An hidden Markov model to estimate homozygous-by-descent probabilities associated with nested layers of ancestors

Too big to purge: persistence of deleterious Mutations in Island populations of the European Barn Owl (Tyto alba)

A key aspect of assessing the risk of extinction/extirpation for a particular wild species or population is the status of inbreeding, but the origin of inbreeding and the current mutational load are also two crucial factors to consider when determining survival probability of a population. In this study, we used samples from 502 barn owls from continental and island populations across Europe, with the aim of quantifying and comparing the level of inbreeding between populations with differing demographic histories. In addition to comparing inbreeding status, we determined whether inbreeding is due to non-random mating or high co-ancestry within the population. We show that islands have higher levels of inbreeding than continental populations, and that this is mainly due to small effective population sizes rather than recent consanguineous mating. We assess the probability that a region is autozygous along the genome and show that this probability decreased as the number of genes present in that region increased. Finally, we looked for evidence of reduced selection efficiency and purging in island populations. Among island populations, we found an increase in numbers of both neutral and deleterious minor alleles, possibly as a result of drift and decreased selection efficiency but we found no evidence of purging.

A comparative analysis reveals the genomic diversity among 8 Muscovy duck populations

The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China. In the 1990s, the commodity Muscovy duck breed "Crimo," cultivated in Europe, entered the Chinese market for consumption and breeding purposes. Due to the different selective breeding processes, Muscovy ducks have various populational traits and lack transparency of their genetic background. To remove this burden in the Muscovy duck breeding process, we analyzed genomic data from 8 populations totaling 83 individuals. We identify 11.24 million single nucleotide polymorphisms (SNPs) and categorized these individuals into the Fujian-bred and the Crimo populations according to phylogenetic analyses. We then delved deeper into their evolutionary relationships through assessing population structure, calculating fixation index (FST) values, and measuring genetic distances. Our exploration of runs of homozygosity (ROHs) and homozygous-by-descent (HBD) uncovered genomic regions enriched for genes implicated in fatty acid metabolism, development, and immunity pathways. Selective sweep analyses further indicated strong selective pressures exerted on genes including TECR, STAT2, and TRAF5. These findings provide insights into genetic variations of Muscovy ducks, thus offering valuable information regarding genetic diversity, population conservation, and genome associated with the breeding of Muscovy ducks.

Genomic Reconstruction of the Successful Establishment of a Feralized Bovine Population on the Subantarctic Island of Amsterdam

The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19th century and revealed contributions from European taurine and Indian Ocean Zebu in the founder ancestry. Comparative analysis of whole-genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. Unlike some populations that have experienced prolonged reductions in effective population size, we did not observe any significant purging of highly deleterious variants. Interestingly, the population's success in the harsh environment can be attributed to preadaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. The Amsterdam Island cattle offers valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It also sheds light on the unique genetic legacies of feral populations, raising ethical questions according to conservation efforts.

MCMC algorithm based on Markov random field in image segmentation

In the realm of digital image applications, image processing technology occupies a pivotal position, with image segmentation serving as a foundational component. As the digital image application domain expands across industries, the conventional segmentation techniques increasingly challenge to cater to modern demands. To address this gap, this paper introduces an MCMC-based image segmentation algorithm based on the Markov Random Field (MRF) model, marking a significant stride in the field. The novelty of this research lies in its method that capitalizes on domain information in pixel space, amplifying the local segmentation precision of image segmentation algorithms. Further innovation is manifested in the development of an adaptive segmentation image denoising algorithm based on MCMC sampling. This algorithm not only elevates image segmentation outcomes, but also proficiently denoises the image. In the experimental results, MRF-MCMC achieves better segmentation performance, with an average segmentation accuracy of 94.26% in Lena images, significantly superior to other common image segmentation algorithms. In addition, the study proposes that the denoising model outperforms other algorithms in peak signal-to-noise ratio and structural similarity in environments with noise standard deviations of 15, 25, and 50. In essence, these experimental findings affirm the efficacy of this study, opening avenues for refining digital image segmentation methodologies.

Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle

BACKGROUND

Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding.

