Maximal ecological diversity exceeds evolutionary diversity in model ecosystems

Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka–Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, although still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.     

Experimental evidence of size-selective harvest and environmental stochasticity effects on population demography,fluctuations and non-linearity

Theory and analyses of fisheries data sets indicate that harvesting can alter population structure and destabilise non-linear processes, which increases population fluctuations. We conducted a factorial experiment on the population dynamics of Daphnia magna in relation to size-selective harvesting and stochasticity of food supply. Harvesting and stochasticity treatments both increased population fluctuations. Timeseries analysis indicated that fluctuations in control populations were non-linear, and non-linearity increased substantially in response to harvesting. Both harvesting and stochasticity induced population juvenescence, but harvesting did so via the depletion of adults, whereas stochasticity increased the abundance of juveniles. A fitted fisheries model indicated that harvesting shifted populations towards higher reproductive rates and larger-magnitude damped oscillations that amplify demographic noise. These findings provide experimental evidence that harvesting increases the non-linearity of population fluctuations and that both harvesting and stochasticity increase population variability and juvenescence.     

The effect of salinity on the reproduction of coastal submerged macrophytes in experimental communities

The effects of salinity on the reproduction of coastal submerged macrophyte species were studied on samples of communities from six seasonal marshes in two outdoor experiments performed in autumn and in spring. The submerged macrophyte communities were submitted to five different salinity levels (0, 1, 2, 4 and 6 g/1 Cl^?1). In a companion paper (Grillas, van Wijck & Bonis 1993) three groups of species were distinguished on the basis of their biomass production over the salinity range 0 to 6 g/1 Cl^?1: (1) glycophytes (non-salt-tolerant species), (2) salt-tolerant species and (3) halo-phytes. This part of the study describes the impact of salinity on the reproduction of the individual species during the two experiments. The species differ in their capacity to reproduce in the autumn; only Zannichelliapedunculata and Tolypella hispánica were able to produce fruits in that season. For all species reproduction was greater in spring and strongly correlated with biomass, except for Chara canescens. Differences in reproductive effort over the salinity range amplified the halophytic nature of Ruppia marítima and Chara canescens and the intolerance of Callitriche truncata and Chara contraria. For the other species, reproductive effort did not differ significantly over the salinity range. Regarding the effect of salinity on biomass and reproductive effort of individual species, there were large differences in the total weight of propagules produced at the community level and in the relative contribution of individual species. The resulting quantitative changes in the species composition of the seed bank could affect the structure of the communities by their effects on the establishment and survival of species populations.     

Coevolution of species colonisation rates controls food-chain length in spatially structured food webs

How the complexity of food webs depends on environmental variables is a long-standing ecological question. It is unclear though how food-chain length should vary with adaptive evolution of the constitutive species. Here we model the evolution of species colonisation rates and its consequences on occupancies and food-chain length in metacommunities. When colonisation rates can evolve, longer food-chains can persist. Extinction, perturbation and habitat loss all affect evolutionarily stable colonisation rates, but the strength of the competition-colonisation trade-off has a major role: weaker trade-offs yield longer chains. Although such eco-evo dynamics partly alleviates the spatial constraint on food-chain length, it is no magic bullet: the highest, most vulnerable, trophic levels are also those that least benefit from evolution. We provide qualitative predictions regarding how trait evolution affects the response of communities to disturbance and habitat loss. This highlights the importance of eco-evolutionary dynamics at metacommunity level in determining food-chain length.     

Mortality rates of desert vegetation during high-intensity drought at Uluru-Kata Tjuta National Park,Central Australia

Precipitation variability and heatwaves are expected to intensify over much of inland Australia under most projected climate change scenarios. This will undoubtedly have impacts on the biota of Australian dryland systems. However, accurate modelling of these impacts is presently impeded by a lack of empirical research on drought/heatwave effects on native arid flora and fauna. During the 2018–2021 Australian drought, many parts of the continent's inland experienced their hottest, driest period on record. Here, we present the results of a field survey in 2021 involving indigenous rangers, scientists and national parks staff who assessed plant dieback during this drought at Ulur u-Kata Tjut a National Park (UKTNP), central Australia. Spatially randomized quadrat sampling of eight common and culturally important plants indicated the following plant death rates across UKTNP (in order of drought susceptibility): desert myrtle (Aluta maisonneuvei subsp. maisonneuvei) (91%), yellow flame grevillea (Grevillea eriostachya) (79%), Maitland's wattle (Acacia maitlandii) (67%), waxy wattle (A. melleodora) (65%), soft spinifex grass (Triodia pungens) (53%), mulga (A. aneura) (42%), desert oak (Allocasuarina decaisneana) (22%) and quandong (Santalum acuminatum) (0%). The sampling also detected that seedling recruitment was absent or minimal for all plants except soft spinifex, while a generalized linear mixed model (GLMM) indicated two-way interactions among species, plant size and stand density as important predictors of drought survival of adult plants. A substantial loss of biodiversity has occurred at UKTNP during the recent drought, with likely drivers of widespread plant mortality being extreme multi-year rainfall deficit (2019 recorded the lowest-ever annual rainfall at UKTNP [27 mm]) and record high summer temperatures (December 2019 recorded the highest-ever temperature [47.1°C]). Our findings indicate that widespread plant death and extensive vegetation restructuring will occur across arid Australia if the severity and frequency of droughts increase under climate change.     

