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Data from: Linking dynamical complexities from activation signals to transcription responses

The transcription of inducible genes involves signaling pathways that induce DNA binding of the downstream transcription factors to form functional promoter states. How the transcription dynamics is linked to the temporal variations of activation signals is far to be fully understood. In this work, we develop a mathematical model with multiple promoter states to address this question. Each promoter state has its own activation and inactivation rates, and is selected randomly with a probability that may change in time. Under the activation of constant signals, our analysis shows that if only the activation rates differ among the promoter states, then the mean transcription level $m(t)$ displays only a monotone or monophasic growth pattern. In a sharp contrast, if the inactivation rates change with the promoter states, then $m(t)$ may display multiphasic growth patterns. Upon the activation of signals that oscillate periodically, $m(t)$ also oscillates later, almost periodically in the same frequency, but the magnitude decreases in the frequency and is almost completely attenuated at large frequencies. This gives a surprising indication that multiple promoter states could filter out the signal oscillation and the noise in the random promoter state selection, as observed in the transcription of a gene activated by p53 in breast carcinoma cells. Our approach may help develop a theoretical framework to integrate coherently the genetic circuit with the promoter states to elucidate the linkage from the activation signal to the temporal profile of transcription outputs.

Data from: Selective breeding and selection mapping using a novel wild-derived heterogeneous stock mice revealed two closely-linked loci for tameness

Tameness is a major behavioral factor for domestication, and can be divided into two potential components: motivation to approach humans (active tameness) and reluctance to avoid humans (passive tameness). We identified genetic loci for active tameness through selective breeding, selection mapping, and association analysis. In previous work using laboratory and wild mouse strains, we found that laboratory strains were predominantly selected for passive tameness but not active tameness during their domestication. To identify genetic regions associated with active tameness, we applied selective breeding over 9 generations for contacting, a behavioural parameter strongly associated with active tameness. The prerequisite for successful selective breeding is high genetic variation in the target population, so we established and used a novel resource, wild-derived heterogeneous stock (WHS) mice from eight wild strains. The mice had genetic variations not present in other outbred mouse populations. Selective breeding of the WHS mice increased the contacting level through the generations. Selection mapping was applied to the selected population using a simulation based on a non-selection model and inferred haplotype data derived from single-nucleotide polymorphisms. We found a genomic signature for selection on chromosome 11 containing two closely linked loci.

Data from: Self-limiting population genetic control with sex-linked genome editors

In male heterogametic species the Y chromosome is transmitted solely from fathers to sons, and is selected for based only on its impacts on male fitness. This fact can be exploited to develop efficient pest control strategies that use Y-linked editors to disrupt the fitness of female descendants. With simple population genetic and dynamic models we show that Y-linked editors can be substantially more efficient than other self-limiting strategies and, while not as efficient as gene drive approaches, are expected to have less impact on non-target populations with which there is some gene flow. Efficiency can be further augmented by simultaneously releasing an autosomal X-shredder construct, in either the same or different males. Y-linked editors may be attractive option to consider when efficient control of a species is desired in some locales but not others.

opencc-zeroDec 2015View details →

Data from: Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Background: Subtilisin-like serine proteases or Subtilases in fungi are important for penetration and colonization of host. In Hypocreales, these proteins share several properties with other fungal, bacterial, plant and mammalian homologs. However, adoption of specific roles in entomopathogenesis may be governed by attainment of unique biochemical and structural features during the evolutionary course. Due to such functional shifts Subtilases coded by different family members of Hypocreales acquire distinct features according to respective hosts and lifestyle. We conducted phylogenetic and DIVERGE analyses and identified important protein residues that putatively assign functional specificity to Subtilases in fungal families/species under the order Hypocreales. Results: A total of 161 Subtilases coded by 10 species from five different families under the fungal order Hypocreales was included in the analysis. Based on the presence of conserved domains, the Subtilase genes were divided into three subfamilies, Subtilisin (S08.005), Proteinase K (S08.054) and Serine-carboxyl peptidases (S53.001). These subfamilies were investigated for phylogenetic associations, protein residues under positive selection and functional divergence among paralogous clades. The observations were co-related with the life-styles of the fungal families/species. Phylogenetic and Divergence analyses of Subtilisin (S08.005) and Proteinase K (S08.054) families of proteins revealed that the paralogous clades were clear-cut representation of familial origin of the protein sequences. We observed divergence between the paralogous clades of plant-pathogenic fungi (Nectriaceae), insect-pathogenic fungi (Cordycipitaceae/Clavicipitaceae) and nematophagous fungi (Ophiocordycipitaceae). In addition, Subtilase genes from the nematode-parasitic fungus Purpureocillium lilacinum made a unique cluster which putatively indicated that the fungus might have developed distinctive mechanisms for nematode-pathogenesis. Our evolutionary genetics analysis revealed evidence of positive selection on the Subtilisin (S08.005) and Proteinase K (S08.054) protein sequences of the entomopathogenic and nematophagous species belonging to Cordycipitaceae, Clavicipitaceae and Ophiocordycipitaceae families of Hypocreales. Conclusions: Our study provided new insights into the evolution of Subtilisin like serine proteases in Hypocreales, a fungal order largely consisting of biological control species. Subtilisin (S08.005) and Proteinase K (S08.054) proteins seemed to play important roles during life style modifications among different families and species of Hypocreales. Protein residues found significant in functional divergence analysis in the present study may provide support for protein engineering in future.

