Find research datasets worth reusing

Data from: A context-dependent induction of natal habitat preference in a generalist herbivorous insect

In many species adults exploit sensory information experienced in their natal habitat when searching for resources. This behavioral plasticity may help animals to establish themselves in new habitats by quickly locating suitable resources and avoiding unsuitable resources in complex environments. However the processes guiding positive or negative natal habitat preference induction (NHPI) remain poorly understood. In the polyphagous moth Spodoptera littoralis, earlier studies have shown that female innate host-plant preference is modulated by larval feeding experience. In this context, the aim of this study was to investigate how variability in food quality associated with habitat olfactory cues can modulate NHPI in this species. We found that larvae showed appetitive or aversive responses to the experienced plant olfactory cues based on their values as predictors of food quality. Furthermore, larval exposure to host-plant olfactory cues alone induced oviposition preference for these plants in adult females, but only when the females had been feeding on high-quality food as larvae. Females reared on poor quality food retained their innate plant oviposition preference as adults. These results show that NHPI in S. littoralis is context-dependent and based on food quality with which olfactory cues are associated. They also suggest that larval experience to plant olfactory cues alone is sufficient to modulate the adult host plant preference. Finally, this study suggests that polyphagous insects with particular innate plant preferences may only show phenotypic plasticity in this trait when the fitness benefits are high.

Data from: Scale dependencies and generalism in host use shape virus prevalence

Processes that generate the distribution of pathogens and their interactions with hosts are not insensitive to changes in spatial scale. Spatial scales and species traits are often selected intentionally, based on practical considerations, ignoring biases that the scale and type of observation may introduce. Specifically, these biases might change the interpretation of disease-diversity relationships that are reported as either 'dilution' or 'amplification' effects. Here, we combine field data of a host-pathogen community with empirical models to test the effects that i) spatial scale and ii) host range have on the relationship between plant-virus infection prevalence and diversity. We show that prevalence-diversity relationships are scale dependent, and can produce opposite effects associated with different habitats at sub-ecosystem scales. The total number of host species of each virus reflected generalism at the ecosystem scale. However, plasticity in host-range resembled habitat-specific specialisation and also changed model predictions. We show that habitat heterogeneity, ignored at larger (ecosystem) spatial scales, influences pathogen distributions. Hence, understanding disease distributions and the evolution of pathogens requires reconciling specific hypotheses of the study with an appropriate spatial scale, or scales, and consideration of traits, such as host range, that might strongly contribute to biotic interactions.

Data from: Speed dependency in α-motoneuron activity and locomotor modules in human locomotion: indirect evidence for phylogenetically conserved spinal circuits

Coordinated locomotor muscle activity is generated by the spinal central pattern generators (CPGs). Vertebrate studies have demonstrated the following two characteristics of the speed control mechanisms of the spinal CPGs: (i) rostral segment activation is indispensable for achieving high-speed locomotion; and (ii) specific combinations between spinal interneuronal modules and motoneuron (MN) pools are sequentially activated with increasing speed. Here, to investigate whether similar control mechanisms exist in humans, we examined spinal neural activity during varied-speed locomotion by mapping the distribution of MN activity in the spinal cord and extracting locomotor modules, which generate basic MN activation patterns. The MN activation patterns and the locomotor modules were analysed from multi-muscle electromyographic recordings. The reconstructed MN activity patterns were divided into the following three patterns depending on the speed of locomotion: slow walking, fast walking and running. During these three activation patterns, the proportion of the activity in rostral segments to that in caudal segments increased as locomotion speed increased. Additionally, the different MN activation patterns were generated by distinct combinations of locomotor modules. These results are consistent with the speed control mechanisms observed in vertebrates, suggesting phylogenetically conserved spinal mechanisms of neural control of locomotion.

