Find research datasets worth reusing

opencc-zeroDec 2021View details →

Data from: Elevational divergence in pigmentation plasticity is associated with selection and pigment biochemistry

Phenotypic plasticity is predicted to evolve in environmentally variable habitats, or those experiencing a high frequency of strong selection. However, the evolution of plasticity may be constrained by costs or physiological constraints. In flowers, UV-absorbing pigmentation ameliorates UV damage to pollen, and is linked with elevated UV exposure. Whether plasticity contributes to this pattern remains unclear. Petals of Argentina anserina have larger UV-absorbing petal areas at high elevations where they experience higher and more variable UV exposure compared to low elevations. We measured UV-induced pigmentation plasticity in high- and low-elevation populations (hereafter, 'high, 'low'), and selection on pigmentation via male fitness. We dissected UV pigment biochemistry using metabolomics to explore biochemical mechanisms underlying plasticity. High displayed positive UV-induced pigmentation plasticity but low lacked plasticity. Selection favored elevated pigmentation under UV in high, supporting adaptive plasticity. In high, UV-absorption was conferred by flavonoids produced in one flavonoid pathway branch. However, in low, UV-absorption was associated with many compounds spanning many branches. Elevated plasticity was thus associated with reduced pigment diversity. Results are consistent with adaptive floral pigmentation plasticity in more extreme and variable environments. We discuss how biochemical underpinnings of pigmentation may permit or constrain the evolution of pigmentation plasticity.

opencc-zeroDec 2021View details →

Genomic data from: Are you ready for the heat? Phenotypic plasticity vs adaptation of heat tolerance in three-spined stickleback

Heat waves constitute a challenge for aquatic ectotherms. However, the thermal tolerance of animals and their individual phenotypic plasticity to respond to heat waves may be influenced by thermal history. We tested these hypotheses by comparing the upper thermal tolerance and the individual capacities of three-spined sticklebacks from populations with different thermal histories to respond to heat waves. Two populations originated from thermally polluted nuclear power plant (NPP) habitats, while four locations represented geographically adjacent control areas. To disentangle the genetic adaptation from the phenotypic plastic response, we measured the individual upper thermal tolerance and the responses at molecular level in common garden conditions before and after a laboratory-mimicked heat wave. We found that the sticklebacks exhibit considerable phenotypic plasticity in thermal tolerance since the heat wave increased fish upper thermal tolerance significantly. The individual plasticity to respond to the heat wave was also negatively correlated to initial thermal tolerance. On the other hand, neither the thermal tolerance nor the plastic responses differed between NPP and control sites despite detection of significant but low genome-wide divergence in 10 out of 15 pairwise comparisons. Our results suggest that five decades of nuclear power plant activity with warmer water has not resulted in a detectable evolutionary change in either the upper thermal tolerance or its plasticity in three-spined sticklebacks potentially rendering them sensitive to frequent heat waves.

opencc-zeroDec 2021View details →

Competition alters species' plastic and genetic response to environmental change

Species react to environmental change via plastic and evolutionary responses. While both of them determine species' survival, most studies quantify these responses only individually. As species occur in communities, competing species may further influence their respective response to environmental change. Yet, how environmental change and competing species combined shape plastic and genetic responses to environmental change remains unclear. Quantifying how species interactions such as competition alter plastic and genetic responses of species to environmental change requires integrating approaches from trait-based, community and evolutionary ecology. We exposed unicellular aquatic organisms to long-term selection of increasing salinity—representing a common and relevant environmental change. Then, we assessed plastic and genetic contributions to phenotypic change in biomass, cell shape, and dispersal ability along increasing levels of salinity in the presence and absence of competition. Species differed in their response to salinity and to competition. The observed trait changes during selection were mainly due to mean trait evolution, and differed whether species evolved in the presence or absence of competition. Moreover, our results show that species' evolutionary and plastic responses to environmental change depended both on the presence of competing species and the magnitude of the environmental change, ultimately determining species persistence. Our results suggest that understanding plastic and genetic responses to environmental change within a community will improve predictions of species' persistence to environmental change.

