Biology subjects

Topaloudis, A.

Publications and source records attributed to Topaloudis, A..

8 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↗

bioRxiv2024

The recombination landscape of the barn owl, from families to populations

Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of recombination landscapes are lacking due to methodological limitations and a dearth of appropriate data. Linkage mapping based on familial data gives unbiased sex-specific broad-scale estimates of recombination while linkage disequilibrium (LD) based inference based on population data provides finer resolution data albeit depending on the effective population size and acting selective forces. In this study, we use a combination of these two methods, using a dataset of whole genome sequences and elucidate the recombination landscape for the Afro-European barn owl (Tyto alba). Linkage mapping allows us to refine the genome assembly to a chromosome-level quality. We find subtle differences in crossover placement between sexes that leads to differential effective shuffling of alleles. LD based estimates of recombination are concordant with family-based estimates and identify large variation in recombination rates within and among linkage groups. Larger chromosomes show variation in recombination rates while smaller chromosomes have a universally high rate which shapes the diversity landscape. We also identify local recombination hotspots in accordance with other studies in birds lacking the PRDM9 gene. However these hotspots show very little evolutionary stability when compared among populations with shallow genetic differentiation. Overall, this comprehensive analysis enhances our understanding of recombination dynamics, genomic architecture, and sex-specific variation in the barn owl, contributing valuable insights to the broader field of avian genomics. Article summaryTo study recombination events we look either in family data or in population data, with each method having advantages over the other. In this study we use both approaches to quantify the barn owl recombination landscape. We find that differences exist between sexes, populations and chromosomes.

genomics↗

bioRxiv2023

Where and when local adaptation happens: lessons from the European barn owl (Tyto alba)

Although local adaptation influences species distributions, its role in driving evolutionary resilience under climate change remains unclear. Current predictive models focus on genetic adaptation to present climates, providing limited insight into future adaptive capacity. We hypothesise that historical responses to climatic shifts can reveal future adaptive potential. Combining ecological niche modelling and genomic analyses, we investigated spatiotemporal patterns and mechanisms of local adaptation of the Western Palearctic barn owl (Tyto alba). Ecological modelling revealed that barn owls now occupy a broader climatic niche than during the Last Glacial Maximum. Genomic analyses indicated ongoing adaptation, with regions under selection linked to environmental factors across all populations. Our findings demonstrate that local adaptation drives evolutionary changes across populations, enabling colonisation of new habitats and shaping responses to climate change in resident populations. We demonstrate that standing genetic diversity plays a crucial role in adaptation to past, present, and future environmental shifts.

evolutionary biology↗

bioRxiv2021

Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean

The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. As a result, apparently identical islands may harbour populations with contrasting histories. Here, we use whole genome sequences of 65 barn owls to investigate the patterns of inbreeding and genetic diversity of insular populations in the eastern Mediterranean Sea. We focus on Crete and Cyprus, islands with similar size, climate and distance to mainland, that provide natural replicates for a comparative analysis of the impacts of microevolutionary processes on isolated populations. We show that barn owl populations from each island have a separate origin, Crete being genetically more similar to other Greek islands and mainland Greece, and Cyprus more similar to the Levant. Further, our data show that their respective demographic histories following colonisation were also distinct. On the one hand, Crete harbours a small population and maintains very low levels of gene flow with neighbouring populations. This has resulted in low genetic diversity, strong genetic drift, increased relatedness in the population and remote inbreeding. Cyprus, on the other hand, appears to maintain enough gene flow with the mainland to avoid such an outcome. Our work provides a comparative population genomic analysis of the effects of neutral processes on a classical island-mainland model system. It provides empirical evidence for the role of stochastic processes in determining the fate of diverging isolated populations.

evolutionary biology↗