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opencc-zeroOct 2020View details →

Magnitude and predictability of pH fluctuations shape plastic responses to ocean acidification

Phenotypic plasticity is expected to facilitate the persistence of natural populations as global change progresses. The attributes of fluctuating environments that favor the evolution of plasticity have received extensive theoretical investigation, yet empirical validation of these findings is still in its infancy. Here, we combine high-resolution environmental data with a laboratory-based experiment to explore the influence of habitat pH fluctuation dynamics on the plasticity of gene expression in two populations of the Mediterranean mussel, Mytilus galloprovincialis. We linked differences in the magnitude and predictability of pH fluctuations in two habitats to population-specific gene expression profiles in ambient and stressful pH treatments. The results presented demonstrate population-based differentiation in gene expression plasticity, whereby mussels native to a habitat exhibiting a large magnitude of pH fluctuations with low predictability display reduced phenotypic plasticity between experimentally imposed pH treatments. This work validates recent theoretical findings on evolution in fluctuating environments using an ecologically important marine bivalve, and suggests that populations inhabiting regions exposed to unpredictably fluctuating selection pressures may exhibit reduced plasticity as global change progresses.

opencc-by-4.0Nov 2020View details →

Code and Data for: "Signs of local adaptation and phenotypic plastic response to elevation shifted between environmental backgrounds in Snapdragon plants"

Code and data for manuscript: "Signs of local adaptation and phenotypic plastic response to elevation shifted between environmental backgrounds in Snapdragon plants"

Fig. 3 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 3. Response curves of three morphological variables of Piaractus mesopotamicus (proportion of increase) respect to dissolved oxygen gradient. Black arrow indicates the DO concentration determined for the inflection point of the reaction norm.

Fig. 1 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 1. Development and reversion of the three morphological variables exposed to nine hours of hypoxia, followed by three hours of normoxia in Piaractus mesopotamicus. (a) lower lip, (b) maxillary, and (c) opercular valve. Capital letters above box plots indicate groups in multiple comparisons (Tukey's tests) after repeated measures ANOVA.

Fig. 4 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 4. Response curves of behavioral and respiratory variables of Piaractus mesopotamicus respect to dissolved oxygen gradient. Black arrow indicates inflection point given by the four parameters logistic function. The curve fitted to data points is not shown for horizontal and vertical movements due to the great dispersion.

Fig. 5 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 5. Comparisons of plasticity among behavioral (a), respiratoy (b) and morphological traits (c) of Piaractus mesopotamicus as measured by the coefficient of variation (CV) across the DO gradient. Capital letters above box plots indicate groups in multiple comparison Tukey's tests after a one way ANOVA. Names of traits as defined in the text.

Fig. 2 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 2. Photographs showing increases in size of the three morphological traits of Piaractus mesopotamicus analyzed exposed to extreme hypoxia: (a) lower lip, (b) maxillary, and (c) opercular valve. White arrow indicates the area where the expansion of dermal tissue occurred.

opencc-by-4.0Jul 2016View details →

Mechanical Response of Foams: Elasticity, Plasticity, and Rearrangements (Supplemental Material)

Supplemental material to <a href="https://openaccess.leidenuniv.nl/handle/1887/40902">Mechanical Response of Foams: Elasticity, Plasticity, and Rearrangements; hdl:1887/40902</a>. The supplemental material consists of 9 videos: S1, S2 Two examples of foam under shear, φ = 0.85 (S1) and φ = 1.25 (S2). The foam is sheared from sCD = − 0.2 to sCD = + 0.2 at γ̇=3 × 10−5 /s. Time and a scale bar are indicated in the top right; the video is sped up 250× . S3,S4 Difference imaging for direct (top) and affine-corrected (bottom) images, for the same systems as in S1 and S2. Both the real space (left) and difference images (right) are shown. The direct difference images are dominated by the affine deformation, while the affine-corrected difference images highlight the nonaffine motion in the system. S5,S6 Tracked particle trajectories for the same systems as in S1 and S2. Particle trajectories are indicated using white curves. Left: direct tracking data, right: affine-corrected tracking data. S7 Compression of a foam from φ = 0.77to φ = 1.41 under ε̇ = − 3 × 10−5 /s. (left) Real space image; (right) from top to bottom: flame graph and log10 A and β from the power law fit Eq. (4.21). Time is indicated on the top left, φ is indicated at the bottom left. With increasing confinement, we observe a transition from fully smooth to fully intermittent behavior. S8,S9 Two examples of foam under shear, φ = 0.9 (S8) and φ = 1.5 (S9). The foam is sheared from sCD = −0.2 to sCD = +0.2 at γ̇=3 × 10−5 /s. At low density, A ≈ 10−6 and β ≈ 1.6 are fairly constant, while we can clearly distinguish the quiet and active periods for the high density foam.

