Biology subjects

Cumer, T.

Publications and source records attributed to Cumer, T..

16 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↗

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↗

bioRxiv2025

PG-SCUnK: measuring pangenome graph representativeness using Single-Copy and Universal K-mers

BackgroundPangenome graphs integrate multiple assemblies to represent non-redundant genetic diversity. However, current evaluations of pangenome graphs rely primarily on technical parameters (e.g., total length, number of nodes/edges, growth curves), which fail to assess how effectively the graph represents homologous stretches across the integrated assemblies. ResultsWe introduce a novel method to quantitatively assess how well a pangenome graph represents its integrated assemblies. Our method quantifies how many single-copy and universal k-mers from the source assemblies are uniquely and completely represented within the graph nodes. Implemented in the open-source tool PG-SCUnK, this approach identifies the fractions of unique, duplicated, and split k-mers, which correlate with short read mapping rates to the pangenome graph. ConclusionsInsights provided by PG-SCUnK facilitate the selection of appropriate parameters to build optimal pangenome graphs. Availability and implementationA bash implementation of the PG-SCUnK workflow is freely available under the GNU GPLv3 license at https://github.com/cumtr/PG-SCUnK/.

bioinformatics↗

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

The genomic architecture of a continuous color polymorphism in the European barn owl (Tyto alba)

The maintenance of color polymorphism in populations has fascinated evolutionary biologists for decades. Studies of color variation in wild populations often focus on discrete color traits exhibiting simple inheritance patterns, while studies on continuously varying traits remain rare. Here, we studied the continuous white to rufous color polymorphism in the European barn owl (Tyto alba). Using a Genome Wide Association approach on whole-genome data of 75 barn owls sampled across Europe, we identified, in addition to a previously known MC1R mutation, two regions involved in this color polymorphism. We show that the combination of the three explains 80.37% (95% credible interval 58.45 to 100%) of the color variation. Among the two newly identified regions, the one on the sexual chromosome (Z) shows a large signal of differentiation in the Swiss population when contrasting individuals with different morph but the same MC1R genotype. We suggest it may play a role in the sexual dimorphism observed locally in the species. These results, uncovering two new genomic regions, provide keys to better understand the molecular bases of the color polymorphism as well as the mechanisms responsible for its maintenance in the European barn owl at both continental and local scales.

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 bases of insularity and ecological divergence in barn owls (Tyto alba) of the Canary Islands

Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba) is thought to have diverged into a subspecies (T. a. gracilirostris) on the eastern islands, Fuerteventura and Lanzarote. Taking advantage of 40 whole-genomes and modern population genomics tools, we provide the first look at the origin and genetic makeup of barn owls of this archipelago. We show that the Canaries hold diverse, long-standing and monophyletic populations with a neat distinction of gene pools from the different islands. Using new method, less sensitive to structure than classical FST, to detect regions involved in local adaptation to the insular environment, we identified a haplotype-like region likely under positive selection in all Canaries individuals. Genes in this region suggest morphological adaptations to insularity. In the eastern islands, where the subspecies T. a. gracilirostris is present, genomic traces of selection pinpoint signs of locally adapted body proportions and blood pressure, consistent with the smaller size of this population living in a hot arid climate. In turn, genomic regions under selection in the western barn owls from Tenerife showed an enrichment in genes linked to hypoxia, a potential response to inhabiting a small island with a marked altitudinal gradient. Our results illustrate the interplay of neutral and adaptive forces in shaping divergence and early onset speciation.