Data from: Age-dependent speciation can explain the shape of empirical phylogenies

Tens of thousands of phylogenetic trees, describing the evolutionary relationships between hundreds of thousands of taxa, are readily obtainable from various databases. From such trees inferences can be made about the underlying macroevolutionary processes, yet remarkably these processes are still poorly understood. Simple and widely used evolutionary null models are problematic: empirical trees show very different imbalance between the sizes of the daughter clades of ancestral taxa compared to what models predict. Obtaining a simple evolutionary model that is both biologically plausible and produces the imbalance seen in empirical trees is a challenging problem, to which none of the existing models provide a satisfying answer. Here we propose a simple, biologically-plausible macroevolutionary model in which the rate of speciation decreases with species age, while extinction rates can vary quite generally. We show that this model provides a remarkable fit to the thousands of trees stored in the online database TreeBase. The biological motivation for the identified age-dependent speciation process may be that recently evolved taxa often colonise new regions or niches and may initially experience little competition. These new taxa are thus more likely to give rise to further new taxa than a taxon that has remained largely unchanged and is therefore well-adapted to its niche. We show that age-dependent speciation may also be the result of different within-species populations following the same laws of lineage splitting to produce new species. As the fit of our model to the tree database shows, this simple biological motivation provides an explanation for a long standing problem in macroevolution.

opencc-zeroDec 2018View details →

Data from: Complex spike synchrony dependent modulation of rat deep cerebellar nuclear activity

The rules determining cerebellar output are not fully understood, but must involve Purkinje cell activity (PCs), as PCs are the major input to deep cerebellar nuclear (DCN) cells (which form the majority of cerebellar output). Here, the influence of PC complex spikes (CSs) was investigated by simultaneously recording DCN activity with CSs from PC arrays in anesthetized rats. Crosscorrelograms were used to identify PCs that were presynaptic to recorded DCN cells (presynaptic PCs). Such PCs were located within rostrocaudal cortical strips and displayed synchronous CS activity. CS-associated modulation of DCN activity included a short-latency post-CS inhibition and long-latency excitations before and after the CS. The amplitudes of the post-CS responses correlated with the level of synchronization among presynaptic PCs. A temporal precision of {less than or equal to} 10 ms was generally required for CSs to be maximally effective. The results suggest that CS synchrony is a key control parameter of cerebellar output.Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

Data from: Time-dependent decline of body-specific attention to the paretic limb in chronic stroke patients

Objective: To examine whether reduced body-specific attention to paretic limb is found in chronic stroke patients in the time-dependent manner. Methods: Twenty-one patients with chronic hemiparesis (10 left and 11 right hemiparesis) after subcortical stroke and 18 age-matched healthy controls were recruited in this study. Standard neuropsychological examinations showed no clear evidence of spatial neglect in all patients. In order to quantitatively measure the spatial attention to paretic hand, a visual detection task for detecting a target appearing on the surface of either a paretic or dummy hand was used. This task can measure the body facilitation effect, which makes faster detection of a target on the body compared with one far from the body. Results: In stroke patients, there was no difference in the reaction time for visual target between on the paretic and the dummy hands, while the healthy participants showed faster detection for the visual target on the real hand than that on dummy one. The Index of the body facilitation effect, subtracting the reaction time for the target-on-paretic hand from that for the target-on-dummy one, was correlated with the duration since onset and with finger function test on the Stroke Impairment Assessment Set. Conclusions: The reduction of the body facilitation effect in paretic limb suggests the decline of body-specific attention to the paretic one in patients with chronic hemiparesis. This decline of the body-specific attention, leading to neglect for paretic limb, will be one of the most serious problems for rehabilitation based on use-dependent plasticity.

Data from: Use of elastic stability analysis to explain the stress-dependent nature of soil strength

The peak and critical state strengths of sands are linearly related to the stress level, just as the frictional resistance to sliding along an interface is related to the normal force. The analogy with frictional sliding has led to the use of a 'friction angle' to describe the relationship between strength and stress for soils. The term 'friction angle' implies that the underlying mechanism is frictional resistance at the particle contacts. However, experiments and discrete element simulations indicate that the material friction angle is not simply related to the friction angle at the particle contacts. Experiments and particle-scale simulations of model sands have also revealed the presence of strong force chains, aligned with the major principal stress. Buckling of these strong force chains has been proposed as an alternative to the frictional-sliding failure mechanism. Here, using an idealized abstraction of a strong force chain, the resistance is shown to be linearly proportional to the magnitude of the lateral forces supporting the force chain. Considering a triaxial stress state, and drawing an analogy between the lateral forces and the confining pressure in a triaxial test, a linear relationship between stress level and strength is seen to emerge from the failure-by-buckling hypothesis.

