nils-herrmann/clean_scirepeval huggingface dataset:
Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros
Venue: Current Biology

Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations . Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans . The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.
Rapid self-assembly of complex biomolecular architectures during mussel byssus biofabrication
Venue: Nature Communications

Protein-based biogenic materials provide important inspiration for the development of high-performance polymers. The fibrous mussel byssus, for instance, exhibits exceptional wet adhesion, abrasion resistance, toughness and self-healing capacity–properties that arise from an intricate hierarchical organization formed in minutes from a fluid secretion of over 10 different protein precursors. However, a poor understanding of this dynamic biofabrication process has hindered effective translation of byssus design principles into synthetic materials. Here, we explore mussel byssus assembly in Mytilus edulis using a synergistic combination of histological staining and confocal Raman microspectroscopy, enabling in situ tracking of specific proteins during induced thread formation from soluble precursors to solid fibres. Our findings reveal critical insights into this complex biological manufacturing process, showing that protein precursors spontaneously self-assemble into complex architectures, while maturation proceeds in subsequent regulated steps. Beyond their biological importance, these findings may guide development of advanced materials with biomedical and industrial relevance.
School formation characteristics and stimuli based modeling of Tetra fish.
Venue: Bioinspiration & Biomimetics

Self-organizing motion is an important yet inadequately understood phenomena in the field of collective behavior. For birds flocks, insect swarms, and fish schools, group behavior can provide a mechanism for defense against predators, better foraging and mating capabilities and increased hydro/aerodynamic efficiency in long-distance migration events. Although collective motion has received much scientific attention, more work is required to model and understand the mechanisms responsible for school initiation and formation, and information transfer within these groups. Here we investigate schooling of Black Tetra (Gymnocorymbus ternetzi) fish triggered by startle stimuli in the form of approaching objects. High-speed video and tagging techniques were used to track the school and individual members. We then measured several variables including reaction times, group formation shapes, fish velocity, group density, and leadership within the group. These data reveal three things: 1) information propagates through the group as a wave, indicating that each fish is not reacting individually to the stimulus, 2) the time taken for information to transfer across the group is independent of group density, and 3) information propagates across large groups faster than would be expected if the fish were simply responding to the motion of their nearest neighbor. A model was then built wherein simulated fish have a simple `stimuli/escape' vector based on a hypothetical field of vision. The model was used to simulate a group of individual fish with initial conditions, size, and stimuli similar to the biological experiments. The model revealed similar behavior to the biological experiments and provide insights into the observed patterns, response times, and wave speeds.
Transitive inference in Polistes paper wasps
Venue: Biology Letters

Transitive inference (TI) is a form of logical reasoning that involves using known relationships to infer unknown relationships (A > B; B > C; then A > C). TI has been found in a wide range of vertebrates but not in insects. Here, we test whether Polistes dominula and Polistes metricus paper wasps can solve a TI problem. Wasps were trained to discriminate between five elements in series (A0B−, B0C−, C0D−, D0E−), then tested on novel, untrained pairs (B versus D). Consistent with TI, wasps chose B more frequently than D. Wasps organized the trained stimuli into an implicit hierarchy and used TI to choose between untrained pairs. Species that form social hierarchies like Polistes may be predisposed to spontaneously organize information along a common underlying dimension. This work contributes to a growing body of evidence that the miniature nervous system of insects does not limit sophisticated behaviours.
Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers
Venue: Cell

Long-range (>10 μm) transport of electrons along networks of Geobacter sulfurreducens protein filaments, known as microbial nanowires, has been invoked to explain a wide range of globally important redox phenomena. These nanowires were previously thought to be type IV pili composed of PilA protein. Here, we report a 3.7 Å resolution cryoelectron microscopy structure, which surprisingly reveals that, rather than PilA, G. sulfurreducens nanowires are assembled by micrometer-long polymerization of the hexaheme cytochrome OmcS, with hemes packed within ∼3.5-6 Å of each other. The inter-subunit interfaces show unique structural elements such as inter-subunit parallel-stacked hemes and axial coordination of heme by histidines from neighboring subunits. Wild-type OmcS filaments show 100-fold greater conductivity than other filaments from a ΔomcS strain, highlighting the importance of OmcS to conductivity in these nanowires. This structure explains the remarkable capacity of soil bacteria to transport electrons to remote electron acceptors for respiration and energy sharing.
Flight activity in pallid swifts Apus pallidus during the non-breeding period
Venue: Journal of Avian Biology