Food-web studies in shallow eutrophic lakes by the Netherlands Institute of Ecology: Main results,knowledge gaps and new perspectives

For more than 20 years scientists of the ‘Food-chain studies’ Group of the former Limnological Institute have been studying interactions within the pelagic food web. Purpose of research was to explain the structure and dynamics of the zooplankton and fish communities in lakes and reservoirs in relation to biotic and abiotic environmental factors. A so-called multi-species approach was used, in which all common and abundant species within a specific ecosystem were studied on the individual and population level with the same degree of detail. The recent results and the scientific approach used are evaluated and the main gaps in knowledge about food-web dynamics in shallow eutrophic lakes are identified and discussed. It is concluded that instead of the purely functional approach used so far, future studies should also include evolutionary aspects which determine the success of an organism in a given environment and that more attention should be paid to central questions in ‘community ecology’. This paper is based on a lecture given by the first author for the Netherlands Society of Aquatic Ecology on May 12th, 1992, in Amsterdam, The Netherlands.     

Computational Fluid Dynamics Analysis of Upper Airway Changes after Protraction Headgear and Rapid Maxillary Expansion Treatment

Clinically, it is common for Class III patients with maxillary skeletal deficiency, which may result in a variety of adverse consequences. Protraction headgear and rapid maxillary expansion (PE) is an effective treatment, but its effect on upper airway hydrodynamics has not been reported. The main purpose of this study was to evaluate the changes of the flow in the upper airway after PE by computational fluid dynamics (CFD). The sample includes fifteen patients (6 males, 9 females, age 11.00 ± 1.00) and the paired T-test was used to analyze the differences between the measured data before and after treatment. The maximum flow velocity decreased from 8.42 ± 0.16 m/s to 6.98 ± 0.36 m/s (p < 0.05), and the maximum shear force decreased from 3.72 ± 1.48 Pa to 2.13 ± 0.18 Pa. The maximum negative pressure decreased from −101.78 ± 33.60 Pa to 58.15 ± 9.16 Pa, only the changes of velopharynx and glossopharynx were statistically significant; while the maximum resistance decreased from 140.88 ± 68.68 Pa/mL/s to 45.95 ± 22.96 Pa/mL/s. PE can effectively reduce the airflow resistance of the upper airway and the probability of airway collapse, thus improving the patient’s ventilation function.     

N-glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study

Various posttranslational modifications like hyperphosphorylation, O-GlcNAcylation, and acetylation have been attributed to induce the abnormal folding in tau protein. Recent in vitro studies revealed the possible involvement of N-glycosylation of tau protein in the abnormal folding and tau aggregation. Hence, in this study, we performed a microsecond long all atom molecular dynamics simulation to gain insights into the effects of N-glycosylation on Asn-359 residue which forms part of the microtubule binding region. Trajectory analysis of the stimulations coupled with essential dynamics and free energy landscape analysis suggested that tau, in its N-glycosylated form tends to exist in a largely folded conformation having high beta sheet propensity as compared to unmodified tau which exists in a large extended form with very less beta sheet propensity. Residue interaction network analysis of the lowest energy conformations further revealed that Phe378 and Lys353 are the functionally important residues in the peptide which helped in initiating the folding process and Phe378, Lys347, and Lys370 helped to maintain the stability of the protein in the folded state.     

A new approach for extracting information from protein dynamics

Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from network science. Most studies build protein dynamics networks from correlation measures, an approach that only works under very specific conditions, instead of the more robust inverse approach. Thus, we apply the inverse approach to the dynamics of protein dihedral angles, a system of internal coordinates, to avoid structural alignment. Using the well-characterized adhesion protein, FimH, we show that our method identifies networks that are physically interpretable, robust, and relevant to the allosteric pathway sites. We further use our approach to detect dynamical differences, despite structural similarity, for Siglec-8 in the immune system, and the SARS-CoV-2 spike protein. Our study demonstrates that using the inverse approach to extract a network from protein dynamics yields important biophysical insights.     

Integrating experimental data with molecular simulations to investigate RNA structural dynamics

Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule Förster resonance energy transfer, or even thermal or mechanical denaturation experiments probe RNA dynamics at different time and space resolutions. Their combination with accurate atomistic molecular dynamics (MD) simulations paves the way for quantitative and detailed studies of RNA dynamics. First, experiments provide a quantitative validation tool for MD simulations. Second, available data can be used to refine simulated structural ensembles to match experiments. Finally, comparison with experiments allows for improving MD force fields that are transferable to new systems for which data is not available. Here we review the recent literature and provide our perspective on this field.