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Endosymbiosis drives evolutionary innovation and underpins the function of diverse ecosystems. The mechanistic origins of symbioses, however, remain unclear, in part because early evolutionary events are obscured by subsequent evolution and genetic drift. This Essay highlights how experimental studies of facultative, host-switched, and synthetic symbioses are revealing the important role of fitness trade-offs between within-host and free-living niches during the early-stage evolution of new symbiotic associations. The mutational targets underpinning such trade-offs are commonly regulatory genes, such that single mutations have major phenotypic effects on multiple traits, thus enabling and reinforcing the transition to a symbiotic lifestyle.

Understanding what structures ecological communities is vital to answering questions about extinctions, environmental change, trophic cascades, and ecosystem functioning. Optimal foraging theory was conceived to increase such understanding by providing a framework with which to predict species interactions and resulting community structure. Here, we use an optimal foraging model and allometries of foraging variables to predict the structure of real food webs. The qualitative structure of the resulting model provides a more mechanistic basis for the phenomenological rules of previous models. Quantitative analyses show that the model predicts up to 65% of the links in real food webs. The deterministic nature of the model allows analysis of the model's successes and failures in predicting particular interactions. Predacious and herbivorous feeding interactions are better predicted than pathogenic, parasitoid, and parasitic interactions. Results also indicate that accurate prediction and modeling of some food webs will require incorporating traits other than body size and diet choice models specific to different types of feeding interaction. The model results support the hypothesis that individual behavior, subject to natural selection, determines individual diets and that food web structure is the sum of these individual decisions.

Great uncertainty exists in the global exchange of carbon between the atmosphere and the terrestrial biosphere. An important source of this uncertainty lies in the dependency of photosynthesis on the maximum rate of carboxylation (Vcmax) and the maximum rate of electron transport (Jmax). Understanding and making accurate prediction of C fluxes thus requires accurate characterization of these rates and their relationship with plant nutrient status over large geographic scales. Plant nutrient status is indicated by the traits: leaf nitrogen (N), leaf phosphorus (P), and specific leaf area (SLA). Correlations between Vcmax and Jmax and leaf nitrogen (N) are typically derived from local to global scales, while correlations with leaf phosphorus (P) and specific leaf area (SLA) have typically been derived at a local scale. Thus, there is no global‐scale relationship between Vcmax and Jmax and P or SLA limiting the ability of global‐scale carbon flux models do not account for P or SLA. We gathered published data from 24 studies to reveal global relationships of Vcmax and Jmax with leaf N, P, and SLA. Vcmax was strongly related to leaf N, and increasing leaf P substantially increased the sensitivity of Vcmax to leaf N. Jmax was strongly related to Vcmax, and neither leaf N, P, or SLA had a substantial impact on the relationship. Although more data are needed to expand the applicability of the relationship, we show leaf P is a globally important determinant of photosynthetic rates. In a model of photosynthesis, we showed that at high leaf N (3 gm−2), increasing leaf P from 0.05 to 0.22 gm−2 nearly doubled assimilation rates. Finally, we show that plants may employ a conservative strategy of Jmax to Vcmax coordination that restricts photoinhibition when carboxylation is limiting at the expense of maximizing photosynthetic rates when light is limiting. Great uncertainty exists in the global exchange of carbon between the atmosphere and the terrestrial biosphere. To reduce this uncertainty we analysed data collected in the literature from across the globe on the maximum rate of carboxylation (Vcmax) and the maximum rate of electron transport (Jmax) in relation to plant nutrient status indicated by the traits: leaf nitrogen (N), leaf phosphorus (P), and specific leaf area (SLA). Vcmax was strongly related to leaf N and increasing leaf P substantially increased the sensitivity of Vcmax to leaf N and in a model of photosynthesis we showed that at high leaf N (3 gm−2) increasing leaf P from 0.05 to 0.22 gm−2 nearly doubled assimilation rates. Finally we show that plants may employ a conservative strategy of Jmax to Vcmax co‐ordination that restricts photoinhibition when carboxylation is limiting at the expense of maximising photosynthetic rates when light is limiting.

