Dieter Ebert

Collagen is the most abundant protein in animals. Its thermal stability depends on its specific amino acid composition within the repeated Gly- _Xaa -Y _aa motifs forming the triple helix structure. Proline increases collagen rigidity, while serine enhances its elasticity—properties that contribute to collagen function and that vary with temperature. Although variation in collagen composition has been linked to temperature adaptation across evolutionary distinct taxa, its role within a species remains unclear. Here, we tested whether collagen genes across populations of the freshwater crustacean, Daphnia magna , show a signature of local adaptation to the ambient temperature. Analysing 39 collagen genes from 215 D. magna populations across three phylogeographic lineages spawning four continents, we found that animals from populations in warmer climates have higher proline and lower serine content in collagen—consistent with enhanced protein stability at higher temperatures. This variation was also associated with experimentally measured upper temperature tolerance. Parallel directional patterns of amino acid change appeared across genetically distinct lineages. Collagen genes also showed strong signatures of positive selection, comparable to that of immune-related genes, supporting a scenario of polygenic molecular role in adaptive responses. Our findings provide evidence of intraspecific molecular evolution in collagen amino acid composition driven by environmental temperature. Additionally, our study bridges macroevolutionary patterns with microevolutionary processes, posing the first intraspecific evidence that collagen genes can contribute to responses to environmental gradients at the molecular level, and thus, advancing our understanding of molecular adaptation of constrained structural proteins in an environmental context.

Daphnia magna is a widely used model organism in ecological genomics, ecotoxicology, and evolutionary biology. While a few genome assemblies of this species of freshwater crustacean are available, disagreements in their chromosomal arrangements point toward scaffolding problems. We present the most contiguous chromosome-level genome assembly of D. magna , the first based on PacBio HiFi sequencing technology. The assembly spans 184.38 Mb and has a scaffold N50 of 12.4 Mb. Eight of ten chromosomal scaffolds consist of mainly two contigs, representing one chromosome arm each. Eleven of 20 telomeric regions are fully resolved. Using a genomic map and comparative genomics, we were able to not only resolve the problems of previous assemblies, but also to demonstrate that some of the scaffolding errors followed a systematic pattern, most likely resulting from mis-joins during Hi-C scaffolding. Additionally, we provide expression profiles for annotated genes derived from different D. magna RNA-seq datasets, enabling rapid assessment of predicted gene expression and identification of potential pseudogenes. The new genomic and transcriptomic resource enables comparative genomic studies on genome architecture, structural variation, and gene family evolution in this important model organism. Significance Statement: Genome assemblies of different individuals of the same species vary as a result of natural genetic variation and assembly errors but distinguishing between these two sources of variation can be challenging. We generated an updated D. magna genome using long, highly-fidelity DNA sequences and a genetic map, revealing that previous assemblies contain systematic errors, including inverted chromosome arms likely due to mis-joins from the widely used Hi-C scaffolding method. The new genome enables identifying real genetic differences among the many already sequenced D. magna individuals from across the species range, allowing to investigate how natural selection shapes large-scale genetic variation, for example, involved in resistance to stressors and parasites.

Predators are often considered regulators of disease in prey populations, a concept central to the "healthy herd hypothesis". This hypothesis suggests that by preferentially removing infected individuals, predators can reduce parasite prevalence. However, predators may also act as disease vectors, facilitating the spread of parasites. We investigated whether stickleback fish ( Gasterosteus aculeatus ) can act as vectors for the transmission of the obligate bacterial parasite Pasteuria ramosa to its Daphnia host, a widespread freshwater zooplanktor. We fed infected D. magna to sticklebacks, and subsequently analysed faecal samples for the presence, viability, and infectivity of parasite transmission stages (= spores). We recovered approximately 60% of the consumed spores from fish faeces and these spores did not suffer from reduced infectivity to D. magna . Additionally, spores associated with sloppy feeding did not reduce infection rates. Thus, consumption of infected hosts by fish does not eliminate the parasite, but in contrary, may contribute to the spread and persistence of P. ramosa in natural populations, potentially influencing parasite dynamics in natural freshwater ecosystems.