opencc-zeroDec 2012View details →

Data from: Fight evolution with evolution: plasmid-dependent phages with a wide host range prevent the spread of antibiotic resistances

The emergence of pathogenic bacteria resistant to multiple antibiotics is a serious worldwide public health concern. Whenever antibiotics are applied, the genes encoding for antibiotic resistance are selected for within bacterial populations. This has led to the prevalence of conjugative plasmids that carry resistance genes and can transfer themselves between diverse bacterial groups. In this study, we investigated whether it is feasible to attempt to prevent the spread of antibiotic resistances with a lytic bacteriophage, which can replicate in a wide range of gram-negative bacteria harboring conjugative drug-resistance conferring plasmids. The counter-selection against the plasmid was shown to be effective, reducing the frequency of multi-resistant bacteria that formed via horizontal transfer by several orders of magnitude. This was true also in the presence of an antibiotic against which the plasmid provided resistance. Majority of the multi-resistant bacteria subjected to phage selection also lost their conjugation capability. Overall this study suggests that, while we are obligated to maintain the selection for the spread of the drug resistances, the 'fight evolution with evolution' approach could help us even out the outcome to our favor.

Data from: Towards an interactive, process‐based approach to understanding range shifts: developmental and environmental dependencies matter

Many species are undergoing distributional changes in response to climate change. However, wide variability in range shifting rates has been observed across taxa, and even among closely-related species. Attempts to link climate-mediated range shifts to traits has often produced weak or conflicting results. Here we investigate interactive effects of developmental processes and environmental stress on the expression of traits relevant to range shifts. We use an individual-based modelling approach to assess how different developmental strategies affect range shift rates under a range of environmental conditions. We find that under stressful conditions, such as at the margins of the species' fundamental niche, investment in prolonged development leads to the greatest rates of range shifting, especially when longer time in development leads to of improved fecundity and dispersal-related traits. However, under benign conditions, and when traits are less developmentally plastic, shorter development times are preferred for rapid range shifts, because higher generational frequency increases the number of individual dispersal events occurring over time. Our results suggest that the ability of a species to range shift depends not only on their dispersal and colonisation characteristics but also how these characteristics interact with developmental strategies. Benefits of any trait always depended on the environmental and developmental sensitivity of life history trait combinations, and the environmental conditions under which the range shift takes place. Without considering environmental and developmental sources of variation in the expression of traits relevant to range shifts, there is little hope of developing a general understanding of intrinsic drivers of range shift potential

opencc-zeroDec 2015View details →

Data from: Susceptibility of Macrosiphum euphorbiae to the parasitoid Aphidius ervi: larval development depends on host aphid genotype

The potato aphid, Macrosiphum euphorbiae Thomas (Hemiptera: Aphididae: Macrosiphini), is a common polyphagous aphid in Europe and North America. However, the factors influencing potato aphid dynamics and susceptibility to natural enemies are largely undescribed, particularly in relation to facultative endosymbiotic bacteria, which can provide protection against parasitism and disease in some aphid species. This study investigated whether potato aphid susceptibility to one of its principal natural enemies, the parasitoid Aphidius ervi Haliday (Hymenoptera: Braconidae: Aphidiinae), varied in relation to aphid genotype and/or endosymbiont presence. Parasitism and aphid fitness assays were conducted on clonal lineages of aphids, harbouring their natural endosymbiont infections, collected over 3 years from separate geographic locations. Parasitized aphids were dissected to quantify parasitoid oviposition, larval development, and mummification. Amongst the 19 clonal lines of M. euphorbiae tested, seven aphid genotypes were identified, and 11 lines harboured one or both of the facultative endosymbionts Hamiltonella defensa Moran et al. and Regiella insecticola Moran et al.; H. defensa infections were associated exclusively with two of the seven M. euphorbiae genotypes. Parasitism resistance was detected in clonal lines belonging to a single aphid genotype and resulted from failure of parasitoid eggs to develop into larvae rather than failure of the parasitoid to oviposit. Contrary with studies of several other aphid species, there was little evidence that H. defensa provided strong protection to M. euphorbiae from parasitism by A. ervi. Furthermore, there were no clear fitness costs to the aphid associated with parasitism resistance or with H. defensa infection. The two M. euphorbiae genotypes in which H. defensa occurred, which included the resistant genotype, exhibited faster development, higher survival, and greater fecundity than the other five aphid genotypes. These findings suggest that biological control of M. euphorbiae using A. ervi alone could exacerbate pest problems by selecting for the fittest parasitism-resistant genotypes.