opencc-by-4.0May 2023View details →

Single-cell datasets for cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2- breast tumor cells

There are 7 files uploaded in the data.tumor_preprocessed.h5ad: Full primary tumor dataset post-feature selection and standardization across three treatment conditions (0, 10, and 100 nM palbociclib). AnnData object format. 14 cell cycle features, phase labels and other cell metadata, and two PHATE dimensions for manifold visualization.T47D_preprocssed.h5ad: Full dataset of main text T47D dataset post-feature selection and standardization across three treatment conditions (0, 10, and 100 nM palbociclib). AnnData object format. 14 cell cycle features,  phase labels and other cell metadata, and two PHATE dimensions for manifold visualization.sketched_integrated.h5ad: After downsample 6,000 (2,000 per condition) from T47D_preprocessed and tumor_preprocessed, we integrate the two datasets into one joint latent space using TRANSACT. Now included in the data are the consensus component columns ('0',..,'13'). AnnData object.sketched_integrated_df.csv: sketched_integrated.h5ad in .csv format.T47D_replicate_preprocessed: Replicate experimental dataset of T47D for supplementary analysis post-feature selection and standardization across three treatment conditions (0, 10, and 100 nM palbociclib). 15 cell cycle features (same 14 but with CDK6).sketched_rep.h5ad: Representative downsample of the T47D_replicate_preprocessed. Selecting 6,000 cells (2,000 for each of the three treatment conditions) using kernel herding sketching. AnnData object.sketched_rep_df.csv: Same data as sketched_rep.h5ad in csv format.T47D_triplicate_preprocessed.h5ad: T47D biological replicate sample collected in triplicate form (three wells for 0, 10, and 100 nM of palbociclib). Wells were joined and the data were sketched down to 20,000 per condition.T47D_triplicate_preprocessed.h5ad: T47D triplicate in .csv form.tumor_2_preprocessed.h5ad: An additional tumor sample from a new patient with the same treatment conditions of palbociclib. Sketched down to 2,000 cells per condition.tumor_2_preprocessed.csv: The additional tumor sample in .csv form. Further description of sketched_integrated: This is the joint dataset between the T47D and primary tumor, after subsampling using kernel herding sketching. This is a dataset consisting of T47D and primary tumor cells resected from a consented patient. The samples were imaged using iterative indirect immunofluorescent imaging (4i) to get proteomic measurements on a single-cell level. The T47D and tumor samples were gathered, cultured, and imaged separately. Each sample was treated with three conditions of CDK4/6 inhibitor palbociclib (control, 10 nM, and 100 nM). Then, we used kernel sketching to representatively downsample each dataset, selecting 2,000 from each of the three treatment conditions (6,000 cells from each of the two sources). We used an integration method called TRANSACT to integrate the two datasets into one shared, latent space. The dataset here is consisting of these 12,000 cells. The columns ('0','1',...'13') are the principal vectors of the joint latent space. After that, there are the columns of the standardized proteomic measurements of different cell cycle effectors, and biological annotations of interest. The standardization is done for each data source separately. Well refers to the treatment condition. 'prb_ratio' is a marker of if a cell is still proliferating or arrested, found by selecting the upper modality of pRB/RB values. 'phase' are cell cycle phase labels found by unsupervised clustering done on a handful of known cell cycle markers.

opencc-by-4.0Nov 2023View details →

SeaPaCS graphic elaboration of the Protocol for marine micro-plastic collection and monitoring in citizen science and for building a L.A.D.I. trawling tool

This  is a graphic elaboration  (in Italian) of the protocol "SeaPaCS deliverable - protocol for plastic monitoring in citizen science" in English and Italian is a deliverable of the SeaPaCS project (Participatory Citizen Science Against Marine Pollution), funded by IMPETUS (project ID 101058677). The protocol  and the visual elaboration has been freely adapted from "LADI and the Trawl" by Coco Coyle with Melissa Novaceski, Emily Wells and Max Liboiron, as published by the Civic Laboratory for Environmental Action Research, August 2016.  The graphic elaboration (as the protocol) in both languages, consists of three parts: 1) how to build a DIY low cost manta trawl device (LADI - Low-Tech Aquatic Detection Debris Instrument) to monitor plastic pollution,  adjusted to materials availability and costs in Italy; 2) how to monitor (the sampling itself and towing procedure); and 3) how to categorize plastic debris back on land.