In a comfort zone and beyond – ecological plasticity of key marine mediators

Copepods of the genus Calanus are the key components of zooplankton. Understanding their response to a changing climate is crucial to predict the functioning of future warmer high-latitude ecosystems. Although specific Calanus species are morphologically very similar, they have different life strategies and roles in ecosystems. In this study, C. finmarchicus and C. glacialis were thoroughly studied with regard to their plasticity in morphology and ecology both in their preferred original water mass (Atlantic vs. Arctic side of the Polar Front) and in suboptimal conditions (due to, e.g., temperature, turbidity, and competition in Hornsund fjord). Our observations show that 'at the same place and time', both species can reach different sizes, take on different pigmentation, be in different states of population development, utilize different reproductive vs. lipid accumulation strategies, and thrive on different foods. Size was proven to be a very mutable morphological trait, especially with regard to reduced length of C. glacialis. Both species exhibited pronounced red pigmentation when inhabiting their preferred water mass. In other domains, C. finmarchicus individuals tended to be paler than C. glacialis individuals. Gonad maturation and population development indicated mixed reproductive strategies, although a surprisingly similar population age structure of the two co-occurring species in the fjord was observed. Lipid accumulation was high and not species-specific, and its variability was due to diet differences of the populations. According to the stable isotope composition, both species had a more herbivorous diatom-based diet in their original water masses. While the diet of C. glacialis was rather consistent among the domains studied, C. finmarchicus exhibited much higher variability in its feeding history (based on lipid composition). Our results show that the plasticity of both Calanus species is indeed impressive and may be regulated differently, depending on whether they live in their 'comfort zone' or beyond it.

Data from: Life histories as mosaics: plastic and genetic components differ among traits that underpin life-history strategies

Life-history phenotypes emerge from clusters of traits that are the product of genes and phenotypic plasticity. If the impact of the environment differs substantially between traits, then life histories might not evolve as a cohesive whole. We quantified the sensitivity of components of the life history to food availability, a key environmental difference in the habitat occupied by contrasting ecotypes, for 36 traits in fast-and slow-reproducing Trinidadian guppies. Our dataset included six putatively independent origins of the slow-reproducing, derived ecotype. Traits varied substantially in plastic and genetic control. Twelve traits were influenced only by food availability (body lengths, body weights), five only by genetic differentiation (inter-birth intervals, offspring sizes), ten by both (litter sizes, reproductive timing), and nine by neither (fat contents, reproductive allotment). Ecotype-by-food interactions were negligible. The response to low food was aligned with the genetic difference between high- and low-food environments, suggesting that plasticity was adaptive. The heterogeneity among traits in environmental sensitivity and genetic differentiation reveals that the components of the life history may not evolve in concert. Ecotypes may instead represent mosaics of trait groups that differ in their rate of evolution.

Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences

The data presented here are those used in the paper : CAYUELA H., JACOB S., SCHTICKZELLE N., VERDONCK R., PHILIPPE H., LAPORTE M., HUET M., BERNATCHEZ L., LEGRAND D. Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences. Oikos. DOI: 10.1111/oik.08846 Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species' response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally-induced phenotypic variation across generations, and can influence adaptation. To date, the genetic control of TGP, its long-term stability, and its potential costs remain largely unknown, mostly because empirical demonstrations of TGP across many generations in several genetic backgrounds are scarce. In the paper of Cayuela et al., we examined how genotype determines the TGP of phenotypic traits related to dispersal, a fundamental process in ecology and evolution. We used an experimental approach in Tetrahymena thermophila, a ciliate model-species, to determine if and how phenotypic changes expressed following a dispersal treatment are inherited over multiple generations. The data include morphological and movement traits, dispersal rates, and cell growth data measured before and after dispersal trials. We considered different genotypes and different populations within each genotype.

