Biology subjects

Almasi, B.

Publications and source records attributed to Almasi, B..

9 recordsLinked to original sources

bioRxiv2026

A chromosome-level, haplotype-resolved genome assembly for the barn owl, Tyto alba

Recent advances in long-read sequencing have enabled near telomere-to-telomere (T2T) assemblies across diverse taxa. However, avian genomes remain challenging due to numerous microchromosomes, small, typically < 20Mb, elements that are gene-, GC-, and repeat-rich. As a consequence, microchromosomes are often missing from genome assemblies. Here, we present a chromosome-level, haplotype-resolved genome assembly for the Western barn owl (Tyto alba). Using a trio-binning strategy with Illumina parental reads combined with PacBio HiFi and Oxford Nanopore Technologies data, we generated two phased contig sets. These were scaffolded into 40 linkage groups using a linkage map. Comparative analyses identified unplaced HiFi scaffolds corresponding to microchromosomes, which we integrated into six additional microchromosomes using long reads information. The two assemblies present 46 chromosomes, matching the karyotype of the species. They exhibit strong synteny between parental haplotypes, except for a [~]38 Mb complex region on chromosome 7 containing nested inversions. This high-quality reference provides the first haplotype-resolved and chromosome-level genome for Strigiformes, enabling fine-scale studies of structural variation and avian genome evolution.

genomics↗

bioRxiv2026

The effect of age and sex on the rate of de novo mutations in barn owls

The rate of new mutations is the ultimate source of genetic variation, and thus, a fundamental quantity in evolution. Mutation rates vary across the tree of life, influenced by selection pressures and life-history traits. Within species, mutation rates and types show subtle differences between sexes as well as a positive association with parental age. Most of the direct estimates come from a few mammal species, often primates, and their generality has not been fully realised. Using 33 parent-offspring trios, we investigate the mutation rate in the barn owl (Tyto alba) and show that this species has a mutation rate of 5.6 x 10-9, matching rates of passerine species with a similar generation time of 2-3 years. Using different phasing methods we show that fathers pass on twice as many mutations as mothers and identify subtle differences in the sex-specific spectra of mutations. We also find that the number of mutations increases with paternal age, bringing direct evidence for germline senescence in birds. While across-species mutation rates and types appear conserved, the potential for within species variation due to age is substantial.

evolutionary biology↗

bioRxiv2025

Benchmarking imputation accuracy in the presence or absence of a reference panel

Whole genome sequencing (WGS) of a large number of samples is costly. Solutions to reduce this cost include targeting a proportion of the genome (e.g. SNP arrays) or lowering the sequencing depth (low-coverage WGS, lcWGS) but both solutions suffer from either genotype missingness or uncertainty. Genomic imputation addresses this problem by inferring missing or uncertain genotypes using a collection of high quality genomic data (a reference panel). However, certain methods can impute a lcWGS dataset without a reference panel. Because the investment into generating a reference panel can be prohibitively expensive in non-model species, a benchmarking of the accuracy of these alternative methods of imputation can help inform study design. Here, we imputed a dataset of 2800 lcWGS in the presence and absence of a reference panel of 502 samples. We used 32 individuals sequenced at both high and low coverage to estimate the accuracy of each method and explored the limitations of lcWGS sample size and reference panel size. Although the best results were achieved with a large reference panel, using only a lcWGS dataset showed accurate imputation, when over 500 samples were used and we account for missing data and low frequency alleles. In addition, imputing with or without a reference panel gave similar results in a GWAS for a polygenic trait but required some quality control in the identification of homozygous-by-descent segments. Thus, while using a reference panel remains the ideal approach, imputation in suitably large lcWGS datasets can provide sufficient accuracy given proper quality control.

genomics↗

bioRxiv2025

Genomic bases of short-term evolution in the wild revealed by long-term monitoring and population-scale sequencing

