nils-herrmann/clean_scirepeval huggingface dataset:
Communication versus waterproofing: the physics of insect cuticular hydrocarbons
Venue: The Journal of Experimental Biology

Understanding the evolution of complex traits is among the major challenges in biology. One such trait is the cuticular hydrocarbon (CHC) layer in insects. It protects against desiccation and provides communication signals, especially in social insects. CHC composition is highly diverse within and across species. To understand the adaptive value of this chemical diversity, we must understand how it affects biological functionality. So far, CHCs have received ample research attention, but their physical properties were little studied. We argue that these properties determine their biological functionality, and are vital to understanding how CHC composition affects their adaptive value. We investigated melting behaviour and viscosity of CHCs from 11 ant species using differential scanning calorimetry and a novel microrheological technique. CHCs began melting below −45°C, and often were entirely liquid only above 30°C. Thus, they formed a solid–liquid mixture under ambient conditions, which contrasts to previous assumptions of entirely solid layers in many species. This may be adaptive as only biphasic CHC layers ensure uniform coating of the insect body, which is necessary for waterproofing. CHC viscosity was mostly between 0.1 and 0.2 Pa s−1, thus similar to motor oils. Surprisingly, chemically different CHC profiles had similar viscosities, suggesting that a certain viscosity level is adaptive and ensures that communication signals can be perceived. With this study, we draw attention to the importance of studying the physics of CHC layers. Only by understanding how chemical and physical mechanisms enable CHC functionality can we understand the causes and consequences of CHC diversification.  Cuticular hydrocarbons protect insects from desiccation and allow chemical communication, and contain both liquid and solid parts. This complex phase behaviour appears vital to ensure biological functioning.
Free-standing spider silk webs of the thomisid Saccodomus formivorus are made of composites comprising micro- and submicron fibers
Venue: Scientific Reports

Our understanding of the extraordinary mechanical and physico-chemical properties of spider silk is largely confined to the fibers produced by orb-weaving spiders, despite the diversity of foraging webs that occur across numerous spider families. Crab spiders (Thomisidae) are described as ambush predators that do not build webs, but nevertheless use silk for draglines, egg cases and assembling leaf-nests. A little-known exception is the Australian thomisid Saccodomus formivorus, which constructs a basket-like silk web of extraordinary dimensional stability and structural integrity that facilitates the capture of its ant prey. We examined the physical and chemical properties of this unusual web and revealed that the web threads comprise microfibers that are embedded within a biopolymeric matrix containing additionally longitudinally-oriented submicron fibers. We showed that the micro- and submicron fibers differ in their chemical composition and that the web threads show a remarkable lateral resilience compared with that of the major ampullate silk of a well-investigated orb weaver. Our novel analyses of these unusual web and silk characteristics highlight how investigations of non-model species can broaden our understanding of silks and the evolution of foraging webs.
The Scaly-foot Snail genome and implications for the origins of biomineralised armour
Venue: Nature Communications

The Scaly-foot Snail, Chrysomallon squamiferum , presents a combination of biomineralised features, reminiscent of enigmatic early fossil taxa with complex shells and sclerites such as sachtids, but in a recently-diverged living species which even has iron-infused hard parts. Thus the Scaly-foot Snail is an ideal model to study the genomic mechanisms underlying the evolutionary diversification of biomineralised armour. Here, we present a high-quality whole-genome assembly and tissue-specific transcriptomic data, and show that scale and shell formation in the Scaly-foot Snail employ independent subsets of 25 highly-expressed transcription factors. Comparisons with other lophotrochozoan genomes imply that this biomineralisation toolkit is ancient, though expression patterns differ across major lineages. We suggest that the ability of lophotrochozoan lineages to generate a wide range of hard parts, exemplified by the remarkable morphological disparity in Mollusca, draws on a capacity for dynamic modification of the expression and positioning of toolkit elements across the genome. The Scaly-foot Snail, Chrysomallon squamiferum , is a model for understanding the evolution of biomineralised armour. Here, the authors present a chromosome-level reference genome assembly and tissue-specific transcriptomic data for this enigmatic organism.
Group structure and kinship in beluga whale societies
Venue: Scientific Reports

Evolutionary explanations for mammalian sociality typically center on inclusive-fitness benefits of associating and cooperating with close kin, or close maternal kin as in some whale societies, including killer and sperm whales. Their matrilineal structure has strongly influenced the thinking about social structure in less well-studied cetaceans, including beluga whales. In a cross-sectional study of group structure and kinship we found that belugas formed a limited number of distinct group types, consistently observed across populations and habitats. Certain behaviours were associated with group type, but group membership was often dynamic. MtDNA-microsatellite profiling combined with relatedness and network analysis revealed, contrary to predictions, that most social groupings were not predominantly organized around close maternal relatives. They comprised both kin and non-kin, many group members were paternal rather than maternal relatives, and unrelated adult males often traveled together. The evolutionary mechanisms that shape beluga societies are likely complex; fitness benefits may be achieved through reciprocity, mutualism and kin selection. At the largest scales these societies are communities comprising all ages and both sexes where multiple social learning pathways involving kin and non-kin can foster the emergence of cultures. We explore the implications of these findings for species management and the evolution of menopause.
A specialized avian seed dispersal system in a dry-fruited non-photosynthetic plant, Balanophora yakushimensis.
Venue: Ecology

