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opencc-zeroDec 2017View details →

Data from: Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains

Species richness is greatest in the tropics and much of this diversity is concentrated in mountains. Janzen (1967) proposed that reduced seasonal temperature variation selects for narrower thermal tolerances and limited dispersal along tropical elevation gradients. These locally adapted traits should, in turn, promote reproductive isolation and higher speciation rates in tropical mountains compared to temperate ones. Here we show that tropical and temperate montane stream insects have diverged in thermal tolerance and dispersal capacity, two key traits that are drivers of isolation in montane populations. Tropical species in each of three insect clades have markedly narrower thermal tolerances and lower dispersal than temperate species, resulting in significantly greater population divergence, higher cryptic species diversity, higher tropical speciation rates, and greater accumulation of species over time. Our study also indicates that tropical montane species, with narrower thermal tolerance and reduced dispersal ability, will be especially vulnerable to rapid climate change.

opencc-by-4.0Jul 2021View details →

Digesta and Plasma Metabolomics of Rainbow Trout Strains with Varied Tolerance of Plant-Based Diets Highlights Potential for Non-Lethal Assessments of Enteritis Development

The replacement of fishmeal in aquafeeds is essential to the sustainability of aquaculture. Besides the procurement of alternative protein sources, fish can also be selected for better performance on plant-based alternative diets. Rainbow trout (Oncorhynchus mykiss) is one such species in which the strain ARS-Selhas been selected for higher growth and enhanced utilization when fed soy-based diets. The aim of this study was to compare fish growth, and plasma and digesta metabolomes between the ARS-Seland two commercial strains (CS-1 and CS-2), when fed a plant-protein diet (PM) and a fishmeal-based diet (FM) and correlate them with the onset of enteritis. An NMR-metabolomics approach was taken to assess plasma and digesta metabolite profiles. Diet and strain showed significant effects on fish growth, with the ARS-Selfish receiving the PM diet reaching the highest final weight at sampling. Multivariate analysis revealed differences between plasma metabolite profiles of ARS-Seland CS (CS-1 considered together with CS-2) PM-fed groups in the early stages of the enteritis development, which was confirmed by a histological approach. In digesta, no differences were observed between groups. As reported in previous studies the ARS-Selstrain performed better than the commercial strains when fed the PM diet.

opencc-zeroJul 2021View details →

Estimating migration of the cold-tolerant leaf beetle Gonioctena quinquepunctata inside a mountain range in a spatially explicit context

The cold-tolerant leaf beetle Gonioctena quinquepunctata displays a large but fragmented European distribution and is restricted to mountain regions in the southern part of its range. Using a RAD-seq-generated large SNP data set (> 10,000 loci), we investigated the geographic distribution of genetic variation within the Vosges mountains, where the species is common. To translate this pattern of variation in an estimate of its capacity to disperse, we simulated SNP data under a spatially explicit model of population evolution and compared the simulated and real data with an approximate Bayesian computation (ABC) approach. For this purpose, we propose a new SNP statistic summarizing genetic variation in a spatially explicit context. The estimated number of effective migrants inferred with this statistic was compared to that derived from a combination of standard population genetic statistics often used in population genetic analyses. We conducted this ABC analysis with a relatively low number of data points compared to traditional ABC analyses, because spatially explicit models require long simulation times. A test of our overall strategy was conducted with simulated data and showed that it could provide a good estimate of the level of dispersal of an organism over its continuous geographic range. We suggest that the lower number of explored data points were at least partially compensated by the much larger number of simulations per data point associated with a large SNP data set. The results of our analyses suggested that this insect disperses well within the Vosges mountains, much more than was initially expected given the current and probably past fragmentation of its habitat and given the results of previous studies on genetic variation in other mountain leaf beetles.

opencc-zeroAug 2021View details →

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-zeroAug 2021View details →

Terrestrial green algae show higher tolerance to dehydration than do their aquatic sister-species: Raw data and analysis files