Understanding how wild populations adapt to rapid environmental change requires linking phenotypic evolution to its genomic basis over contemporary timescales. This remains challenging because genetic and environmental effects are often intertwined. Here, we leverage a 30-year study of Swiss barn owls (Tyto alba) to explore this process. During this period, owls have evolved darker plumage and increased spottiness, two melanin-based traits associated with fitness. Whole-genome sequencing of 3,102 individuals reveals that these traits are largely controlled by few loci of major effect with partially overlapping architectures. Temporal allele frequency analyses show subtle but consistent shifts at these loci. Simulations indicate that genetic drift alone cannot explain these changes, whereas models incorporating selection do. Our findings demonstrate that selection on a small number of loci can drive rapid phenotypic evolution in the wild. This work underscores the adaptive potential of natural populations and the value of long-term genomic monitoring under accelerating climate change.

evolutionary biology↗

bioRxiv2025

Growth effects and the underlying genetic architecture of inbreeding depression in a wild raptor

1Despite its potentially devastating effects, the prevalence and underlying mechanisms of inbreeding depression in wild populations are still relatively under-explored. Here, we use whole-genome sequence data from >3,000 wild barn owls from Switzerland to investigate the presence, severity, and genetic architecture of inbreeding depression in three morphological traits. Using a combination of linear models (accounting for age) and non-linear models (to measure growth effects) we clearly show inbreeding depression is present in this population. Moreover, by breaking-down the timing of the effects we also have a better ability to detect inbreeding depression, as in some traits we find that it manifests during juvenile growth, and in others during adulthood. To our knowledge this is the first study to show direct evidence for inbreeding depression during the crucial early life weight gain period in a wild animal. We further show that certain trait-specific patterns may reflect differences in environmental influences across life stages, as we find that heritability is often lower before adulthood. We also use two classes of genomic inbreeding coefficients: FROH and FUniW, and while the directionality of effects is equivalent, the strength of evidence regarding the presence of inbreeding depression differs depending on the coefficient used. This discrepancy might give some insight into the frequency distribution of responsible variants, as each coefficient weights variants differently based on their population frequencies. Finally, an assessment of local genomic inbreeding effects highlights a handful of regions with significantly deleterious effects, alongside many regions with a smaller contribution to the observed inbreeding depression. Overall, we provide a comprehensive overview of the effects of inbreeding in this wild population, highlighting the dynamic interplay between environmental influences and the selection pressure against inbred individuals.

evolutionary biology↗

bioRxiv2023

Stealth hunters: landing force predicts hunting success in Barn Owls

Predator-prey arms races have led to the evolution of finely-tuned disguise strategies. While the theoretical benefits of predator camouflage are well established, no study has yet been able to quantify its consequences for hunting success in natural conditions. We used high-resolution movement data to quantify how barn owls (Tyto alba) conceal their approach when using a sit-and-wait strategy. We hypothesized that hunting barn owls would modulate their landing force, potentially reducing noise levels in the vicinity of prey. Analysing 87,957 landings by 163 individuals equipped with GPS tags and accelerometers, we show that barn owls reduce their landing force as they approach their prey, and that landing force predicts the success of the following hunting attempt. Landing force also varied with the substrate, being lowest on man-made poles in field boundaries. The physical environment therefore affects the capacity for sound camouflage, providing an unexpected link between predator-prey interactions and land-use. Finally, hunting strike forces in barn owls were the highest recorded in any bird, relative to body mass, highlighting the range of selective pressures that act on landings and the capacity of these predators to modulate their landing force. Overall, our results provide the first measurements of landing force in a wild setting, revealing a new form of motion-induced sound camouflage and its link to hunting success.