Future climate change may reshape ecological communities not only by increasing mean temperature, but also by altering the consequences of increasingly frequent heatwaves. Predicting these effects requires understanding how background warming interacts with short heatwaves in natural communities, where responses can arise through direct thermal stress and species interactions. We tested this using 32 outdoor freshwater mesocosms exposed to sustained near-future warming while capturing a documented natural heatwave. Warming raised temperature maxima that exceeded the thermal threshold of the pond snail, a main grazer in the community. Warmed communities showed lower grazer abundance, increased macrophyte and insect herbivore abundance, reduced phytoplankton biomass, and lower zooplankton density. Complementary assays showed that heatwave-level temperatures promoted macrophyte growth and reduced grazer survival, whereas reduced zooplankton performance mainly reflected indirect warming effects via food-web cascades. Thus, near-future warming can amplify natural heatwave impacts by exceeding consumer thermal thresholds and propagating through species interactions.

The Red Queen model of host–parasite coevolution is based on time-lagged negative frequency-dependent selection resulting from highly specific interactions of the antagonists within populations. This model has been the preferred theory for explaining the elevated levels of genetic diversity and even trans-species polymorphisms found in the disease genes of many organisms, including humans. Several genomic analyses with plants and animals revealed reduced spatial differentiation and balancing selection at disease genes; however, the geographic distribution of disease-related phenotypes has not been studied. Filling this gap is important, as balancing selection acts on phenotypes, expected to create an even distribution of phenotypes across space. Daphnia magna, a host with strong evidence of Red Queen coevolution, shows a strong pattern of isolation by distance and phylogeographic population structure. Here, we analyse the distribution of resistance phenotypes from 236 populations across 4 continents in response to 14 isolates of the coevolving pathogen Pasteuria ramosa. Polymorphisms for resistance phenotypes show a rather even geographic distribution without isolation by distance and little difference among phylogeographic host clades, coinciding with patterns expected for traits under balancing selection. This finding strongly supports the Red Queen model of antagonistic coevolution by negative frequency-dependent selection. This article is part of the theme issue ‘Exploring negative frequency dependent selection across levels: from genetics to ecology and back again’.

Collagen-like proteins (CLPs) serve many pathogenic bacteria as adhesins to attach to host tissue. It was suggested that CLPs are a major determinant in the coevolution of the model system Daphnia (Crustacean) and its virulent pathogen Pasteuria ramosa (Bacillota). We analyzed 5 new high-quality genomes of P. ramosa originating from three host species. CLP genes underwent a radiation in P. ramosa. Genome comparison showed a high synteny, with few structural variations, mainly involving CLPs and transposases, both of which underwent recent multiplications. While most CLP genes are conserved, the presence/absence of some CLP genes varies among isolates. Our findings suggest a rapid radiation of CLP genes. These observations, derived from the first published genomes of P. ramosa, are consistent with the notion of rapid Pasteuria–Daphnia coevolution, as previously suggested for this highly specific host-parasite system.

Understanding how parasites spread is crucial for preventing infections and predicting epidemic dynamics. These efforts are challenging for environment‐borne parasites because transmission is host density‐independent. We monitored the dynamics of Pasteuria ramosa , a common bacterial parasite of Daphnia magna with prolonged free‐living transmission stages (spores). Spores are released into the sediment from decaying host cadavers. Transmission is believed to happen from sediment to host, though recent work has challenged this assumption, suggesting that transmission may also happen in the water column. We collected water samples during an epidemic and found infectious spore levels in the water, thus confirming this transmission pathway. Water column infectivity correlated with epidemic dynamics, suggesting that this pathway contributes to disease dynamics. We demonstrated experimentally that spores have a low sedimentation rate, suggesting that once suspended in the water, they remain in suspension for extended periods. We excluded that spores are released in the free water through macroinvertebrate predation or decomposition of sinking dead Daphnia , thus suggesting that perturbation transfers spores from the sediment to the water, potentially by water birds and large zooplankton. This research contributes insights into the transmission of environment‐borne parasites, emphasizing the importance of considering the physical environment and ecological community.