Diverse algae possess the ability to recover from extreme desiccation without forming specialized resting structures. Green algal genera such as Tetradesmus (Sphaeropleales, Chlorophyceae) contain temperate terrestrial, desert, and aquatic species, providing an opportunity to compare physiological traits associated with the transition to land in closely related taxa. We subjected six species from distinct habitats to three dehydration treatments varying in relative humidity (RH 5%, 65%, 80%) followed by short- and long-term rehydration. We tested the capacity of the algae to recover from dehydration using the effective quantum yield of photosystem II as a proxy for physiological activity. The degree of recovery was dependent both on the habitat of origin and the dehydration scenario, with terrestrial, but not aquatic species, recovering from dehydration. Distinct strains of each species responded similarly to dehydration and rehydration, with the exception of one aquatic strain that recovered from the mildest dehydration treatment. Cell ultrastructure was uniformly maintained in both aquatic and desert species during dehydration and rehydration, but staining with an amphiphilic styryl dye indicated damage to the plasma membrane from osmotically-induced water loss in the aquatic species. These analyses demonstrate that terrestrial Tetradesmus possess a vegetative desiccation tolerance phenotype, making these species ideal for comparative omics studies.

opencc-zeroAug 2021View details →

Genetic variation for upper thermal tolerance diminishes within and between populations with increasing acclimation temperature in Atlantic salmon

Populations may counteract lasting temperature changes or recurrent extremes through plasticity or adaptation. However, it remains underexplored how outbreeding, either naturally, unintentionally, or facilitated, may modify a local response potential and whether genotype-by-environment interactions or between-trait correlations can restrict this potential. We quantified population differences and outbreeding effects, within-population genetic variation, and plasticity of these, for thermal performance proxy traits using 32 pedigreed wild, domesticated, and wild-domesticated Atlantic salmon families reared under common-garden conditions. Following exposure to ambient cold (11.6°C) or ~4- and ~8-degree warmer summer temperatures, populations differed notably for body length and critical thermal maximum (CTmax) and for thermal plasticity of length, condition, and CTmax, but not for haematocrit. Line-cross analysis suggested mostly additive and some dominant outbreeding effects on means and solely additive outbreeding effects on plasticity. Heritability was detected for all traits. However, with increasing acclimation temperature, differences in CTmax between populations and CTmax heritability diminished, and CTmax breeding values re-ranked. Furthermore, CTmax and body size were negatively correlated at the genetic and phenotypic levels, and there was indirect evidence for a positive correlation between growth potential and thermal performance breadth for growth. Thus, population differences (including those between wild and domesticated populations) in thermal performance and plasticity may present a genetic resource in addition to the within-population genetic variance to facilitate, or impede, thermal adaptation. However, unfavourable genotype-by-environment interactions and negative between-trait correlations may generally hamper joint evolution in response to increase in average temperature and temporary extremes.

opencc-zeroSep 2021View details →

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.

opencc-by-4.0Sep 2021View details →

Supporting data for 'Fast universal quantum gate above the fault-tolerance threshold in silicon'

Data supporting for paper 'Fast universal quantum gate above the fault-tolerance threshold in silicon'. All the data are stored in the HDF5 format that can be conveniently loaded by the xarray Python package.

opencc-zeroSep 2021View details →

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.

opencc-by-4.0Sep 2021View details →

GTTAtlas - Metabolomics atlas of oral 13C-glucose tolerance test in mice

GTTAtlas - Metabolomics atlas of oral 13C6-glucose tolerance test in mice GTTAtlas web application: <a href="https://gttatlas.metabolomics.fgu.cas.cz">https://gttatlas.metabolomics.fgu.cas.cz</a> Repository of LC–MS data in *.abf format: <a href="https://repository.metabolomics.fgu.cas.cz/">https://repository.metabolomics.fgu.cas.cz/</a> LC–MS platforms: <a href="https://www.metabolomics.fgu.cas.cz">https://www.metabolomics.fgu.cas.cz</a> LIMeX platforms: BEH Amide positive, BEH amide negative, HSS T3 negative, BEH C18 positive, BEH C18 positive-TG,  BEH C18 negative LC−MS system: Vanquish UHPLC System (Thermo Fisher Scientific, Bremen, Germany) coupled to a Q Exactive Plus mass spectrometer (Thermo Fisher Scientific) Samples: plasma, liver, pancreas, kidney, heart, gastrocnemius muscle, soleus muscle, duodenum, jejunum, ileum, subcutaneous adipose tissue, epididymal adipose tissue, brown adipose tissue. Time points: 0, 15, 30, 60, 120, 180, 240 minutes

opencc-zeroSep 2021View details →

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-zeroOct 2021View details →

Towards an understanding of the latitudinal patterns in thermal tolerance and vulnerability of woody plants under climate warming