animal behavior and cognition↗

bioRxiv2020

Experimental manipulation of body size alters senescence in hydra

Body size has a fundamental impact on the ecology and physiology of animals. Large size, for instance, is often associated with increased fecundity and reproductive success. A persistent correlation between body size and individual longevity is also observed across the animal world, although this relationship proved difficult to understand due to the inseparability of body size from growth rate and the widespread collinear relationship between body size with other life history traits. Here, we used Hydra oligactis, a freshwater cnidarian with high tissue plasticity and inducible ageing as an experimental system to understand the causal roles of body size on reproduction and senescence. We first show that large size predicts accelerated sexual development, increased fecundity and reduced survival in a population sample of this species kept under common garden conditions in the laboratory. Next, using phenotypic engineering, we experimentally increased or decreased body size by reciprocally grafting pieces of the body column differing in size between hydra polyps. Experimentally reduced body size was associated with delayed sexual development and reduced fecundity. In parallel, post-reproductive survival was significantly higher in polyps with reduced size. These results suggest that small hydra can physiologically detect their reduced body size and adjust reproductive decisions to achieve a higher post-reproductive survival. Our observations offer a new perspective on why smaller individuals within a species live longer by suggesting a growth-independent link between body size, reproduction and senescence.

evolutionary biology↗

bioRxiv2019

Survival of adult barn owls is linked to corticosterone levels

Glucocorticoid hormones, such as corticosterone, are fundamental in the translation of external stimuli into physiological adjustments that promote the survival of an organism in face of changes in its environment. At baseline levels, corticosterone is crucial in regulating daily life metabolism and energy expenditure, whereas the acute corticosterone response promotes short-term physiological and behavioral responses to unpredictable environmental challenges. Given their different physiological effects and their role in mediating fitness components, it is still unclear whether and how inter-individual variation in baseline corticosterone levels and acute stress-response levels can affect the survival of organisms. We used 13 years of capture-recapture and dead recovery data combined with 11 years of corticosterone measurements taken on breeding barn owls (Tyto alba) to investigate how survival probability varies in relation to baseline and stress-induced corticosterone levels. Our study shows that males with a higher level of both baseline and stress-induced corticosterone levels have a higher probability of surviving than individuals with lower corticosterone levels. In females, survival probability was higher in individuals presenting elevated stress-induced corticosterone levels but was not significantly associated to baseline corticosterone levels. Our results suggest that in the barn owl the stress-induced corticosterone response is a better proxy of adult survival than baseline corticosterone levels. Further studies investigating the link between corticosterone levels and different fitness components as well as the environmental factors (e.g. weather, development conditions, disease and predation risk) leading to such endocrine phenotypes are needed to identify the costs and benefits of presenting high and low corticosterone profiles.

evolutionary biology↗

bioRxiv2019

Reproductive success in the barn owl is linked to partner compatibility in glucocorticoid levels

In biparental species, reproductive success depends not only on the quality of the parents, the care they each provide and many environmental factors such as territory quality and food availability, but also on the ability of the parents to collaborate and divide reproductive tasks. Because hormones, such as corticosterone (CORT), modulate physiological and behavioural functions that are associated to reproductive success, hormonal compatibility between pair members is likely to have consequences on reproductive success. Here, we investigated in the barn owl (Tyto alba) whether baseline and stress-induced CORT levels are correlated between breeding partners and whether this correlation is associated to fitness parameters (i.e., clutch size, offspring number and body mass). We found that the combination of CORT levels in the two partners predicts reproductive parameters. Pairs with similar baseline CORT levels during incubation produced more fledglings than pairs with dissimilar baseline CORT levels. On the other hand, pairs showing dissimilar stress-induced CORT responses during the period of offspring rearing produced more fledglings than pairs with similar stress-induced responses. Offspring body mass was associated only with maternal (baseline and stress-induced) CORT levels and depended on the context with baseline CORT being potentially adjusted to environmental conditions but also to the energetic demand of reproduction. Hence, to produce large broods good quality mothers might increase their baseline CORT to meet the energetic demand of the brood, while mothers in unfavourable habitats may have smaller broods but still need to increase baseline CORT to cope with the environmental challenges. Taken together, the results show that the association between parental CORT levels and reproductive success are context-dependent and rely on the combination of parental CORT levels. Assuming that CORT levels reflect investment in parental care, our study suggests that parents coordinate their reproductive activities in a complex way to ensure a high reproductive success.

evolutionary biology↗