Data from: Phenotype-dependent selection underlies patterns of sorting across habitats: the case of stream-fishes

Spatial and temporal heterogeneity within landscapes influences the distribution and phenotypic diversity of individuals both within and across populations. Phenotype-habitat correlations arise either through phenotypes within an environment altering through the process of natural selection or plasticity, or phenotypes remaining constant but individuals altering their distribution across environments. The mechanisms of non-random movement and phenotype-dependent habitat choice may account for associations within highly heterogeneous systems, such as streams, where local adaptation may be negated, plasticity too costly and movement is particularly important. Despite growing attention, however, few empirical tests have yet to be conducted. Here we provide a test of phenotype-dependent habitat choice and ask: 1) if individuals collected from a single habitat type continue to select original habitat; 2) if decisions are phenotype-dependent and functionally related to habitat requirements; and 3) if phenotypic-sorting continues despite increasing population density. To do so we both conducted experimental trials manipulating the density of four stream-fish species collected from either a single riffle or pool and developed a game-theoretical model exploring the influence of individuals' growth rate, sampling and competitive abilities as well as interference on distribution across two habitats as a function of density. Our experimental trials show individuals selecting original versus alternative habitats differed in their morphologies, that morphologies were functionally related to habitat-type swimming demands, and that phenotypic-sorting remained significant (although decreased) as density increased. According to our model this only occurs when phenotypes have contrasting habitat preferences and only one phenotype disperses (i.e. selects alternatives) in response to density pressures. This supports our explanation that empirical habitat selection was due to a combination of collecting a fraction of mobile individuals with different habitat preferences and the exclusion of individuals via scramble competition at increased densities. Phenotype-dependent habitat choice can thereby account for observed patterns of natural stream-fish distribution.

opencc-zeroDec 2011View details →

Data from: Identification of glucose kinase dependent and independent pathways for carbon control of primary metabolism, development and antibiotic production in Streptomyces coelicolor by quantitative proteomics

Members of the soil-dwelling prokaryotic genus Streptomyces are indispensable for the recycling of complex polysaccharides, and produce a wide range of natural products. Nutrient availability is a major determinant for the switch to development and antibiotic production in streptomycetes. Carbon catabolite repression (CCR), a main signaling pathway underlying this phenomenon, was so far considered fully dependent on the glycolytic enzyme glucose kinase (Glk). Here we provide evidence of a novel Glk-independent pathway in Streptomyces coelicolor, using advanced proteomics that allowed the comparison of the expression of some 2,000 proteins, including virtually all enzymes for central metabolism. While CCR and inducer exclusion of enzymes for primary and secondary metabolism and precursor supply for natural products is mostly mediated via Glk, enzymes for the urea cycle, as well as for biosynthesis of the γ-butyrolactone Scb1 and the responsive cryptic polyketide Cpk are subject to Glk-independent CCR. Deletion of glkA led to strong downregulation of biosynthetic proteins for prodigionin and calcium-dependent antibiotic (CDA) in mannitol-grown cultures. Repression of bldB, bldN, and its target bldM explains the poor development of S. coelicolor on solid-grown cultures containing glucose. A new model for carbon catabolite repression in streptomycetes is presented.

