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Feldmeyer, B.

Publications and source records attributed to Feldmeyer, B..

At least 19 recordsLinked to original sources

Climate change intensifies rapid genomic selection beyond the ancestral niche of Fagus sylvatica

As climate change accelerates, the persistence of long-lived organisms increasingly depends on their capacity to adapt in situ. While phenotypic plasticity provides an immediate buffer, it remains uncertain whether forest trees can evolve rapidly enough to track shifting climatic niches. Here, we investigate the adaptive potential of European beech (Fagus sylvatica L.), a keystone temperate species, by leveraging different growth classes as a quasi-time-series. This approach allows us to compare growth classes established under the relatively stable climate of the early 20th century against those regenerating under contemporary warming (+1.1{degrees}C global mean temperature increase). Integrating pool-seq data from three growth classes across 43 sites in Germany with satellite-derived environmental stress indicators, we characterised past, current and projected future climate-driven selection. We detected rapid, genome-wide selective sweeps between the oldest and youngest growth classes, particularly in sites already exceeding their historical climatic niche (defined as the 95% confidence interval of pre-warming conditions). Notably, selection signatures have shifted over time: while older classes show signatures related to biotic interactions, younger cohorts exhibit intense selection on genes managing abiotic heat and drought stress. In the warmest regions, we estimated exceptionally high selection coefficients (s{approx}2), suggesting intense selection where beech trees exceed their ancestral niche. In older growth classes, distance and geology account for genetic differences between populations but in young growth classes climate is the primary factor, highlighting the importance of climate change. However, predictive modelling reveals a critical threshold to this resilience. While adaptive potential appears sufficient to maintain population persistence under low-emission scenarios (SSP1-2.6), high-emission trajectories (SSP5-8.5) are projected to rapidly outpace the species evolutionary capacity. These findings demonstrate that while trees can undergo remarkably rapid genomic shifts, the sheer velocity of unmitigated climate change threatens to exceed the fundamental limits of forest adaptation.

evolutionary biology↗

Pervasive and dynamic release of Cryptic Genetic Variation in Chironomus riparius: Rethinking adaptation in fluctuating environments

The interplay between phenotypic plasticity and cryptic genetic variation (CGV) is crucial for understanding adaptation, yet the prevailing paradigm suggests CGV is primarily exposed under novel or extreme conditions. By examining gene expression responses along a natural temperature gradient in Chironomus riparius, we challenged this view. We found that the vast majority of expressed genes (63%) exhibit dynamic CGV, where interindividual expression variability scales continuously with distance from the selectively optimal temperature, a pattern also observed in higher-level traits like mutation rate and ROS levels. Genes with lower overall expression levels were less temperature-regulated, and thermal reaction norm shapes varied with gene function. Unexpectedly, thermally plastic genes were more pleiotropic, often acting as hub genes, while CGV in gene expression was associated with lower pleiotropy. This pattern, and the observed strong recurrent selection on plastic genes with CGV, aligns with C. ripariuss adaptation to its highly fluctuating environment through selective tracking. We propose that this continuous, dynamic release of genetic variation is a necessary and inherent outcome of the polygenic nature of traits. This model fundamentally reshapes our understanding of adaptation, implying that populations can gradually and continuously adapt without requiring harsh conditions to expose hidden diversity. This leads to smoother adaptive landscapes, enhancing rapid adaptation and facilitating evolutionary innovation in the face of ongoing environmental change.

evolutionary biology↗

Dissecting Oxidative Stress and Organismic Response to various Temperature Regimes in the midge C. riparius

Oxidative stress, driven by reactive oxygen species (ROS), poses a major challenge for organisms facing temperature fluctuations. This study provides the first direct in vivo measurements of ROS production in an insect, Chironomus riparius, across a broad range of ecologically relevant temperatures. We observed a U-shaped pattern of oxidative stress, with minimal ROS levels within an optimal thermal window (12-18{degrees}C) and significantly elevated stress at both cold and warm extremes. Crucially, our findings reveal distinct underlying molecular mechanisms for ROS generation at these extremes: at low temperatures, ROS production is predominantly of the superoxide group, linked to hypoxia-induced hemoglobin autoxidation. Conversely, at high temperatures, the hydrogen peroxide group dominates, associated with increased metabolic rate and heat stress signaling pathways. Transcriptomic analysis shows that C. ripariuss antioxidant defense system adapts accordingly, selectively upregulating mechanisms to counteract the specific dominant ROS type at different temperatures. This mechanistically differentiated oxidative stress and the modulated organismic response profoundly impacts the overall ecological success and evolution of C. riparius as a model for thermal stress in ectotherms. Summary StatementThis study shows that cold and heat stress activate different oxidative damage pathways in midge larvae, explaining how organisms face unique physiological limits in thermal extremes.

