Biology subjects

Lucek, K.

Publications and source records attributed to Lucek, K..

7 recordsLinked to original sources

bioRxiv2026

DNA metabarcoding samples from nest soil and beaks outperform samples from talons and faeces when identifying diversity of white-tailed eagle diet in South Greenland

DNA metabarcoding is an emerging approach to study diets across a broad range of species but requires careful optimisation of the sample collection method and substrate used. The suitability of different sample types to identify the diet of the target species remains under investigated. Here, we address these knowledge gaps by collecting four different sample types - faeces, beak swabs, talon swabs, and soil samples - during nest visits of white-tailed eagles (Haliaeetus albicilla) during the 2025 breeding season in South Greenland. We further investigated whether some eagle dietary taxa could act as vectors for microplastic pollution. Our analyses revealed a broad diet, with 25 dietary taxa for white-tailed eagles. Lumpfish (Cyclopterus lumpus) was the most frequently detected dietary taxon in the diet, which was composed of 75 % fish, 19 % birds, and 7 % mammals. Our findings indicate that diets varied strongly between nesting sites. Although each sample type was efficient in capturing diet, soil and beak swabs were most promising for eagles and gave comparable results. On the other hand, faeces provided a distinct dietary profile with a reduced detection of fish, while requiring an increased sample size, and talon swabs missed rare food items. Finally, we recovered microplastic contamination in 33 % of our samples, but no dietary taxon was associated with microplastic pollution. Taken together our results underline the overlooked value of soil from nests to provide dietary information and highlight the necessity to deepen our knowledge of Arctic food webs and their microplastic contamination.

ecology↗

bioRxiv2026

Contrasting signatures of interspecific gene flow in the Atlantic Forest endemic butterfly Heliconius besckei

Gene flow between diverging species can reshuffle genomic variation and greatly influence the speciation process, sometimes reinforcing, sometimes eroding species boundaries. However, the effect of ecological and historical processes on the patterns of introgression remains poorly understood. Here, we focus on the evolutionary history of Heliconius besckei, a geographically restricted butterfly endemic to the Brazilian Atlantic Forest, together with the mimetic H. melpomene nanna, the sympatric non-mimetic H. ethilla narcaea, and its closely related H. numata robigus. Using whole-genome sequencing, genome-wide tests of introgression, demographic modelling and palaeoclimatic species distribution models, we tested the extent and timing of interspecific gene flow in relation to mimicry, ecological context, and changes in geographic overlap. Despite strong genomic differentiation among the four focal Heliconius species, we detected widespread signatures of interspecific gene flow, greatly influenced by geographical overlap. Demographic models including post-divergence gene flow were better supported than strict-isolation models. In addition, genome-wide introgression analyses showed more numerous and larger candidate introgressed regions between H. besckei and H. ethilla narcaea, consistent with recurrent opportunities for exchange between these currently sympatric species. Species distribution models further recovered repeated expansions of suitable habitat for H. besckei during cold periods, providing a potential geographic context for secondary contact within the Atlantic Forest. Together, our results reveal recurrent gene flow occurring under different temporal, geographic, and potentially selective contexts, and show that the evolutionary history of a geographically restricted lineage can be shaped by repeated genetic exchange while substantial species differentiation is maintained.

evolutionary biology↗

bioRxiv2026

Dynamic holocentric genomes facilitate divergent evolutionary paths through chromosomal rearrangements, hybrid dysfunction, and recombination suppression

Theory predicts chromosomal rearrangements (CRs) to promote reproductive isolation and local adaptation by disrupting meiosis and altering recombination landscapes. These processes are especially important in holocentric organisms, whose diffuse centromeres facilitate CRs. Here, we investigated the genomic origins and evolutionary consequences of CRs in the holocentric sedge Carex laevigata, a species with extreme intraspecific chromosome-number variation (2n = 69-84). Establishing chromosome-scale genome assemblies, experimental crosses involving more than one thousand living plants throughout three generations and eight years, linkage mapping, and Quantitative Trait Loci (QTL) analyses, we identified extensive CRs among karyotypically distinct populations. Breakpoint regions of CRs were enriched in GC-rich and repetitive sequences, particularly LTR-Gypsy elements, suggesting recurrent genomic regions prone to structural instability. Inter-cytotype hybrids formed complex meiotic configurations and showed reduced germination success, consistent with hybrid dysfunction associated with increasing chromosomal divergence. Rearranged chromosomes exhibited strong recombination suppression and segregation distortion near breakpoint regions and within inverted segments. QTL analyses further identified fitness-related loci associated with both rearranged and collinear chromosomes. Together, our results corroborate theoretical predictions providing novel empirical evidence that CRs arise preferentially in structurally fragile genomic regions and contribute to genomic divergence through hybrid dysfunction and recombination suppression.

plant biology↗

bioRxiv2026

Genomic insights into the karyotypic radiation of a narrow endemic holocentric plant Carex helodes

