Find research datasets worth reusing

Data from: A new theory of plant-microbe nutrient competition resolves inconsistencies between observations and model predictions

Terrestrial plants assimilate anthropogenic CO2 through photosynthesis and synthesizing new tissues. However, sustaining these processes requires plants to compete with microbes for soil nutrients, which therefore calls for an appropriate understanding and modeling of nutrient competition mechanisms in Earth System Models (ESMs). Here, we survey existing plant-microbe competition theories and their implementations in Earth System Models (ESMs). We found no consensus regarding the representation of nutrient competition and that observational and theoretical support for current implementations are weak. To reconcile this situation, we applied the Equilibrium Chemistry Approximation (ECA) theory to plant-microbe nitrogen competition in a detailed grassland 15N tracer study and found that competition theories in current ESMs fail to capture observed patterns and the ECA prediction simplifies the complex nature of nutrient competition and quantitatively matches the 15N observations. Since plant carbon dynamics are strongly modulated by soil nutrient acquisition, we conclude that (1) predicted nutrient limitation effects on terrestrial carbon accumulation by existing ESMs may be biased and (2) our ECA-based approach may improve predictions by mechanistically representing plant-microbe nutrient competition.

opencc-zeroDec 2013View details →

Data from: Linking niche theory to ecological impacts of successful invaders: insights from resource fluctuation-specialist herbivore interactions

1. Theories of species coexistence and invasion ecology are fundamentally connected and provide a common theoretical framework for studying the mechanisms underlying successful invasions and their ecological impacts. Temporal fluctuations in resource availability and differences in life-history traits between invasive and resident species are considered as likely drivers of the dynamics of invaded communities. Current critical issues in invasion ecology thus relate to the extent to which such mechanisms influence coexistence between invasive and resident species, and to the ability of resident species to persist in an invasive-dominated ecosystem. 2. We tested how a fluctuating resource and species traits differences may explain and help predict long-term impacts of biological invasions in forest specialist insect communities. We used a simple invasion system comprising closely related invasive and resident seed-specialized wasps (Hymenoptera: Torymidae) competing for a well-known fluctuating resource, and displaying divergent diapause, reproductive and phenological traits. 3. Based on extensive long-term field observations (1977-2010), we developed a combination of mechanistic and statistical models aiming to (i) obtain a realistic description of the population dynamics of these interacting species over time, and (ii) clarify the respective contributions of fluctuation-dependent and fluctuation-independent mechanisms to long-term impact of invasion on the population dynamics of the resident wasp species. 4. We showed that a fluctuation-dependent mechanism was unable to promote coexistence of the resident and invasive species. Earlier phenology of the invasive species was the main driver of invasion success, enabling the invader to exploit an empty niche. Phenology also had the greatest power to explain the long-term negative impact of the invasive on the resident species, through resource preemption. 5. This study provides strong support for the critical role of species differences in interspecific competition outcomes within animal communities. Our mechanisticstatistical approach allows disentangling the critical drivers of the dynamics of coexistence and exclusion within novel species assemblages, following both intentional and non-intentional species introductions.

opencc-zeroJun 2021View details →

The Hydroperoxyl Radical Scavenging Activity of Sulfuretin: Insights from Theory

This dataset contains data from the calculations described in the paper: "Nguyen Thi Hoa, Do Thi My Hang, Do Phu Hieu, Huynh Van Truong, Loc Phuoc Hoang, Adam Mechler and Quan V. Vo*. (2021), The Hydroperoxyl Radical Scavenging Activity of Sulfuretin: Insights from Theory. Royal Society Open Science. 2021. The thermodynamic and kinetic calculations were applied to evaluate the HOO· radical scavenging activity of sulfuretin (SFR) in the gas phase and solvents (water and pentyl ethanoate) by the M06-2X/6-311++G(d,p) level of theory. SFR is predicted to be an excellent HOO• scavenger in water at pH = 7.40 with koverall = 4.75´107 M-1 s-1, principally due to an increase in the activity of the anionic form following the single electron transfer mechanism. Consistently the activity of the neutral form is more prominent in the nonpolar environment with koverall = 1.79´104 M-1 s-1 following the formal hydrogen transfer mechanism. Thus it is predicted that SFR exhibits better HOO· antiradical activity than typical antioxidants such as resveratrol, ascorbic acid, and Trolox in the lipid medium. The hydroperoxyl radical scavenging of SFR in the aqueous solution is ~530 times faster than that of Trolox and similar to ascorbic acid or resveratrol. This suggests that SFR is a promising radical scavenger in physiological environments.