ecology↗

The Genomic Basis of Social Parasitism: A Geographical Mosaic of Behavioural, Chemical, and Environmental Adaptations in a Widespread Host-Parasite System

Coevolutionary dynamics in host-parasite systems are driven by reciprocal selection and environmental pressures. When parasite and host are closely related and have similar evolutionary potentials, evolution may follow parallel trajectories, affecting the same traits and underlying genes. We investigated coevolution and its genomic basis in the dulotic ant parasite Temnothorax americanus and its host T. longispinosus across a broad climatic gradient using population genomics, genome-wide association and transcriptome analyses. Population genomics revealed a striking contrast: panmictic host populations versus structured parasite populations, consistent with geographic mosaic dynamics. Genomic responses to parasite prevalence were strongly asymmetric: hosts showed strong selection on immune and structural defence genes, potentially with pleiotropic social functions. Parasites exhibited weaker signals, often in regulatory genes linked to behavioural shifts critical for raiding. Both species displayed shared genomic signatures of climate adaptation (e.g., desiccation resistance, stress response), suggesting convergent physiological responses. Genes associated with host-parasite encounters (mechanosensation, circadian rhythms, venom) also showed parallel selection. Behavioural traits such as aggression showed limited genomic signals but potentially higher transcriptional plasticity. Associations with chemical traits revealed shared selection on genes involved in cuticular hydrocarbon biosynthesis and chemosensory perception, indicating evolutionary coupling of signal production and perception. Constitutive gene expression patterns diverged: host expression correlated with parasite prevalence, while parasite expression was more strongly linked to climate, reflecting contrasting regulatory pressures. Our study demonstrates how differing population structures, asymmetric reciprocal selection, and environmental context shape divergent genomic trajectories of coadaptation, reflecting distinct evolutionary architectures across a heterogeneous landscape.

evolutionary biology↗

Predicting forest tree leaf phenology under climate change using satellite monitoring and population-based GWAS

Leaf phenology, a critical determinant of plant fitness and ecosystem function, is undergoing rapid shifts due to climate change, yet its complex genetic and environmental drivers remain incompletely understood. Understanding the genetic basis of phenological adaptation is crucial for forecasting forest responses to a changing climate. Here, we integrate multi-year satellite-derived phenology from 46 Fagus sylvatica (European beech) populations across Germany with a population-based genome-wide association study to dissect the environmental and genetic drivers of leaf-out day (LOD) and leaf shedding day (LSD). We show that environmental factors, particularly temperature forcing and water availability, are the primary drivers of LOD variation, while LSD is influenced by a more complex suite of climatic cues. Our genomic analysis identifies candidate genes associated with LOD and LSD, primarily linked to circadian rhythms and dormancy pathways, respectively. Furthermore, genomic prediction models incorporating these loci accurately reconstruct past phenological dynamics, providing a powerful framework to forecast forest vulnerability and adaptation to future climate change.

evolutionary biology↗

Convergent Evolutionary Traces of Genomic Innovations and Depletions in Socially Parasitic Ants

Parasitism, a common strategy across life, often involves genomic reduction. Socially parasitic "slavemaking" ants provide an excellent model to study the evolution of this lifestyle. Here, we compared the genomes of four closely related, independently evolved parasite-host pairs and their outgroups to identify convergent patterns. While genome size and gene numbers remain relatively stable, parasites show increased positive and relaxed selection, more putative de novo genes which have recently emerged from previously non-coding regions, and a significant loss of chemical receptors, particularly those associated with the evolution of sociality. Hosts, however, retain many duplicated genes. Gene co-expression networks associated with nest-defence in hosts are rather conserved, while the network structure of raiding parasites is much more variable and reflects the independent evolutionary origin of social parasitism. Our findings suggest that while hosts primarily rely on existing molecular mechanisms for defence, parasite genome evolution is characterised by extensive, convergent gene loss, innovation, and network rewiring.

evolutionary biology↗

Transcriptomics predicts Artificial Light at Night's (ALAN) impact on fitness: nightly illumination alters gene expression pattern and negatively affects fitness components in the midge Chironomus riparius (Diptera:Chironomidae)

