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Data from: Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change

Understanding the dynamics of molecular adaptation is a fundamental goal of evolutionary biology. While adaptation to constant environments has been well characterized, the effects of environmental complexity remain seldom studied. One simple but understudied factor is the rate of environmental change. Here we used experimental evolution with RNA viruses to investigate whether evolutionary dynamics varied based on the rate of environmental turnover. We used whole-genome next-generation sequencing to characterize evolutionary dynamics in virus populations adapting to a sudden versus gradual shift onto a novel host cell type. In support of theoretical models, we found that when populations evolved in response to a sudden environmental change, mutations of large beneficial effect tended to fix early, followed by mutations of smaller beneficial effect; as predicted, this pattern broke down in response to a gradual environmental change. Early mutational steps were highly parallel across replicate populations in both treatments. The fixation of single mutations was less common than sweeps of associated "cohorts" of mutations, and this pattern intensified when the environment changed gradually. Additionally, clonal interference appeared stronger in response to a gradual change. Our results suggest that the rate of environmental change is an important determinant of evolutionary dynamics in asexual populations.

Data from: A model of urban scaling laws based on distance dependent interactions

Socio-economic related properties of a city grow faster than a linear relationship with the population, in a log–log plot, the so-called superlinear scaling. Conversely, the larger a city, the more efficient it is in the use of its infrastructure, leading to a sublinear scaling on these variables. In this work, we addressed a simple explanation for those scaling laws in cities based on the interaction range between the citizens and on the fractal properties of the cities. To this purpose, we introduced a measure of social potential which captured the influence of social interaction on the economic performance and the benefits of amenities in the case of infrastructure offered by the city. We assumed that the population density depends on the fractal dimension and on the distance-dependent interactions between individuals. The model suggests that when the city interacts as a whole, and not just as a set of isolated parts, there is improvement of the socio-economic indicators. Moreover, the bigger the interaction range between citizens and amenities, the bigger the improvement of the socio-economic indicators and the lower the infrastructure costs of the city. We addressed how public policies could take advantage of these properties to improve cities development, minimizing negative effects. Furthermore, the model predicts that the sum of the scaling exponents of social-economic and infrastructure variables are 2, as observed in the literature. Simulations with an agent-based model are confronted with the theoretical approach and they are compatible with the empirical evidences.

Data from: Cyclic population dynamics and density-dependent intransitivity as pathways to coexistence between co-occurring annual plants

1. Recent studies have brought renewed attention to the importance of complex species interactions - notably intransitive interactions - to patterns of plant community diversity. One underappreciated avenue through which intransitivity can occur is through cyclic population dynamics. Though such cyclic intransitive relationships have been extensively studied in predator-prey systems, evidence of their importance in competitive communities, notably plant communities, is more limited. Most studies of coexistence in plant communities assume fixed-point coexistence even while utilizing models that allow for cyclic population dynamics. 2. In this paper, we explore the potential for density-dependent, cyclic population dynamics and intransitivity in a model for annual plants. We then examine how these density-dependent cycles impact mutual invasibility and ultimately stable coexistence between plant species pairs. We do this using data collected from four co-occurring annual plant species living in natural wildflower communities in SW Western Australia. To maximize the number of biologically plausible pathways by which coexistence mediated by density-dependent cyclic intransitivity can occur, we use an annual plant model that allows for competitive direct interactions, facilitative direct interactions, and higher-order interactions between species. 3. Results from our empirically-parameterized model suggest that monocultures of all four focal species can have cyclic solutions with periodicity greater than 1 under sunny ("open") or shaded field conditions. Cyclic patterns drive variation in annual abundance patterns, with stable solutions for persistent monocultures and invasibility potential (the capacity of one population to invade another) common. Mutual invasibility in the face of cyclic population dynamics was found for just one of six species pairs, only under open environmental conditions. Our results illustrate the potential for cyclic intransitivity to both drive and prevent stable coexistence in environmentally heterogeneous biological communities. 4. Synthesis. We provide analytical and empirical evidence that coexistence in competitive communities (annual plants) can be achieved under non-equilibrium circumstances, through density-dependent cyclic intransitivity. Our results suggest that cyclic population dynamics may be common and important for coexistence dynamics in some types of communities. In such communities, the exploration of stable coexistence should therefore include consideration of cyclic as well as fixed-point equilibria for maximal accuracy.

