nils-herrmann/clean_scirepeval huggingface dataset:
Hedgehog signaling is necessary and sufficient to mediate craniofacial plasticity in teleosts
Venue: Proceedings of the National Academy of Sciences of the United States of America

Phenotypic plasticity has emerged as an important concept in evolutionary biology. It is thought to contribute to an organism’s ability to adapt to environmental change within a single generation, which may facilitate survival and increase fitness. Furthermore, plasticity has the potential to bias the direction and/or speed of evolution by changing patterns of phenotypic variation and exposing new genetic variation to selection (i.e., flexible stem evolution). Our understanding of this important phenomenon is incomplete owing to limited knowledge of the molecular underpinnings of reaction norm evolution. Using the teleost feeding apparatus as a model, we explore this open question and show that the Hh signaling pathway underlies the ability of this structure to respond plastically to alternate feeding regimes. Phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes under different environmental conditions, is critical for the origins and maintenance of biodiversity; however, the genetic mechanisms underlying plasticity as well as how variation in those mechanisms can drive evolutionary change remain poorly understood. Here, we examine the cichlid feeding apparatus, an icon of both prodigious evolutionary divergence and adaptive phenotypic plasticity. We first provide a tissue-level mechanism for plasticity in craniofacial shape by measuring rates of bone deposition within functionally salient elements of the feeding apparatus in fishes forced to employ alternate foraging modes. We show that levels and patterns of phenotypic plasticity are distinct among closely related cichlid species, underscoring the evolutionary potential of this trait. Next, we demonstrate that hedgehog (Hh) signaling, which has been implicated in the evolutionary divergence of cichlid feeding architecture, is associated with environmentally induced rates of bone deposition. Finally, to demonstrate that Hh levels are the cause of the plastic response and not simply the consequence of producing more bone, we use transgenic zebrafish in which Hh levels could be experimentally manipulated under different foraging conditions. Notably, we find that the ability to modulate bone deposition rates in different environments is dampened when Hh levels are reduced, whereas the sensitivity of bone deposition to different mechanical demands increases with elevated Hh levels. These data advance a mechanistic understanding of phenotypic plasticity in the teleost feeding apparatus and in doing so contribute key insights into the origins of adaptive morphological radiations.
Prey Exploits the Auditory Illusions of Eavesdropping Predators
Venue: The American Naturalist

Mating signals have evolved to attract target receivers, even to the point of exploiting receivers through perceptual manipulation. Signals, however, can also expose signalers to nontarget receivers, including predators and parasites, and thus have also evolved to decrease enemy attraction. Here we show that male tree frogs (Smilisca sila) reduce their attractiveness to eavesdropping enemies (bats and midges) by overlapping their calls at near-perfect synchrony with the calls of neighboring conspecifics. By producing calls that closely follow those of other males, synchronizing S. sila take advantage of an auditory illusion where enemies are more attracted to the leading call. Female S. sila, however, are less susceptible to this illusion. Thus, synchronization among signaling males can result in acoustic crypsis from predators without affecting female attraction. Given the widespread use of conspicuous mating signals and eavesdropping enemies, perceptual exploitation of eavesdroppers is likely a common driver of signal evolution.
The high speed radular prey strike of a fish-hunting cone snail
Venue: Current Biology

Cone snails are venomous marine gastropods that hydraulically propel a hollow, chitinous radular harpoon into prey . This radular harpoon serves both as projectile and conduit for venom delivery. In the fish-hunting cone snail Conus catus, the radular harpoon is also utilized to tether the snail to its prey, rapidly paralyzed by neuroexcitatory peptides [2,3]. Effective prey capture in C. catus requires both fast-acting neurotoxins and a delivery system quick enough to exceed the prey fish's rapid escape responses . We report here that the cone snail's prey strike is one of the fastest in the animal kingdom. A unique cellular latch mechanism prevents harpoon release until sufficient pressure builds and overcomes the forces of the latch, resulting in rapid acceleration into prey . The radular harpoon then rapidly decelerates as its bulbous base reaches the end of the proboscis, a distensible hydrostatic skeleton extended toward the prey , with little slowing during prey impalement. The velocities achieved are the fastest movements of any mollusk and exceed previous estimates by over an order of magnitude .
The potential of the solitary parasitoid Microctonus brassicae for the biological control of the adult cabbage stem flea beetle, Psylliodes chrysocephala
Venue: Entomologia Experimentalis Et Applicata

The cabbage stem flea beetle (CSFB), Psylliodes chrysocephala L. (Coleoptera: Chrysomelidae), is a major pest of oilseed rape, Brassica napus L. (Brassicaceae), within the UK and continental Europe. Following the withdrawal of many broad‐spectrum pesticides, most importantly neonicotinoids, and with increased incidence of pyrethroid resistance, few chemical control options remain, resulting in the need for alternative pest management strategies. We identified the parasitoid wasp Microctonus brassicae (Haeselbarth) (Hymenoptera: Braconidae) within CSFB collected from three independent sites in Norfolk, UK. Parasitism of adult CSFB was confirmed, and wasp oviposition behaviour was described. Moreover, we show that within captive colonies parasitism rates are sufficient to generate significant biological control of CSFB populations. A sequence of the M. brassicae mitochondrial cytochrome oxidase 1 (MT‐CO1) gene was generated for rapid future identification. Moroccan specimens of Microctonus aethiopoides (Loan), possessing 90% sequence similarity, were the closest identified sequenced species. This study represents the first description published in English of this parasitoid of the adult cabbage stem flea beetle.
Automatic control: the vertebral column of dogfish sharks behaves as a continuously variable transmission with smoothly shifting functions
Venue: The Journal of Experimental Biology

During swimming in dogfish sharks, Squalus acanthias, both the intervertebral joints and the vertebral centra undergo significant strain. To investigate this system, unique among vertebrates, we cyclically bent isolated segments of 10 vertebrae and nine joints. For the first time in the biomechanics of fish vertebral columns, we simultaneously characterized non-linear elasticity and viscosity throughout the bending oscillation, extending recently proposed techniques for large-amplitude oscillatory shear (LAOS) characterization to large-amplitude oscillatory bending (LAOB). The vertebral column segments behave as non-linear viscoelastic springs. Elastic properties dominate for all frequencies and curvatures tested, increasing as either variable increases. Non-linearities within a bending cycle are most in evidence at the highest frequency, 2.0 Hz, and curvature, 5 m−1. Viscous bending properties are greatest at low frequencies and high curvatures, with non-linear effects occurring at all frequencies and curvatures. The range of mechanical behaviors includes that of springs and brakes, with smooth transitions between them that allow for continuously variable power transmission by the vertebral column to assist in the mechanics of undulatory propulsion.  Characterization of non-linear elasticity and viscosity throughout the bending oscillation reveals that the shark vertebral column behaves as both a spring and a brake, with smooth transitions between them for continuously variable power transmission.
Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life
Venue: Genome Biology

Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown. By parent-offspring whole genome sequencing, we estimate a mutation rate (3.38 ×  10−6 per bp per generation) that is two orders of magnitude higher than reported for any non-viral organism, with 93–98% of mutations being RIP-associated. RIP mutations are, however, relatively rare in coding sequence, in part because RIP preferentially attacks GC-poor long duplicates that interact in three dimensional space, while coding sequence duplicates are rare, GC-rich, short, and tend not to interact. Despite this, with over 5 coding sequence mutations per genome per generation, the mutational burden is an order of magnitude higher than the previously highest observed. Unexpectedly, the majority of these coding sequence mutations appear not to be the direct product of RIP being mostly in non-duplicate sequence and predominantly not C→T mutations. Nonetheless, RIP-deficient strains have over an order of magnitude fewer coding sequence mutations outside of duplicated domains than RIP-proficient strains. Neurospora crassa has the highest mutation rate and mutational burden of any non-viral life. While the high rate is largely due to the action of RIP, the mutational burden appears to be RIP-associated but not directly caused by RIP.
Dynamic pigmentary and structural coloration within cephalopod chromatophore organs
Venue: Nature Communications

Chromatophore organs in cephalopod skin are known to produce ultra-fast changes in appearance for camouflage and communication. Light-scattering pigment granules within chromatocytes have been presumed to be the sole source of coloration in these complex organs. We report the discovery of structural coloration emanating in precise register with expanded pigmented chromatocytes. Concurrently, using an annotated squid chromatophore proteome together with microscopy, we identify a likely biochemical component of this reflective coloration as reflectin proteins distributed in sheath cells that envelop each chromatocyte. Additionally, within the chromatocytes, where the pigment resides in nanostructured granules, we find the lens protein Ω- crystallin interfacing tightly with pigment molecules. These findings offer fresh perspectives on the intricate biophotonic interplay between pigmentary and structural coloration elements tightly co-located within the same dynamic flexible organ - a feature that may help inspire the development of new classes of engineered materials that change color and pattern.Chromatophores in cephalopod skin are known for fast changes in coloration due to light-scattering pigment granules. Here, authors demonstrate structural coloration facilitated by reflectin in sheath cells and offer insights into the interplay between structural and pigmentary coloration elements.
Species richness and redundancy promote persistence of exploited mutualisms in yeast
Venue: Science

Species richness maintains mutualisms Mutualistic communities of species that benefit each other are ubiquitous in ecosystems and are important for ecosystem functioning. However, the relationship between the persistence of mutualisms and species richness has remained unclear. Vidal et al. used a synthetic mutualism in brewer's yeast to experimentally test whether species richness buffers mutualistic communities against exploitation by species that do not provide benefits in return. They showed that richer mutualist communities survive exploitation more often than pairwise mutualisms and that higher species richness and functional redundancy allow mutualist communities to persist in the presence of exploiters. These results provide experimental support for the hypothesis that species richness is necessary for the function and maintenance of mutualistic communities. Science, this issue p. 346 Experiments with yeast show that species richness buffers against loss of mutualistic interactions in ecological communities. Mutualisms, or reciprocally beneficial interspecific interactions, constitute the foundation of many ecological communities and agricultural systems. Mutualisms come in different forms, from pairwise interactions to extremely diverse communities, and they are continually challenged with exploitation by nonmutualistic community members (exploiters). Thus, understanding how mutualisms persist remains an essential question in ecology. Theory suggests that high species richness and functional redundancy could promote mutualism persistence in complex mutualistic communities. Using a yeast system (Saccharomyces cerevisiae), we experimentally show that communities with the greatest mutualist richness and functional redundancy are nearly two times more likely to survive exploitation than are simple communities. Persistence increased because diverse communities were better able to mitigate the negative effects of competition with exploiters. Thus, large mutualistic networks may be inherently buffered from exploitation.
Longer-lived tropical songbirds reduce breeding activity as they buffer impacts of drought
Venue: Nature Climate Change

Droughts are expected to increase in frequency and severity with climate change. Population impacts of such harsh environmental events are theorized to vary with life history strategies among species. However, existing demographic models generally do not consider behavioural plasticity that may modify the impact of harsh events. Here we show that tropical songbirds in the New and Old Worlds reduced reproduction during drought, with greater reductions in species with higher average long-term survival. Large reductions in reproduction by longer-lived species were associated with higher survival during drought than predrought years in Malaysia, whereas shorter-lived species maintained reproduction and survival decreased. Behavioural strategies of longer-lived, but not shorter-lived, species mitigated the effect of increasing drought frequency on long-term population growth. Behavioural plasticity can buffer the impact of climate change on populations of some species and differences in plasticity among species related to their life histories are critical for predicting population trajectories. Climate change impacts on population dynamics will depend on species’ life history strategies. In contrast to short-lived species, longer-lived tropical songbirds reduced reproduction during drought, leading to higher survival and mitigating the effect on long-term population growth.
Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection
Venue: Proceedings of the National Academy of Sciences of the United States of America

Several nodule-specific cysteine-rich (NCR) peptides expressed in a model legume Medicago truncatula exhibit potent antimicrobial activity. However, their structure–activity relationships and mechanisms of action against fungal pathogens of plants are still largely unknown. A small highly cationic peptide NCR044 with potent antifungal activity has been identified. This peptide has a unique highly dynamic structure and exhibits multifaceted mechanisms of action against a fungal pathogen Botrytis cinerea. Exogenous application of this peptide confers resistance to a gray mold disease caused by B. cinerea in tobacco and tomato plants as well as postharvest products. Our work paves the way for future development of NCR peptides as spray-on antifungal agents. In the indeterminate nodules of a model legume Medicago truncatula, ∼700 nodule-specific cysteine-rich (NCR) peptides with conserved cysteine signature are expressed. NCR peptides are highly diverse in sequence, and some of these cationic peptides exhibit antimicrobial activity in vitro and in vivo. However, there is a lack of knowledge regarding their structural architecture, antifungal activity, and modes of action against plant fungal pathogens. Here, the three-dimensional NMR structure of the 36-amino acid NCR044 peptide was solved. This unique structure was largely disordered and highly dynamic with one four-residue α-helix and one three-residue antiparallel β-sheet stabilized by two disulfide bonds. NCR044 peptide also exhibited potent fungicidal activity against multiple plant fungal pathogens, including Botrytis cinerea and three Fusarium spp. It inhibited germination in quiescent spores of B. cinerea. In germlings, it breached the fungal plasma membrane and induced reactive oxygen species. It bound to multiple bioactive phosphoinositides in vitro. Time-lapse confocal and superresolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, subsequent accumulation in the cytoplasm, and elevated levels in nucleoli of germlings. Spray-applied NCR044 significantly reduced gray mold disease symptoms caused by the fungal pathogen B. cinerea in tomato and tobacco plants, and postharvest products. Our work illustrates the antifungal activity of a structurally unique NCR peptide against plant fungal pathogens and paves the way for future development of this class of peptides as a spray-on fungistat/fungicide.
Vividly coloured poppy flowers due to dense pigmentation and strong scattering in thin petals
Venue: Journal of Comparative Physiology A-neuroethology Sensory Neural and Behavioral Physiology

The flowers of poppies (Papaveraceae) exhibit bright colours, despite their thin and floppy petals. We investigated the optical properties of flowers of Papaver rhoeas, P. dubium, Meconopsis cambrica and Argemone polyanthemos using a combined approach of anatomy, spectrophotometry and optical modelling. The petals of Papaver flowers are composed of only three cell layers, an upper and lower epidermal layer, which are densely filled with pigment, and an unpigmented mesophyll layer. Dense pigmentation together with strong scattering structures, composed of serpentine cell walls and air cavities, cause the striking poppy colours. We discuss how various aspects of the optical signal contribute to the flower’s visibility to pollinators.
Pupil Diameter Tracks Statistical Structure in the Environment to Increase Visual Sensitivity
Venue: The Journal of Neuroscience

Pupil diameter determines how much light hits the retina and, thus, how much information is available for visual processing. This is regulated by a brainstem reflex pathway. Here, we investigate whether this pathway is under the control of internal models about the environment. This would allow adjusting pupil dynamics to environmental statistics to augment information transmission. We present image sequences containing internal temporal structure to humans of either sex and male macaque monkeys. We then measure whether the pupil tracks this temporal structure not only at the rate of luminance variations, but also at the rate of statistics not available from luminance information alone. We find entrainment to environmental statistics in both species. This entrainment directly affects visual processing by increasing sensitivity at the environmentally relevant temporal frequency. Thus, pupil dynamics are matched to the temporal structure of the environment to optimize perception, in line with an active sensing account.  When light hits the retina, the pupil reflexively constricts. This determines how much light and thus how much information is available for visual processing. We show that the rate at which the pupil constricts and dilates is matched to the temporal structure of our visual environment, although this information is not directly contained in the light variations that usually trigger reflexive pupil constrictions. Adjusting pupil diameter in accordance with environmental regularities optimizes information transmission at ecologically relevant temporal frequencies. We show that this is the case in humans and macaque monkeys, suggesting that the reflex pathways that regulate pupil diameter are under some degree of cognitive control across primate species.
Moving pieces in a cellular puzzle: a cryptic peptide from the scorpion toxin Ts14 activates AKT and ERK signaling and decreases cardiac myocyte contractility via dephosphorylation of phospholamban.
Venue: Journal of Proteome Research

