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opencc-by-4.0Mar 2018View details →

Interaction of one-dimensional trivial and non-trivial travelling waves in a three-species competition-diffusion system

We consider the situation where an exotic species w invades an ecosystem inhabited by two native species u and v. All species are competing for the same limited resource. Supposing that u and v are not able to coexist in the absence of the invader, we want to determine whether a successful invasion by w may allow all species to coexist (competitor-mediated coexistence). Mathematically, this problem can be modelled by the following three-species competition-diffusion system \( \left\{ \begin{alignedat}{6} u_t &= d_1 \, \Delta u &&+ (r_1 &&- u &&- b_{12} \, v &&- b_{13} \, w &&)\,u, \\ v_t &= d_2 \, \Delta v &&+ (r_2 &&- v &&- b_{21} \, u &&- b_{23} \, w &&)\,v, \\ w_t &= d_3 \, \Delta w &&+ (r_3 &&- w &&- b_{31} \, u &&- b_{32} \, v &&)\,w, \end{alignedat} \right.\) where all parameters are positive constants. We are interested in the case in which the invading species is weaker than the native ones, i.e., it is not able to survive in the diffusion-free system obtained by setting d1 = d2 = d3 = 0. We fix all parameters as \( \begin{aligned} & d_1 = d_2 = d_3 = 1, \\ & r_1 = r_2 = 28, \\ & \begin{aligned} b_{12} &= 22/21, & b_{13} &= 4, \\ b_{21} &= 1.87, & b_{23} &= 3/4, \\ b_{31} &= 26/21, & b_{32} &= 22/21, \\ \end{aligned} \end{aligned}\) and leave r3, which measures the strength of the exotic species, as a free parameter. Depending on the value of r3, the invasion can be either successful or not and competitor-mediated coexistence may or may not occur. It turns out that if r3 lies in a certain range of values, the three-species competition-diffusion system admits two planarly stable travelling wave solutions. In the movies here presented, the result of the interaction of these two waves in one spatial dimension is reported for several value of r3. For relatively higher values of the free parameter, the relative velocity of the interacting waves is small and they merge into a single travelling pulse. As r3 decreases, the relative velocity of the two waves becomes larger and they merge into a breathing wave (a travelling pulse whose width is oscillating). If r3 is even smaller, the trivial wave is reflected as a leftward-moving non-trivial wave.

opencc-by-4.0Mar 2018View details →

Interaction of planarly stable trivial and non-trivial travelling waves in a three-species competition-diffusion system

We consider the situation where an exotic species w invades an ecosystem inhabited by two native species u and v. All species are competing for the same limited resource. Supposing that u and v are not able to coexist in the absence of the invader, we want to determine whether a successful invasion by w may allow all species to coexist (competitor-mediated coexistence). Mathematically, this problem can be modelled by the following three-species competition-diffusion system \( \left\{ \begin{alignedat}{6} u_t &= d_1 \, \Delta u &&+ (r_1 &&- u &&- b_{12} \, v &&- b_{13} \, w &&)\,u, \\ v_t &= d_2 \, \Delta v &&+ (r_2 &&- v &&- b_{21} \, u &&- b_{23} \, w &&)\,v, \\ w_t &= d_3 \, \Delta w &&+ (r_3 &&- w &&- b_{31} \, u &&- b_{32} \, v &&)\,w, \end{alignedat} \right.\) where all parameters are positive constants. We are interested in the case in which the invading species is weaker than the native ones, i.e., it is not able to survive in the diffusion-free system obtained by setting d1 = d2 = d3 = 0. We fix all parameters as \( \begin{aligned} & d_1 = d_2 = d_3 = 1, \\ & r_1 = r_2 = 28, \\ & \begin{aligned} b_{12} &= 22/21, & b_{13} &= 4, \\ b_{21} &= 1.87, & b_{23} &= 3/4, \\ b_{31} &= 26/21, & b_{32} &= 22/21, \\ \end{aligned} \end{aligned}\) and leave r3, which measures the strength of the exotic species, as a free parameter. Depending on the value of r3, the invasion can be either successful or not and competitor-mediated coexistence may or may not occur. It turns out that if r3 lies in a certain range of values, the three-species competition-diffusion system admits two planarly stable travelling wave solutions. In the movies here presented, the result of the interaction of these two waves in two spatial dimensions is reported for several value of r3. The species u, v and w are denoted by the red, green and blue colours respectively. The yellow line marks the interface between the species u and v. As the value of the free parameter decreases, we observe a transition from a regular spiral pattern, to a breathing spiral and finally to a complex spatio-temporal pattern born from the break-up of the spiral. This complex pattern may be either periodic or chaotic in the long run, as can be seen in the movies for longer time intervals T.

opennotspecifiedJan 2016View details →

Fig. 1 3D in Towards a sound definition of Skeneidae (Mollusca, Vetigastropoda): 3D interactive anatomy of the type species, Skenea serpuloides (Montagu, 1808) and comments on related taxa

Fig. 1 3D reconstructions of the body and tentacles of Skenea serpoloides. a Latero-frontal view on the right side, mantle roof transparent. b Latero-frontal view on the left side, mantle roof transparent. c Frontal view, mantle roof transparent. d Right side view onto epipodial tentacle and epipodial sense organ, mantle roof removed. a, b SMNH-

opennotspecifiedFeb 2011View details →

Fig. 2 in Flowering phenology of co-occurring Asteraceae: a matter of climate, ecological interactions, plant attributes or of evolutionary relationships among species?

Fig. 2 Number of Asteraceae species growing in Chaco Serrano forests of La Serranita-Los Aromos that bear flowers during each month of the year; for calculation, see text in Material and methods Section

opennotspecifiedFeb 2011View details →

Fig. 1 in Flowering phenology of co-occurring Asteraceae: a matter of climate, ecological interactions, plant attributes or of evolutionary relationships among species?

Fig. 1 Diagram of phylogenetic relationships between Asteraceae taxa studied in this work (adapted from Panero and Crozier 2008; Panero and Funk 2008)

opennotspecifiedFeb 2011View details →

Fig. 4 in Flowering phenology of co-occurring Asteraceae: a matter of climate, ecological interactions, plant attributes or of evolutionary relationships among species?

Fig. 4 Plot of PCA scores for 43 co-occurring Asteraceae species in Chaco Serrano forests of La Serranita-Los Aromos, showing first two principal component axes from analysis of flowering phenology considering plant traits and taxonomic membership. Vectors corre-

opencc-by-4.0Aug 2024View details →

Data for Coevolution and temporal dynamics of species interactions shape species coexistence

This dataset is the one used in our preprint "<a href="https://doi.org/10.1101/2024.08.08.607160">Coevolution and temporal dynamics of species interactions shape species coexistence</a>". R codes to analyse these data can be found here: <a href="https://github.com/f-duchenne/Evolution_pheno_vs_morpho">https://github.com/f-duchenne/Evolution_pheno_vs_morpho</a> flow_pheno_empirical.csv and poll_pheno_empirical.csv contain the empirical phenological parameters for plant and pollinator species, respectively: the mean activity day (mu) and its standard deviation (sde) representing the duration of the activity period. matrices_empirical_networks.RData contains an R object with the 17 networks used. Plants are in rows and pollinators in columns, with each cell representing the average interaction value across sampling rounds, corrected by abundances. You can access it in R via: <div> <pre><code>#load data load("matrices_empirical_networks.RData") #see the structure (a list of 17 networks) str(networks) #access the first network networks[[1]]</code></pre> <pre> </pre> </div>

opencc-zeroJul 2021View details →

Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota

Background and objectives Slowing the spread of antimicrobial resistance is urgent if we are to continue treating infectious diseases successfully. There is increasing evidence microbial interactions between and within species are significant drivers of resistance. On one hand, cross-protection by resistant genotypes can shelter susceptible microbes from the adverse effects of antibiotics, reducing the advantage of resistance. On the other hand, antibiotic-mediated killing of susceptible genotypes can alleviate competition and allow resistant strains to thrive (competitive release). Here, by observing interactions both within and between species in microbial communities sampled from humans, we investigate the potential role for cross-protection and competitive release in driving the spread of ampicillin resistance in the ubiquitous gut commensal and opportunistic pathogen Escherichia coli. Methodology Using anaerobic gut microcosms comprising E. coli embedded within gut microbiota sampled from humans, we tested for cross-protection and competitive release both within and between species in response to the clinically important beta-lactam antibiotic ampicillin. Results While cross-protection gave an advantage to antibiotic-susceptible E. coli in standard laboratory conditions (well-mixed LB medium), competitive release instead drove the spread of antibiotic-resistant E. coli in gut microcosms (ampicillin boosted growth of resistant bacteria in the presence of susceptible strains). Conclusions and implications Competition between resistant strains and other members of the gut microbiota can restrict the spread of ampicillin resistance. If antibiotic therapy alleviates competition with resident microbes by killing susceptible strains, as here, microbiota-based interventions that restore competition could be key for slowing the spread of resistance.

opencc-zeroJul 2021View details →

Data from: Long-term and interactive effects of different mammalian consumers on growth, survival and recruitment of dominant tree species

Throughout the world, numerous tree species are reported to be in decline, either due to increased mortality of established trees or reduced recruitment. The situation appears especially acute for oaks, which are dominant features of many landscapes in the northern hemisphere. Although numerous factors have been hypothesized to explain reductions in tree performance, vertebrate herbivores and granivores may serve as important drivers of these changes. Here, using data from 8- and 14-year-old exclosure experiments, we evaluated the individual and interactive effects of large and small mammalian herbivores on the performance of three widespread oak species in California – coast live oak (Quercus agrifolia), California black oak (Q. kelloggii) and Oregon white oak (Q. garryana). Although impacts varied somewhat by species and experiment, herbivory by black-tailed deer (Odocoileus hemionus columbianus) reduced the height and survival of juvenile coast live oaks and altered their architecture, as well as reduced the abundance of black oak seedlings, the richness of woody species and the cover of non-oak woody species. Small mammals (Microtus californicus and Peromyscus maniculatus) had even more widespread effects, reducing the abundance of black oak seedlings and the height and cover of all three oak species. We also detected numerous interactions between small mammals and deer, with one herbivore having positive or negative effects on oak abundance and cover when the other herbivore was either present or absent. For example, deer often had negative effects on seedling abundance only when, or even more so when, small mammals were present. In summary, mammalian consumers play crucial roles in limiting oak recruitment by reducing seedling abundance, maintaining trees in stunted states and preventing them from reaching sapling stages and becoming reproductive. Interactions between large and small mammals can also alter the intensity and direction of their effects on trees.

opencc-zeroAug 2021View details →

Supplementary information from: Species interactions have predictable impacts on diversification

A fundamental goal of ecology is to reveal generalities in the myriad types of interactions among species, such as competition, mutualism, and predation. Another goal is to explain the enormous differences in species richness among groups of organisms. Here, we show how these two goals are intertwined: we find that different types of species interactions have predictable impacts on rates of species diversification, which underlie richness patterns. Based on a systematic review, we show that interactions with positive fitness effects for individuals of a clade (e.g. insect pollination for plants) generally increase that clade's diversification rates. Conversely, we find that interactions with negative fitness effects (e.g. predation for prey, competition) generally decrease diversification rates. The sampled clades incorporate all animals and land plants, encompassing ~90% of all described species across life. Overall, we show that different types of local-scale species interactions can predictably impact large-scale patterns of diversification and richness.

opencc-by-4.0Aug 2021View details →

Mitonuclear interactions alter sex-specific longevity in a species without sex chromosomes

Data submission accompanies a manuscript submitted to Proceedings of the Royal Society B entitled "Mitonuclear interactions alter sex-specific longevity in a species without sex chromosomes" by Flanagan, Li, and Edmands. Data files include longevity, mtDNA content, DNA damage, and sample information. All analyses are performed in a single R Markdown file.

opencc-zeroAug 2021View details →

Interactive effects of tree species mixture and climate on foliar and woody trait variation in a widely distributed deciduous tree

Despite increasing reports of severe drought and heat impacts on forest ecosystems, community-level processes, which could potentially modulate tree responses to climatic stress, are rarely accounted for. While numerous studies indicate a positive effect of species diversity on a wide range of ecosystem functions and services, little is known about how species interactions influence tree responses to climatic variability. We quantified the intraspecific variation in 16 leaf and wood physiological, morphological, and anatomical traits in mature beech trees (Fagus sylvatica L.) at six sites located along a climatic gradient in the French Alps. At each site, we studied pure beech and mixed stands with silver fir (Abies alba Mill.) or downy oak (Quercus pubescens Willd.). We tested how functional traits differed between the two species mixtures (pure vs. mixed stands) within each site and along the climatic gradient. We found significant changes in many traits along the climatic gradient as conditions progressively got drier and warmer. Independent of the mixture, reduced leaf-level CO2 assimilation, stomatal size, and thicker leaf cuticles, consistent with a more conservative resource use strategy, were found. At the drier sites, higher foliar stable carbon isotopic composition (d13C), thicker mesophyll tissues, and lower specific leaf area (SLA) in pure stands suggests that beech had more acquisitive traits there compared to mixed stands. At the wetter sites, trees in beech-silver fir mixtures had higher chlorophyll concentration, lower d13C, larger xylem vessels, and higher SLA, suggesting a more acquisitive resource use strategy in mixed stands than in pure stands. Our work revealed that species interactions are significant modulators of functional traits, and that they can be just as important drivers of intraspecific trait variation as climatic conditions. We show that downy oak mixtures lead to an adaptive drought response by common beech in dry environments. In contrast, in milder climates, interactions with silver fir seem to increase beech' resource acquisition and productivity. These findings highlight a strong context-dependency and imply that incorporating local interspecific interactions in research on climate impacts could improve our understanding and predictions of forest dynamics.

Figure 5 in Are spider communities influenced by urbanisation? An approach using species and guilds resolutions and their interaction with the anthropogenic environment

Figure 5. Nonmetric multidimensional scaling of ambush hunters species collected, stress value: 0.12. References: Urban sites location = black circles; Suburban sites location = grey triangles.

Figure 3 in Are spider communities influenced by urbanisation? An approach using species and guilds resolutions and their interaction with the anthropogenic environment

Figure 3. Comparison between sampling site location of mean and SEM Shannon-Weaver index (a) and Shannon evenness index (b) of total spiders collected and per guild assessed by ANOVA. Location references: Urban = black bars; Suburban = grey bars. * = p <0.05.

Figure 4 in Are spider communities influenced by urbanisation? An approach using species and guilds resolutions and their interaction with the anthropogenic environment

Figure 4. Nonmetric multidimensional scaling of all species collected, stress value: 0.14. References: Urban sites = black circles; Suburban sites = grey triangles.

Figure 1 in Are spider communities influenced by urbanisation? An approach using species and guilds resolutions and their interaction with the anthropogenic environment

Figure 1. Sample sites in Cordoba city, Argentina. Circles = urban and triangles = suburban sites. The zoom-window shows urbanisation degree categories measured and radii (Map adapted from García et al. 2018).

opennotspecifiedJun 2021View details →

Figure 4 in Review of the interactions of an ecological keystone species, Aechmea distichantha Lem. (Bromeliaceae), with the associated fauna

Figure 4. Bipartite nets showing the relative proportion of interactions of Aechmea distichantha with animals registered for the different taxonomic groups classified according to the (a) use of the plant, (b) trophic level and (c) type (resource involved) of herbivory and ordered following the 'as few crossings of interactions as possible' criteria. Boxes represent the number of morphospecies, and categories and paths represent the number of interactions.

opennotspecifiedJun 2021View details →

Figure 3 in Review of the interactions of an ecological keystone species, Aechmea distichantha Lem. (Bromeliaceae), with the associated fauna

Figure 3. (a) Number of animal species associated with, and (b) number of interactions established with A. distichantha. In both graphs, the records are ordered taxonomically according to Hyman (1940).

opennotspecifiedJun 2021View details →

Figure 2 in Review of the interactions of an ecological keystone species, Aechmea distichantha Lem. (Bromeliaceae), with the associated fauna

Figure 2. Evolution of the number of publications from the 1960s to the present grouped in 10-year periods about interactions of Aechmea distichantha with animals in the mid-latitudes of South America.