opencc-by-4.0Nov 2023View details →

A step towards understanding plastic complexity: antimony speciation in consumer plastics and synthetic textiles revealed by XAS - supporting data

This dataset contains all data related to "A step towards understanding plastic complexity: antimony speciation in consumer plastics and synthetic textiles revealed by XAS"

Variation in personality shaped by evolutionary history, genotype, and developmental plasticity in response to feeding modalities in the Arctic charr

Animal personality has been shown to be influenced by both genetic and environmental factors and shaped by natural selection. Currently, little is known about mechanisms influencing the development of personality traits. This study examines the extent to which personality development is genetically influenced and/or environmentally responsive (plastic). We also investigated the role of evolutionary history, assessing whether personality traits could be canalized along a genetic and ecological divergence gradient. We tested the plastic potential of boldness in juveniles of five Icelandic Arctic charr morphs (Salvelinus alpinus), including two pairs of sympatric morphs, displaying various degrees of genetic and ecological divergence from the ancestral anadromous charr, split between treatments mimicking benthic vs. pelagic feeding modalities. We show that differences in mean boldness are mostly affected by genetics. While the benthic treatment led to bolder individuals overall, the environmental effect was rather weak, suggesting that boldness lies under strong genetic influence with reduced plastic potential. Finally, we found hints of differences by morphs in boldness canalization through reduced variance and plasticity, and higher consistency in boldness within morphs. These findings provide new insights into how behavioural development may impact adaptive diversification.

Experimental evolution under varying sex ratio and behavioral plasticity in response to perceived competitive environment independently affect calling effort in male crickets

The operational sex ratio (OSR) is a key component influencing the magnitude of sexual selection driving the evolution of male sexual traits, but males often also retain the ability to plastically modulate trait expression depending on the current environment. Here we employed an experimental evolution approach to determine whether the OSR affects the evolution of male calling effort in decorated crickets, a costly sexual trait, and whether plasticity in calling effort is altered by the OSR under which males have evolved. Calling effort of males from two selection regimes maintained at different OSRs over 18–20 generations (male- versus female-biased) was recorded at two different levels of perceived competition, in the absence of rivals or in the presence of an experimentally muted competitor. The effect of the OSR on the evolution of male calling effort was modest and in the opposite direction predicted by theory. Instead, the immediate competitive environment strongly influenced male calling effort as males called more in the presence of a rival, revealing considerable plasticity in this trait. This increased calling effort came at a cost, however, as males confined with a muted rival experienced significantly higher mortality.

Data from: movement or plasticity: acoustic responses of a torrent frog to stream geophony

Vocalization is the main form of communication in many animals, including frogs, which commonly emit advertisement calls to attract females and maintain spacing. In noisy environments such as streams, mechanisms to maximize signaling efficiency may include vocal plasticity and/or movement of individuals to quieter sections, but which strategy is used is still uncertain. We investigated the influence of stream geophony on the advertisement call of the torrent frog Hylodes perere in the Atlantic Rainforest, southeastern Brazil. In a mark-recapture study, we tested if males remain in their territories and thus adjust their advertisement calls to maximize their communication. We ran mixed linear and generalized models to verify the relation of call parameters and stream geophony, body size and environmental temperature. We found that males remained in the same location across time, increased call intensity in noisier environments but did not reduce call effort. Males also increased the dominant frequency in these situations, suggesting a modulation in this parameter. Our results indicate that territoriality is an important factor to males to increase call intensity to surpass stream noise instead of repositioning along the stream. However, because call effort was maintained, we suggest that sexual selection is crucial in this system, favoring males that better detect others and adjust their call efficiency. This is the first study to evaluate simultaneously frog movements and adaptations to geophony, which contributes to the investigation of the concomitant environmental and sexual selective pressures in species that communicate in noisy environments.