Predicting spatial patterns in thermal tolerance and vulnerability of species under climate warming remains a challenge. Current knowledge is mainly from experiment-based thermal physiology of limited numbers of ectotherms, yet large-scale evaluations on plants remain elusive. Here, using distribution maps with spatial resolutions of 20×20 km for 5628 woody species in China, we propose a novel approach, i.e. thermal distribution curves, to describe species' realized thermal niches, and then estimate their thermal tolerance and warming risks under projected climate warming in 2050s and 2070s. We find that species' vulnerability and potential local extinction risks within grid cells decrease with latitude and increase with aridity due to narrow thermal tolerance of species located at low latitudes and arid regions. Over 90% of species could still tolerate future warming in most areas, indicating relatively optimistic expectation of potential local extinctions. Our study presents a new framework to quantify climate warming impacts on a large number of species without sufficient physiological information, and provides fundamental references for conservation planning under climate change.

opencc-by-4.0Oct 2021View details →

Negative regulation of IMD contributes to disease tolerance during systemic bacterial infection in Drosophila

Data and R code for Negative regulation of IMD contributes to disease tolerance during systemic bacterial infection in Drosophila

opencc-zeroOct 2022View details →

Data from: Does tolerance allow bonobos to outperform chimpanzees on a cooperative task? A conceptual replication of Hare et al., 2007

Across various taxa, social tolerance is thought to facilitate cooperation, and many species are treated as having species-specific patterns of social tolerance. Yet studies that assess wild and captive bonobos and chimpanzees result in contrasting findings. By replicating a cornerstone experimental study on tolerance and cooperation in bonobos and chimpanzees (Hare et al., 2007 Cur. Biol. 17, 619–623), we aim to understand whether current discrepant findings may result from noise, methodological differences, or behavioural variability. We tested bonobos and chimpanzees housed at the same facility in a co-feeding and cooperation task. Food was placed on dishes located on both ends or in the middle of a platform. In the co-feeding task, the tray was simply made available to the ape duos, whereas in the cooperation task the apes had to simultaneously pull at both ends of a rope attached to the platform to retrieve the food. In contrast to the published findings, bonobos and chimpanzees co-fed to a similar degree, indicating a similar level of tolerance. However, bonobos cooperated more than chimpanzees when the food was monopolizable, which replicates the original study. Our findings call into question the interpretation that at the species level bonobos cooperate to a higher degree because they are inherently more tolerant.

Data from: A test of the competitive ability – cold tolerance trade-off hypothesis in seasonally breeding beetles

Closely related species that use similar resources often differ in their seasonal patterns of activity, but the factors that limit their distributions across seasons are unknown for most species. One hypothesis to explain seasonal variation in the distributions of species involves a trade-off between competitive ability and cold tolerance, where tolerance to the cold compromises competitive ability in warmer (benign) temperatures, either at the level of the individual or population. We tested both individual-level and population-level mechanisms of this hypothesis in two co-occurring species of temperate burying beetles (Silphidae: Nicrophorus sayi, N. orbicollis) that differ in their seasonal patterns of activity. We measured cold tolerance, breeding activity as a function of temperature, and competitive ability as a function of temperature and season. Consistent with our hypothesis, the mid-season N. orbicollis was less able to function at the cold temperatures that characterize early spring, when the early-season N. sayi is most active. The larger beetle, however, always won one-on-one competitive trials at warm temperatures, regardless of species, inconsistent with an individual-level trade-off. N. orbicollis was usually larger and successful when competing for the same carrion later in the season, mostly because of its larger population size, consistent with a trade-off between competitive ability and cold tolerance acting at the population level. Our findings suggest that cold temperatures limit the mid-season N. orbicollis from earlier spring emergence, while competitive pressure from the more abundant, larger N. orbicollis constrains the early-season N. sayi from remaining active through the summer.

Data from: Heat tolerance variation reveals vulnerability of tropical herbivore-parasitoid interactions to climate change

Assessing the heat tolerance (CTmax) of organisms is central to understand the impact of climate change on biodiversity. While both environment and evolutionary history affect CTmax, it is unclear how these factors and their interplay influence ecological interactions, communities, and ecosystems under climate change. We collected and reared caterpillars and parasitoids from canopy and ground layers in different seasons in a tropical rainforest. We tested the CTmax and Thermal Safety Margins (TSM) of these food webs with implications for how species interactions could shift under climate change. We identified strong influence of phylogeny in herbivore-parasitoid community heat tolerance. The TSM of all insects were narrower in the canopy and parasitoids had lower heat tolerance compared to their hosts. Our CTmax-based simulation showed higher herbivore-parasitoid food web instability under climate change than previously assumed, highlighting the vulnerability of parasitoids and related herbivore control in tropical rainforests, particularly in the forest canopy.