Flight activity recorders have recently confirmed that alpine and common swifts spend the majority of their non-breeding period on the wing, which may last 6–10 months. Here we test the hypothesis that the closely related pallid swift, a species with a breeding distribution around the Mediterranean, lead a similar aerial life-style during its migration and wintering periods. The pallid swift usually lays two clutches in one season and therefore spends more time in the breeding area than the common swift. We successfully tracked four pallid swifts with data loggers that record light for geolocation and acceleration every 5 min to monitor flight activity. The birds wintered south of the Sahel in west Africa from the Ivory Coast to Cameroon. The pallid swifts spent the majority of their non-breeding time in flight, especially the first two months after leaving the breeding area in autumn, while a few landing events occurred during the winter. The total time grounded was < 1%, similar to that of the common and alpine swifts. The mass specific flight metabolic rate of swifts is similar to the average non-breeding metabolic rate of a long distance terrestrial migrant, suggesting swifts are not more likely to procure oxidative damage as a consequence of continuous flight than other migrants. The open airspace used by swifts may provide a relatively safe habitat that explain the high survival rate found in swifts.
Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade‐off in sperm evolution
Venue: Journal of Evolutionary Biology

Sperm morphology varies enormously across the animal kingdom. Whilst knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterized by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light and scanning electron microscopy, we examined among‐species correlations between the occurrence of sperm head abnormalities and sperm morphology, as well as the correlation between sperm head abnormalities and two indicators of sperm competition. We found that species with more helically shaped sperm heads (i.e., a wider helical membrane and more pronounced cell waveform) had a higher percentage of abnormal sperm heads than species with less helical sperm (i.e., relatively straight sperm) and that sperm head traits were better predictors of head abnormalities than total sperm length. In contrast, there was no correlation between sperm abnormalities and the level of sperm competition. Given that songbird species with more pronounced helical sperm have higher average sperm swimming speed, our results suggest an evolutionary trade‐off between sperm performance and the structural integrity of the sperm head. As such, susceptibility to morphological abnormalities may constrain the evolution of helical sperm morphology in songbirds.
Wake-induced ‘slaloming’ response explains exquisite sensitivity of seal whisker-like sensors
Venue: Journal of Fluid Mechanics

Blindfolded harbour seals are able to use their uniquely shaped whiskers to track vortex wakes left by moving animals and identify objects that passed by 30 s earlier, an impressive feat, as the flow features have velocities as low as $1~\text{mm}~\text{s}^{-1}$ . The seals sense while swimming, hence their whiskers are sensitive enough to detect small-scale changes in the flow, while rejecting self-generated flow noise. Here we identify and illustrate a novel flow mechanism, causing a large-amplitude ‘slaloming’ whisker response, which allows artificial whiskers with the identical unique undulatory geometry as those of the harbour seal to detect the features of minute flow fluctuations when placed within wakes. Whereas in open water the whisker responds with very low-amplitude vibration, once within a wake, it oscillates with large amplitude and, importantly, its response frequency coincides with the Strouhal frequency of the upstream cylinder, making the detection of an upstream wake and an estimation of the size and shape of the wake-generating body possible. This mechanism has some similarities with the flow mechanisms observed in actively controlled propulsive foils within upstream wakes and trout swimming behind bluff cylinders in a stream, but there are also differences caused by the unique whisker morphology, which enables it to respond passively and within a much wider parametric range.
Contrasting Behavior of Antifreeze Proteins: Ice Growth Inhibitors and Ice Nucleation Promoters.
Venue: Journal of Physical Chemistry Letters

Several types of natural molecules interact specifically with ice crystals. Small antifreeze proteins (AFPs) adsorb to particular facets of ice crystals, thus inhibiting their growth, whereas larger ice-nucleating proteins (INPs) can trigger the formation of new ice crystals at temperatures much higher than the homogeneous ice nucleation temperature of pure water. It has been proposed that both types of proteins interact similarly with ice and that, in principle, they may be able to exhibit both functions. Here we investigated two naturally occurring antifreeze proteins, one from fish, type-III AFP, and one from beetles, TmAFP. We show that in addition to ice growth inhibition, both can also trigger ice nucleation above the homogeneous freezing temperature, providing unambiguous experimental proof for their contrasting behavior. Our analysis suggests that the predominant difference between AFPs and INPs is their molecular size, which is a very good predictor of their ice nucleation temperature.
In situ enrichment of microbial communities on polarized electrodes deployed in alkaline hot springs
Venue: Journal of Power Sources