The emission of artificial light at night (ALAN) is rapidly increasing worldwide. Yet, evidence for its detrimental effects on various species is accumulating. While the effects of ALAN on phenotypic traits have been widely investigated, effects on the molecular level are less well understood. Here we aimed to integrate the effects of ALAN at the transcriptomic and the phenotypic level. We tested these effects on Chironomus riparius, a multivoltine, holometabolous midge with high ecological relevance for which genomic resources are available. We performed life-cycle experiments in which we exposed midges to constant light and control conditions for one generation. We observed higher EmT50 and reduced fertility under ALAN. From the observed decline in population size due to the reduced fertility, we predicted the population size to decline to 1% after 200 days. The transcriptomic analysis revealed expression changes of genes related to circadian rhythmicity, moulting, catabolism and oxidative stress. From the transcriptomic analysis we hypothesised that under ALAN, oxidative stress is increased, and that moulting begins earlier. We were able to confirm both hypotheses in two posthoc experiments, showing that transcriptomics are a powerful tool in predicting physiological outcomes before they are even observable.

molecular biology↗

Reference genome of the ant Lasius platythorax

Ants are a highly diversified insect family of the order Hymenoptera, with many fascinating characteristics such as eusociality, chemical communication, farming, or social parasitism. Moreover, ants frequent a wide variety of habitats from dry deserts, grasslands, and savannas to cold temperate forests. The ability of ants to inhabit such diverse habitat ranges demonstrates their adaptability and ecological resilience. However, little is known about the genetic underpinnings of this vast array of traits and their adaptive potential. Here, we generated a high-quality genome assembly for the ant species Lasius platythorax using long-read PacBio HiFi in combination with chromatin conformation capture (Hi-C) sequencing. We successfully assembled the genome into 15 chromosome-level scaffolds ranging from 7.9 to 19.2 Mb and encompassing 204.6 Mb out of 235.3 Mb (total assembly), and a BUSCO score of 86% (Hymenoptera_odb10). Comparative genomics between the two sister species will provide insights into the genomic basis of trait differentiation.

genomics↗

Age- and caste-independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus

Social insects are models for phenotypic plasticity: the generation of different phenotypes from the same genotype. Ant queens and workers differ not only in their morphology and behaviour, but also in their fecundity and lifespan, which is often several times higher in queens. However, the gene regulatory mechanisms underlying these differences are not yet well understood. Since ant queens can live and reproduce for more than two decades, they need to protect their germline from the activity of transposable elements (TEs). This protection may be redundant in short-lived, often sterile workers. We have analysed the expression of two protective classes of smallRNAs, microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), in different tissues, castes, and age classes of the ant species Temnothorax rugatulus. We show that piRNAs are particularly active in the ovaries of queens. TEs are clear targets of the piRNAs in this ant species, and piRNA-specific sequence signatures in the ovaries of all queens regardless of age indicate that young and old queens have similarly active piRNA pathways. Interestingly, the reduced ovaries of the workers also showed the same level of piRNA activity. This was not only the case in young, fertile workers from queenless nests, but also in the presumably older foragers, which have almost completely regressed ovaries. These findings suggest that the germline in these ants is invariably protected by piRNA activity, irrespective of ovarian development. The brain and thorax of queens also contained piRNAs, but at lower levels, and the piRNA-specific ping-pong signatures were strongly reduced in these tissues. We also annotated and analysed miRNAs in different tissues. We confidently detected the expression of 304 miRNAs. Of these, 10 were enriched in the brain and three to the thorax, whereas 83 were specific to the ovaries. 105 miRNAs were found to be expressed in all three tissues. We also identified miRNAs whose expression potentially is related to ant caste, fecundity, and age, suggesting that caste-specific gene activity may be regulated in part by miRNAs. In contrast, our studies of piRNA activity indicate similar profiles across caste, fecundity and age groups, but strong tissue specificity with the highest piRNA mediated TE protection in the germline.

ecology↗

Phenotypic drought stress prediction of European beech (Fagus sylvatica) by genomic prediction and remote sensing

Current climate change species response models usually not include evolution. We integrated remote sensing with population genomics to improve phenotypic response prediction to drought stress in the key forest tree European beech (Fagus sylvatica L.). We used whole-genome sequencing of pooled DNA from natural stands along an ecological gradient from humid-cold to warm-dry climate. We phenotyped stands for leaf area index (LAI) and moisture stress index (MSI) for the period 2016-2022. We predicted this data with matching meteorological data and a newly developed genomic population prediction score in a Generalised Linear Model. Model selection showed that addition of genomic prediction decisively increased the explanatory power. We then predicted the response of beech to future climate change under evolutionary adaptation scenarios. A moderate climate change scenario would allow persistence of adapted beech forests, but not worst-case scenarios. Our approach can thus guide mitigation measures, such as allowing natural selection or proactive evolutionary management.

evolutionary biology↗

Genomic profiling of climate adaptation in Aedes aegypti along an altitudinal gradient in Nepal indicates non-gradual expansion of the disease vector

