Biology subjects

Zielinski, P.

Publications and source records attributed to Zielinski, P..

8 recordsLinked to original sources

bioRxiv2025

Citizen science and detailed searches reveal widespread occurrence of hybrid-like Syrian x Great-spotted woodpeckers

The Syrian Woodpecker (hereafter SW) expansion into Europe since the end of the 19th century has enabled its hybridisation with the Great spotted Woodpecker (hereafter GW). This phenomenon, however, has generally been considered sporadic. Here, we examined the occurrence of mixed pairs and hybrids based on our own field observations and citizen science data. Interspecific pairs and individuals of SW and GW were found to be generally scarce but occurred in all parts of the area investigated, not only at the edges of the SWs range. The proportion of hybrid occurrence in woodpecker populations was found to be similar across the whole SWs range in Europe and in both urban and rural populations. However, on a local level, hybrids seemed to be more abundant in certain regions, for example, E Austria, Moravia, SE Poland, W Russia, S Ukraine, Bulgaria, E Greece and W Turkey. Generally, females were 1.4 times more frequent among hybrids. Three major phenotypical hybrid forms were identified: GW-like, SW-like, and intermediate, with first two forms being more frequent in the central and south of Europe respectively. Whereas proportion of the intermediate form was relatively constant across the whole range of hybrid occurrence. The results indicate that hybrids of the two species have become significant part of woodpecker populations and thus should be considered in research and nature conservation projects.

zoology↗

bioRxiv2025

Demographic history inferred from an inversion-rich spruce bark beetle genome

The demographic history of species inferred from whole-genome data provides quantitative insights into key biological parameters such as population size changes and divergence times. Reliable estimates often require data that have not been affected by selection. Extensive research, however, indicates that many species harbour multiple polymorphic chromosomal inversions, which often evolve under different selective pressures. Consequently, inversions can influence genome-wide patterns of variation and subsequent evolutionary inferences. In this study, we used genome-wide data from over 300 spruce bark beetle (Ips typographus) individuals from 23 populations across Europe to reconstruct their demographic history and to investigate the impact of a complex polymorphic inversion landscape (covering approximately 28% of the beetle genome) on demographic inference. We used two complementary methods, Pairwise Sequential Markovian Coalescent (PSMC) and Site Frequency Spectrum (SFS)-based modelling, and revealed a Late Pleistocene divergence ([~]79 kya) between populations from the southern and northern parts of the species European range, and a long-term effective population size of [~]250,000. The southern group underwent significant population expansion after this divergence event, whereas the northern group expanded during the Holocene ([~]7 kya). Recent population size estimates suggest that the southern group is twice as large as the northern group. Neglecting the presence of chromosomal inversions did not significantly affect the model selection procedure and resulted in relatively small biases in the estimated demographic parameters. This study provides information on the historical population dynamics of the spruce bark beetle and improves our understanding of the influence of a complex genomic architecture on the inference of evolutionary history.

evolutionary biology↗

bioRxiv2025

Selection inference in a complex genomic landscape: the role of inversions in the spruce bark beetle

Understanding the genetic basis of adaptation is a key objective in evolutionary biology. Although advances in genomic selection scans have greatly improved our ability to detect signatures of adaptation, distinguishing true signals from false positives remains challenging. This task is particularly difficult in regions of reduced recombination, such as polymorphic inversions. In this study, we examine the genome-wide landscape of selection in the European spruce bark beetle (Ips typographus), Europes most destructive forest pest, which has one of the most complex inversion-associated recombination landscapes known. Using simulation-based analyses and whole-genome resequencing data from 312 individuals across 23 populations, we applied two complementary selection scan methods (nSL and {Lambda}) to assess how inversions influence the detection of adaptive signals. Simulations revealed that the two selection scan methods differ in their susceptibility to false-positive signals within inversions and that partitioning data by inversion genotype (i.e., homozygote classes) can substantially reduce these errors. Consistent with the results of our simulations, our empirical data showed that inversions are highly enriched for selection signals when all inversion genotypes are analyzed but are depleted when only homozygotes are considered. This demonstrates that focusing on homozygote genotypes allows for a more precise identification of putative selection targets and haplotype-specific signals, as it overcomes the confounding effects of suppressed recombination in heterokaryotypic individuals. In contrast, the detection of selection in collinear regions was largely unaffected by the presence of inversions. Our findings highlight that inversions may play an important role in shaping adaptation, underscoring the need to account for species-specific genomic architecture when interpreting signals from selection scans. Author summaryDetecting the genetic basis of adaptation is one of the main goals in evolutionary biology. However, it is often difficult to tell whether selection signals identified by genome scans truly reflect natural selection signatures or are simply artefacts of genome structure. In this study, we examined how polymorphic inversions affect the detection of selection in the European spruce bark beetle, one of Europes most destructive forest pests. First, we assessed two selection scan methods using simulation approach. Second, we tested the influence of polymorphic inversion on the selection inference using genome-wide data from 23 beetle populations. We showed that inversions can create false signals of selection when all individuals are analyzed together but by separating individuals according to their inversion genotypes, we were able to distinguish potential adaptive regions from false positives. Our results demonstrate that accounting for genomic architecture is crucial for identifying selection signatures and provide practical guidelines for studying species with inversion-rich genomes.