opencc-zeroDec 2013View details →

Data from: Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation in Busseola fusca (Lepidoptera: Noctuidae)

Current population genetic models fail to cope with genetic differentiation for species with large, contiguous and heterogeneous distribution. We show that in such a case, genetic differentiation can be predicted at equilibrium by circuit theory, where conductance corresponds to abundance in species distribution models (SDM). Circuit-SDM approach was used for the phylogeographic study of the lepidopteran cereal stemborer Busseola fusca Füller (Noctuidae) across sub-Saharan Africa. Species abundance was surveyed across its distribution range. SDM models were optimized and selected by cross validation. Relationship between observed matrices of genetic differentiation between individuals, and matrices of resistance distance was assessed through Mantel tests and redundancy discriminant analyses (RDA). A total of 628 individuals from 130 localities in 17 countries were genotyped at 7 microsatellite loci. Six population clusters were found based on a Bayesian analysis. The eastern margin of Dahomey Gap between East and West Africa was the main factor of genetic differentiation. The SDM projections at present, last interglacial and last glacial maximum periods were used for estimation of circuit resistance between locations of genotyped individuals. For all periods of time, when using either all individuals or only East-African individuals, partial Mantel r and RDA analyses conditioning on geographic distance were found significant. Under future projections (year 2080), partial r and RDA significance were different. From this study, it is concluded that analytical solutions provided by circuit theory are useful for the evolutionary management of populations and for phylogeographic analysis when coalescence times are not accessible by approximate Bayesian simulations.

Data from: Ecology of tern flight in relation to wind, topography and aerodynamic theory

Flight is an economic mode of locomotion, because it is both fast and relatively cheap per unit of distance, enabling birds to migrate long distances and obtain food over large areas. The power required to fly follows a U-shaped function in relation to airspeed, from which context dependent 'optimal' flight speeds can be derived. Crosswinds will displace birds away from their intended track unless they make compensatory adjustments of heading and airspeed.We report on flight track measurements in five geometrically similar tern species ranging one magnitude in body mass, from both migration and the breeding season at the island of O ¨ land in the Baltic Sea. When leaving the southern point of O ¨ land, migrating Arctic and common terns made a 608 shift in track direction, probably guided by a distant landmark. Terns adjusted both airspeed and heading in relation to tail and sidewind, where coastlines facilitated compensation. Airspeed also depended on ecological context (searching versus not searching for food), and it increased with flock size. Species-specific maximum range speed agreed with predicted speeds from a new aerodynamic theory. Our study shows that the selection of airspeed is a behavioural trait that depended on a complex blend of internal and external factors.

Data from: Dispersal and diversity in experimental metacommunities: linking theory and practice

There has been a recent rise in the number of experiments investigating the effect of dispersal on diversity, with many of the predictions for these tests derived from metacommunity theory. Despite the promise of linking observed relationships between dispersal and diversity to underlying metacommunity processes, empirical studies have faced challenges in providing robust tests of theory. We review experimental studies that have tested how dispersal affects metacommunity diversity to determine why shortcomings emerge, and to provide a framework for empirical tests of theory that capture the processes structuring diversity in natural metacommunities. We first summarize recent experimental work to outline trends in results and to highlight common methods that cause a misalignment between empirical studies and the processes described by theory. We then identify the undesired implications of three widely used experimental methods that homogenize metacommunity structure or species traits, and present alternative methods that have been used to successfully integrate experiments and theory in a biologically relevant way. Finally, we present methodological and theoretical insights from three related ecological fields (coexistence, food web and priority effects theory) that, if integrated into metacommunity experiments, could help isolate the independent and joint effects of local interactions and dispersal on diversity, and reveal the mechanisms underlying observed dispersal–diversity patterns. Together, these methods can provide stronger tests of existing theory and stimulate new theoretical explorations.

