genetically distinct, while the other four populations showed signs of recent admixture. Estimated effective population sizes and m-ratios were low within most populations, suggesting loss of alleles due to recent genetic drift. Positive FIS values, high average individual inbreeding coefficients, and high degrees of inferred relatedness among individuals suggested that inbreeding is taking place in some populations. FST values were high, and analysis of molecular variance indicated genetic divergence among populations. These indicators suggest that Clinch Dace populations are subject to the genetic processes that are characteristic of small and isolated populations.

Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line.

With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (FROH ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10-5 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.

Effects of inbreeding and selection on heritability estimates of production traits of Holstein cattle under selection

Inbreeding and selection are forces that affect heritability, important to selection in livestock species. So, this study aims to relate those forces in a Holstein population under selection for superior milk production. Inbreeding coefficients was calculated considering 3 generations, after the individual inbreeding coefficient was calculated, inbred (7.92±2.72) and non-inbred group (0.46±0.38) were formed. The genetic variance was higher for the inbred group and for the residual variance was lower. As result, those variance changes resulted in higher heritability for all traits analyzed for the inbred group. For the levels of inbreeding observed in this study, the selection for higher productions possibly masked the effects of inbreeding.

Evidence of an Absence of Inbreeding Depression in a Wild Population of Weddell Seals (Leptonychotes weddellii).

Inbreeding depression can reduce the viability of wild populations. Detecting inbreeding depression in the wild is difficult; developing accurate estimates of inbreeding can be time and labor intensive. In this study, we used a two-step modeling procedure to incorporate uncertainty inherent in estimating individual inbreeding coefficients from multilocus genotypes into estimates of inbreeding depression in a population of Weddell seals (Leptonychotes weddellii). The two-step modeling procedure presented in this paper provides a method for estimating the magnitude of a known source of error, which is assumed absent in classic regression models, and incorporating this error into inferences about inbreeding depression. The method is essentially an errors-in-variables regression with non-normal errors in both the dependent and independent variables. These models, therefore, allow for a better evaluation of the uncertainty surrounding the biological importance of inbreeding depression in non-pedigreed wild populations. For this study we genotyped 154 adult female seals from the population in Erebus Bay, Antarctica, at 29 microsatellite loci, 12 of which are novel. We used a statistical evidence approach to inference rather than hypothesis testing because the discovery of both low and high levels of inbreeding are of scientific interest. We found evidence for an absence of inbreeding depression in lifetime reproductive success, adult survival, age at maturity, and the reproductive interval of female seals in this population.

Inbreeding evaluation using microsatellite confirmed inbreeding depression in growth in the Fenneropenaeus chinensis natural population.

Understanding inbreeding depressions (IBDs), the effect on the phenotypic performance of inbreeding, is of major importance for evolution and conservation genetics. Inbreeding depressions in aquatic animals were well documented in a domestic or captive population, while there is less evidence of inbreeding depression in natural populations. Chinese shrimp, Fenneropenaeus chinensis, is an important species in both aquaculture and fishery activities in China. To investigate inbreeding depression in natural populations, four Fenneropenaeus chinensis natural populations (Huanghua, Qinhuangdao, Qingdao, and Haiyang) were collected from the Bohai and Yellow seas. Microsatellite markers were used to evaluate individual inbreeding coefficients (F) of all samples. Furthermore, the effects of inbreeding on growth traits were investigated. The results showed marker-based F was continuous and ranged from 0 to 0.585, with an average of 0.191 ± 0.127, and there was no significant difference among the average F of the four populations. Regression analysis using the four populations showed inbreeding had a very significant (p < 0.01) effect on body weight. When analyzing a single population, regression coefficients were also all negative and those in Huanghua and in Qingdao were significant at the level of p < 0.05 and < 0.01, respectively. Inbreeding depressions, expressed as the percent change in body weight per 10% increase in F, were 2.75% in Huanghua, 2.22% in Qingdao, and 3.69% in all samples. This study provided a piece of rare evidence of inbreeding depression in natural populations and also guidance toward the conservation of wild Fenneropenaeus chinensis resources.