The long-standing notion that genotypes map to phenotypes through simple one gene–one trait relationships continues to shape both research in the life sciences and public understanding, with implications for policy and funding priorities. Yet this paradigm is increasingly recognized as inadequate for explaining continuous phenotypic variation and the complex genetic architectures of the genotype–phenotype map. Modern genetics emerged from the early 20th-century synthesis of Mendelian and biometric schools of heredity, with R.A. Fisher demonstrating early on how multiple discrete loci could collectively produce continuous variation. Despite this fundamental insight, Mendelism—with its focus on single genes and standardized genetic backgrounds—became the dominant framework, shaping current genetics research and molecular biology as well as science education. The advent of large-scale genomic data has revealed yet again the limitations of this reductionist approach. Evidence from quantitative genetics now shows that most phenotypes arise from complex networks of many interdependent genes and their dynamic responses to environmental perturbations. Here we trace the historical roots of how Mendelian classical genetics departed from the biometric school to create the current predominant paradigm in genetics, despite fundamentally unresolved issues. Moving on from this one-sided paradigm will require systematic development of integrative, evolutionarily grounded experimental approaches that better capture the multigenic and context-dependent nature of inheritance. Achieving such an extended perspective will require methodological innovation, including advances in large-scale (e.g. automated) phenotyping. Dedicated research programs will be necessary to advance a new era of genetic research into the complex mechanisms underlying phenotypic variation.

We provide a general theoretical explanation for a longstanding result in spatial ecology: weak dispersal among habitat patches promotes local biodiversity. Using analytical approximations of spatial Lotka–Volterra competition models, we show that species persistence in heterogeneous landscapes can be expressed as a function of regional abundance and local invasion growth rates. We further demonstrate that local multispecies coexistence is governed by the feasibility domain, linking spatial coexistence to a structural property of nonspatial competitive systems. Together, these results explain why weak dispersal increases local species richness and why this effect strengthens with landscape size. We test these predictions using numerical simulations and find that the theory breaks down only when both dispersal and competitive interactions are very strong, in which case dispersal has a unimodal effect on coexistence. In contrast, landscape size retains a positive effect on coexistence whenever an effect is detectable. We then apply the theory to long-term data from a natural Daphnia metacommunity. We detect strong preemptive competition among species and find no detectable effect of dispersal rate on local coexistence, whereas species co-occurrence increases with local landscape size, as predicted by theory. Together, our results identify how dispersal, interaction strength, and landscape size jointly regulate biodiversity in competitive systems.

The link between host density and parasite population size is well-established. However, while high host density facilitates parasite transmission, it may negatively impact parasites through more intense competition and/or more intense host immune defence. We assessed the performance of individually tagged female salmon lice (Lepeophtheirus salmonis), an ectoparasite of Atlantic salmon (Salmo salar), under experimental low and high host density conditions, the latter mimicking salmon aquaculture conditions. Lice at high density exhibit greater pre-reproductive mortality, reduced growth, delayed maturation, smaller adult sizes and lower fecundity. Adult size in salmon lice correlates negatively with age at maturity and positively with early fecundity, lifetime fecundity and lifespan. Thus, lice in high-density host populations perform poorly across all life-history traits, probably owing to stronger immune responses of hosts initially exposed to higher parasite doses. This study suggests density-dependent regulation of parasites in intensive agriculture, where hosts are farmed at high densities. Our results further suggest that salmon lice in aquaculture may be selected for greater resistance to host immune defence. As host populations now consist overwhelmingly of farmed fish, continued research is essential to understand the implications for wild salmonids, which are frequently infected by lice originating from farms.