Rates of phenotypic plasticity in thermal tolerance

An individual's fitness cost associated with environmental change likely depends on the rate of adaptive phenotypic plasticity, and yet our understanding of plasticity rates in an ecological and evolutionary context remains limited. We provide the first quantitative synthesis of existing plasticity rate data, focusing on acclimation of temperature tolerance in ectothermic animals, where we demonstrate applicability of a recently proposed analytical approach. The analyses reveal considerable variation in plasticity rates of this trait among species, with half-times (how long it takes for the initial deviation from the acclimated phenotype to be reduced by 50% when individuals are shifted to a new environment) ranging from 3.7 to 770.2 h. Furthermore, rates differ among higher taxa, being higher for amphibians and reptiles than for crustaceans and fishes, and with insects being intermediate. We argue that a more comprehensive understanding of phenotypic plasticity will be attained through increased focus on the rate parameter.

Data and code from: Experimental evolution of environmental tolerance, acclimation, and physiological plasticity in a randomly fluctuating environment

Environmental tolerance curves, representing absolute fitness against the environment, are an empirical assessment of the fundamental niche, and emerge from the phenotypic plasticity of underlying phenotypic traits. Dynamic plastic responses of these traits can lead to acclimation effects, whereby recent past environments impact current fitness. Theory predicts that higher levels of phenotypic plasticity should evolve in environments that fluctuate more predictably, but there have been few experimental tests of these predictions. Specifically, will still lack experimental evidence for evolution of acclimation effects in response to environmental predictability. Here, we exposed 25 genetically diverse populations of the halotolerant microalgae Dunaliella salina to different constant salinities, or to randomly fluctuating salinities, for over 200 generations. The fluctuating treatments differed in their autocorrelation, which determines the similarity of subsequent values, and thus environmental predictability. We then measured acclimated tolerance surfaces, mapping population growth rate against past (acclimation) and current (assay) environments. We found that experimental mean and variance in salinity caused the evolution of niche position (optimal salinity) and breadth, with respect to not only current but also past (acclimation) salinity. We also detected weak but significant evidence for evolutionary changes in response to environmental predictability, with higher predictability leading notably to an upwards shift in optimal salinities and stronger acclimation effect of past environment on current fitness. We further showed that these responses are related to the evolution of plasticity for intracellular glycerol, the major osmoregulatory mechanism in this species. However the direction of plasticity evolution did not match simple theoretical predictions. Our results underline the need for a more explicit consideration of the dynamics of environmental tolerance and its underlying plastic traits to reach a better understanding of ecology and evolution in fluctuating environments.

Tolerance of coralline algae to ocean warming and marine heatwaves

Ocean warming (OW) and marine heatwaves (MHWs) rapidly transform marine ecosystems, especially when they impact keystone or foundation species. Foundation species such as kelps, fucoids and corals are highly sensitive to heat stress, which threatens the future of temperate seaweed forests and tropical reefs. However, functioning and resilience of these systems also rely on the less conspicuous coralline algae, whose thermal tolerances have gone largely untested. Here, we examined the sensitivity of four temperate coralline algal morphotypes from three different species to four realistic present-day and future OW and MHW scenarios (ambient [16°C constant]; ambient+MHW [16°C baseline + a symmetric two-week heatwave with a peak intensity of 18.7°C]; future [18.7°C constant]; future+MHW [18.7°C baseline + a symmetric two-week heatwave with a peak intensity of 21.4°C]). Photo-physiology (e.g., Fv/Fm) and calcification physiology (e.g., proxies for calcifying fluid saturation state Ω CF ) were generally unaffected by the treatments, implying a high thermo-tolerance of our study species compared to other important marine foundation species. We ascribe this mainly to their photosynthetic apparatus that, unlike in other photoautotrophs, continued to function under heat stress. Experimental evidence presented here and elsewhere implies that coralline algae are likely to continue to play their crucial ecological roles in a warming ocean. Yet, such predictions are fraught with uncertainty due to the substantial gaps in our knowledge. We attempt to highlight some of these gaps and aim to present potential physiological underpinnings of their thermo-tolerance.