Data from: Revising traditional theory on the link between plant body size and fitness under competition: evidence from old-field vegetation

The selection consequences of competition in plants have been traditionally interpreted based on a "size-advantage" hypothesis – that is, under intense crowding/competition from neighbors, natural selection generally favors capacity for a relatively large plant body size. However, this conflicts with abundant data, showing that resident species body size distributions are usually strongly right-skewed at virtually all scales within vegetation. Using surveys within sample plots and a neighbor-removal experiment, we tested: (1) whether resident species that have a larger maximum potential body size (MAX) generally have more successful local individual recruitment, and thus greater local abundance/density (as predicted by the traditional size-advantage hypothesis); and (2) whether there is a general between-species trade-off relationship between MAX and capacity to produce offspring when body size is severely suppressed by crowding/competition – that is, whether resident species with a larger MAX generally also need to reach a larger minimum reproductive threshold size (MIN) before they can reproduce at all. The results showed that MIN had a positive relationship with MAX across resident species, and local density – as well as local density of just reproductive individuals – was generally greater for species with smaller MIN (and hence smaller MAX). In addition, the cleared neighborhoods of larger target species (which had relatively large MIN) generally had – in the following growing season – a lower ratio of conspecific recruitment within these neighborhoods relative to recruitment of other (i.e., smaller) species (which had generally smaller MIN). These data are consistent with an alternative hypothesis based on a 'reproductive-economy-advantage' – that is, superior fitness under competition in plants generally requires not larger potential body size, but rather superior capacity to recruit offspring that are in turn capable of producing grand-offspring – and hence transmitting genes to future generations – despite intense and persistent (cross-generational) crowding/competition from near neighbors. Selection for the latter is expected to favor relatively small minimum reproductive threshold size and hence – as a tradeoff – relatively small (not large) potential body size.

opencc-zeroDec 2013View details →

Data from: Moving on with foraging theory: incorporating movement decisions into the functional response of a gregarious shorebird

1. Models relating intake rate to food abundance and competitor densities (generalized functional response models) can predict forager distributions and movements between patches, but we lack understanding of how distributions and small-scale movements by the foragers themselves affect intake rates. 2. Using a state-of-the-art approach based on continuous-time Markov chain dynamics, we add realism to classic functional response models by acknowledging that the chances to encounter food and competitors are influenced by movement decisions, and, vice versa, that movement decisions are influenced by these encounters. 3. We used a multi-state modelling framework to construct a stochastic functional response model in which foragers alternate between three behavioural states: searching, handling and moving. 4. Using behavioural observations on a molluscivore migrant shorebird (red knot, Calidris canutus canutus), at its main wintering area (Banc d'Arguin, Mauritania), we estimated transition rates between foraging states as a function of conspecific densities and densities of the two main bivalve prey. 5. Intake rate decreased with conspecific density. This interference effect was not due to decreased searching efficiency, but resulted from time lost to avoidance movements. 6. Red knots showed a strong functional response to one prey (Dosinia isocardia), but a weak response to the other prey (Loripes lucinalis). This corroborates predictions from a recently developed optimal diet model that accounts for the mildly toxic effects due to consuming Loripes. 7. Using model-averaging across the most plausible multi-state models, the fully parameterized functional response model was then used to predict intake rate for an independent dataset on habitat choice by red knot. 8. Comparison of the sites selected by red knots with random sampling sites showed that the birds fed at sites with higher than average Loripes and Dosinia densities, i.e. sites for which we predicted higher than average intake rates. 9. We discuss the limitations of Holling's classical functional response model that ignores movement and the limitations of contemporary movement ecological theory ignoring consumer-resource interactions. With the rapid advancement of technologies to track movements of individual foragers at fine spatial scales, the time seems ripe to integrate descriptive tracking studies with stochastic movement-based functional response models.

opencc-zeroDec 2012View details →

Data from: Testing sex ratio theory with the malaria parasite Plasmodium mexicanum in natural and experimental infections

The malaria parasite (Plasmodium) life history accords well with the assumptions of Local Mate Competition (LMC) of sex ratio theory. Within a single meal of the blood-feeding vector, sexually dimorphic gametocyte cells produce gametes (females produce 1, males several) that mate and undergo sexual recombination. The theory posits several factors drive the Plasmodium sex ratio: male fecundity (gametes/ male gametocyte), number and relative abundance of parasite clones, and gametocyte density. We measured these traits for the lizard malaria parasite, P. mexicanum, with a large sample of natural infections and infections from experiments which manipulated clonal diversity. Sex ratio in single-clone infections was slightly female-biased, but matched predictions of theory for this low-fecundity species. Sex ratio was less female-biased in clonally diverse infections as predicted by LMC for the experimental, but not natural infections. Gametocyte density was not positively related to sex ratio. These results are explained by the P. mexicanum life history of naturally low clonal diversity and high gametocyte production. This is the first study of a natural malaria system that examines all traits relevant to LMC in individual vertebrate hosts and suggests a striking example of sex ratio theory having significance for human public health.