Data from: Ecdysteroid hormones link the juvenile environment to alternative adult life histories in a seasonal insect

The conditional expression of alternative life strategies is a widespread feature of animal life and a pivotal adaptation to life in seasonal environments. To optimally match suites of traits to seasonally changing ecological opportunities, animals living in seasonal environments need mechanisms linking information on environmental quality to resource allocation decisions. The butterfly Bicyclus anynana expresses alternative adult life histories in the alternating wet and dry seasons of its habitat as endpoints of divergent developmental pathways triggered by seasonal variation in preadult temperature. Pupal ecdysteroid hormone titers are correlated with the seasonal environment, but whether they play a functional role in coordinating the coupling of adult traits in the alternative life histories is unknown. Here, we show that manipulating pupal ecdysteroid levels is sufficient to mimic in direction and magnitude the shifts in adult reproductive resource allocation normally induced by seasonal temperature. Crucially, this allocation shift is accompanied by changes in ecologically relevant traits, including timing of reproduction, life span, and starvation resistance. Together, our results support a functional role for ecdysteroids during development in mediating strategic reproductive investment decisions in response to predictive indicators of environmental quality. This study provides a physiological mechanism for adaptive developmental plasticity, allowing organisms to cope with variable environments.

Data from: The role of transcriptomes linked with responses to light environment on seedling mortality in a subtropical forest, China

Differences in seedling survival in trees have a lasting imprint on seedling, juvenile and adult community structure. Identifying the drivers of these differences, therefore, is a critical research objective that ultimately requires knowledge regarding how organismal function interacts with the local environment to influence survival rates. In tree communities, differences in light use strategies are frequently invoked to explain differences in seedling demographic performance through growth and survival trade-offs. For example, shade-tolerant species grow slowly and have higher survival rates, whereas shade-intolerant species grow quickly but have lower survival rates. Thus, functional traits related to photosynthesis should be strong predictors of demographic rates, but results in the literature are mixed indicating that additional or alternative information regarding organismal function should be considered. Here, we provide a community-wide inventory of transcriptomes in a subtropical tree community. This information is utilized to determine the degree to which species share homologous genes related to gene ontologies for light use and harvesting. These species similarities are used in neighbourhood generalized linear mixed-effects models of seedling survival that evaluated seedling survival as a function of the transcriptomic, functional trait and phylogenetic composition of the local neighbourhood. The results show neighbourhood similarity in three of the 15 gene ontologies evaluated are significantly related to survival rates based on neighbourhood composition. For two of these ontologies, survival rates increase when neighbours are similar in their gene tree composition indicating the importance of abiotic filtering and performance hierarchies. Synthesis. The present work takes a novel approach by sequencing the transcriptomes of naturally co-occurring tree species in a subtropical forest in China. The results show that the transcriptomic similarity of species is a significant predictor of differential survival. The study demonstrates that exploring the functional genomic similarity of non-model species in nature has the potential to increase the breadth and depth of our understanding of how gene function influences species co-occurrence and population dynamics in communities.

opencc-zeroDec 2014View details →

Data from: Face patch resting state networks link face processing to social cognition