METHODS

We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (FPED), on the correlation between uniting gametes (FUNI), on the genomic relationship matrix (FGRM), on excess homozygosity (FHET), or on homozygous-by-descent (HBD) segments (FHBD).

RESULTS

FUNI and FGRM were sensitive to used allele frequencies, whereas FHET and FHBD were more robust. We detected significant ID for four traits related to height and length; FHBD and FUNI presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments.

CONCLUSIONS

Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding.

Estimation of inbreeding, between-breed genomic relatedness and definition of sub-populations in red-pied cattle breeds

Currently, enhancing the collaboration between related breeds is of main importance to increase the competitivity and the sustainability of local breeds. One type of collaboration is the development of an across-breed reference population that will allow a better management of local breeds. For this purpose, the genomic relatedness between the local target breed and possible breeds to be included in the reference population should be estimated. In Europe, there are several local red-pied cattle breeds that would benefit from this kind of collaboration. However, how different red-pied cattle breeds from the Benelux are related to each other and can collaborate is still unclear. The objectives of this study were therefore: (1) to estimate the level of inbreeding of the East Belgian Red and White (EBRW), the Red-Pied of the Ösling (RPO) and Dutch red-pied cattle breeds; (2) to determine the genomic relatedness of several red-pied cattle breeds, with a special focus on two endangered breeds: the EBRW and the RPO, and (3) based on the second objective, to detect animals from other breeds that were genomically close enough to be considered as advantageous in the creation of an across-breed reference population of EBRW or RPO. The estimated inbreeding levels based on runs of homozygosity were relatively low for almost all the studied breeds and especially for the EBRW and RPO. This would imply that inbreeding is currently not an issue in these two endangered breeds and that their sustainability is not threatened by their level of inbreeding. The results from the principal component analysis, the phylogenetic tree and the clustering all highlighted that the EBRW and RPO breeds were included in the genomic continuum of the studied red-pied cattle breeds and can be therefore considered as genomically close to Dutch red-pied cattle breeds, highlighting the possibility of a collaboration between these breeds. Especially, EBRW animals were closely related to Deep Red and Improved Red animals while, to a lesser extent, the RPO animals were closely related to the Meuse-Rhine-Yssel breed. Based on these results, we could use distance measures, based either on the principal component analysis or clustering, to detect animals from Dutch breeds that were genomically closest to the EBRW or RPO breeds. This will finally allow the building of an across-breed reference population for EBRW or RPO for further genomic evaluations, considering these genomically closest animals from other breeds.

Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization

Genomic measures of inbreeding based on identical-by-descent (IBD) segments are increasingly used to measure inbreeding and mostly estimated on SNP arrays and whole-genome sequencing (WGS) data. However, some softwares recurrently used for their estimation assume that genomic positions which have not been genotyped are nonvariant. This might be true for WGS data, but not for reduced genomic representations and can lead to spurious IBD segments estimation. In this project, we simulated the outputs of WGS, two SNP arrays of different sizes and RAD-sequencing for three populations with different sizes and histories. We compare the results of IBD segments estimation with two softwares: runs of homozygosity (ROHs) estimated with PLINK and homozygous-by-descent (HBD) segments estimated with RZooRoH. We demonstrate that to obtain meaningful estimates of inbreeding, RZooRoH requires a SNPs density 11 times smaller compared to PLINK: ranks of inbreeding coefficients were conserved among individuals above 22 SNPs/Mb for PLINK and 2 SNPs/Mb for RZooRoH. We also show that in populations with simple demographic histories, distribution of ROHs and HBD segments are correctly estimated with both SNP arrays and WGS. PLINK correctly estimated distribution of ROHs with SNP densities above 22 SNPs/Mb, while RZooRoH correctly estimated distribution of HBD segments with SNPs densities above 11 SNPs/Mb. However, in a population with a more complex demographic history, RZooRoH resulted in better distribution of IBD segments estimation compared to PLINK even with WGS data. Consequently, we advise researchers to use either methods relying on excess homozygosity averaged across SNPs or model-based HBD segments calling methods for inbreeding estimations.

Challenges in quantifying genome erosion for conservation

Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.