opencc-by-sa-4.0Nov 2015View details →

Data from ``Developments in Stochastic Coupled Cluster Theory: The initiator approximation and application to the Uniform Electron Gas''

We describe further details of the Stochastic Coupled Cluster method and a diagnostic of such calculations, the shoulder height, akin to the plateau found in Full Configuration Interaction Quantum Monte Carlo. We describe an initiator modification to Stochastic Coupled Cluster Theory and show that initiator calculations can be extrapolated to the unbiased limit.  We apply this method to the 3D 14-electron uniform electron gas and present complete basis set limit values of the CCSD and previously unattainable CCSDT correlation energies for up to $r_s=2$, showing a requirement to include triple excitations to accurately calculate energies at high densities.

FIGURE 22 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 22. Spectrograms and corresponding oscillograms of the advertisement calls of two anuran species, exemplifying the presence of parallel frequency bands in the spectrogram, although at comparatively low FFT resolution (256; Hanning window function), not representing harmonics, but resulting from a high pulse rate. Left: Section of the advertisement call of Elachistocleis sp., with a pulse rate of 245 pulses/second and a total call duration of 2000‒3040 ms. Right: Advertisement call of Physalaemus albonotatus, with seven recognizable and modulated frequency bands. Its call is exceptionally fastly pulsed, with an approximate rate of 470 pulses/second. Figures modified and data taken from Köhler (2000). Spectrograms and oscillograms produced with CoolEdit Pro.

FIGURE 8 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 8. Comparative oscillograms of notes of four anuran species, illustrating differences in amplitude modulation and respective differences in descriptive terminology, particularly the bioacoustical application of the term pulse as defined herein.

FIGURE 5 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 5. Spectrograms and oscillograms of anuran advertisement calls conforming to the general sound categories proposed by Beeman (1998) for animals (and slightly modified herein). All graphics produced with the R package Seewave (Sueur et al. 2008a), from recordings of AmphibiawebEcuador.org (Hypsiboas tetete: Hylidae), Dendrobates.org (Andinobates fulguritus: Dendrobatidae), Vences et al. (2006) (Rhombophryne coronata: Microhylidae), Du Preez & Carruthers (2009) (Ptychadena anchietae: Ptychadenidae; Tomopterna marmorata and Amietia angolensis: Pyxicephalidae), Cocroft et al. (2001) (Ceratophrys cornuta: Ceratophryidae), Elliot et al. (2009) (Dryophytes andersonii: Hylidae). All spectrograms at Hanning window function, 512 bands resolution.

FIGURE 3 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 3. Two calls of Dryophytes andersonii (recording taken from Elliot et al. 2009) depicted in exemplary spectrogram, oscillogram and power spectrum, showing units and explaining details and analytical purpose of the graphs. Graphs were produced with the R package Seewave (Sueur et al. 2008a).

FIGURE 2 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 2. Vocal sac variation in anurans. Except for Ceratophrys cranwelli (emitting a warning call with open mouth) and the pictured specimens of Hyperolius (emitting advertisement calls with aggressive components in male-male combat) all pictured specimens are emitting advertisement calls. Phrynobatrachus alleni is suspected to use its yellow vocal sac for visual signalling, and a visual function is also probable for the bright white vocal sacs of the two Guibemantis species, and of other frogs. All hyperoliids (such as Hyperolius viridiflavus shown here) have gular glands on the vocal sac that might have a visual function, in addition to probably producing pheromones (Starnberger et al. 2013). Note that the distinction between vocal sac types is not always clear; for instance, the vocal sacs of Rana temporaria and Boophis tsilomaro can be considered as partially paired subgular and partially paired lateral. All photos by the authors except Trachycephalus typhonius and Pseudopaludicola jaredi (by Daniel Loebmann).