Faces transmit a wealth of social information. How this information is exchanged between face-processing centers and brain areas supporting social cognition remains largely unclear. Here we identify these routes using resting state functional magnetic resonance imaging in macaque monkeys. We find that face areas functionally connect to specific regions within frontal, temporal, and parietal cortices, as well as subcortical structures supporting emotive, mnemonic, and cognitive functions. This establishes the existence of an extended face-recognition system in the macaque. Furthermore, the face patch resting state networks and the default mode network in monkeys show a pattern of overlap akin to that between the social brain and the default mode network in humans: this overlap specifically includes the posterior superior temporal sulcus, medial parietal, and dorsomedial prefrontal cortex, areas supporting high-level social cognition in humans. Together, these results reveal the embedding of face areas into larger brain networks and suggest that the resting state networks of the face patch system offer a new, easily accessible venue into the functional organization of the social brain and into the evolution of possibly uniquely human social skills.

Data from: Risky business: linking Toxoplasma gondii infection and entrepreneurship behaviours across individuals and countries

Disciplines such as business and economics often rely on the assumption of rationality when explaining complex human behaviours. However, growing evidence suggests that behaviour may concurrently be influenced by infec- tious microorganisms. The protozoan, Toxoplasma gondii, infects an estimated 2 billion people worldwide and has been linked to behavioural alterations in humans and other vertebrates. Here we integrate primary data from college students and business professionals with national-level information on cultural attitudes toward business to test the hypothesis that T. gondii infection influences individual as well as societal-scale entre- preneurship activities. Using a saliva-based assay, we found that students (n 1⁄4 1495) who tested IgG positive for T. gondii exposure were 1.4 more likely to major in business and 1.70 more likely to have an emphasis in 'management and entrepreneurship' over other business-related emphases. Among professionals attending entrepreneurship events, T. gondii-positive individuals were 1.8 more likely to have started their own business com- pared with other attendees (n 1⁄4 197). Finally, after synthesizing and combining country-level databases on T. gondii infection from the past 25 years with the global entrepreneurship monitor of entrepreneurial activity, we found that infection prevalence was a consistent, positive predictor of entrepreneurial activity and intentions at the national scale, regardless of whether previously identified economic covariates were included. Nations with higher infection also had a lower fraction of respondents citing 'fear of failure' in inhibiting initiating new business ventures. While correlational, these results highlight the linkage between parasitic infection and complex human behaviours, including those relevant to business, entrepreneurship, and economic productivity.

Data from: Linking species thermal tolerance to elevational range shifts in upland dung beetles

Climate warming has been proposed as the main cause of the recent range shifts seen in many species. Although species' thermal tolerances are thought to play a key role in determining responses to climate change, especially in ectotherms, empirical evidence is still limited. We investigate the connection between species' thermal tolerances, elevational range and shifts in the lower elevational limit of dung beetle species (Coleoptera, Aphodiidea) in an upland region in the northwest of England. We measured thermal tolerances in the laboratory, and used current and historical distribution data to test specific hypotheses about the area's three dominant species, particularly the species most likely to suffer from warming: Agollinus lapponum. We found marked differences between species in their minimum and maximum thermal tolerance and in their elevational range and patterns of abundance. Overall, differences in thermal limits among species matched the abundance patterns along the elevation gradient expected if distributions were constrained by climate. A. lapponum abundance increased with elevation and this species showed lower maximum and minimum thermal limits than Acrossus depressus, for which abundance declined with elevation. Consistent with lower tolerance to high temperature, we recorded an uphill retreat of the low elevation limit of A. lapponum (177 m over 57 years) in line with the increase in summer temperature observed in the region over the same period. Moreover, this species has been replaced at low and mid-elevations by the other two warm-tolerant species (A. depressus and Agrilinus ater). Our results provide empirical evidence that species' thermal tolerance constrains elevational ranges and contributes to explain the observed responses to climate warming. A mechanistic understanding of how climate change directly affects species, such as the one presented here, will provide a robust base to inform predictions of how individual species and whole assemblages may change in the future.