Diet-induced changes in titer support a discrete response of Wolbachia-associated plastic recombination in Drosophila melanogaster

Plastic recombination in Drosophila melanogaster has been associated with a variety of extrinsic and intrinsic factors such as temperature, starvation, and parasite infection. The bacterial endosymbiont Wolbachia pipientis has also been associated with plastic recombination in D. melanogaster. Wolbachia infection is pervasive in arthropods and this infection induces a variety of phenotypes in its hosts, the strength of which can depend on bacterial titer. Here, we test the hypothesis that the magnitude of Wolbachia-associated plastic recombination in D. melanogaster depends on titer. To manipulate titer, we raised Wolbachia-infected and uninfected flies on diets that have previously been shown to increase or decrease Wolbachia titer relative to controls. We measured recombination in treated and control individuals using a standard backcrossing scheme with two X-linked visible markers. Our results recapitulate previous findings that Wolbachia infection is associated with increased recombination rate across the yellow-vermillion interval of the X chromosome. Our data show no significant effect of diet or diet by Wolbachia interactions on recombination, suggesting that diet-induced changes in Wolbachia titer have no effect on the magnitude of plastic recombination. These findings represent one of the first steps toward investigating Wolbachia-associated plastic recombination and demonstrate that the phenotype is a discrete response rather than a continuous one.

Endocrine disruption from plastic pollution and warming interact to increase the energetic cost of growth in a fish

Energetic cost of growth determines how much food-derived energy is needed to produce a given amount of new biomass, and thereby influences energy transduction between trophic levels. Growth and development are regulated by hormones and are therefore sensitive to changes in temperature and environmental endocrine disruption. Here we show that the endocrine disruptor bisphenol A at an environmentally relevant concentration (BPA; 10 µg l⁻¹) decreased fish (Danio rerio) size at 30 oC water temperature. Under the same conditions, it significantly increased metabolic rates and the energetic cost of growth across development. In contrast, BPA decreased cost of growth at cooler temperatures (24 °C). BPA-mediated changes in cost of growth were not associated with mitochondrial efficiency (P/O ratios [i.e., ADP used/oxygen consumed] and respiratory control ratios) although BPA did increase mitochondrial proton leak. In females, BPA decreased age at maturity at 24 oC but increased it at 30 oC, and it decreased the gonadosomatic index suggesting reduced investment into reproduction. Our data reveal a potentially serious emerging problem: increasing water temperatures resulting from climate warming together with endocrine disruption from plastic pollution can impact animal growth efficiency, and hence the dynamics and resilience of animal populations and the services these provide.

opencc-zeroFeb 2022View details →

Multiple modes of selection can influence the role of phenotypic plasticity in species' invasions: Evidence from a manipulative field experiment

In exploring the roles of phenotypic plasticity in the establishment and early evolution of invading species, little empirical attention has been given to the importance of correlational selection acting upon suites of functionally related plastic traits in nature. We illustrate how this lack of attention has limited our ability to evaluate plasticity's role during invasion and also, the costs and benefits of plasticity. We addressed these issues by transplanting clones of European-derived Plantago lanceolata L. genotypes into two temporally variable habitats in the species' introduced range in North America. Phenotypic selection analyses were performed for each habitat to estimate linear, quadratic, and correlational selection on phenotypic trait values and plasticities in the reproductive traits: flowering onset, spike and scape lengths. Also, we measured pairwise genetic correlations for our "colonists". Results showed that 1) correlational selection acted on trait plasticity after transplantation, 2) selection favored certain combinations of genetically correlated and uncorrelated trait values and plasticities, 3) Using signed, instead of absolute, values of plasticity in analyses facilitated the detection of correlational selection on trait value-plasticity combinations and their adaptive value. Based on our results, we urge future studies on species invasions to: 1) measure correlational selection and 2) retain signed values of plasticity in order to better discriminate between adaptive and maladaptive plasticity.

opencc-zeroFeb 2022View details →

Maintenance of phenotypic plasticity is linked to oxidative stress in spadefoot toad larvae