opencc-zeroDec 2019View details →

Data from: High fat diet induces microbiota-dependent silencing of enteroendocrine cells

Enteroendocrine cells (EECs) are specialized sensory cells in the intestinal epithelium that sense and transduce nutrient information. Consumption of dietary fat contributes to metabolic disorders, but EEC adaptations to high fat feeding were unknown. Here, we established a new experimental system to directly investigate EEC activity in vivo using a zebrafish reporter of EEC calcium signaling. Our results reveal that high fat feeding alters EEC morphology and converts them into a nutrient insensitive state that is coupled to endoplasmic reticulum (ER) stress. We called this novel adaptation 'EEC silencing'. Gnotobiotic studies revealed that germ-free zebrafish are resistant to high fat diet induced EEC silencing. High fat feeding altered gut microbiota composition including enrichment of Acinetobacter species, and we identified an Acinetobacter strain sufficient to induce EEC silencing. These results establish a new mechanism by which dietary fat and gut microbiota modulate EEC nutrient sensing and signaling.

opencc-zeroDec 2014View details →

Data from: The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

Although genome scans have become a popular approach towards understanding the genetic basis of local adaptation, the field still does not have a firm grasp on how sampling design and demographic history affect the performance of genome scans on complex landscapes. To explore these issues, we compared 20 different sampling designs in equilibrium (i.e. island model and isolation by distance) and nonequilibrium (i.e. range expansion from one or two refugia) demographic histories in spatially heterogeneous environments. We simulated spatially complex landscapes, which allowed us to exploit local maxima and minima in the environment in 'pair' and 'transect' sampling strategies. We compared FST outlier and genetic–environment association (GEA) methods for each of two approaches that control for population structure: with a covariance matrix or with latent factors. We show that while the relative power of two methods in the same category (FST or GEA) depended largely on the number of individuals sampled, overall GEA tests had higher power in the island model and FST had higher power under isolation by distance. In the refugia models, however, these methods varied in their power to detect local adaptation at weakly selected loci. At weakly selected loci, paired sampling designs had equal or higher power than transect or random designs to detect local adaptation. Our results can inform sampling designs for studies of local adaptation and have important implications for the interpretation of genome scans based on landscape data.

Data from: Climate effects on growth, body condition and survival depend on the genetic characteristics of the population

Climatic change is expected to affect individual life-histories and population dynamics, potentially increasing vulnerability to extinction. The importance of genetic diversity has been highlighted for adaptation and population persistence. However, whether responses of life-history traits to a given environmental condition depend on the genetic characteristics of a population remains elusive. Here we tested this hypothesis in the lizard Zootoca vivipara, by simultaneously manipulating habitat humidity, a major climatic predictor of Zootoca's distribution, and adult male colour morph frequency, a trait with genome-wide linkage. Interactive effects of humidity and morph frequency had immediate effects on growth and body condition of juveniles and yearlings, and on adult survival, and delayed effects on offspring size. In yearlings, higher humidity led to larger female body size, and lower humidity led to higher male compared to female survival. In juveniles and yearlings, some treatment effects were compensated over time. The results show that individual responses to environmental conditions depend on the population's colour morph frequency, age class and sex, and that these affect intra- and inter-age class competition. Moreover, humidity affected the competitive environment, rather than imposing trait-based selection on specific colour morphs. This indicates that species' responses to changing environments, e.g. to climate change, are highly complex, and difficult to accurately reconstruct and predict without information on the genetic characteristics and demographic structure of populations.