Data from: Linking Darwin's naturalisation hypothesis and Elton's diversity‐invasibility hypothesis in experimental grassland communities

1. Darwin's naturalisation hypothesis posing that phylogenetic distance of alien species to native residents predicts invasion success, and Elton's diversity‐invasibility hypothesis posing that diversity of native communities confers resistance to invasion, are both rooted in ideas of species coexistence. Because the two hypotheses are inherently linked, the mechanisms underlying them may interact in driving the invasion success. Even so, these links and interactions have not been explicitly disentangled in one experimental study before. 2. To disentangle the links between the two hypotheses, we used 36 native grassland herbs to create greenhouse mesocosms with 90 grassland communities of different diversities, and introduced each of five herbaceous alien species as seeds and seedlings. We used phylogeny and four functional traits (plant height, specific leaf area, leaf size, seed mass) to calculate different measures of phylogenetic and functional distance and diversity. Specifically, we tested how the alien‐native distance (phylogenetic or functional) and the native diversity (phylogenetic or functional) affected each other in their effects on germination, seedling survival, growth and reproduction of the aliens. 3. Overall, our results supported both hypotheses. Multivariate functional distance based on four traits jointly had stronger positive effects than phylogenetic distance and the univariate ones based on each trait separately. Moreover, the aliens were more successful if they were more competitive by being taller and having larger leaves with a lower SLA than the native residents. Univariate functional diversity based on each trait separately had stronger negative effects than phylogenetic and multivariate functional diversity. Most importantly, we found that the effects of alien‐native phylogenetic and multivariate functional distance became stronger as diversity increased. Our analyses with single traits also showed that the strength of the effects of both alien‐native hierarchical functional distances (indicative of competitive inequalities) and absolute functional distances (indicative of niche differences) increased at higher diversities, where competition is more severe. 4. SynthesisOur study explicitly demonstrates for the first time how the mechanisms underlying the two classical invasion hypotheses interact in driving invasion success in grassland communities. This may help to explain some of the puzzling results of studies testing either of the two hypotheses.

Data from: Testing the phenotype-linked fertility hypothesis in the presence and absence of inbreeding

The phenotype-linked fertility hypothesis suggests that females can judge male fertility by inspecting male phenotypic traits. This is because male sexually selected traits might correlate with sperm quality if both are sensitive to factors that influence male condition. A recent meta-analysis found little support for this hypothesis, suggesting little or no shared condition dependence. However, we recently reported that in captive zebra finches (Taeniopygia guttata) inbreeding had detrimental effects both on phenotypic traits and on measures of sperm quality, implying that variation in inbreeding could induce positive covariance between indicator traits and sperm quality. Therefore, we here assess empirically the average strength of correlations between phenotypic traits (courtship rate, beak colour, tarsus length) and measures of sperm quality (proportion of functional sperm, sperm velocity, sperm length) in populations of only outbred individuals and in mixed populations consisting of inbreds (F = 0.25) and outbreds (F = 0). As expected, phenotype sperm-trait correlations were stronger when the population contained a mix of inbred and outbred individuals. We also found unexpected heterogeneity between our two study populations, with correlations being considerably stronger in a domesticated population than in a recently wild-derived population. Correlations ranged from essentially zero among outbred-only wild-derived birds (mean Fisher's Zr ± SE = 0.03 ± 0.10) to moderately strong among domesticated birds of mixed inbreeding status (Zr ± SE = 0.38 ± 0.08). Our results suggest that, under some conditions, the phenotype-linked fertility hypothesis might apply.

Data from: Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL

The domesticated crop maize and its wild progenitor, teosinte, have been used in numerous experiments to investigate the nature of divergent morphologies. This study examines a poorly understood region on the fifth chromosome of maize associated with a number of traits under selection during domestication using a QTL mapping population specific to the fifth chromosome. In contrast with other major domestication loci in maize where large effect, highly pleiotropic, single genes are responsible for phenotypic effects, our study found the region on chromosome five fractionates into multiple QTL regions, none with singularly large effects. The smallest 1.5 LOD support interval for a QTL contained 54 genes, one of which was a MADS MIKCC transcription factor, a family of proteins implicated in many developmental programs. We also used simulated trait datasets to investigate the power of our mapping population to identify QTL for which there is a single underlying causal gene. This analysis showed that while QTL for traits controlled by single genes can be accurately mapped, our population design can detect no more than ~4.5 QTL per trait even when there are 100 causal genes. Thus when a trait is controlled by 5 or more genes in the simulated data, the number of detected QTL can represent a simplification of the underlying causative factors. Our results show how a QTL region with effects on several domestication traits may be due to multiple linked QTL of small effect as opposed to a single gene with large and pleiotropic effects.