Phenotypic plasticity allows organisms to improve the match between their phenotype and heterogeneous environments. Theoretical models have argued that costs of maintaining the sensory and response machinery necessary for adaptive phenotypic plasticity are important determinants to the evolution of plasticity. Despite recurrent arguments invoking putative metabolic costs associated with maintenance of cellular machinery, no studies have yet attempted to quantify it from a molecular standpoint. Here we experimentally examine physiological differences across genotypes (sibships) of spadefoot toad larvae with different degrees of plasticity in response to predator cues. We observed marked differences across sibships in developmental, growth and morphological responses to predators, and tested whether increased plasticity was associated with oxidative stress or immune suppression. We observed that more plastic sibships experienced higher antioxidant enzymatic activity when reared in the absence of predator cues, i.e. not expressing their plastic responses. The degree of plasticity was also associated with higher lipid peroxidation and slightly greater granulocyte-to-lymphocyte ratio. Higher antioxidant activity in highly plastic sibships suggests that maintenance of phenotypic plasticity may be linked to energy demanding metabolic processes. Our findings suggest that having the potential to produce plastic responses may incur oxidative and immunological costs. In the long term, such maintenance costs may erode individual fitness and even constrain the evolution of plasticity. To our knowledge, this is the first empirical evidence indicating the existence of a physiological cost to the maintenance of phenotypic plasticity.

opencc-zeroFeb 2022View details →

Thermal plasticity of setae of the second limb of Daphnia

These data are associated with a study that tests the hypothesis of thermal plasticity in the rigid setae of the second limb of Daphnia. The data are body size and length measurements (mm) of three limb setae (limb 2; endite 2). The second seta is often called the "rigid" seta because it is heavily chitinized. In all, 300 specimens of Daphnia (including Daphnia umbra and Daphnia galeata) were dissected from four sets of clonal thermal transfers and seasonal variants from nature. Specimens of D. galeata were cultured under identical conditions save temperature (10 and 20◦C). Clonal neonates were reciprocally transferred across temperature regimes to determine the degree of postnatal plasticity.

zenodo32/100

Raw data to "Macrophage Plasticity and Polarization Are Altered in the Experimental Model of Multiple Sclerosis"

Background: Macrophages have been identified as one of the major effectors of inflammation and demyelination in both MS and its animal model, experimental autoimmune encephalomyelitis (EAE). However, the activation and heterogeneity of macrophages in MS is not fully understood. Results: We performed a complete immunophenotyping of M1 and M2 macrophages from EAE and control mice through polychromatic flow cytometry. We found that M1 macrophages possessed a higher proinflammatory profile in EAE compared to control mice, since they expressed higher levels of activation/co-stimulatory markers (iNOS, CD40 and CD80) (Table 1), cytokines/chemokines (IL-6, IL-12, CCL2 and CXCL10) (Table 2) and a higher expression of Toll-like receptors (TLR2) 2 and 5 (Table 3). On the contrary, M2 of EAE mice lost their M2-like phenotype by showing a decreased expression of their signature markers CD206, CD11c, CD44 and CCL22, and a concomitant upregulation of several M1 makers such as iNOS, CD40, CD80/CD86 (Table 1) and proinflammatory CCL22 (Table 2) and TLR4 and 8. Conclusions: Our data account for a phenotypic alteration of M1/M2 balance during MS and this can be of crucial importance not only for a better understanding of the immunopathology of this neurodegenerative disease but also to potentially develop new macrophage-centered therapeutic strategies

opencc-by-4.0Feb 2022View details →

Data from: The genetic basis of variation in sexual aggression: evolution versus social plasticity

Male sexual aggression towards females is a form of sexual conflict that can result in increased fitness for males through forced copulations or coercive matings at the cost of female lifetime fitness. We used male fruit flies (Drosophila melanogaster) as a model system to uncover the genomic contributions to variation in forced copulation, both due to standing variation in a wild population, and due to plastic changes associated with variation in social experience. We used RNAseq to analyze whole-transcriptome differential expression in male head tissue associated with evolved changes in forced copulation from lineages previously selected for high and low forced copulation rate (Dukas et al., 2020), and in male flies with varying forced copulation rates due to social experience. We identified hundreds of genes associated with evolved and plastic variation in forced copulation, however only a small proportion (27 genes) showed consistent differential expression due to both modes of variation. We confirmed this trend of low concordance in gene expression effects across broader sets of genes significant in either the evolved or plastic analyses using multivariate approaches. The gene ontology terms neuropeptide hormone activity and serotonin receptor activity were significantly enriched in the set of significant genes. Of 7 genes chosen for RNAi knockdown validation tests, knockdowns of 4 genes showed the expected effect on forced copulation behaviours. Taken together, our results provide important information about the apparently independent genetic architectures that underlie natural variation in sexual aggression due to evolution and plasticity.