evolutionary biology↗

bioRxiv2024

On the ecology of Acinetobacter baumannii - jet stream rider and opportunist by nature

The natural reservoirs of the nosocomial pathogen Acinetobacter baumannii are not well defined. We previously identified white storks as a model system to study the ecology of A. baumannii. Having screened more than 1,300 white stork nestlings over a period of six years across different regions of Poland and Germany (overall isolation rate of [~]29.5%), including food chain analyses and environmental samplings, we come up with a detailed picture of the dynamics and diversity of A. baumannii in their natural habitats. Adult storks, rather than being stably colonized with strains of A. baumannii which are successively transferred to their offspring, instead initially encounter these bacteria while foraging. Among their common food sources, consisting of earthworms, small mammals, and insects, we identified earthworms as a potential source of A. baumannii, but more so the associated soil as well as plant roots. Through this, hotspot soil and compost habitats were identified which enable population dynamics to be studied over the course of the year. We demonstrate that sterilized plant material is rapidly colonized by airborne A. baumannii suggesting they patrol to search for novel habitats, being opportunist by nature. The prevalence of A. baumannii exhibited a strong seasonality and peaked during summer. The strains we collected in Poland and Germany represent more than 50% of the worldwide known diversity in terms of the intrinsic OXA-51-like {beta}-lactamase. A set of [~]400 genomes was determined and compared to a diverse set of publicly available genomes. Our pan-genome estimate of the species ([~]51,000 unique genes) more than doubles the amount proposed by previous studies. Core-genome based phylogenetic analyses illustrated numerous links between wildlife isolates and hospital strains, including ancient as well as recent intercontinental transfer. Our data further suggest massive radiation within the species early after its emergence, matching with human activity during the Neolithic. Deforestation in particular seemed to set the stage for this bloom as we found that forests do not provide conducive conditions for the proliferation of A. baumannii. In contrast, wet and nutrient-rich soil alongside rivers sampled during the summer can yield an isolation rate of [~]30%. Linking published work on the interaction between A. baumannii and fungi and on aspergillosis as a major cause of mortality in white stork nestlings to our findings, we hypothesized that fungi and A. baumannii share a long history of coevolution. Interaction studies revealed the capability of A. baumannii to adhere to fungal spores and to suppress spore germination. Taken together, the intrinsic resistance endowment and potential to acquire antibiotic resistance can be explained by coevolution with antibiotic-producing fungi and other microorganisms within soil, and resistance to desiccation stress and radiation can be interpreted in the light of intercontinental hitchhiking through fungal spores. Originality - SignificanceThe ecology of the nosocomial pathogen Acinetobacter baumannii remains poorly understood outside the hospital. Here, we present the most comprehensive study on its environmental biology to date, after having collected more than 1,450 independent isolates of which around 400 were whole genome-sequenced. This study more than doubles the size of the pan-genome of the species, illustrating both the diversity of our collection and the bias of previous work, but also the bottleneck for the establishment of lineages within the hospital environment. We reached isolation rates of about 30% both in white stork (Ciconia ciconia) nestlings and in soil samples when considering for sampling all preferences of A. baumannii we uncovered. Thus, it is now possible to study the ecology and evolution of A. baumannii in nature at an unprecedented temporal and spatial resolution. We describe the worldwide spread of A. baumannii lineages in nature as an ancient phenomenon that even surpasses that of human-associated bacteria in magnitude. This is likely due to airborne spread, putatively facilitated by association with fungal spores. We propose that A. baumannii is an opportunist by nature, using airborne patrolling to rapidly enter new suitable habitats consisting of organic matter in early stages of decomposition. Our collective data suggest that A. baumannii, early after its speciation, went through massive radiation during the Neolithic, likely due to deforestation, settlement and farming producing numerous favorable habitats. Their natural lifestyle, which requires rapid adaptability to various habitats as well as tolerance to desiccation, radiation and antibiotic stress, perfectly predispose these opportunistic pathogens to establish within the hospital setting. Comparison of genomes from environmental and clinical isolates will now enable studies of the adaptive evolution of environmental bacteria towards multidrug-resistant opportunistic pathogens.

microbiology↗

bioRxiv2023

Complex genomic landscape of inversion polymorphism in Europe's most destructive forest pest