opencc-zeroMay 2019View details →

Data from: A link between heritable parasite resistance and mate choice in dung beetles

Parasites play a central role in the adaptiveness of sexual reproduction. Sexual selection theory suggests a role for parasite resistance in the context of mate choice, but the evidence is mixed. The parasite-mediated sexual selection (PMSS) hypothesis derives a number of predictions, among which that resistance to parasites is heritable, and that female choice favours parasite resistance genes in males. Here we tested the PMSS hypothesis using the dung beetle Onthophagus taurus, a species that can be heavily parasitised by Macrocheles merdarius mites, which are known to affect adult survival. We investigated the heritability of resistance to M. merdarius, as well as whether female O. taurus impose a mating bias against males susceptible to mite infestation. Female choice for parasite resistance is difficult to disentangle from the possibility that females are simply choosing less parasitised males due to naturally selected benefits of avoiding contracting those parasites. This is especially likely for ectoparasites, such as mites. We tackled this problem by performing a mate choice trial first, and then measuring a male's resistance to mite infestation. Resistance to mite infestation exhibited significant levels of additive genetic variance. Although we found no relationship between mating success and parasite resistance, males with greater resistance to infestation mated for longer. If females control copula duration, given that short copulations often result in mating failure, female choice could act on parasite resistance.

opencc-zeroDec 2012View details →

Data from: A genomic island linked to ecotype divergence in Atlantic cod

The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome-wide or localized in "genomic mosaics" during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or "genomic island", as potentially associated with ecological divergence and suggest a selective sweep involved in ecological divergence. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although underlying mechanisms are still unknown, the results suggest that "genomic mosaics" of differentiation may even be found under high levels of gene flow, and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.

Data from: Linking phenological shifts to species interactions through size-mediated priority effects

1. Inter-annual variation in seasonal weather patterns causes shifts in the relative timing of phenological events of species within communities, but we currently lack a mechanistic understanding of how these phenological shifts affect species interactions. Identifying these mechanisms is critical to predicting how inter-annual variation affects populations and communities. 2. Species' phenologies, particularly the timing of offspring arrival, play an important role in the annual cycles of community assembly. We hypothesize that shifts in relative arrival of offspring can alter interspecific interactions through a mechanism called size-mediated priority effects (SMPE), in which individuals that arrive earlier can grow to achieve a body size advantage over those that arrive later. 3. In this study, we used an experimental approach to isolate and quantify the importance of SMPE for species interactions. Specifically, we simulated shifts in relative arrival of the nymphs of two dragonfly species to determine the consequences for their interactions as intraguild predators. 4. We found that shifts in relative arrival altered not only predation strength but also the nature of predator-prey interactions. When arrival differences were great, SMPE allowed the early arriver to prey intensely upon the late arriver, causing exclusion of the late arriver from nearly all habitats. As arrival differences decreased, the early arriver's size advantage also decreased. When arrival differences were smallest, there was mutual predation, and the two species coexisted in similar abundances across habitats. Importantly, we also found a nonlinear scaling relationship between shifts in relative arrival and predation strength. Specifically, small shifts in relative arrival caused large changes in predation strength while subsequent changes had relatively minor effects. 5. These results demonstrate that SMPE can alter not only the outcome of interactions but also the demographic rates of species and the structure of communities. Elucidating the mechanisms that link phenological shifts to species interactions is crucial for understanding the dynamics of seasonal communities as well as for predicting the effects of climate change on these communities.

opencc-zeroDec 2018View details →

Data from: Blood-brain barrier impairment and hypoperfusion are linked in cerebral small vessel disease

Objective: To investigate the link between BBB permeability and CBF and the relation with white matter hyperintensities (WMHs) in cerebral small vessel disease (cSVD). Methods: Twenty-seven patients with cSVD received dynamic susceptibility contrast and dynamic contrast-enhanced MRI to determine CBF and BBB permeability (expressed as leakage rate and volume), respectively. Structural MR images were segmented into normal appearing white matter (NAWM) and WMHs, for which a perilesional zone was defined. In these regions, we investigated the BBB permeability, CBF, and their relation using Pearson correlation r. Results: We found a decrease in CBF of 2.2 mL/min/100g(p<0.01) and an increase in leakage volume of 0.7%(p<0.01) per mm closer to the WMHs in the perilesional zones. Lower CBF values correlated with higher leakage measures in the NAWM and WMHs (-0.53