The family Balanophoraceae are among the most unusual of plants because they have aberrant vegetative bodies, highly reduced flowers, and small and reduced embryos (Hansen 1972, Gonzalez et al. 2019). Because the plants lack chlorophyll and are incapable of photosynthesis, they draw nutrition from other organisms. Indeed, like the well-known parasitic plant, Rafflesia, members of the Balanophoraceae acquire both water and nutrients from host plants. They are, therefore, highly specialized root parasites.
Sexual and natural selection on pollen morphology in Taraxacum.
Venue: American Journal of Botany

PREMISE
Spiny pollen has evolved independently in multiple entomophilous lineages. Sexual selection may act on exine traits that facilitate male mating success by influencing the transfer of pollen from the anther to the body of the pollinator, while natural selection acts to increase pollen survival. We postulated that relative to sexual congeners, apomictic dandelions undergo relaxed selection on traits associated with male mating success.



We explored sexual selection on exine traits by measuring the propensity for Taraxacum spp. pollen to attach to hairs of flower-visiting bumblebees (Bombus spp.) or flies (Diptera: Syrphidae and Muscoidea) and assessed natural selection by testing whether pollen traits defend against consumption.



Pollen picked up by bumblebees exhibited a narrower subset of spine-spacing phenotypes, consistent with stabilizing selection. Flies picked up larger pollen from flowers than expected at random. Surveys of corbiculae (pollen basket) contents from foraging bumblebees and feces of flies showed that pollen grains consumed by both kinds of visitors are similar in spine characteristics and size to those produced by the donor. When bees visit inflorescences of apomictic T. officinale, they pick up pollen with spine-spacing phenotypes above the mean and shifted toward those of sexual T. ceratophorum.



We demonstrate that traits under sexual selection during pollen pickup vary among pollinators, while natural selection for pollen defense is nil in T. ceratophorum. In hybrid zones between apomictic and sexual dandelions, pollen traits place apomictic donors at a dispersal disadvantage, potentially reinforcing reproductive isolation.
Reduced immune responsiveness contributes to winter energy conservation in an Arctic bird
Venue: The Journal of Experimental Biology

Animals in seasonal environments must prudently manage energy expenditure to survive the winter. This may be achieved through reductions in the allocation of energy for various purposes (e.g. thermoregulation, locomotion, etc.). We studied whether such trade-offs also include suppression of the innate immune response, by subjecting captive male Svalbard ptarmigan (Lagopus muta hyperborea) to bacterial lipopolysaccharide (LPS) during exposure to either mild temperature (0°C) or cold snaps (acute exposure to −20°C), in constant winter darkness when birds were in energy-conserving mode, and in constant daylight in spring. The innate immune response was mostly unaffected by temperature. However, energy expenditure was below baseline when birds were immune challenged in winter, but significantly above baseline in spring. This suggests that the energetic component of the innate immune response was reduced in winter, possibly contributing to energy conservation. Immunological parameters decreased (agglutination, lysis, bacteriostatic capacity) or did not change (haptoglobin/PIT54) after the challenge, and behavioural modifications (anorexia, mass loss) were lengthy (9 days). While we did not study the mechanisms explaining these weak, or slow, responses, it is tempting to speculate they may reflect the consequences of having evolved in an environment where pathogen transmission rate is presumably low for most of the year. This is an important consideration if climate change and increased exploitation of the Arctic would alter pathogen communities at a pace outwith counter-adaption in wildlife.  Adaptation to the thermally extreme and pathogenically pristine high Arctic may select for year-round energy conservation at the expense of permanently reduced innate immune function.
Self-organization of river vegetation leads to emergent buffering of river flows and water levels
Venue: Proceedings of The Royal Society B: Biological Sciences