Range expansion can promote the evolution of plastic generalism in coarse-grained landscapes

Phenotypic plasticity is one way for organisms to deal with variable environments through generalism. However, plasticity is not found universally and its evolution may be constrained by costs and other limitations such as complexity: the need for multiple mutational steps before the adaptation is realized. Theory predicts that greater experienced heterogeneity, such as organisms may encounter when spatial heterogeneity is fine-grained relative to dispersal, should favor the evolution of a broader niche. Here we tested this prediction via simulation. We found that, contrary to classical predictions, coarse-grained landscapes can be the most favorable for the evolution of plasticity, but only when populations encountered those landscapes through range expansion. During these range expansions, coarse-grained landscapes select for each step in the complex mutational pathway to plastic generalism by blocking the dispersal of specialists. These circumstances provide ecological opportunities for innovative mutations that change the niche. Our results indicate a new mechanism by which range expansion and spatially structured landscapes interact to shape evolution, and reveal that the environments in which a complex adaptation has the highest fitness may not be the most favorable for its evolution.

opencc-zeroMar 2024View details →

Data from: Hatching plasticity is associated with a more advanced stage at hatching in an Ambystoma with terrestrial eggs

These data are from a 2019 study of embryonic development in marbled salamander (Ambystoma opacum) and ringed salamander (Ambystoma annulatum). Egg masses were collected in Arkansas in the fall of 2019 and transported to the University of North Carolina Asheville. Clutches were split and embryos were reared in one of two environments mimicking the terrestrial environment typical of A. opacum nests and the aquatic environment typical of A. annulatum egg masses. Response variables recorded include number of embryos that hatched, age (days) at hatching, Harrison stage at hatching, and dry mass at hatching.

opencc-zeroMar 2024View details →

Neglected patterns of variation in transgenerational plasticity: The importance of different sources of environmental variation differs across ages and sexes in a cyprinid fish

Adaptive transgenerational plasticity (TGP) requires individuals to integrate environmental experience across multiple sources. However, few empirical studies have considered that the relative relevance of certain sources might vary across ontogeny and sexes. Here, we address this knowledge gap by studying inducible antipredator defenses, one of the most convincing examples of TGP. We assessed individual and combined effects of perceived high predation risk in mothers, fathers, caring males and personal environments on the morphology of juvenile, adult male and adult female cyprinids Pimephales promelas. Parental rather than personal environmental experience determined morphological defense expression across ages and sexes, likely because parents had a longer sampling period. In juveniles and adult males, egg-mediated environmental experience outweighed sperm-mediated environmental experience in the induction of body shape differences, likely because eggs can transmit information beyond epigenomes. However, in adult females, where body shape responses can be interpreted as life-history plasticity, information from egg and sperm were equally important, likely resulting from different integration mechanisms between morphological and life-history plasticity. The importance of care-mediated relative to gamete-mediated variation changed between juveniles and adult males, likely because they represent short- and long-term environmental experience, respectively. Instead, in adult females, both sources were again equally important, potentially owing to lag-times of life-history plasticity. Parental care intensity only contributed marginally to defense formation. These results highlight age- and sex-specific prioritization of different environmental experiences so as to generate optimal phenotypes.

opencc-zeroApr 2024View details →

Data from: Turbidity drives plasticity in the eyes and brains of an African cichlid

Natural variation in environmental turbidity correlates with variation in the visual sensory system of many fishes, suggesting that turbidity may act as a strong selective agent on visual systems. Since many aquatic systems experience increased turbidity due to anthropogenic perturbations, it is important to understand the degree to which fish can respond to rapid shifts in their visual environment, and whether such responses can occur within the lifetime of an individual. We examined if developmental exposure to turbidity (Clear <5 NTU, Turbid ~9 NTU) influenced the size of morphological structures associated with vision in the African cichlid Pseudocrenilabrus multicolor. Parental fish were collected from two sites (clear swamp, turbid river) in western Uganda. F1 broods from each population were split and reared under clear and turbid rearing treatments until maturity. We measured morphological traits associated with the visual sensory system (eye diameter, pupil diameter, axial length, brain mass, optic tectum volume) over the course of development. Age was significant in explaining variation in visual traits even when standardized for body size, suggesting an ontogenetic shift in the relative size of eyes and brains. When age groups were analyzed separately, young fish reared in turbid water grew larger eyes than fish reared in clear conditions. Population was important in the older age category, with swamp-origin fish having relatively larger eyes and optic lobes relative to river-origin fish. Plastic responses during development of fish may be important in responding to a more variable visual environment associated with anthropogenically induced turbidity.

opencc-by-4.0Apr 2024View details →

Physical characterization of agricultural plastic mulching films

The excel file regards the radiometric properties of the source material mulching films.  The radiometric tests were carried out at the University of Bari. The mulching films were used for the generation of microplastic test materials. The Italian mulching films were buried at the experimental field at the University of Bari.