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↗

bioRxiv2021

Landscape and climatic variations of the Quaternary shaped multiple secondary contacts among barn owls (Tyto alba) of the Western Palearctic

The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a narrow secondary contact zone between the two in Anatolia. Nonetheless, we also show that barn owls re-colonized Europe after the glaciation from two distinct glacial refugia: a western one in Iberia and an eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.

evolutionary biology↗

bioRxiv2021

Unexpected post-glacial colonisation route explains the white colour of barn owls (Tyto alba) from the British Isles

The climate fluctuations of the Quaternary shaped the movement of species in and out of glacial refugia. In Europe, the majority of species followed one of the described traditional postglacial recolonization routes from the southern peninsulas towards the north. Like most organisms, barn owls are assumed to have colonized the British Isles by crossing over Doggerland, a land bridge that connected Britain to northern Europe. However, while they are dark rufous in northern Europe, barn owls in the British Isles are conspicuously white, a contrast that could suggest selective forces are at play on the islands. However, analysis of known candidate genes involved in colouration found no signature of selection. Instead, using whole genome sequences and species distribution modelling, we found that owls colonised the British Isles soon after the last glaciation, directly from a white coloured refugium in the Iberian Peninsula, before colonising northern Europe. They would have followed a yet unknown post-glacial colonization route to the Isles over a westwards path of suitable habitat in now submerged land in the Bay of Biscay, thus not crossing Doggerland. As such, they inherited the white colour of their Iberian founders and maintained it through low gene flow with the mainland that prevents the import of rufous alleles. Thus, we contend that neutral processes likely explain this contrasting white colour compared to continental owls. With the barn owl being a top predator, we expect future research will show this unanticipated route was used by other species from its paleo community.

evolutionary biology↗

bioRxiv2020

A novel assay for tracking carboxylesterase gene amplifications conferring organophosphate resistance in the mosquito Aedes aegypti: from experimental evolution to field application

By altering gene expression and creating paralogs, genomic amplifications represent a key component of short-term adaptive processes. In insects, the use of insecticides can select gene amplifications causing an increased expression of detoxification enzymes, supporting the usefulness of these DNA markers for monitoring the dynamics of resistance alleles in the field. In this context, the present study aims to characterise a genomic amplification event associated with resistance to organophosphate insecticides in the mosquito Aedes aegypti and to develop a molecular assay to monitor the associated resistance alleles in the field. An experimental evolution experiment using a composite population from Laos supported the association between the over-transcription of multiple contiguous carboxylesterase genes on chromosome 2 and resistance to multiple organophosphate insecticides. Combining whole genome sequencing and qPCR on specific genes confirmed the presence of a ~100 Kb amplification spanning at least five carboxylesterase genes at this locus with the co-existence of multiple structural duplication haplotypes. Field data confirmed their circulation in South-East Asia and revealed high copy number polymorphism among and within populations suggesting a trade-off between this resistance mechanism and associated fitness costs. A dual-colour multiplex TaqMan assay allowing the rapid detection and copy number quantification of this amplification event in Ae. aegypti was developed and validated on field populations. The routine use of this novel assay will improve the tracking of resistance alleles in this major arbovirus vector.

evolutionary biology↗

bioRxiv2020

BAdabouM: a genomic structural variations discovery tool for polymorphism analyses

Genomic Structural Variations (SVs) are known to impact the evolution of genomes and to have consequences on individuals fitness. Nevertheless, they remain challenging to detect in whole genome re-sequencing (WGS) data. Lots of methods detecting SVs are described in the literature but they might be hard to install, have non-trivial settings, do not detect all SVs categories and have generally high levels of false positive. Here we introduce BAdabouM, a fast (C written) and easy to install SVs discovery tool. BAdabouM auto evaluates read length, library size and mean coverage to set thresholds specific to each experiment. BAdabouM interprets multiple SVs signatures (reads aligned with a split, non-concordant mapped pairs or uneven coverage) to detect insertions, deletions, copy number variations, inversions, and translocations at single-nucleotide resolution. When compared with two widely used methods on simulated and real datasets, BAdabouM was faster, exhibited a similar accuracy with a good concordance on SVs detected, and detected significantly more insertions. BAdabouM was more reproducible to detect independently SVs across individuals, which is a clear advantage when characterizing population polymorphism. Furthermore, BAdabouM demonstrated a superior ability to detect breakpoints with a base pair resolution. BAdabouM proved to be efficient, fast and accurate to detect SVs, and handle. BAdabouM is a complementary method to be used for a more comprehensive detection of SVs, and is especially suited for studying polymorphism for all types of SVs with a high accuracy.