Holocentric chromosomes allow rapid genome changes through chromosomal rearrangements such as fissions, fusions, inversions or translocations. The plant genus Carex shows one of the highest rates of karyotypic evolution among holocentric organisms. We studied the genomic patterns underlying chromosomal rearrangements in the karyotypic radiation of the narrow endemic species Carex helodes (2n = 68-75). Comparing genome assemblies of C. helodes from the two karyologically distinct extremes of its European distribution, revealed a striking number of eight chromosomal rearrangements including fusions, translocations and inversions. Genomic breakpoints are gene-poor and TE-rich, corroborating findings in other species and suggesting common genomic characteristics that facilitate the evolution and establishment of chromosomal rearrangements. We identified a chromosomal inversion exhibiting patterns of purifying selection and enrichment in functional genes that potentially mediate rearrangement tolerance. Conversely, another inversion displayed elevated sequence divergence and enrichment in response to temperature stress and phosphate limitation, matching key environmental variables that differ between the study localities. The establishment of chromosomal rearrangements along Carex helodes European populations was likely driven by demographic bottlenecks and distinct genomic features at breakpoints. Our findings provide preliminary evidence on the rearrangement role in population differentiation either as reproductive barriers or as genomic islands of differentiation.

genomics↗

bioRxiv2026

Transposable elements underlie chromosomal fusions and fissions in a highly species-rich group of butterflies

Chromosomal fusions and fissions reshape karyotypes, recombination landscapes and patterns of speciation, yet the molecular mechanisms underlying their formation remain poorly understood. Comparing 37 chromosome-level Erebia genomes, a butterfly genus with exceptionally high rates of chromosomal rearrangements, we identify more than 250 fusion and fission events and characterise over one hundred breakpoints. Breakpoints and homologous regions in the most closely related species with the unfused chromosomal state are significantly enriched for repetitive elements, particularly R1-like LINE retrotransposons. This provides evidence for the implication of a specific LINE family in inter-chromosomal rearrangements that promote species diversification. R1-like elements at breakpoints are longer than copies in other genomic regions, consistent with ectopic recombination requiring sufficient sequence length and similarity. However, the burst of rearrangements in the youngest and most species-rich Erebia clade does not coincide with increased R1-like activity, indicating that repeat dynamics does not solely account for the elevated rates of fusion and fission. Indeed, we detect lineage-specific gains and losses of genes involved in DNA repair and chromatin organisation that coincide with this burst, suggesting a genomic context that facilitates chromosomal fusions and fissions. Our findings refine the role of repetitive elements in inter-chromosomal rearrangements, identify a candidate substrate for ectopic recombination in Lepidoptera, and establish a framework for understanding how karyotypic diversity arises.

evolutionary biology↗

bioRxiv2025

Chromosome Size as a Universal Predictor of Recombination Rate: Insights from Holocentric and Monocentric Systems

Recombination is a fundamental evolutionary process essential for generating genetic diversity, facilitating adaptation, and driving speciation. However, direct measurement of recombination rate remains challenging, as standard methods--such as chiasma counts or genetic linkage maps--are labor-intensive and often infeasible for non-model species. In this study, we identify chromosome number and mean chromosome size as practical proxies for genome-wide recombination rate by analyzing genetic map data from 73 insect species and supplementary analyses of 157 monocentric flowering plants. We confirm the long-standing hypothesis that monocentric species have nearly twice as many crossovers per chromosome as holocentric species, reflecting structural constraints imposed by diffuse centromeres. Using both ordinary and phylogenetically informed Bayesian regression models, we show that recombination rate increases with chromosome number and decreases with mean chromosome size. Crucially, mean chromosome size is a significantly better predictor, particularly in holocentric species. This insight enables recombination rate estimation in thousands of species with known genome and chromosome sizes, thereby allowing hypothesis testing at scales previously unattainable. Building on these results, we present predictive models applicable to poorly studied holocentric plants. Overall, our study highlights the pivotal role of chromosome architecture in recombination evolution and provides an accessible framework for evolutionary genomic research across diverse lineages. Article summaryWhy do some species have more genetic shuffling than others? We investigated 73 insect species with detailed genetic maps and found that mean chromosome size is the best predictor of genome-wide recombination rate, not the number of chromosomes. This means we can now estimate recombination rates even in species where genetic maps are unavailable, using only genome size and chromosome number. We also show that chromosome structure matters--species with a single centromere per chromosome (monocentric) have nearly double the recombination compared to those with diffuse centromeres (holocentric). These insights open new doors for studying evolution across many organisms.

genetics↗

bioRxiv2023

A macroevolutionary role for chromosomal fusion and fission in Erebia butterflies

The impact of large-scale chromosomal rearrangements, such as fusions and fissions, on speciation is a long-standing conundrum. We assessed whether bursts of change in chromosome numbers resulting from chromosomal fusion and fission are related to increased speciation rates in Erebia, one of the most species-rich and karyotypically variable butterfly groups. We established a genome-based phylogeny and employed state-dependent birth-death models to infer trajectories of karyotype evolution across this genus. We demonstrated that rates of anagenetic chromosomal changes (i.e. along phylogenetic branches) exceed cladogenetic changes (i. e. at speciation events), but when cladogenetic changes occur, they are mostly associated with chromosomal fissions rather than fusions. Moreover, we found that the relative importance of fusion and fission differs among Erebia clades of different ages, where especially in younger, more karyotypically diverse clades, speciation is more frequently associated with chromosomal changes. Overall, our results imply that chromosomal fusions and fissions have contrasting macroevolutionary roles and that large-scale chromosomal rearrangements are associated with bursts of species diversification.

evolutionary biology↗