BackgroundDriven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging trends of vector expansion. ResultsBy applying whole genome analyses and genotype-environment associations to populations of the main dengue vector Ae. aegypti, sampled along an altitudinal temperature gradient in Nepal (200- 1300m), we identify adaptive traits and describe the species genomic footprint of climate adaptation to colder ecoregions. We found two clusters of differentiation with significantly different allele frequencies in genes associated to climate adaptation between the highland population (1300m) and all other lowland populations ([≤] 800 m). We revealed non-synonymous mutations in 13 of the candidate genes associated to either altitude, precipitation or cold tolerance and identified an isolation-by-environment differentiation pattern. ConclusionOther than the expected gradual differentiation along the altitudinal gradient, our results reveal a distinct genomic differentiation of the highland population. This finding either indicates a differential invasion history to Nepal or local high-altitude adaptation explaining the populations phenotypic cold tolerance. In any case, this highland population can be assumed to carry pre-adapted alleles relevant for the species invasion into colder ecoregions worldwide that way expanding their climate niche.

genomics↗

Selective effects of a short transient environmental fluctuation on a natural population

Natural populations experience continuous and often transient changes of environmental conditions. These in turn may result in fluctuating selection pressures leading to variable demographic and evolutionary population responses. Rapid adaptation as short-term response to a sudden environmental change has in several cases been attributed to polygenic traits, but the underlying genomic dynamics and architecture are poorly understood. In this study, took advantage of a natural experiment in an insect population by monitoring genome-wide allele frequencies before and after a cold snap event. Whole genome pooled sequencing of time series samples revealed ten selected haplotypes carrying ancient polymorphisms, partially with signatures of balancing selection. By constantly cold exposing genetically variable individuals in the laboratory, we could demonstrate with whole genome resequencing i) among the survivors, the same alleles rose in frequency as in the wild and ii) that the identified variants additively predicted fitness (survival time) of its bearers. Finally, by simultaneously sequencing the genome and the transcriptome of cold exposed individuals we could tentatively link some of the selected SNPs to the cis- and trans-regulation of genes and pathways known to be involved in cold response of insects, like Cytochrome P450 and fatty acid metabolism. Altogether, our results shed light on the strength and speed of selection in natural populations and the genomic architecture of its underlying polygenic trait. Population genomic time series data thus appear as promising tool for measuring the selective tracking of fluctuating selection in natural populations.

evolutionary biology↗

Evidence for a conserved queen-worker genetic toolkit across slave-making ants and their ant hosts

The ecological success of social Hymenoptera (ants, bees, wasps) depends on the division of labour between the queen and workers. Each caste is highly specialised in its respective function in morphology, behaviour and life-history traits, such as lifespan and fecundity. Despite strong defences against alien intruders, insect societies are vulnerable to social parasites, such as workerless inquilines or slave-making (dulotic) ants. Here, we investigate whether gene expression varies in parallel ways between lifestyles (slave-making versus host ants) across five independent origins of ant slavery in the "Formicoxenus-group" of the ant tribe Crematogastrini. As caste differences are often less pronounced in slave-making ants than non-parasitic ants, we also compare the transcriptomes of queens and workers in these species. We demonstrate a substantial overlap in expression differences between queens and workers across taxa, irrespective of lifestyle. Caste affects the transcriptomes much more profoundly than lifestyle, as indicated by 37 times more genes being linked to caste than to lifestyle and by multiple caste-associated gene modules with strong connectivity. However, several genes and one gene module are linked to the slave-making lifestyle across the independent origins, pointing to some evolutionary convergence. Finally, we do not find evidence for an interaction between caste and lifestyle, indicating that caste differences remain consistent even when species switch to a parasitic lifestyle. Our findings are a strong indication for the existence of a core set of genes whose expression is linked to the queen and worker caste in this ant taxon, supporting the "genetic toolkit" hypothesis.

evolutionary biology↗

Comparative transcriptome analysis of noble crayfish and marbled crayfish immune response to Aphanomyces astaci challenges