Effects of inbreeding on reproduction and fitness traits in a closed flock of Nilagiri sheep, an endangered Indian breed

The objective of this study was to investigate the effect of inbreeding on reproductive and fitness traits in Nilagiri sheep. Information on pedigree of 6430 animals collected during the year of 1965–2015 by Sheep Breeding Research Station (SBRS) in Sandynallah were used for analysis. Inbreeding coefficient (F) was calculated from pedigree information using Wright’s method. The average inbreeding per cent was 1.82% in the whole population studies (6430 animals). The average inbreeding per cent was 3.9% for 3007 no. of inbred animals. The effect of inbreeding on most of the reproduction and fitness traits were significant and depression due to inbreeding was evident.The significant effect of inbreeding on reproduction traits viz., age at first service (AFS), weight at first service (WFS), age at first lambing (AFL) and fitness traits viz., tupping percent (TP), number of lambs weaned per ewe mated (NLWEM), number of lambs weaned per ewe lambing (NLWEL) and total lambs weaned per ewe over lifetime (TLWE) was studied using a general linear model, with individual inbreeding coefficient as covariate. The partial regression coefficient for AFC, WFS, AFL, TP, NLWEM, NLWEL and TLWE were 1.28 days, −0.25 kg, 8.13 days, −0.02%, −0.028, −0.017 and −0.182 per 1 per cent increase in inbreeding for Nilagiri sheep. Survival and litter size were not affected by inbreeding. In general, inbreeding had a depressive effect on most of the reproduction and fitness traits. Inbreeding in the population has to be restricted through methods such as introduction of unrelated animals or following co-ancestry based mating system.

Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse

BackgroundEstimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou’s ancestral, Kalinowski’s ancestral, Kalinowski’s new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.ResultsThe mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated.ConclusionsUltimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.

Variabilidade genética do gado Guzerat criado no norte do Brasil, com base na análise do pedigree

ABSTRACT Genealogical data comprised 45,711 animals born between 1901 and 2016, with 48,127 animals in the pedigree file. Population structure was analyzed in terms of pedigree completeness, individual inbreeding coefficient (F), generation interval (L), rate of inbreeding (ΔF), effective population size (Ne), effective number of founders (ff), and effective number of ancestors (fa). The herd initially consisted of 13 bulls and 14 cows, and there were variations in the number of selected bulls and cows throughout the analyzed period, with 2,575 bulls, 13,691 cows, and 45,711 births recorded at the end of 2016. In total, 48.81% of the cows had only one progeny. Most dams (47.59%) were between three and seven years old, with a mean L in the population of 7.9 years. According to the results, 52.75% of the cows, 44.92% of the bulls, and 63.71% of the calves of the Guzerat breed in the northern region of Brazil showed some degree of inbreeding, with small-magnitude coefficients (0.56, 0.83, and 0.71% for cows, bulls, and calves, respectively). This fluctuation did not hinder the genetic evolution of the herd in the region. The effective population size does not seem to compromise the maintenance of genetic variability in the breed.

A joint likelihood estimator of relatedness and allele frequencies from a small sample of individuals

Abstract As a key parameter in population genetics, relatedness has found wide applications in molecular ecology, evolutionary biology, conservation, forensics and in studies of human inheritable diseases. It is defined as the probability that two individuals share an allele due to recent common ancestry. Many estimators have been developed to estimate relatedness from genotype data. However, they are invariably biased when a sample is small or contains a high proportion of close relatives, because allele frequencies required for inferring relatedness are poorly estimated in both cases under the impracticable and yet indispensable assumption of a large sample of unrelated genotypes. In this study, I develop a likelihood method to estimate relatedness and allele frequencies jointly from a sample of multilocus genotypes. I propose an expectation maximization (EM) algorithm to update allele frequencies and the nine condensed identical by descent (IBD) coefficients () of each pair of sampled individuals iteratively till convergence. Relatedness between and inbreeding coefficients of individuals is then calculated from the estimated nine IBD coefficients. The EM algorithm is also implemented in the reduced non‐inbreeding model () to estimate three condensed IBD coefficients () and relatedness. Using simulated and empirical data, I show that the new method is much less biased and more accurate than previous methods, providing almost unbiased relatedness and inbreeding estimates, when the sampled individuals are few or/and contain many close relatives. The EM algorithm for the likelihood estimator is fast enough to handle a sample with thousands of individuals and millions of markers, thanks to the parallelization using openMP and MPI. The method is implemented in a software package, EMIBD9, that runs on all major computer platforms. This study shows allele frequencies and relatedness, although highly correlated and difficult to disentangle from each other when the only information available is a sample of multilocus genotypes, can be estimated jointly from genotype data of diallelic and multiallelic markers in a likelihood framework. The new method and software are especially useful for analysing small samples (such as ancient samples from museums, or samples from endangered species) and samples with a strong genetic structure.