Plasticity and evolution shape the scaling of metabolism and excretion along a geothermal temperature gradient

Physiological rates are heavily dependent on temperature and body size. Most current predictions of organisms' response to environmental warming are based on the assumption that key physiological rates like metabolism and excretion scale independently with body size and temperature and will not evolve. However, temperature is a significant driver for phenotypic variability in the allometric scaling and thermal sensitivity of physiological rates within ectotherm species, suggesting that evolution may play a role in shaping these parameters. We common-reared six populations of western mosquitofish that have recently established (~100 years ago) in geothermal springs along a broad thermal gradient (19-33°C) to determine whether these scaling parameters are affected by evolutionary and/or plastic responses to warming over ecological timescales. Each population was reared at four different temperatures (23, 26, 30 and 32°C). We measured routine metabolic and nitrogen excretion rates on mosquitofish across a wide body size range. We found evidence for plasticity, but not evolution, increasing the allometric scaling of metabolic rate with temperature. Plasticity in metabolism allometry reflected a decrease in thermal sensitivity at smaller body sizes. We found evidence for evolution of phenotypic plasticity on the allometry of excretion rate, reflecting evolutionary differences in how thermal sensitivity varies with body size across different populations. Evolutionary differences in excretion rate scaling did not influence the relationship between excretion and metabolism across rearing temperatures, suggesting that warming does not affect the balance between mosquitofish energy demands and nutrient recycling rates.

Plasticity in floral longevity and sex-phase duration of Lobelia siphilitica in response to simulated pollinator declines

Premise: Pollinator declines can reduce the quantity and quality of pollination services, resulting in less pollen deposited on flowers and lower seed production by plants. In response to these reductions, plants can increase the opportunity for pollination by plastically adjusting their floral traits, including floral longevity and sex-phase duration. However, studies of plant responses to pollinator declines have primarily focused on floral evolution across generations rather than plasticity in floral traits within a generation. Methods: To test whether plants can respond to pollinator declines by plastically adjusting their floral traits, we simulated declines by experimentally reducing pollinator access to Lobelia siphilitica plants, and measuring floral longevity and male- and female-phase duration. We also measured daily display size and phenotypic gender to test whether plasticity in floral longevity and sex-phase duration affected inflorescence traits. Results: We found that experimentally reducing pollination extended the male-phase duration of early-season flowers and the longevity of late-season flowers. However, plants with an extended male phase did not have a more male-biased phenotypic gender, and plants with an extended floral longevity did not have a larger daily display. Conclusions: Our results suggest that L . siphilitica plants can respond to pollinator declines by plastically adjusting both the longevity and sex-phase duration of their flowers. Consequently, plasticity in floral traits could be one mechanism by which plants respond to decreases in pollination services caused by pollinator declines.

opencc-by-4.0Nov 2021View details →

zenodo32/100

A calcium-based plasticity model for predicting long-term potentiation and depression in the neocortex

This dataset contains all (>1000) cell pairs as the Blue Brain Projects <a href="https://github.com/BlueBrain/EModelRunner">EModelRunner</a> packages as well as analysis code and analysed data used for the figures of our <a href="https://www.biorxiv.org/content/biorxiv/early/2020/04/20/2020.04.19.043117.full.pdf">preprint</a>: "A calcium-based plasticity model predicts long-term potentiation and depression in the neocortex". More documentation will follow in the upcoming days. Updates: v1.1 (31/12/2021): updated READMEs within cell_packages, added 2 extra authors for their contribution in EModelRunner. v1.2 (31/12/2021): same as v1.1 but w/o MacOS junk v1.3 (11/01/2022): added analysis notebooks v2.0 (11/01/2022): same as v1.3 but w/o MacOS junk and proper version number v2.1 (14/03/2022): fetching data from websites when possible instead of providing the downloaded csv files.

zenodo32/100

Source Data_Selective plasticity of callosal neurons following TBI.