The discovery of the ability of microorganisms to exchange electrons with inert electrodes has triggered new areas in fundamental and applied research. However, the field is currently limited to several known electrochemically active microorganisms enriched and isolated in research laboratories. An alternative strategy is to enrich such microorganisms in their native environment by allowing them to exchange electrons with polarized solid electrodes. The use of this approach is currently limited because of a lack of available tools. We developed a low-cost, battery-operated potentiostat that is capable of controlling the potential of a working electrode and can be deployed and operated remotely, allowing the enrichment of microorganisms on electrodes in their native environment. The device was tested in four alkaline hot springs in Heart Lake Geyser Basin in Yellowstone National Park (with a temperature ranging from 45 οC to 91 οC and a relatively constant pH of 8.5–8.7). Microbial community analysis showed a change in microbial community structure after 32 days of polarization. The impact of polarization on microbial community was most substantial on the electrodes that generated the highest cathodic and anodic currents, suggesting a direct impact of polarization on electrode microbial community.
Gyroscopic stabilization minimizes drag on Ruellia ciliatiflora seeds
Venue: Journal of the Royal Society Interface

Fruits of Ruellia ciliatiflora (Acanthaceae) explosively launch small (2.5 mm diameter × 0.46 mm thick), disc-shaped seeds at velocities over 15 m s−1, reaching distances of up to 7 m. Through high-speed video analysis, we observe that seeds fly with extraordinary backspin of up to 1660 Hz. By modelling the seeds as spinning discs, we show that flying with backspin is stable against gyroscopic precession. This stable backspin orientation minimizes the frontal area during flight, decreasing drag force on the seeds and thus increasing dispersal distance. From high-speed video of the seeds' flight, we experimentally determine drag forces that are 40% less than those calculated for a sphere of the same volume and density. This reduces the energy costs for seed dispersal by up to a factor of five.
Collective ventilation in honeybee nests
Venue: Journal of the Royal Society Interface

European honey bees (Apis mellifera) live in large congested nest cavities with a single opening that limits passive ventilation. When the local air temperature exceeds a threshold, the nests are actively ventilated by bees fanning their wings at the nest entrance. Here, we show that colonies with relatively large nest entrances use an emergent ventilation strategy where fanning bees self-organize to form groups, separating regions of continuous inflow and outflow. The observed spatio-temporal patterns correlate the air velocity and air temperature along the entrances to the distribution of fanning bees. A mathematical model that couples these variables to known fanning behaviour of individuals recapitulates their collective dynamics. Additionally, the model makes predictions about the temporal stability of the fanning group as a function of the temperature difference between the environment and the nest. Consistent with these predictions, we observe that the fanning groups drift, cling to the entrance boundaries, break-up and reform as the ambient temperature varies over a period of days. Overall, our study shows how honeybees use flow-mediated communication to self-organize into a steady state in fluctuating environments.
Phototactic tails: Evolution and molecular basis of a novel sensory trait in sea snakes
Venue: Molecular Ecology

Dermal phototaxis has been reported in a few aquatic vertebrate lineages spanning fish, amphibians and reptiles. These taxa respond to light on the skin of their elongate hind‐bodies and tails by withdrawing under cover to avoid detection by predators. Here, we investigated tail phototaxis in sea snakes (Hydrophiinae), the only reptiles reported to exhibit this sensory behaviour. We conducted behavioural tests in 17 wild‐caught sea snakes of eight species by illuminating the dorsal surface of the tail and midbody skin using cold white, violet, blue, green and red light. Our results confirmed phototactic tail withdrawal in the previously studied Aipysurus laevis, revealed this trait for the first time in A. duboisii and A. tenuis, and suggested that tail photoreceptors have peak spectral sensitivities between blue and green light (457–514 nm). Based on these results, and an absence of photoresponses in five Aipysurus and Hydrophis species, we tentatively infer that tail phototaxis evolved in the ancestor of a clade of six Aipysurus species (comprising 10% of all sea snakes). Quantifying tail damage, we found that the probability of sustaining tail injuries was not influenced by tail phototactic ability in snakes. Gene profiling showed that transcriptomes of both tail skin and body skin lacked visual opsins but contained melanopsin (opn4x) in addition to key genes of the retinal regeneration and phototransduction cascades. This work suggests that a nonvisual photoreceptor (e.g., Gq rhabdomeric) signalling pathway underlies tail phototaxis, and provides candidate gene targets for future studies of this unusual sensory innovation in reptiles.
Bacterial chemolithoautotrophy via manganese oxidation
Venue: Nature