Population genomic consequences of life-history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers.

Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life-history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200 m geographical gap of no intermediate habitat. Individual inbreeding coefficients (FIS ) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1 km) scales. Finally, YNP adaptation does not reuse a widespread inversion that underlies M. guttatus life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life-history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.

Detection of Cryptic Sex in Automictic Populations: Theoretical Expectations and a Case Study in Cataglyphis Desert Ants

Reproductive strategies are diverse and a whole continuum of mixed systems lies between strict sexuality and strict clonality (apomixis), including automixis, a parthenogenetic mode of reproduction involving a meiosis and increasing homozygosity over generations. These various systems impact the genetic structure of populations, which can therefore be used to infer reproductive strategies in natural populations. Here, we first develop a mathematical model, validated by simulations, to predict heterozygosity and inbreeding in mixed sexual-automictic populations. It highlights the predominant role of the rate of heterozygosity loss experienced during automixis (γ), which is locus dependent. Whenγis low, mixed populations behave like purely sexual ones until sex becomes rare. In contrast, whenγis high, the erosion of genetic diversity is tightly correlated to the rate of sex, so that the individual inbreeding coefficient can inform on the ratio of sexual/asexual reproduction. In the second part of this study, we used our model to test the presence of cryptic sex in a hybridogeneticCataglyphisant where new queens are produced parthenogenetically, leaving males with an apparent null fitness while they are essential to colony development as sperm is required to produce workers. Occasional sexual production of queens could resolve this paradox by providing males some fertile progeny. To determine whether this occurs in natural populations, we simulated genotypic datasets in a population under various regimes of sexual vs. asexual reproduction for queen production and compared the distribution of inbreeding, expected heterozygosity and inter-individual relatedness coefficients with those observed in a natural population ofCataglyphis mauritanicausing microsatellites. Our simulations show that the distribution of inter-individual relatedness coefficients was particularly informative to assess the relative rate of sexual/asexual reproduction, and our dataset was compatible with pure parthenogenesis but also with up to 2% sexual reproduction. Our approach, implemented in an R script, should be useful to assess reproductive strategies in other biological models.

Genetic effects of long-term captive breeding on the endangered pygmy hog.

Long-term captive populations often accumulate genetic changes that are detrimental to their survival in the wild. Periodic genetic evaluation of captive populations is thus necessary to identify deleterious changes and minimize their impact through planned breeding. Pygmy hog (Porcula salvania) is an endangered species with a small population inhabiting the tall sub-Himalayan grasslands of Assam, India. A conservation breeding program of pygmy hog from six founders has produced a multi-generational captive population destined for reintroduction into the wild. However, the impact of conservation breeding on its genetic diversity remained undocumented. Here, we evaluate temporal genetic changes in 39 pygmy hogs from eight consecutive generations of a captive population using genome-wide SNPs, mitochondrial genomes, and MHC sequences, and explore the relationship between genetic diversity and reproductive success. We find that pygmy hog harbors a very low genome-wide heterozygosity (H) compared to other members of the Suidae family. However, within the captive population we find excess heterozygosity and a significant increase in H from the wild-caught founders to the individuals in subsequent generations due to the selective pairing strategy. The MHC and mitochondrial nucleotide diversities were lower in captive generations compared to the founders with a high prevalence of low-frequency MHC haplotypes and more unique mitochondrial genomes. Further, even though no signs of genetic inbreeding were observed from the estimates of individual inbreeding coefficient F and between individuals (FIS) in each generation, the kinship coefficient showed a slightly increasing trend in the recent generations, due to a relatively smaller non-random sample size compared to the entire captive population. Surprisingly, male pygmy hogs that had higher heterozygosity also showed lower breeding success. We briefly discuss the implications of our findings in the context of breeding management and recommend steps to minimize the genetic effects of long-term captive breeding.