Global climate change is expected to impact hydrodynamic conditions in stream ecosystems. There is limited understanding of how stream ecosystems interact and possibly adapt to novel hydrodynamic conditions. Combining mathematical modelling with field data, we demonstrate that bio-physical feedback between plant growth and flow redistribution triggers spatial self-organization of in-channel vegetation that buffers for changed hydrological conditions. The interplay of vegetation growth and hydrodynamics results in a spatial separation of the stream into densely vegetated, low-flow zones divided by unvegetated channels of higher flow velocities. This self-organization process decouples both local flow velocities and water levels from the forcing effect of changing stream discharge. Field data from two lowland, baseflow-dominated streams support model predictions and highlight two important stream-level emergent properties: vegetation controls flow conveyance in fast-flowing channels throughout the annual growth cycle, and this buffering of discharge variations maintains water depths and wetted habitat for the stream community. Our results provide important evidence of how plant-driven self-organization allows stream ecosystems to adapt to changing hydrological conditions, maintaining suitable hydrodynamic conditions to support high biodiversity.
Improved color constancy in honey bees enabled by parallel visual projections from dorsal ocelli
Venue: Proceedings of the National Academy of Sciences of the United States of America

Color sensing requires a capacity to discount the changing color of natural light. We present a biologically validated mathematical solution to this classic problem based on honey bee color vision. The observed spectral tuning of two simple ocellar photoreceptors in the honey bee allows for an optimal color constancy solution to different light environments, including standard CIE ( illuminations, natural forest light, sunlight, or shade. The model is fully supported by a neural pathway potentially allowing for the transfer of spectral information originating from the ocellar photoreceptors to the centralized information processing regions in the brain and explains previously observed behavioral results. This solution to color constancy can be implemented into color imaging systems to enable accurate color interpretation. How can a pollinator, like the honey bee, perceive the same colors on visited flowers, despite continuous and rapid changes in ambient illumination and background color? A hundred years ago, von Kries proposed an elegant solution to this problem, color constancy, which is currently incorporated in many imaging and technological applications. However, empirical evidence on how this method can operate on animal brains remains tenuous. Our mathematical modeling proposes that the observed spectral tuning of simple ocellar photoreceptors in the honey bee allows for the necessary input for an optimal color constancy solution to most natural light environments. The model is fully supported by our detailed description of a neural pathway allowing for the integration of signals originating from the ocellar photoreceptors to the information processing regions in the bee brain. These findings reveal a neural implementation to the classic color constancy problem that can be easily translated into artificial color imaging systems.
The Protective Role of Bark and Bark Fibers of the Giant Sequoia (Sequoiadendron giganteum) during High-Energy Impacts
Venue: International Journal of Molecular Sciences

The influences of (1) a high fiber content, (2) the arrangement of fibers in fiber groups, and (3) a layered hierarchical composition of the bark of the giant sequoia (Sequoiadendron giganteum) on its energy dissipation capability are analyzed and discussed regarding the relevance for an application in bioinspired components in civil engineering. The giant sequoia is native to the Sierra Nevada (USA), a region with regular rockfalls. It is thus regularly exposed to high-energy impacts, with its bark playing a major protective role, as can be seen in the wild and has been proven in laboratory experiments. The authors quantify the fundamental biomechanical properties of the bark at various length scales, taking into account its hierarchical setup ranging from the integral level (whole bark) down to single bark fibers. Microtensile tests on single fibers and fiber pairs give insights into the properties of single fibers as well as the benefits of the strong longitudinal interconnection between single fibers arranged in pairs. Going beyond the level of single fibers or fiber pairs, towards the integral level, quasistatic compression tests and dynamic impact tests are performed on samples comprising the whole bark (inner and outer bark). These tests elucidate the deformation behavior under quasistatic compression and dynamic impact relevant for the high energy dissipation and impact-damping behavior of the bark. The remarkable energy dissipation capability of the bark at the abovementioned hierarchical levels are linked to the layered and fibrous structure of the bark structurally analyzed by thin sections and SEM and µCT scans.
IGF1R is an entry receptor for respiratory syncytial virus
Venue: Nature

Pneumonia resulting from infection is one of the leading causes of death worldwide. Pulmonary infection by the respiratory syncytial virus (RSV) is a large burden on human health, for which there are few therapeutic options 1 . RSV targets ciliated epithelial cells in the airways, but how viruses such as RSV interact with receptors on these cells is not understood. Nucleolin is an entry coreceptor for RSV 2 and also mediates the cellular entry of influenza, the parainfluenza virus, some enteroviruses and the bacterium that causes tularaemia 3 , 4 . Here we show a mechanism of RSV entry into cells in which outside-in signalling, involving binding of the prefusion RSV-F glycoprotein with the insulin-like growth factor-1 receptor, triggers the activation of protein kinase C zeta (PKCζ). This cellular signalling cascade recruits nucleolin from the nuclei of cells to the plasma membrane, where it also binds to RSV-F on virions. We find that inhibiting PKCζ activation prevents the trafficking of nucleolin to RSV particles on airway organoid cultures, and reduces viral replication and pathology in RSV-infected mice. These findings reveal a mechanism of virus entry in which receptor engagement and signal transduction bring the coreceptor to viral particles at the cell surface, and could form the basis of new therapeutics to treat RSV infection. Respiratory syncytial virus enters cells by binding to cell-surface IGFR1, which activates PKCζ and induces trafficking of the NCL coreceptor to the RSV particles at the cell surface.
Torque and Angular-Momentum Transfer in Merging Rotating Bose-Einstein Condensates.
Venue: Physical Review Letters