Manganese is one of the most abundant elements on Earth. The oxidation of manganese has long been theorized1—yet has not been demonstrated2–4—to fuel the growth of chemolithoautotrophic microorganisms. Here we refine an enrichment culture that exhibits exponential growth dependent on Mn(II) oxidation to a co-culture of two microbial species. Oxidation required viable bacteria at permissive temperatures, which resulted in the generation of small nodules of manganese oxide with which the cells associated. The majority member of the culture—which we designate ‘Candidatus Manganitrophus noduliformans’—is affiliated to the phylum Nitrospirae (also known as Nitrospirota), but is distantly related to known species of Nitrospira and Leptospirillum. We isolated the minority member, a betaproteobacterium that does not oxidize Mn(II) alone, and designate it Ramlibacter lithotrophicus. Stable-isotope probing revealed 13CO2 fixation into cellular biomass that was dependent upon Mn(II) oxidation. Transcriptomic analysis revealed candidate pathways for coupling extracellular manganese oxidation to aerobic energy conservation and autotrophic CO2 fixation. These findings expand the known diversity of inorganic metabolisms that support life, and complete a biogeochemical energy cycle for manganese5,6 that may interface with other major global elemental cycles. A co-culture of two newly identified microorganisms—‘Candidatus Manganitrophus noduliformans’ and Ramlibacter lithotrophicus—exhibits exponential growth that is dependent on manganese(II) oxidation, demonstrating the viability of this metabolism for supporting life.
Unique structural features of a bacterial autotransporter adhesin suggest mechanisms for interaction with host macromolecules
Venue: Nature Communications

Autotransporters are the largest family of outer membrane and secreted proteins in Gram-negative bacteria. Most autotransporters are localised to the bacterial surface where they promote colonisation of host epithelial surfaces. Here we present the crystal structure of UpaB, an autotransporter that is known to contribute to uropathogenic E. coli (UPEC) colonisation of the urinary tract. We provide evidence that UpaB can interact with glycosaminoglycans and host fibronectin. Unique modifications to its core β-helical structure create a groove on one side of the protein for interaction with glycosaminoglycans, while the opposite face can bind fibronectin. Our findings reveal far greater diversity in the autotransporter β-helix than previously thought, and suggest that this domain can interact with host macromolecules. The relevance of these interactions during infection remains unclear.Autotransporter proteins are localised to the bacterial surface and promote colonisation of host epithelial surfaces. Here, the authors present the crystal structure of autotransporter UpaB and show evidence for distinct binding sites for glycosaminoglycans and host fibronectin.
The central role of Clark's nutcracker in the dispersal and establishment of whitebark pine
Venue: Oecologia

SummaryWhitebark pine (Pinus albicaulis) is known to have its seeds harvested and cached in the soil by Clark's Nutcracker (Nucifraga columbiana), and unretrieved seeds are known to be capable of germinating and establishing new pines. Many other vertebrates also harvest and feed on these seeds, however, and the roles of these animals as dispersers and establishers of whitebark pine has been uncertain. This work demonstrates that birds other than the nutcracker, rodents, and other mammals do not have the requisite behaviors to systematically disperse or establish whitebark pine, and that the pine is therefore dependent on the nutcracker for its regeneration. These findings support previous suggestions that Clark's Nutcracker is a specialized frugivore that has profoundly influenced the ecology and the evolution of whitebark pine.
Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism
Venue: PLOS Biology

Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. Although much progress has been made in understanding the mechanisms of planar leaf development, it is unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. Here, we use 3D imaging and cellular and clonal analysis, combined with computational modelling, to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. We show that the transformation from a near-spherical form at early developmental stages to an oblate spheroid with a straightened ventral midline in the mature form can be accounted for by spatial variations in rates and orientations of growth. Different hypotheses regarding spatiotemporal control predict distinct patterns of cell shape and size, which were tested experimentally by quantifying cellular and clonal anisotropy. We propose that orientations of growth are specified by a proximodistal polarity field, similar to that hypothesised to account for Arabidopsis leaf development, except that in Utricularia, the field propagates through a highly curved tissue sheet. Independent evidence for the polarity field is provided by the orientation of glandular hairs on the inner surface of the trap. Taken together, our results show that morphogenesis of complex 3D leaf shapes can be accounted for by similar mechanisms to those for planar leaves, suggesting that simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies.