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opencc-zeroJun 2021View details →

Phylogenetic patterns of trait and trait plasticity evolution: Insights from tadpoles

Environmental heterogeneity has led to widespread evolution of phenotypic plasticity in all taxonomic groups. Although phenotypic plasticity has been examined from multiple perspectives, few studies have examined evolutionary patterns of plasticity within a phylogeny. We conducted common-garden experiments on 20 species of tadpoles, spanning three families, exposed for 4 weeks to a control, predator cues, or reduced food (i.e., increased intraspecific competition). We quantified tadpole activity, growth, and relative morphology and found widespread differences in species responses to predator cues and reduced food. We detected pervasive phylogenetic signals in traits within each environment, but phylogenetic signal was much less common in the trait plasticities. Among different models of continuous character evolution, Brownian Motion and Ornstein Uhlenbeck models provided better fits to the data than the Early Burst model. Tadpole activity level in predator environments had much higher evolutionary rates than in the control and reduced-food environments; we did not see this pattern in the other traits. In comparing traits versus trait plasticities, activity evolved much faster than the plasticity of activity whereas morphological traits evolved much slower than morphological plasticities . Collectively, these results suggest that traits and trait plasticities can exhibit dramatically different evolutionary patterns.

opencc-zeroJul 2021View details →

Interindividual plasticity in metabolic and thermal tolerance traits from populations subjected to recent anthropogenic heating

To better understand temperature's role in the interaction between local evolutionary adaptation and physiological plasticity, we investigated acclimation effects on metabolic performance and thermal tolerance among natural Fundulus heteroclitus populations from different thermal environments. F. heteroclitus populations experience large daily and seasonal temperature variations, as well as local mean temperature differences across their large geographic cline. In this study, we focus on three populations: one locally heated (32°C) by thermal effluence (TE) from the Oyster Creek Nuclear Generating Station, NJ and two nearby reference populations that do not experience local heating (28°C). After acclimation to 12°C or 28°C, we quantified whole animal metabolic rate (WAM), critical thermal maximum (CTMax) and substrate specific cardiac metabolic rate (CaM, substrates: glucose, fatty acids, lactate plus ketones plus ethanol, and endogenous [i.e., no added substrates]) in ~160 individuals from these three populations. Populations showed few significant differences due to large interindividual variation within each population and variation in acclimation response within any single trait. In general, for WAM and CTMax the interindividual variation in acclimation response (log2 ratio 28°C/12°C) was a function of performance at 12°C with greater acclimation response for individuals that had lower 12°C performance. In contrast, for CaM the rates when acclimated and assayed at 12°C or 28°C were nearly identical. The small differences in CaM between 12°C and 28°C temperature were partially explained by cardiac remodeling where individuals acclimated to 12°C had larger hearts than individuals acclimated to 28°C, resulting in a higher CaM rate per unit heart mass at 28°C than 12°C. Correlation among physiological traits were dependent on acclimation temperature. For example, WAM was negatively correlated with CTMax at 12°C but positively correlated at 28°C. Additionally, glucose substrate supported higher cardiac metabolism than fatty acid, and fatty acid supported higher cardiac metabolism than LKA or endogenous. However, these responses were highly variable with some individuals using much more FA than glucose. These data suggest a complex relationship between specific, temperature-dependent physiological traits.

opencc-zeroJul 2021View details →

Effect of Environmental Weathering on Biodegradation of Biodegradable Plastic Mulch Films under Ambient Soil and Composting Conditions

Plastic mulch films contribute to better crop production. Concerns for lack of sustainable disposal methods for conventional polyethylene (PE) mulch led to development of biodegradable plastic mulches (BDMs) that can be soil-incorporated or composted after use. Environmental weathering of BDMs during crop growth reduces their mechanical strength and alters the molecular structure of their polymeric components. However, the impact of weathering on BDMs' biodegradability is not fully understood. The biodegradability of agriculturally weathered and unweathered BDMs in soil and compost was compared using standardized laboratory tests (ASTM D5988 and D5338) using four BDMs (experimental polylactic acid and polyhydroxyalkanoate-based film [PLA/PHA] and three commercially available polybutyrate [PBAT]-based BDMs). In soil, biodegradation of weathered PLA/PHA was greater than its unweathered counterpart. For PBAT-based BDMs, the extent of biodegradation varied. A decrease of the weight-averaged molecular weight (Mw) of PBAT and PLA and thermostability of PLA, PHA, PBAT, and starch components was observed during biodegradation in the soil. The proportion of the minor components PHA and starch decreased during biodegradation, indicating preferential utilization of PHA over PLA and starch over PBAT by microbes. Bacterial abundance was significantly higher than fungal abundance in soil and was more prominent in soil adjacent to weathered than unweathered BDM treatments. Under composting conditions, unweathered PBAT-enriched mulches yielded higher CO2 evolution than their weathered counterpart. Together, these results suggest that environmental weathering enhances biodegradation of BDMs and mulch's polymeric constituents also influence the microbial degradation, more so for bacterial than fungal communities.

High plasticity in marmoset monkey vocal development from infancy to adulthood

The vocal behavior of human infants undergoes dramatic changes across their first year, while becoming increasingly speech-like. Surprisingly, vocal development in nonhuman primates has been assumed to be largely predetermined and completed within the first postnatal months. Contradicting this assumption, we found a dichotomy between the development of call features and vocal sequences in marmoset monkeys suggestive of a role for experience. While changes in call features were related to physical maturation, sequences of and transitions between calls remained flexible until adulthood. As in humans, marmoset vocal behavior developed in stages correlated with motor and social development stages. These findings are evidence for a prolonged phase of plasticity during marmoset vocal development, a crucial primate evolutionary preadaptation for the emergence of vocal learning and speech.

Evaluating the fitness consequences of plasticity in tolerance to pesticides

In a rapidly changing world, phenotypic plasticity may be a critical mechanism allowing populations to rapidly acclimate when faced with novel anthropogenic stressors. Theory predicts that if exposure to anthropogenic stress is heterogeneous, plasticity should be maintained as it allows organisms to avoid unnecessary expression of costly traits (i.e. phenotypic costs) when stressors are absent. Conversely, if exposure to stressors becomes constant, costs or limits of plasticity may lead to evolutionary trait canalization (i.e. genetic assimilation). While these concepts are well-established in theory, few studies have examined whether these factors explain patterns of plasticity in natural populations facing anthropogenic stress. Using wild populations of wood frogs that vary in plasticity in tolerance to pesticides, the goal of this study was to evaluate the environmental conditions under which plasticity is expected to be advantageous or detrimental. We found that when pesticides were absent, more plastic populations exhibited lower pesticide tolerance and were more fit than less plastic populations, likely avoiding the cost of expressing high tolerance when it was not necessary. Contrary to our predictions, when pesticides were present, more plastic populations were as fit as less plastic populations, showing no signs of costs or limits of plasticity. Amidst unprecedented global change, understanding the factors shaping the evolution of plasticity will become increasingly important.

opencc-zeroDec 2019View details →

Phenotypic plasticity in chemical defence allows butterflies to diversify host use strategies

Hostplant specialization is a major force driving ecological niche partitioning and diversification in insect herbivores. The cyanogenic defences of Passiflora plants keeps most herbivores at bay, but not larvae of Heliconius butterflies, which can both sequester and biosynthesize cyanogenic compounds. Here, we demonstrate that both Heliconius cydno chioneus, a host plant generalist, and H. melpomene rosina, a specialist, have remarkable plasticity in their chemical defence. When feeding on Passiflora species with cyanogenic compounds they can readily sequester, both species downregulate the biosynthesis of these compounds. In contrast, when fed on Passiflora plants that do not contain cyanogenic glucosides that can be sequestered, both species increase biosynthesis. This biochemical plasticity comes at a significant fitness cost for specialist like H. m. rosina, as growth rates for this species negatively correlate with biosynthesis levels, but not for a generalist like H. c. chioneus. In exchange, H. m rosina has increased performance when sequestration is possible as on its specialised hostplant. In summary, phenotypic plasticity in biochemical responses to different host plants offers these butterflies the ability to widen their range of potential host within the Passiflora genus, while maintaining their chemical defences.

Perineuronal nets in HVC and plasticity in male canary song

Songbirds learn their vocalizations during developmental sensitive periods of song memorization and sensorimotor learning. Some seasonal songbirds, called open-ended learners, recapitulate transitions from sensorimotor learning and song crystallization on a seasonal basis during adulthood. In adult male canaries, sensorimotor learning occurs each year in autumn and leads to modifications of the syllable repertoire during successive breeding seasons. We previously showed that perineuronal nets (PNN) expression in song control nuclei decreases during this sensorimotor learning period. Here we explored the causal link between PNN expression in adult canaries and song modification by enzymatically degrading PNN in HVC, a key song control system nucleus. Three independent experiments identified limited effects of the PNN degradation in HVC on the song structure of male canaries. They clearly establish that presence of PNN in HVC is not required to maintain general features of crystallized song. Some suggestion was collected that PNN are implicated in the stability of song repertoires but this evidence is too preliminary to draw firm conclusions and additional investigations should consider producing PNN degradations at specified time points of the seasonal cycle. It also remains possible that once song has been crystallized at the beginning of the first breeding season, PNN no longer play a key role in determining song structure; this could be tested by treatments with chondroitinase ABC at key steps in ontogeny. It would in this context be important to develop multiple stereotaxic procedures allowing the simultaneous bilateral degradation of PNN in several song control nuclei for extended periods.

Plasticity of the gastrocnemius elastic system in response to decreased work and power demand during growth

Elastic energy storage and release can enhance performance that would otherwise be limited by the force-velocity constraints of muscle. While functional influence of a biological spring depends on tuning between components of an elastic system (the muscle, spring, driven mass, and lever system), we do not know whether elastic systems systematically adapt to functional demand. To test whether altering work and power generation during maturation alters the morphology of an elastic system, we prevented growing guinea fowl (Numida Meleagris) from jumping. At maturity, we compared the jump performance of our treatment group to that of controls and measured the morphology of the gastrocnemius elastic system. We found that restricted birds jumped with lower jump power and work, yet there were no significant between-group differences in the components of the elastic system. Further, subject-specific models revealed no difference in energy storage capacity between groups, though energy storage was most sensitive to variations in muscle properties (most significantly operating length and least dependent on tendon stiffness). We conclude that the gastrocnemius elastic system in the guinea fowl displays little to no plastic response to decreased demand during growth and hypothesize that neural plasticity may explain performance variation.

Urbanization extends flight phenology and leads to local adaptation of seasonal plasticity in Lepidoptera

Urbanization is globally gaining force and challenges biodiversity but has recently also emerged as an agent of evolutionary change. Seasonal phenology and life-cycle regulation are essential processes that urbanization is likely to alter through both the urban-heat-island effect (UHI) and artificial-light-at-night (ALAN). However, how UHI and ALAN affect the evolution of seasonal adaptations has received little attention. Here, we test for urban evolution of seasonal life-history plasticity, specifically changes in the photoperiodic induction of diapause in two lepidopterans, Pieris napi (Pieridae) and Chiasmia clathrata (Geometridae). We used long-term data from standardized monitoring and citizen science observation schemes to compare yearly phenological flight curves in six cities in Finland and Sweden to those of adjacent rural populations. This analysis showed for both species that flight seasons are longer and end later in most cities, suggesting a difference in timing of diapause induction. Then, we used common-garden experiments to test whether evolution of the photoperiodic reaction norm for diapause could explain these phenological changes for a subset of these cities. These experiments demonstrated a genetic shift for both species in urban areas towards a lower daylength threshold for direct development, consistent with predictions based on the UHI but not ALAN. The correspondence of this genetic change to the results of our larger-scale observational analysis of in situ flight phenology indicates that it may be widespread. These findings suggest that seasonal life-cycle regulation evolves in urban ectotherms and may contribute to eco-evolutionary dynamics in cities.

opencc-by-4.0Sep 2021View details →

Heat waves affect prey and predators differently via developmental plasticity: who may benefit most from global warming?

Dataset of the results in the article: Heat waves affect prey and predators differently via developmental plasticity: who may benefit most from global warming? in Pest Management Science. <a href="https://doi.org/10.1002/ps.6722">https://doi.org/10.1002/ps.6722</a> This research was funded by the Austrian Science Fund (FWF).

Genetic differentiation underlies seasonal variation in thermal tolerance, body size, and plasticity in a short-lived copepod

Organisms experience variation in the thermal environment on several different temporal scales, with seasonality being particularly prominent in temperate regions. For organisms with short generation times, seasonal variation is experienced across, rather than within, generations. How this variation affects the seasonal evolution of thermal tolerance and phenotypic plasticity is understudied, but has direct implications for the thermal ecology of these organisms. Here we document intra-annual patterns of thermal tolerance in two species of Acartia copepods (Crustacea) from a highly seasonal estuary, showing strong variation across the annual temperature cycle. Common garden, split-brood experiments indicate that this seasonal variation in thermal tolerance, along with seasonal variation in body size and phenotypic plasticity, is likely affected by genetic polymorphism. Our results show that adaptation to seasonal variation is important to consider when predicting how populations may respond to ongoing climate change.

Limited plasticity in thermally tolerant ectotherm populations: evidence for a trade-off

Many species face extinction risks owing to climate change, and there is an urgent need to identify which species' populations will be most vulnerable. Plasticity in heat tolerance, which includes acclimation or hardening, occurs when prior exposure to a warmer temperature changes an organism's upper thermal limit. The capacity for thermal acclimation could provide protection against warming, but prior work has found few generalizable patterns to explain variation in this trait. Here, we report the results of, to our knowledge, the first meta-analysis to examine within-species variation in thermal plasticity, using results from 20 studies (19 species) that quantified thermal acclimation capacities across 78 populations. We used meta-regression to evaluate two leading hypotheses. The climate variability hypothesis predicts that populations from more thermally variable habitats will have greater plasticity, while the trade-off hypothesis predicts that populations with the lowest heat tolerance will have the greatest plasticity. Our analysis indicates strong support for the trade-off hypothesis because populations with greater thermal tolerance had reduced plasticity. These results advance our understanding of variation in populations' susceptibility to climate change and imply that populations with the highest thermal tolerance may have limited phenotypic plasticity to adjust to ongoing climate warming.

Phenotypic plasticity versus ecotypic differentiation under recurrent summer drought in two drought-tolerant pine species

1. Despite worldwide reports of high tree mortality, growing evidence indicates that many tree species are well adapted to survive repeated dry spells. The drought resilience of trees is related to their phenotypic plasticity and ecotypic differentiation. Whether these two mechanisms act at the same organisational level of a tree and involve similar plant traits is still unknown. 2. We assessed phenotypic plasticity and ecotypic differentiation across four populations of Pinus sylvestris and Pinus nigra seedlings grown for three years under a recurrent summer drought treatment or well-watered control conditions in a common garden. We measured the response to the summer drought treatment of a total of 26 traits including shoot and needle morphology, needle anatomy, and foliar macronutrients, and related the traits to the growing season water deficit (GSWD) at the location of the seed origin. 3. Foliar phenotypic plasticity in response to recurrent summer drought was surprisingly low, with the needle length and the fraction of mesophyll and phloem tissue adjusting to some extent. In comparison, shoot morphological traits were much more plastic in both species with predominant responses to the summer drought stress including shorter and less numerous apical and lateral shoots. These three traits were also correlated with GSWD at the seed origin, indicating local adaptation. In contrast, between-population variation of foliar morphological and anatomical traits, and macronutrients were mostly unrelated to the GSWD at the seed origin. 4. Consequently, phenotypic plasticity and ecotypic differentiation occurred at the same level of organisation and in the same plant traits, i.e. shoot morphology. This combination of plasticity and ecotypic differentiation allowed P. sylvestris and P. nigra seedlings to rapidly acclimate to recurrent and long-lasting dry-spells. 5. Synthesis: P. sylvestris and P. nigra seedlings showed considerable ecotypic differentiation and phenotypic plasticity of shoot morphological traits, and not foliar traits. Acclimation to recurrent severe summer drought was achieved by reducing shoot growth.

opencc-by-4.0Oct 2021View details →

Dataset for the study Sensitive period for the plasticity of alpha activity in humans

Raw EEG data in european data format (EDF) format. Descriptive and clinical data of the subjects in textual tab delimited format. Columns report for each subject: group (blind/severely impaired, BSI or sighted, S), code, gender, age expressed in decimal years, age bin, degree of visual impairment, diagnosis, motor coordination impairment classification (MCI, 1 = not impaired, 2 = impaired), and hypotonia classification (1 = not impaired, 2 = impaired).  NA correspond to undefined classification. Visual experience is crucial for the development of neural processing. For example, alpha activity development is a vision-dependent mechanism. Indeed, studies report no alpha activity is present in blind adults. Nevertheless, studies have not investigated the developmental trajectory of this activity in infants and children with blindness. Here, we hypothesize that the difference in neural activity of blind compared to sighted subjects is: absent at birth, progressive with age, specifically occipital and linked to a gradual motor impairment. Therefore, we consider spectral power of resting-state EEG and its association with motor impairment indices, in blind subjects and in sighted controls between 0 and 11 years of age. Blind subjects show posterior alpha activity during the first three years of life, although weaker and slower maturing compared to sighted subjects. The first great differentiation between blind and sighted subjects occurs between 3 and 6 years of age. Starting in this period, reduced alpha activity increases the probability of motor impairment in blind subjects, likely because of impaired perception/interaction. These results show that visual experience mediates the neural mechanisms generating alpha oscillations during the first years of life, suggesting that it is a sensitive period for the plasticity of this process.

opencc-by-4.0Apr 2021View details →

DeepPlastic: An Open Source Image Dataset for Epipelagic Marine Plastic Detection

Deep Plastic <ul> <li>Enhanced Object Detection for Epipelagic Plastic.</li> <li>This repository contains source code for the method developed in <a href="https://arxiv.org/pdf/2105.01882.pdf">DeepPlastic: Identifying Marine Plastic In The Epipelagic Zone using Computer Vision and Deep Learning</a></li> <li> Information: </li> <li>Paper: [Coming Soon]</li> <li>YouTube video of Results: <a href="https://youtu.be/8zBdFxaK4Os">https://youtu.be/8zBdFxaK4Os</a></li> <li> Object Detection Model </li> <li>Four models: YOLOv4, YOLOv5, MobileSSD, Faster RCNN Inception V2</li> <li>Small efficient and high precision models can be used for real-time object detection.</li> <li>Model architecture and implementation details: <a href="https://arxiv.org/">https://arxiv.org/</a></li> <li>Weights for YOLOv4 and YOLOv5 are provided in the model/ <ul> <li>YOLOv4: best. weights; use <a href="https://drive.google.com/file/d/1YOTtZ2cHbqgxHukzLp01OVsUoa2CwwXs/view?usp=sharing">best.weights</a></li> <li>YOLOv5: best.pt; use <a href="https://drive.google.com/file/d/14mBOhtLrE2d3hudqjwBZmawKAvTF4zxS/view?usp=sharing">best.pt</a></li> </ul> </li> <li> Google Colab Links Note: Click on File and Save Copy in Drive. If you try to edit my file it'll ask you for permission and send me an email. Please make your own copy. </li> <li>YOLOv5: <a href="https://colab.research.google.com/drive/1_qzbpBWkNfxQ0ny-DvsKicCeM0aFU4eW?usp=sharing">https://colab.research.google.com/drive/1_qzbpBWkNfxQ0ny-DvsKicCeM0aFU4eW?usp=sharing</a></li> <li> DeepTrash DataSet </li> <li>1900 training images, 637 test images, 637 validation images (60, 20, 20 split)</li> <li>Field images taken from Lake Tahoe, San Francisco Bay and Bodega Bay in CA.</li> <li>Deep Sea images are from JAMSTEK JEDI dataset: <a href="http://www.godac.jamstec.go.jp/">http://www.godac.jamstec.go.jp/</a></li> </ul>

opencc-zeroOct 2021View details →

Cross-species transcriptomics uncovers genes underlying genetic accommodation of developmental plasticity in spadefoot toads

That hardcoded genomes can manifest as plastic phenotypes responding to environmental perturbations is a fascinating feature of living organisms. How such developmental plasticity is regulated at the molecular level is beginning to be uncovered aided by the development of -omic techniques. Here, we compare the transcriptome-wide responses of two species of spadefoot toads with differing capacity for developmental acceleration of their larvae in the face of a shared environmental risk: pond drying. By comparing gene expression profiles over time and performing cross-species network analyses, we identified orthologues and functional gene pathways whose environmental sensitivity in expression have diverged between species. Genes related to lipid, cholesterol and steroid biosynthesis and metabolism make up most of a module of genes environmentally responsive in one species, but canalized in the other. The evolutionary changes in the regulation of the genes identified through these analyses may have been key in the genetic accommodation of developmental plasticity in this system.

opencc-by-4.0Dec 2018View details →

Stochastic synaptic plasticity underlying compulsion in an addiction model

Data set for article published in Nature: Pascoli 2018 https://doi.org/10.1038/s41586-018-0789-4

opencc-by-4.0Nov 2022View details →

Plasticization of a Semicrystalline Metallosupramolecular Polymer Network

Data set divided in folders according to the Figures in the manuscript and supporting information

opencc-zeroNov 2022View details →

Within-generation and transgenerational social plasticity interact during rapid adaptive evolution

The effects of within-generation plasticity versus transgenerational plasticity on trait expression are poorly understood, but important for evaluating plasticity's evolutionary consequences. We tested how genetics, within-generation plasticity, and transgenerational plasticity jointly shape traits influencing rapid evolution in the field cricket Teleogryllus oceanicus. In Hawaiian populations attacked by acoustically-orienting parasitoid flies, a protective, X-linked variant ("flatwing") eliminates male acoustic sexual signals. Silent males rapidly spread to fixation, dramatically changing the acoustic environment. First, we found evidence supporting flatwing-associated pleiotropy in juveniles: pure-breeding flatwing males and females exhibit greater locomotion than those with normal-wing genotypes. Second, within-generation plasticity caused homozygous-flatwing females developing in silence, which mimics all-flatwing populations, to attain lower adult body condition and reproductive investment than those experimentally exposed to song. Third, maternal song exposure caused transgenerational plasticity in offspring, affecting adult, but not juvenile, size, condition, and reproductive investment. This contrasted with behavioral traits, which were only influenced by within-generation plasticity. Fourth, we matched and mismatched maternal and offspring social environments and found that transgenerational plasticity sometimes interacted with within-generation plasticity and sometimes opposed it. Our findings stress the importance of evaluating the plasticity of different traits and stages across generations when evaluating their fitness consequences and role in adaptation.