When rotating classical fluid drops merge together, angular momentum can be advected from one to another due to the viscous shear flow at the drop interface. It remains elusive what the corresponding mechanism is in inviscid quantum fluids such as Bose-Einstein condensates (BECs). Here we report our theoretical study of an initially static BEC merging with a rotating BEC in three-dimensional space along the rotational axis. We show that a solitonlike sheet, resembling a corkscrew, spontaneously emerges at the interface. Rapid angular-momentum transfer at a constant rate universally proportional to the initial angular-momentum density is observed. Strikingly, this transfer does not necessarily involve fluid advection or drifting of the quantized vortices. We reveal that the corkscrew structure can exert a torque that directly creates angular momentum in the static BEC and annihilates angular momentum in the rotating BEC. Uncovering this intriguing angular-momentum transport mechanism may benefit our understanding of various coherent matter-wave systems, spanning from atomtronics on chips to dark matter BECs at cosmic scales.
Physical limits of flight performance in the heaviest soaring bird
Venue: Proceedings of the National Academy of Sciences of the United States of America

Flapping flight is extremely costly for large birds, yet little is known about the conditions that force them to flap. We attached custom-made “flight recorders” to Andean condors, the world’s heaviest soaring birds, documenting every single wingbeat and when and how individuals gained altitude. Remarkably, condors flapped for only 1% of their flight time, specifically during takeoff and when close to the ground. This is particularly striking as the birds were immature. Thus, our results demonstrate that even inexperienced birds can cover vast distances over land without flapping. Overall, this can help explain how extinct birds with twice the wingspan of condors could have flown. Flight costs are predicted to vary with environmental conditions, and this should ultimately determine the movement capacity and distributions of large soaring birds. Despite this, little is known about how flight effort varies with environmental parameters. We deployed bio-logging devices on the world’s heaviest soaring bird, the Andean condor (Vultur gryphus), to assess the extent to which these birds can operate without resorting to powered flight. Our records of individual wingbeats in >216 h of flight show that condors can sustain soaring across a wide range of wind and thermal conditions, flapping for only 1% of their flight time. This is among the very lowest estimated movement costs in vertebrates. One bird even flew for >5 h without flapping, covering ∼172 km. Overall, > 75% of flapping flight was associated with takeoffs. Movement between weak thermal updrafts at the start of the day also imposed a metabolic cost, with birds flapping toward the end of glides to reach ephemeral thermal updrafts. Nonetheless, the investment required was still remarkably low, and even in winter conditions with weak thermals, condors are only predicted to flap for ∼2 s per kilometer. Therefore, the overall flight effort in the largest soaring birds appears to be constrained by the requirements for takeoff.
Mechanisms and consequences of flight polyphenisms in an outbreaking bark beetle species
Venue: The Journal of Experimental Biology

Flight polyphenisms naturally occur as discrete or continuous traits in insects. Discrete flight polyphenisms include winged and wingless morphs, whereas continuous flight polyphenisms can take the form of short- or long-distance fliers. The mountain pine beetle (Dendroctonus ponderosae) exhibits polyphenic variation in flight distance but the consequences of this flight variation on life history strategies of beetles is unknown. This study assessed the effect of flight on two particular aspects of beetle biology: (1) an energetic trade-off between flight distance and host colonisation capacity; and (2) the relationship between flight distance and pheromone production. A 23 h flight treatment was applied to a subset of beetles using computer-linked flight mills. After flight treatment, both flown and unflown (control) beetles were given the opportunity to colonise bolts of host trees, and beetles that entered hosts were aerated to collect pheromone. A trade-off occurred between initiation of host colonisation and percentage body mass lost during flight, which indicates energy use during flight affects host acceptance in female mountain pine beetles. Furthermore, production of the aggregation pheromone trans-verbenol by female beetles was influenced by both percentage body mass lost during flight and flight distance. Male production of exo-brevicomin was affected by beetle condition following flight but not by the energy used during flight. These novel results give new insight into the polyphenic flight behaviour of mountain pine beetles. Flight variation is adaptive by acting to maintain population levels through safe and risky host colonisation strategies. These findings suggest mechanisms that facilitate the extremities of the continuous flight polyphenism spectrum. These opposing mechanisms appear to maintain the high variation in flight exhibited by this species.  The relationship between energy use during flight and host colonisation in the mountain pine beetle suggests potential selection mechanisms maintaining flight polyphenisms.