Data from: Rev7 and 53BP1/Crb2 prevent RecQ helicase-dependent hyper-resection of DNA double-strand breaks

Poly(ADP ribose) polymerase inhibitors (PARPi) target cancer cells deficient in homology-directed repair of DNA double-strand breaks (DSBs). In preclinical models, PARPi resistance is tied to altered nucleolytic processing (resection) at the 5' ends of a DSB. For example, loss of 53BP1 or Rev7/MAD2L2/FANCV derepresses resection to drive PARPi resistance, although the mechanisms are poorly understood. Long-range resection can be catalyzed by two machineries: the exonuclease Exo1, or the combination of a RecQ helicase and Dna2. Here, we develop a single cell microscopy assay that allows the distinct phases and machineries of resection to be interrogated simultaneously in living S. pombe cells. Using this assay, we find that the 53BP1 orthologue and Rev7 specifically repress long-range resection through the RecQ helicase-dependent pathway, thereby preventing hyper-resection. These results suggest that 'rewiring' of BRCA1-deficient cells to employ an Exo1-independent hyper-resection pathway is a driver of PARPi resistance.

opencc-zeroDec 2015View details →

Data from: How reliably can we infer diversity-dependent diversification from phylogenies?

Slowdowns in lineage accumulation in phylogenies suggest that speciation rates decline as diversity increases. Likelihood methods have been developed to detect such diversity dependence. However, a thorough test of whether such approaches correctly infer diversity dependence is lacking. Here, we simulate phylogenetic branching under linear negative diversity-dependent and diversity-independent models and estimate from the simulated phylogenies the maximum-likelihood parameters for three different conditionings – on survival of the birth–death process given the crown age, on tree size (N) and on tree size given the crown age. We report the accuracy of recovering the simulation parameters and the reliability of the model selection based on the χ2 likelihood ratio test. Parameter estimate accuracy: Conditioning on survival given the crown age yields a severe bias of the carrying capacity K towards N and an upward bias of the speciation rate, particularly in clades where diversity-dependent feedbacks are still weak (N « K). Conditioning on N yields an overestimate of K and an underestimate of speciation rate, particularly when saturation has been reached. Dual conditioning yields relatively unbiased parameter estimates on average, but the deviation from the true value for any single estimate may be large. Model selection reliability: The frequency of incorrectly rejecting a diversity-independent model when the simulation was diversity-independent (type I error) differs substantially from the significance level α used in the likelihood ratio test, rendering the likelihood ratio test inappropriate. The frequency of correctly rejecting the diversity-independent model when the simulation was diversity-dependent (power) is larger when the clade is closer to equilibrium and for conditioning on crown age. We conclude that conditioning on crown age has the best statistical properties overall, but caution that parameter estimates may be biased. To assess parameter uncertainty in future studies of diversity dependence on real data, we recommend parametric bootstrapping, examination of the likelihood surface and comparison of estimates across the types of conditioning. To assess model selection reliability, we discourage the use of the χ2 likelihood ratio test or AIC (which are equivalent in this case), but recommend a likelihood ratio test based on parametric bootstrap. We illustrate this method for the diversification of Dendroica warblers.

Data from: Scale-dependent role of demography and dispersal on the distribution of populations in heterogeneous landscapes

Both dispersal and local demographic processes determine a population's distribution among habitats of varying quality, yet most theory, experiments, and field studies have focused on the former. We use a generic model to show how both processes contribute to a population's distribution, and how the relative importance of each mechanism depends on scale. In contrast to studies only considering habitat-dependent dispersal, we show that predictions of ideal free distribution (IFD) theory are relevant even at landscape scales, where the assumptions of IFD theory are violated. This is because scales that inhibit one process, promote the other's ability to drive populations to the IFD. Furthermore, because multiple processes can generate IFDs, the pattern alone does not specify a causal mechanism. This is important because populations with IFDs generated by dispersal or demography respond much differently to shifts in resource distributions.