Some Genetic and Environmental Effects on Equine Asthma in Polish Konik Horses.

Simple SummaryEquine Asthma (EA) is a blanket term covering inflammatory diseases of the lower airways in horses. It includes mild-to-moderate equine asthma, which affects horses of any age, and severe equine asthma, which is typically seen in horses older than 7 years of. Relationships of the disease’s occurrence with sex or breed have been proven. However, some authors consider genetic background a predisposing factor, due to the fact that in some bloodlines a clinical form of asthma is more frequently observed. This indicates serious breeding and economic consequences. This study aimed to identify the factors affecting predisposition to severe equine asthma in the population of Polish Konik horses and some environmental and inbreeding effects on the disease. Generally, in the observed population, EA is negligibly affected by the factors analysed. Individual inbreeding effects on asthma were not confirmed by various statistical approaches, but significant maternal inbreeding effects were observed. These results are very important from the perspective of the currently implemented genetic resource conservation programme.Current knowledge of the genetic and environmental backgrounds of equine asthma seems to be insufficient, especially for primitive horse breeds. The main objectives of this study were to estimate the effects of sex, birth period, stud, parentage line and inbreeding on asthma morbidity in Polish Konik horses. Records of 274 horses (housed in two studs) were analysed. These animals were allocated to maternal and paternal lines. Individual inbreeding coefficients were extracted from the additive relationship matrix. Horses underwent diagnosis based on observation of the basic symptoms (high frequency of coughing and excessive nasal discharge). Subsequently, some horses (28 individuals) were clinically examined to confirm the earlier observations. Generally, no significant effects of parentage line on heaves morbidity were identified by the use of logistic regression, although the Pearson’s chi-squared test had shown that individuals of some maternal and paternal lines had a predisposition to severe equine asthma. It was concluded that the individual inbreeding level is not associated with the incidence of EA, but a significant effect of the maternal inbreeding coefficient may be observed. It was also found that there is some variability in the incidence of this disease between studs.

Genetic diversity of the Nenets reindeer breed based on microsatellite markers

Research objective To conduct a comparative analysis of the genetic diversity of the Nenets reindeer breed (Rangifer tarandus tarandus) in Russia using a new microsatellite panel. Material and methods used In total, 228 individuals from four populations of the Nenets (47 samples), Yamalo-Nenets (151), and Khant-Mansi (30) regions of the Russian Federation were studied. The new panel consists of 16 microsatellite loci: 10 dinucleotide loci - Rt6, BMS1788, Rt30, Rt1, Rt9, Rt7, Rt24, FCB193, BMS745, NVHRT16 and 6 tetranucleotide STR markers - OheQ, C217, C32, T40, C276, C143. GeneMapper ID-X 1.4 software (Applied Biosystems) used to analyze the obtained data. The statistical analysis was performed in the R package, 3.6.1 version (R Core Team, 2019). Research results For 16 microsatellite loci 132 alleles were found, from 2 alleles (locus C217) to 16 alleles (locus OheQ). The average number of alleles per locus for all samples was 8.25. The smallest number of alleles per sample was observed in the samples of reindeer from the Nen.NAO and Nen.KhMAO, 103 alleles, and the largest from the Nen.YaNAO, 119. Allelic richness (Ar) ranged from 5.85 to 6.25. For each sample, the distribution of individual inbreeding coefficients f was constructed. We can talk about the presence of inbreeding in all samples, since the high values of f indicate a decrease in the heterozygosity of individual genomes in the samples due to inbreeding. The Polymorphism Information Content (PIC) values were calculated for each pair of “locus-sample” which were estimated based on the number and frequency of alleles at the locus. The average PIC value turned out not to be very high: 0.613 ± 0.049. The highest levels of polymorphism were obtained for 3 loci: Rt9 (PIC = 0.906), OheQ (PIC = 0.913), and Rt1 (PIC = 0.920). It is proposed to investigate the polymorphism of microsatellite loci of all four Russian reindeer breeds. The following will be determined for each breed: genetic structure, its effective number, inbreeding coefficient; the degree of differentiation between the breeds has been established. As a result of a detailed analysis we will build a model for the demographic history of the reindeer.