Data from: Linking system-wide impacts of RNA polymerase mutations to the fitness cost of rifampin resistance in Pseudomonas aeruginosa

Fitness costs play a key role in the evolutionary dynamics of antibiotic resistance in bacteria by generating selection against resistance in the absence of antibiotics. Although the genetic basis of antibiotic resistance is well understood, the precise molecular mechanisms linking the genetic basis of resistance to its fitness cost remain poorly characterized. Here, we examine how the system-wide impacts of mutations in the RNA polymerase (RNAP) gene rpoB shape the fitness cost of rifampin resistance in Pseudomonas aeruginosa. Rifampin resistance mutations reduce transcriptional efficiency, and this explains 76% of the variation in fitness among rpoB mutants. The pleiotropic consequence of rpoB mutations is that mutants show altered relative transcript levels of essential genes. We find no evidence that global transcriptional responses have an impact on the fitness cost of rifampin resistance as revealed by transcriptome sequencing (RNA-Seq). Global changes in the transcriptional profiles of rpoB mutants compared to the transcriptional profile of the rifampin-sensitive ancestral strain are subtle, demonstrating that the transcriptional regulatory network of P. aeruginosa is robust to the decreased transcriptional efficiency associated with rpoB mutations. On a smaller scale, we find that rifampin resistance mutations increase the expression of RNAP due to decreased termination at an attenuator upstream from rpoB, and we argue that this helps to minimize the cost of rifampin resistance by buffering against reduced RNAP activity. In summary, our study shows that it is possible to dissect the molecular mechanisms underpinning variation in the cost of rifampin resistance and highlights the importance of genome-wide buffering of relative transcript levels in providing robustness against resistance mutations. IMPORTANCE Antibiotic resistance mutations carry fitness costs. Relative to the characteristics of their antibiotic-sensitive ancestors, resistant mutants show reduced growth rates and competitive abilities. Fitness cost plays an important role in the evolution of antibiotic resistance in the absence of antibiotics; however, the molecular mechanisms underlying these fitness costs is not well understood. We applied a systems-level approach to dissect the molecular underpinnings of the fitness costs associated with rifampin resistance in P. aeruginosa and showed that most of the variation in fitness cost can be explained by the direct effect of resistance mutations on the enzymatic activity of the mutated gene. Pleiotropic changes in transcriptional profiles are subtle at a genome-wide scale, suggesting that the gene regulatory network of P. aeruginosa is robust in the face of the direct effects of resistance mutations.

Data from: Defector clustering is linked to cooperation in a pathogenic bacterium

Spatial clustering is thought to favour the evolution of cooperation because it puts cooperators in a position to help each other. However, clustering also increases competition. The fate of cooperation may depend on how much cooperators cluster relative to defectors, but these clustering differences have not been the focus of previous models and experiments. By competing siderophore-producing cooperator and defector strains of the opportunistic pathogen Pseudomonas aeruginosa in experimental microhabitats, we found that at the spatial scale of individual interactions, cooperator clustering lowers cooperation, but defector clustering favours cooperation. A theoretical model and individual-based simulations show these counterintuitive effects can arise when competition and cooperation occur at a single resource-determined scale, with population dynamics crucially allowing cooperators and defectors to cluster differently. The results suggest that cooperation relies on the regulation of sufficient defector clustering relative to cooperator clustering, which may be important in bacteria, social amoeba, and cancer inhibition.

Data from: Aspiration-based coevolution of link weights promotes cooperation in the spatial prisoner's dilemma game

In this article, we propose an aspiration-based coevolution of link weights, and we explore how this affects the evolution of cooperation in the spatial prisoner's dilemma game. In particular, an individual will increase the weight of its link to its neighbors only if the payoff received via this interaction will exceed a pre-defined aspiration. Conversely, if the received payoff is below this aspiration, the link weight with the corresponding neighbor will be decreased. Our simulation results show that an appropriate aspiration level leads to a high-cooperation plateau, whereas a too high or a too low aspiration will impede the evolution of cooperation. We explain these findings with a comprehensive analysis of transition points and with a systematic analysis of typical configuration patterns. The presented results provide further theoretical insights with regards to the impact of different aspiration levels on cooperation in human societies.