Data from: Habitat-mediated carry-over effects lead to context dependent outcomes of species interactions

1. When individuals disperse, their performance in newly colonized habitats can be influenced by the conditions they experienced in the past, leading to environmental carry-over effects. While carry-over effects are ubiquitous in animal and plant systems, their impact on species interactions and coexistence are largely ignored in traditional coexistence theory. 2. Here we used a combination of modelling and experiments with two competing species to examine when and how such environmental carry-over effects influence community dynamics and competitive exclusions. 3. We found that variation in the natal habitat quality of colonizing individuals created carry-over effects which altered competitive coefficients, fecundity and mortality rates, and extinction probabilities of both species. As a consequence, the dynamics of competitive exclusion within and across habitat types was contingent on the natal habitat of colonizing individuals, indicating that spatial carry-over effects can fundamentally alter the dynamics and outcome of interspecific competition. 4. Interestingly, carry-over effects persistently influenced dynamics in systems with interspecific competition for the entire duration of the experiment while carry-over effects were transient and only influenced initial dynamics in single-species populations. Thus carry-over effects can be enhanced by species interactions, suggesting that their long-term effects may often not be accurately predicted by single-species studies. 5. Given that carry-over effects are ubiquitous in heterogeneous landscapes, our results provide a novel mechanism that could help explain variation in the structure of natural communities.

Data from: Abundance-dependent effects of neighborhood dissimilarity and growth rank reversal in a Neotropical forest

Why tropical forests harbor an exceptional number of species with striking differences in abundances remains an open question. We propose a theoretical framework to address this question in which rare species may have different extirpation risks depending on species ranks in tree growth and sensitivities to neighborhood interactions. To evaluate the framework, we studied tree growth and its responses to neighborhood dissimilarity (ND) in traits and phylogeny for 146 species in a Neotropical forest. We found that tree growth was positively related to ND, and common species were more strongly affected by ND than rare species, which may help delay dominance of common species. Rare species grew more slowly at the community-wide average ND than common species. But rare species grew faster when common species tended to dominate locally, which may help reduce extirpation risk of rare species. Our study highlights that tree growth rank among species depends on their responses to neighborhood interactions, which can be important in fostering diversity maintenance in tropical forests.

Data from: Cell cycle-dependent differentiation dynamics balances growth and endocrine differentiation in the pancreas

Organogenesis relies on the spatiotemporal balancing of differentiation and proliferation driven by an expanding pool of progenitor cells. In the mouse pancreas, lineage tracing at the population level has shown that the expanding pancreas progenitors can initially give rise to all endocrine, ductal, and acinar cells but become bipotent by embryonic day 13.5, giving rise to endocrine cells and ductal cells. However, the dynamics of individual progenitors balancing self-renewal and lineage-specific differentiation has never been described. Using three-dimensional live imaging and in vivo clonal analysis, we reveal the contribution of individual cells to the global behaviour and demonstrate three modes of progenitor divisions: symmetric renewing, symmetric endocrinogenic, and asymmetric generating a progenitor and an endocrine progenitor. Quantitative analysis shows that the endocrine differentiation process is consistent with a simple model of cell cycle–dependent stochastic priming of progenitors to endocrine fate. The findings provide insights to define control parameters to optimize the generation of β-cells in vitro.

Data from: Experience-dependent mushroom body plasticity in butterflies: consequences of search complexity and host range

An ovipositing insect experiences many sensory challenges during her search for a suitable host plant. These sensory challenges become exceedingly pronounced when host range increases, as larger varieties of sensory inputs have to be perceived and processed in the brain. Neural capacities can be exceeded upon information overload, inflicting costs on oviposition accuracy. One presumed generalist strategy to diminish information overload is the acquisition of a focused search during its lifetime based on experiences within the current environment, a strategy opposed to a more genetically determined focus expected to be seen in relative specialists. We hypothesized that a broader host range is positively correlated with mushroom body (MB) plasticity, a brain structure related to learning and memory. To test this hypothesis, butterflies with diverging host ranges (Polygonia c-album, Aglais io and Aglais urticae) were subjected to differential environmental complexities for oviposition, after which ontogenetic MB calyx volume differences were compared among species. We found that the relative generalist species exhibited remarkable plasticity in ontogenetic MB volumes; MB growth was differentially stimulated based on the complexity of the experienced environment. For relative specialists, MB volume was more canalized. All in all, this study strongly suggests an impact of host range on brain plasticity in Nymphalid butterflies.