In many species, polymorphic inversions underlie complex phenotypic polymorphisms and facilitate local adaptation in the face of gene flow. Multiple polymorphic inversions can co-occur in a genome, but the prevalence, evolutionary significance, and limits to complexity of genomic inversion landscapes remain poorly understood. Here, we examine genome-wide variation in one of Europes most destructive forest pests, the spruce bark beetle Ips typographus, scan for polymorphic inversions, and test whether inversions are involved in key adaptations in this species. We analyzed 240 individuals from 18 populations across the species European range and, using a whole-genome resequencing approach, identified 27 polymorphic inversions covering approximately 28% of the genome. The inversions vary in size and in levels of intra-inversion recombination, are highly polymorphic across the species range, and often overlap, forming a complex genomic architecture. We test several mechanisms, including directional selection, overdominance and associative overdominance that can contribute to the maintenance of inversion polymorphisms in the genome. We show that the heterogeneous inversion landscape is likely maintained by the combined action of several evolutionary forces and that inversions are enriched in odorant receptor genes encoding key elements of recognition pathways for host plants, mates, and symbiotic fungi. Our results indicate that the genome of this major forest pest of growing social, political, and economic importance harbors one of the most complex inversion landscapes described to date posing a question about limits of genomic architecture complexity.

evolutionary biology↗

bioRxiv2019

Pervasive introgression of MHC genes in newt hybrid zones

Variation in the vertebrate major histocompatibility complex (MHC) genes is crucial for fighting pathogen assault. Because new alleles confer a selective advantage, MHC should readily introgress between species, even under limited hybridization. Using replicated transects through two hybrid zones between strongly reproductively isolated newts, we demonstrated recent and ongoing MHC introgression. Its extent correlated with the age of contact. In the older zone, MHC similarity between species within transects exceeded that of between transects within species, implying pervasive introgression - a massive exchange of MHC genes, not limited to specific variants. In simulations, the observed pattern emerged under the combined action of balancing selection and hybridization, but not when these processes acted separately. Thus, massive introgression at advanced stages of divergence can introduce novel and restore previously lost MHC variation, boosting the adaptive potential of hybridizing taxa. In consequence, MHC genes may be the last to stop introgressing between incipient species.

evolutionary biology↗

bioRxiv2019

Time elapsed between choices in a probabilistic task correlates with repeating the same decision.

Reinforcement learning causes an action that yields a positive outcome more likely to be taken in the future. Here, we investigate how the time elapsed from an action affects subsequent decisions. Groups of C57BL6/J mice were housed in IntelliCages with access to water and chow ad libitum; they also had access to bottles with a reward: saccharin solution, alcohol or a mixture of the two. The probability of receiving a reward in two of the cage corners changed between 0.9 and 0.3 every 48 h over a period of ~33 days. As expected, in most animals, the odds of repeating a corner choice were increased if that choice was previously rewarded. Interestingly, the time elapsed from the previous choice also influenced the probability of repeating the choice, and this effect was independent of previous outcome. Behavioral data were fitted to a series of reinforcement learning models. Best fits were achieved when the reward prediction update was coupled with separate learning rates from positive and negative outcomes and additionally a "fictitious" update of the expected value of the nonselected choice. Additional inclusion of a time-dependent decay of the expected values improved the fit marginally in some cases.

animal behavior and cognition↗

bioRxiv2016

Isolation and Gene Flow in a Speciation Continuum in Newts

Because reproductive isolation often evolves gradually, differentiating lineages may retain the potential for genetic exchange for prolonged periods, providing an opportunity to quantify and understand the fundamental role of gene flow during speciation. Here we delimit taxa, reconstruct the phylogeny and infer gene flow in newts of the Lissotriton vulgaris species complex based on 74 nuclear markers sampled from 127 localities. We demonstrate that distinct lineages along the speciation continuum in newts exchange nontrivial amounts of genes, affecting their evolutionary trajectories. By integrating a wide array of methods, we delimit nine taxa and show that two principle factors have driven their genetic differentiation: time since the last common ancestor determining levels of shared ancestral polymorphism, and shifts in geographic distributions determining the extent of secondary contact. Post-divergence gene flow, indicative of evolutionary non-independence, has been most extensive between sister and non-sister taxa in Central Europe, while four southern European lineages have acquired the population genetic hallmarks of independent species (L. graecus, L. kosswigi, L. lantzi, L. schmidtleri). We obtained strong statistical support for widespread mtDNA introgression, previously suggested by discordance between mtDNA phylogeny and morphology. Our study suggests that long-term evolution in structured populations that may periodically exchange genes may be common: although some of these populations may become extinct or fuse, others will acquire complete reproductive isolation and will carry signatures of this complex history in their genomes.

evolutionary biology↗