Data from: What is behind the variation in mate quality dependent sex ratio adjustment? – A meta-analysis

Theory predicts that parents adjust the sex ratio of their brood to the sexually selected traits of their mate because the reproductive success of sons may be more dependent on inherited paternal attractiveness than that of daughters. Empirical studies vary in terms of whether they support the theory, and this variation has often been regarded as evidence against sex ratio adjustment or has been ascribed to methodological differences. Applying phylogenetic meta-analyses, we aimed to find biological explanations for the variation observed in songbirds. In particular, we tested the role extra-pair paternity, because infidelity occurs in the majority of these species and may reduce the adaptive value of adjusting brood sex ratio to the phenotype of the social mate. However, we found that the variation in effect sizes was unrelated to the proportion of extra-pair paternity. Thus future studies should consider that mate quality dependent sex ratio adjustment may be driven by direct (material) rather than indirect (genetic) benefits. We also tested if the effect sizes are influenced by whether the focal male trait is indeed under sexual selection as it is assumed by the sex allocation theory. We found that for male traits with proven role in sexual selection, effect sizes significantly differed from the null expectation of random production of sons and daughters. For male traits with only presumed sexual role in sexual selection, the deviation from the null expectation was less convincing, and the effect sizes were significantly smaller. This result indicates that studies that neglect the assumptions of the hypotheses concerned, may lead to the underestimation of the mean effect size and, eventually, false conclusions.

Data from: Diflunisal inhibits prestin by chloride-dependent mechanism

The motor protein prestin is a member of the SLC26 family of anion antiporters and is essential to the electromotility of cochlear outer hair cells and for hearing. The only direct inhibitor of electromotility and the associated charge transfer is salicylate, possibly through direct interaction with an anion-binding site on prestin. In a screen to identify other inhibitors of prestin activity, we explored the effect of the non-steroid anti-inflammatory drug diflunisal, which is a derivative of salicylate. We recorded prestin activity by whole-cell patch clamping HEK cells transiently expressing prestin and mouse outer hair cells. We monitored the impact of diflunisal on the prestin-dependent non-linear capacitance and electromotility. We found that diflunisal triggers two prestin-associated effects: a chloride independent increase in the surface area and the specific capacitance of the membrane, and a chloride dependent inhibition of the charge transfer and the electromotility in outer hair cells. We conclude that diflunisal affects the cell membrane organization and inhibits prestin-associated charge transfer and electromotility at physiological chloride concentrations. The inhibitory effects on hair cell function are noteworthy given the proposed use of diflunisal to treat neurodegenerative diseases.

Data from: Diversity-dependent evolutionary rates in early Paleozoic zooplankton

The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here we analyse the species-level fossil record of early Paleozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and lower-than-average values of diversity tend to be followed by negative and positive diversification rates, we construct a non-parametric, empirically scaled, diversity-independent null model by randomizing the observed diversification rates with respect to time. Comparing observed correlations between diversity and diversification rate to those expected from this diversity-independent model, we find evidence for negative diversity-dependence, accounting for up to 12% of the variance in diversification rate, with maximal correlation at a temporal lag of ~1 million years. Diversity-dependence persists throughout the Ordovician and Silurian, despite a major increase in the strength and frequency of extinction and speciation pulses in the Silurian. In contrast to some previous work, we find that diversity-dependence affects rates of speciation and extinction nearly equally on average, although subtle differences emerge when we compare the Ordovician and Silurian.

opencc-zeroDec 2015View details →

Data from: Mutualists or parasites? Context-dependent influence of symbiotic fly larvae on carnivorous investment in the Albany pitcher plant

Carnivorous plants allocate more resources to carnivorous structures under nutrient-limited conditions, and relative investment can also be influenced by animals (infauna) that live in association with these plants and feed on their prey. We investigated these effects within a population of the pitcher plant Cephalotus follicularis containing varying densities of larvae of the fly Badisis ambulans. For plants with a relatively high proportion of adult pitchers, increasing larval density was associated with lower relative leaf allocation to new pitcher buds. For plants with relatively few adult pitchers, however, there was greater relative leaf allocation to pitcher buds with increasing larval density. In a field experiment, there was no significant effect of experimental larval presence or absence on the change in carbon-to-nitrogen (C/N) ratio of plants. Although the direction of the correlation between B. ambulans larvae and relative investment in carnivorous and non-carnivorous structures depends on the relative number of mature structures, whether the larvae enhance or reduce nutrient stress under different conditions remains unclear. The change in C/N was, however, less variable for pitchers that contained larvae, suggesting a stabilizing effect. Eighteen of 52 experimental pitchers were damaged by an unknown species, causing the pitcher fluid to drain. These pitchers were significantly more likely to survive if they contained larvae. These results suggest that the relationship between infauna and host varies with the initial resource status and environmental context of the host plant.