Source data for the paper in Nature Communication: Selective plasticity of callosal neurons in the adult contralesional cortex following murine traumatic brain injury.

opencc-by-4.0Mar 2022View details →

Male adaptive plasticity can explain the evolution of sexual perception costs

Sensory perception of environmental cues has been shown to trigger plastic responses that can induce important fitness costs, including the dramatic modulation of ageing across distant taxa. For example, male Drosophila melanogaster suffer a marked decrease in fitness, including faster reproductive and actuarial ageing, if they perceive female cues but fail to mate shortly after (ageing via sexual perception). While this has been a breakthrough for our understanding of the mechanisms of ageing, it poses the question as to why such plastic responses evolved. Here, we used D. melanogaster to ask whether sexual perception costs may be a by-product of plastic adaptive responses to female cues. We found that: a) short-term (1 day) perception of female cues prior to mating opportunities increases male relative lifetime reproductive success in a competitive environment, b) medium-term (3-7 days) perception is neutral, and c) long-term (15 days) perception leads to reproductive costs. We then ran mathematical simulations under a wide range of socio-sexual and demographic scenarios to show that such plastic male responses can be adaptive whenever mating rates fluctuate within the range experienced by D. melanogaster and other insects in the wild, suggesting this may be a widespread strategy in nature. Finally, we show that, because the short-term benefits of plastic responses will be mostly acquired by high-quality males while long-term costs will be mostly paid by low-quality males, sexual perception can significantly magnify sexual selection (15-27% average increase in the opportunity for selection).

Meta-analysis of phenotypic plasticity in response to thermal treatments in invertebrates

Populations must adapt to environmental changes to remain viable. Both evolution and phenotypic plasticity contribute to adaptation, with plasticity possibly being more important for coping with rapid change. Adaptation is complex in species with separate sexes, as the sexes can differ in the strength or direction of natural selection, the genetic basis of trait variation, and phenotypic plasticity. Many species show sex differences in plasticity, yet how these differences influence extinction susceptibility remains unclear. We first extend theoretical models of population persistence in changing environments and show that persistence is affected by sexual dimorphism for phenotypic plasticity, trait genetic architecture, and sex-specific selection. Our models predict that female-biased adaptive plasticity—particularly in traits with modest-to-low cross-sex genetic correlations— typically promotes persistence, though we also identify conditions where sexually monomorphic or male-biased plasticity promotes persistence. We then perform a meta-analysis of sex-specific plasticity under manipulated thermal conditions. Although examples of sexually dimorphic plasticity are widely observed, systematic sex differences are rare. An exception—cold resistance—is systematically female-biased and represents a trait wherein sexually dimorphic plasticity might elevate population viability in changing environments. We discuss our results in light of debates about the roles of evolution and plasticity in extinction susceptibility.

Epigenetics underpins phenotypic plasticity of protandrous sex change in fish

Phenotypic plasticity is an important driver of species resilience. Often mediated by epigenetic changes, phenotypic plasticity enables individual genotypes to express variable phenotypes in response to environmental change. Barramundi (Lates calcarifer) is a protandrous (male-first) sequential hermaphrodite that exhibit plasticity in length-at-sex change between geographic regions. This plasticity is likely to be mediated by changes in DNA methylation (DNAm), a well-studied epigenetic modification. However, region-specific relationships between length, sex and DNAm in sequential hermaphrodites were previously unreported. To investigate these relationships, here we compare DNAm in four conserved vertebrate sex-determining genes in male and female barramundi of differing lengths from three regions of northern Australia. Despite a strong association between increasing length and male-to-female sex change, the data reveal that DNAm becomes more sex-specific (rather than more female-specific) with length. Significant differences in DNAm between males and females of similar lengths suggest that female-specific DNAm arises rapidly during sex change, rather than gradually with growth. The findings also reveal that region-specific differences in length-at-sex change are accompanied by differences in DNAm, and were concurrent with variability in remotely sensed sea temperature and salinity. Together, these findings provide the first in situ evidence for epigenetically and environmentally mediated sex change in a protandrous hermaphrodite, and offer significant insight into the molecular and ecological processes governing the marked and unique plasticity of sex in fish.