Introduction of invasive North American crayfish species and their pathogen Aphanomyces astaci has significantly contributed to the decline of European freshwater crayfish populations. In this study, noble crayfish, a susceptible native European species, and marbled crayfish, an invasive disease-resistant species, were challenged with haplogroup A (low virulence) and haplogroup B (high virulence) strain of A. astaci. Hepatopancreatic tissue was isolated 3 and 21 days post-challenge. Our results revealed strong up-regulation in expression levels of the prophenoloxidase cascade immune-related genes in the haplogroup B challenged noble crayfish 3 days post-challenge. In the marbled crayfish, we observed an up-regulation of immune system relevant genes (DSCAM, AP, ALFs, CTLs and hemocyanin) 3 days post-challenge. This response highlights the marbled crayfish capability of building the immune tolerance. Furthermore, we successfully characterised several novel immune related gene groups in both crayfish species, contributing to our current understanding of crayfish immune related genes landscape. Graphical abstracta) Study species noble crayfish (Astacus astacus) in purple and marbled crayfish (Procambarus virginalis) in green challenged with the pathogen Aphanomyces astaci haplogroup A (Hap A) strain of low virulence and haplogroup B (Hap B) strain of high virulence. b) Sampling scheme of the infection experiment: 5 individuals were taken from the experiment three- and 21-days post-challenge. From each individual, a hepatopancreas sample was taken, followed by RNA isolation and sequencing. c) De novo transcriptome assembly and annotation were conducted for each species. d) Differential gene expression analysis revealed the distinct immune response in the noble crayfish 3 days post-challenge with the Hap B strain of A. astaci and marbled crayfish 3 days post-challenge with the Hap A strain of A. astaci. Immune related DEGs were not present in either species 21 days post-challenge with A. astaci. e) Noble crayfish challenged with the Hap B strain of A. astaci were acutely infected and ultimately moribund, while the A. astaci Hap A challenged marbled crayfish showed high resistance to the pathogen, resulting infected without any mortality. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/445163v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@d1830aorg.highwire.dtl.DTLVardef@f2196forg.highwire.dtl.DTLVardef@63c8f2org.highwire.dtl.DTLVardef@11da1b6_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

Convergent loss of chemoreceptors across independent origins of slave-making in ants

The evolution of an obligate parasitic lifestyle often leads to the reduction of morphological and physiological traits, which may be accompanied by loss of genes and functions. Slave-maker ants are social parasites that exploit the work force of closely related ant species for social behaviours such as brood care and foraging. Recent divergence between these social parasites and their hosts enables comparative studies of gene family evolution. We sequenced the genomes of eight ant species, representing three independent origins of ant slavery. During the evolution of eusociality, chemoreceptor genes multiplied due to the importance of chemical communication in societies. We investigated evolutionary patterns of chemoreceptors in relation to slave-making in ants. We found that slave-maker ant genomes harboured only half as many gustatory receptors as their hosts, potentially mirroring the outsourcing of foraging tasks to host workers. In addition, parasites had fewer odorant receptors and their loss shows patterns of convergence across origins of parasitism, representing a rare case of convergent molecular evolution. This convergent loss of specific odorant receptors suggests that selective deprivation of receptors is adaptive. The 9-exon odorant receptor subfamily, previously linked to social evolution in insects, was significantly enriched for convergent loss across the three origins of slavery in our study, indicating that the transition to social parasitism in ants is accompanied by the loss of receptors that are likely important for mediating eusocial behaviour. Overall, gene loss in slave-maker ants suggests that a switch to a parasitic lifestyle accompanies relaxed selection on chemical perception.

genomics↗

Genomic basis of drought resistance in Fagus sylvatica

In the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated SNPs throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. A SNP-assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding. Impact StatementEuropean beech harbours substantial genetic variation at genomic loci associated with drought resistance and the loci identified in this study can help to accelerate and monitor adaptation to climate change.

plant biology↗

A high-quality genome assembly from short and long reads for the non-biting midge Chironomus riparius (Diptera)

BackgroundChironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species.\n\nFindingsMaking use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species and the respective recombination rate as one of the first insect recombination rates at all.\n\nConclusionsThe genome and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in detail. The estimated recombination rate will help evolutionary biologist gain a better understanding of commonalities and differences of genomic patterns in insects.

genomics↗

Gene expression is stronger associated with behaviour than with age and fertility in ant workers

The ecological success of social insects is based on division of labour, not only between queens and workers, but also among workers. Whether a worker tends the brood or forages is strongly influenced by age, fertility and nutritional status, with brood carers being younger, more fecund and corpulent. Here, we experimentally disentangle behaviour from age and fertility in Temnothorax longispinosus ant workers and analyse how these parameters are linked to whole-body gene expression. Our transcriptome analysis reveals four times more genes associated with behaviour than with age and only few fertility-associated genes. Brood carers exhibited an upregulation of genes involved in lipid biosynthesis, whereas foragers invested in metabolism. Additional simulations revealed that the experimental disassociation of co-varying factors reduces transcriptomic noise, potentially explaining discrepancies between transcriptomic studies on worker behaviour in other social insects. Our study highlights the influence of nutritional status on task choice in ant workers.

evolutionary biology↗