FIGURE 11 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 11. Box plots of Q 10 values reported in the literature for four call traits in 20 different species of amphibians. The red line indicates no temperature effects (Q 10 = 1). CD, call duration; DF, dominant frequency; PR, pulse rate; CR, call rate.

FIGURE 15 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 15. Spectrograms and oscillograms showing intra-specific call variation in two treefrog species from Madagascar, exemplifying the need to account for the possibility of different call / note types and of strong influence of motivation when taxonomically interpreting bioacoustical differences. (A) Males of Boophis at Antsatramidola, Madagascar, were emitting two very different types of calls, one of which might represent a territorial call. However, we never heard the two calls from the same individuals and therefore in the field were convinced of the presence of two morphologically cryptic species. Subsequent genetic study revealed that the individuals were all conspecific with B. tampoka and emitting two different call types (Köhler et al. 2007; Vences et al. 2011). (B) Boophis ankaratra emits long series of notes. Typical note repetition rate is reflected by the call from Manjakatompo, emitted by a male in the presence of several other calling males. At Itremo, during a dry evening, only few specimens were sporadically calling and obviously were in a state of low sexual motivation; despite a slightly higher temperature, note repetition rate was much lower at this occasion. Spectrograms produced with CoolEdit Pro at Hanning window function, 256 bands resolution.

FIGURE 21 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 21. Spectrograms and oscillograms showing frog advertisement calls with components at frequencies higher than usually reported, partly reaching into the ultrasound spectrum. In these four frog species, the dominant frequency is below 10 kHz but harmonics are visible at much higher frequency. Eleutherodactylus iberia (from Bahia de Taco, Cuba) and Stumpffia sp. [Ca6 Vieites et al. 2009] (from Andasibe, Madagascar) are miniaturized frogs with <11 mm snout-vent length (SVL) whereas Eleutherodactylus [Ca4 Rodríguez et al. 2010b] and Platypelis barbouri are small sized frogs around 20 mm SVL. Note that frequency of the spectrograms goes up to 40 kHz. Eleutherodactylus [Ca4] has almost no frequency components in the ultrasound spectrum, yet frequency reaches distinctly above 10 kHz, much higher than usually reported for frogs. Recordings were made with ultrasound microphone Ultramic200k (Dodotronic, Italy). Graphics produced with the R package Seewave (Sueur et al. 2008a). All spectrograms produced at Hanning window function, 1024 bands resolution. Format of candidate species names follows Padial et al. (2010).

FIGURE 7 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 7. Concordance and discordance among call centered and note centered approaches to name sound units in anuran vocalizations. The upper two schematic spectrograms show examples where both approaches lead to the same categorization of sounds. (A) A single tonal sound is repeated after regular silent intervals of longer duration than the sounds. There is no defined duration of the series of sounds; if undisturbed, calling could go on for minutes or hours. In both approaches, one sound unit would be a call, and the note-centered approach would define each call consisting of a single note. (B) Series of rapidly repeated sounds, each composed of a series of bursts of sound energy. Because these bursts are <10 ms in duration they are defined as pulses. The call-centered approach does not define each major subunit as call because the silent intervals between them are much shorter than the units themselves; thus, both approaches agree in defining the units as notes. (C) This species emits clearly defined and stereotyped series of sounds, each series being separated by variable intervals from the next series. The note-centered approach defines one coherent entity of sound emission as a call; hence, each sound series unit is a call, and the subunits are notes. In contrast, the call-centered approach defines each sound unit as a call (and each series as a call series) because it is separated from other such units by a long silent interval. (D) This species emits two distinct kinds of pulsatile sound units, of which one is much longer than the other. Because the combination of sounds is emitted as coherent entity, in the note centered approach the entire sound emission is a call and the sound units are notes of two types, of which one is arranged in a series. In the call-centered approach, each sound unit is a call because they are separated by long silent intervals from the next unit. Two call types can be distinguished and one of these is arranged in a call series.

FIGURE 4 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 4. Comparative spectrograms of a call of Dryophytes andersonii, all drawn with Hanning window function, showing the effect of different FFT resolution on the graphic representation of calls. Each spectrogram shows the identical 300 ms section of a recording. Note that with higher FFT settings, the spectral detail of the call representation increases. At lower FFT settings, the temporal pattern of the call is more clearly recognizable. Call recording taken from Elliot et al. (2009). Graphics produced with the R package Seewave (Sueur et al. 2008a).