bioinformatics↗

bioRxiv2020

Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats

The male-specific part of the Y-chromosome is in mammalian and many other species the longest haplotype that is inherited without recombination. By its paternal transmission it has a small effective population size in species with dominant males. In several species, Y-chromosomal haplotypes are sensitive markers of population history and introgression. Previous studies have identified in domestic goats four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic differentiation and several regional variants. In this study we used published whole-genome sequences of 70 male goats from 16 modern breeds, 11 ancient-DNA samples and 29 samples from seven wild goat species. We identified single-copy male-specific SNPs in four scaffolds, containing SRY, ZFY, DBY with SSX3Y and UTY, and USP9Y with UMN2001, respectively. Phylogenetic analyses indicated haplogroups corresponding to the haplotypes Y1B, Y2A and Y2B, respectively, but Y1A was split into Y1AA and Y1AB. All haplogroups were detected in ancient DNA samples from southeast Europe and, with the exception of Y1AB, in the bezoar goat, which is the wild ancestor of the domestic goats. Combining these data with those of previous studies and with genotypes obtained by Sanger sequencing or the KASP assay yielded haplogroup distributions for 132 domestic breeds or populations. The phylogeographic differentiation indicated paternal population bottlenecks on all three continents. This possibly occurred during the Neolithic introductions of domestic goats to those continents with a particularly strong influence in Europe along the Danubian route. This study illustrates the power of the Y-chromosomal haplotype for the reconstructing the history of mammalian species with a wide geographic range.

genetics↗

bioRxiv2018

Double-digest RAD-sequencing: do wet and dry protocol parameters impact biological results?

O_LINext-generation sequencing technologies have opened a new era of research in genomics. Among these, restriction enzyme-based techniques such as restriction-site associated DNA sequencing (RADseq) or double-digest RAD-sequencing (ddRADseq) are now widely used in many population genomics fields. From DNA sampling to SNP calling, both wet and dry protocols have been discussed in the literature to identify key parameters for an optimal loci reconstruction.\nC_LIO_LIThe impact of these parameters on downstream analyses and biological results drawn from RADseq or ddRADseq data has however not been fully explored yet. In this study, we tackled this issue by investigating the effects of ddRADseq laboratory (i.e. wet protocol) and bioinformatics (i.e. dry protocol) settings on loci reconstruction and inferred biological signal at two evolutionary scale using two systems: a complex of butterfly species (Coenonympha sp.) and populations of Common beech (Fagus sylvatica).\nC_LIO_LIResults suggest an impact of wet protocol parameters (DNA quantity, number of PCR cycles during library preparation) on the number of recovered reads and SNPs, the number of unique alleles and individual heterozygosity. We also found that bioinformatic settings (i.e. clustering and minimum coverage thresholds) impact loci reconstruction (e.g. number of loci, mean coverage) and SNP calling (e.g. number of SNPs, heterozygosity). We however do not detect an impact of parameter settings on three types of analysis performed with ddRADseq data: measure of genetic differentiation, estimation of individual admixture, and demographic inferences. In addition, our work demonstrates the high reproducibility and low rate of genotyping inconsistencies of the ddRADseq protocol.\nC_LIO_LIThus, our study highlights the impact of wet parameters on ddRADseq protocol with strong consequences on experimental success and biological conclusions. Dry parameters affects loci reconstruction and descriptive statistics but not biological conclusion for the two studied systems. Overall, this study illustrates, with others, the relevance of ddRADseq for population and evolutionary genomics at the inter- or intraspecific scales.\nC_LI

molecular biology↗