Cryptic peptides (cryptides) are biologically active peptides formed after proteolysis of native precursors present in animal venoms, for example. Proteolysis is an overlooked post-translational modification (PTM) that increases venom complexity. The tripeptide KPP (Lys-Pro-Pro) is a peptide encrypted in the C-terminus of Ts14 - a 25-mer peptide from the venom of Tityus serrulatus scorpion that has a positive impact on the cardiovascular system, inducing vasodilation and reducing arterial blood pressure of hypertensive rats, among other beneficial effects. A previous study reported that KPP and its native peptide Ts14 act via activation of the bradykinin receptor B2 (B2R). However, the cellular events underlying the activation of B2R by KPP are unknown. To study the cell signaling triggered by the Ts14 cryptide KPP, we incubated cardiac myocytes isolated from C57BL/6 mice with KPP (10-7 mol.L-1) for 0 min, 5 min or 30 min and explored the proteome and phosphoproteome. Our results showed that KPP regulated cardiomyocyte proteins associated with, but not limited to, apoptosis, muscle contraction, protein turnover, and the respiratory chain. We also reported that KPP led to AKT phosphorylation, activating AKT and its downstream target eNOS. We also observed that KPP led to dephosphorylation of phospholamban (PLN) at its activation sites (S16 and T17) leading to reduced contractility of treated cardiomyocytes. Some cellular targets reported here for KPP (e.g., AKT, PLN and ERK) have already been reported to protect cardiac tissue of hypoxia-induced injury. Hence, this study suggests potential beneficial effects of this scorpion cryptide that needs to be further investigated, for example as a drug lead for cardiac infarction.
Friend or Foe? Orb-Weaver Spiders Inhabiting Ant–Acacias Capture Both Herbivorous Insects and Acacia Ant Alates
Venue: Journal of Insect Science

The orb-weaver spiders Eustala oblonga (Chickering) and Eustala illicita (O. Picard-Cambridge) (Araneae: Araneidae) inhabit the ant-defended acacias Vachellia melanocerus (Beurling) and Vachellia collinsii (Safford) ), respectively, in Panama. These spiders do not capture patrolling Pseudomyrmex ants but exploit their plant-protection services to escape predation. What effect the spiders have on the ant-acacia mutualisms is unknown. They may provide an additional layer of plant defense by capturing flying herbivorous insects in their webs. Alternatively, the spiders may disrupt the ant–acacia mutualisms by capturing alate acacia ants during nuptial flights. We evaluated these two hypotheses by sampling insects flying through acacia foliage and by identifying prey remains in webs. The proportions of insects captured on sticky card traps and in webs varied with taxonomic order and ecological role. Herbivorous insects greatly outnumbered other groups captured on sticky cards and were captured in spiders’ webs in both acacia species but made up a minority of prey remains in webs. Instead, insect predators and parasitoids made up the majority of prey remains and were comprised primarily by alate ant mutualists of the host acacias. These results provide indirect support for both hypotheses and suggest that the spiders potentially both benefit and harm their host ant-acacia mutualisms. The net effect of spider exploitation, however, is unclear and is likely based on both the effectiveness of plant protection from herbivory provided by the spiders relative to that provided by acacia ants, as well as the overall proportion of the ant reproductive caste the spiders actually capture.