opencc-zeroDec 2011View details →

Data from: Condition dependence of a multicomponent sexual display trait in Drosophila serrata

Theory predicts that costly sexual displays should evolve condition dependence if the marginal fitness gain from trait exaggeration is greater for high- than for low-condition individuals and that the strength of condition dependence should increase with the strength of directional selection. While there is substantial support for the first prediction, evidence for the latter is much weaker. We undertook a quantitative test of this prediction for a multivariate sexual display consisting of a suite of contact pheromones termed "cuticular hydrocarbons" (CHCs) in Drosophila serrata. We performed a dietary manipulation of condition (i.e., the pool of metabolic resources available for allocation to fitness-enhancing traits) within a half-sibling breeding design, thereby also providing insight into the genetic basis of condition dependence. As predicted, the linear combination of CHCs under the strongest sexual selection from female mate preferences was unusually condition dependent relative to other CHC combinations within the population (P = .049). A significant positive correlation also existed between the strengths of condition dependence and sexual selection among different CHC blends (r = 0.482, P < .001). Finally, sires varied in their response to the dietary manipulation, demonstrating significant genetic variance in condition dependence. Our results are consistent with the evolution of heightened condition dependence of sexual displays in response to persistent sexual selection.

opencc-zeroDec 2015View details →

Data from: Simultaneous age-dependent and age-independent sexual selection in the lekking black grouse (Lyrurus tetrix)

Individuals' reproductive success is often strongly associated with their age, with typical patterns of early-life reproductive improvement and late-life senescence. These age-related patterns are due to the inherent trade-offs between life-history traits competing for a limited amount of resources available to the organisms. In males, such trade-offs are exacerbated by the resource requirements associated with the expression of costly sexual traits, leading to dynamic changes in trait expression throughout their life span. Due to the age dependency of male phenotypes, the relationship between the expression of male traits and mating success can also vary with male age. Hence, using longitudinal data in a lekking species with strong sexual selection – the black grouse Lyrurus tetrix – we quantified the effects of age, life span and age of first lek attendance (AFL) on male annual mating success (AMS) to separate the effects of within-individual improvement and senescence on AMS from selective (dis)appearance of certain phenotypes. Then, we used male AMS to quantify univariate and multivariate sexual selection gradients on male morphological and behavioural traits with and without accounting for age and age-related effects of other traits. Male AMS increased with age, and there was no significant reproductive senescence. Most males never copulated, and of the ones that did, the majority had only one successful year. Life span was unrelated to AMS, but early AFL tended to lead to higher AMS at ages 1–3. AMS was related to most morphological and behavioural traits when male age was ignored. Accounting for age and age-specific trait effects (i.e. the interaction between a trait and age) reduced the magnitude of the selection gradients and revealed that behavioural traits are under consistent sexual selection, while sexual selection on morphological traits is stronger in old males. Therefore, sexual selection in black grouse operates primarily on male behaviour and morphological traits may act as additional cues to supplement female choice. These results demonstrate the multifaceted influence of age on both fitness and sexual traits and highlight the importance of accounting for such effects when quantifying sexual selection.

opencc-zeroDec 2018View details →

Data from: Context-dependent strategies of food allocation among offspring in a facultative cooperative breeder

Natural selection should favor adoption of parental strategies that maximize fitness when allocating investment among offspring. In birds, begging displays often convey information of nestling need and quality, allowing parents to make adaptive food allocation decisions. We investigated how adults utilized cues likely to represent nestling competitive ability (begging position) and need (begging intensity), and a cue independent of nestling control (nestling sex) to distribute food among nestlings in a facultative cooperative breeder, the black-throated tit (Aegithalos concinnus). We found that parents reduced their efforts when helped, suggesting that parents of helped broods would have the potential to satisfy nestling needs more than unhelped parents. This suggestion was supported by the fact that nestling mass increased faster in helped than in unhelped nests. We found no effect of nestling sex on food allocation, but, as predicted, we found that adults responded differently to begging signals in relation to the presence of helpers and brood size. First, helped parents were more responsive to nestling begging intensity than parents without helpers. Second, female parents and helpers had a stronger preference for nestling begging position in large than in small broods. Third, the preference for nestling begging position was greater for unhelped than for helped female parents. These results provide evidence that carers adjust their preference for different offspring begging signals based on availability of food resources.

Data from: Geometric morphometrics reveal altered corpus callosum shape in pyridoxine-dependent epilepsy

Objective: To evaluate the features and maturational changes in overall callosal shape in patients with pyridoxine-dependent epilepsy (PDE). Methods: Measurements were conducted through landmark based geometric morphometrics applied on cerebral MRIs of PDE patients and age-matched control subjects. The outline of the corpus callosum was manually traced in the midsagittal plane. 300 semi-landmarks along the outline were collected and underwent statistical generalized Procrustes analysis. An allometric regression was applied to evaluate the callosal shape due to growth over time. Results: 38 patients with PDE and 38 age- and sex-matched control subjects were included. Mean age at the time of the MRI in the patient group was 9.3 years (median 6.3 years, range 0.01- 48 years). Significant differences (p<0.01) in the mean callosal shape between patients and controls were found. The allometric regression model revealed significant shape variations (p<0.01) between the two study groups across the developmental course after controlling for the effect of callosal size on shape. This latter effect turned out to be significant as well (p<0.001). Conclusions: Patients with PDE show an altered callosal shape and variations in callosal ontogeny which are likely secondary to the underlying genetic defect with abnormal function of antiquitin, the product of the ALDH7A1 gene.

opencc-zeroDec 2013View details →

Data from: Quality attracts parasites: host condition-dependent chemo-orientation of trematode larvae

1. Environmental factors impairing physiological condition of organisms are assumed to predispose them to parasite infections. This is because host immune function is typically condition-dependent. However, poor physiological condition has been reported to reduce host susceptibility to parasites in various systems. 2. We examined whether such an effect can be due to altered exposure of hosts to active parasite transmission stages by investigating chemo-orientation of free-swimming cercariae larvae of a parasite Echinoparyphium aconiatum towards its snail host Lymnaea stagnalis. 3. We used both long-term and short-term feeding treatments to manipulate the body condition and physiological traits related to food processing in experimental (i.e. target) snails and measured the preference of cercariae towards snail-conditioned water (SCW) over clean water. 4. We found that chemo-orientation of cercariae depended on the nutritional status of target snails. High physiological condition (long-term feeding) attracted parasites, but cercariae did not show preference towards SCW from individuals in poor physiological condition (long-term starvation). Food processing (short-term feeding treatments) did not affect chemo-orientation. 5. Our results suggest that host condition-dependent chemo-orientation of parasite larvae is a likely mechanism explaining the reduced susceptibility of snails to infection due to food limitation in our study system. In general, the use of condition-dependent host cues can be highly beneficial for parasites as it increases their transmission to high-quality hosts. Furthermore, evolving counter adaptations to such a transmission strategy can be very difficult for hosts.

Data from: Density regulation in Northeast Atlantic fish populations: density dependence is stronger in recruitment than in somatic growth

1. Population regulation is a central concept in ecology, yet in many cases its presence and the underlying mechanisms are difficult to demonstrate. The current paradigm maintains that marine fish populations are predominantly regulated by density-dependent recruitment. 2. While it is known that density-dependent somatic growth can be present too, its general importance is unknown and most practical applications neglect it. This study aimed to close this gap by for the first time quantifying and comparing density dependence in growth and recruitment over a large set of fish populations. 3. We fitted density-dependent models to time series data on population size, recruitment and age-specific weight from commercially exploited fish populations in the Northeast Atlantic Ocean and the Baltic Sea. Data were standardised to enable a direct comparison within and among populations, and estimated parameters were used to quantify the impact of density regulation on population biomass. 4. Statistically significant density dependence in recruitment was detected in a large proportion of populations (70%) whereas for density dependence in somatic growth the prevalence of density dependence depended heavily on the method (26% and 69%). Despite age-dependent variability, the density dependence in recruitment was consistently stronger among age groups and between alternative approaches that use weight-at-age or weight increments to assess growth. Estimates of density-dependent reduction of biomass underlined these results: 97% of populations with statistically significant parameters for growth and recruitment showed a larger impact of density-dependent recruitment on population biomass. 5. The results reaffirm the importance of density-dependent recruitment in marine fishes, yet they also show that density dependence in somatic growth is not uncommon. Further, the results are important from an applied perspective because density dependence in somatic growth affects productivity and catch composition, and therefore the benefits of maintaining fish populations at specific densities.

Data from: Distance-dependent pattern blending can camouflage salient aposematic signals

The effect of viewing distance on the perception of visual texture is well known: spatial frequencies higher than the resolution limit of an observer's visual system will be summed and perceived as a single combined colour. In animal defensive colour patterns, distance-dependent pattern blending may allow aposematic patterns, salient at close range, to match the background to distant observers. Indeed, recent research has indicated that reducing the distance from which a salient signal can be detected can increase survival over camouflage or conspicuous aposematism alone. We investigated whether the spatial frequency of conspicuous and cryptically coloured stripes affects the rate of avian predation. Our results are consistent with pattern blending acting to camouflage salient aposematic signals effectively at a distance. Experiments into the relative rate of avian predation on edible model caterpillars found that increasing spatial frequency (thinner stripes) increased survival. Similarly, visual modelling of avian predators showed that pattern blending increased the similarity between caterpillar and background. These results show how a colour pattern can be tuned to reveal or conceal different information at different distances, and produce tangible survival benefits.

Data from: Insights into the roles of CMK-1 and OGT-1 in interstimulus interval-dependent habituation in Caenorhabditis elegans

Habituation is a ubiquitous form of non-associative learning observed as a decrement in responding to repeated stimulation that cannot be explained by sensory adaptation or motor fatigue. One of the defining characteristics of habituation is its sensitivity to the rate at which training stimuli are presented – animals habituate faster in response to more rapid stimulation. The molecular mechanisms underlying this interstimulus interval (ISI)-dependent characteristic of habituation remain unknown. In this article we use behavioral neurogenetic and bioinformatic analyses in the nematode Caenorhabiditis elegans to identify the first molecules that modulate habituation in an ISI-dependent manner. We show that the Caenorhabditis elegans orthologs of Ca2+/calmodulin-dependent kinases CaMK1/4, CMK-1, and O-linked N-acetylglucosamine (O-GlcNAc) transferase, OGT-1, both function in primary sensory neurons to inhibit habituation at short ISIs and promote it at long ISIs. In addition, both cmk-1 and ogt-1 mutants display a rare mechanosensory hyper-responsive phenotype, i.e. larger mechanosensory responses than wild-type. Overall, our work identifies two conserved genes that function in sensory neurons to modulate habituation in an ISI-dependent manner, providing the first insights into the molecular mechanisms underlying the universally observed phenomenon that habituation has different properties when stimuli are delivered at different rates.

opencc-zeroDec 2014View details →

Data from: Experimental evidence of condition-dependent sexual dimorphism in the weakly dimorphic antler fly, Protopiophila litigata (Diptera: Piophilidae)

Sexually dimorphic traits have a history of directional selection for exaggeration in at least one sex. Theory suggests that traits targeted by persistent selection should evolve heightened condition dependence whereby their expression reflects the availability and processing efficiency of metabolic resources. This joint dependence of sexual dimorphism and condition dependence on directional selection should result in a positive correlation between the extent of sexual dimorphism and the strength of condition dependence. However, because direct phenotypic evidence is predominately from species with highly exaggerated male traits, it remains unclear whether condition-dependent sexual dimorphism is characteristic of species with more typical levels of dimorphism. We manipulated condition via larval diet and quantified sex-specific responses in adult body size and shape in a moderately dimorphic dipteran species, the antler fly Protopiophila litigata. While dimorphism did not increase with diet quality within any trait, among traits the extent of dimorphism was positively associated with the strength of condition dependence in males but not females, as previously reported for highly dimorphic species. This finding suggests that a shared developmental basis to condition dependence and sexual dimorphism can arise via sexual selection on males even in lineages lacking highly exaggerated male traits.