Eutrophication and climate change are two of the most pressing environmental issues affecting up to 50% of aquatic ecosystems worldwide. Mitigation strategies to reduce the impact of environmental change are complicated by inherent difficulties of predicting the long-term impact of multiple stressors on natural populations. Here, we investigated the impact of temperature, food levels and carbamate insecticides, in isolation and in combination, on current and historical populations of the freshwater grazer Daphnia . We used common garden and competition experiments on historical and modern populations of D. magna ‘resurrected’ from a lake with known history of anthropogenic eutrophication and documented increase in ambient temperature over time. We found that these populations response dramatically differed between single and multiple stressors. Whereas warming alone induced similar responses among populations, warming combined with insecticides or food limitation resulted in significantly lower fitness in the population historically exposed to pesticides. These results suggest that the negative effect of historical pesticide exposure is magnified in the presence of warming, supporting the hypothesis of synergism between chemical pollution and other stressors.

Microbial experimental evolution allows studying evolutionary dynamics in action and testing theory predictions in the lab. Experimental evolution in chemostats (i.e. continuous flow through cultures) has recently gained increased interest as it allows tighter control of selective pressures compared to static batch cultures, with a growing number of efforts to develop systems that are easier and cheaper to construct. This protocol describes the design and construction of a multiplexed chemostat array (dubbed “mesostats”) designed for cultivation of algae in 16 concurrent populations, specifically intended for studying adaptation to herbicides. We also present control data from several experiments run on the system to show replicability, data illustrating the effects of common issues like leaks, contamination and clumps, and outline possible modifications and adaptations of the system for future research.

Mass extinctions are considered to be quintessential examples of Court Jester drivers of macroevolution, whereby abiotic pressures drive a suite of extinctions leading to huge ecosystem changes across geological timescales. Most research on mass extinctions ignores species interactions and community structure, limiting inference about which and why species go extinct, and how Red Queen processes that link speciation to extinction rates affect the subsequent recovery of biodiversity, structure and function. Here, we apply network reconstruction, secondary extinction modelling and community structure analysis to the Early Toarcian (Lower Jurassic; 183 Ma) Extinction Event and recovery. We find that primary extinctions targeted towards infaunal guilds, which caused secondary extinction cascades to higher trophic levels, reproduce the empirical post-extinction community most accurately. We find that the extinction event caused a switch from a diverse community with high levels of functional redundancy to a less diverse, more densely connected community of generalists. Recovery was characterised by a return to pre-extinction levels of some elements of community structure and function prior to the recovery of biodiversity. Full ecosystem recovery took ~7 million years at which point we see evidence of dramatically increased vertical structure linked to the Mesozoic Marine Revolution and modern marine ecosystem structure. Mass extinctions have repeatedly restructured communities through geological time, but biotic interactions are rarely considered in investigations of extinction dynamics and ecosystem recovery. Here the authors present evidence that secondary extinction cascades were important during a Jurassic hyperthermal extinction event and that it took over 7 million years for community structure to fully recover.

In Tigray, northern Ethiopia, there is a long tradition of peaceful coexistence between spotted hyenas (Crocuta crocuta) and humans. While historically the coexistence has been relatively stable, we assessed the impact of the recent war in Tigray on this coexistence. We investigated the effects of war on the scavenging and hunting behavior of spotted hyenas, and the consequences for local people in Tigray. We compared current spotted hyena foraging at six battle sites with six control sites across Tigray using diet analysis, hyena abundance through playback experiments, and assessed human−wildlife interactions via semistructured interviews in 1200 households. Spotted hyena diets at both site types consisted exclusively of domestically derived prey; however, the composition of prey species differed significantly (χ2 = 64.03, df = 6, p = 0.001). Human hair was prevalent in hyena scats from battle sites but was absent in scats collected from the control sites. In total, 318 hyenas responded to 48 call stations, response rates were significantly higher at battle sites (x¯ $$ \\overline{x} $$  = 36.7 ± 9.7 SD) than at control sites (x¯ $$ \\overline{x} $$  = 16.3 ± 14.6 SD). There were several lines of evidence that human−wildlife interactions were more negative. Reported livestock predation was 18.85% higher at battle sites, with 78.5% of depredation events occurring during the war, compared to 6% pre‐war and 15.5% post‐war. We conclude that changes in hyena feeding behavior during the war and siege period can be linked to changes in the availability of scavengable food sources. These results yield insight not only into the consequences of war for the people of Tigray but also into how the many armed conflicts in regions with large scavenger/carnivore populations may have long‐lasting impacts on human−wildlife conflict around the globe. Spotted hyena diet and habitat shifts are driven by war and conflict in Ethiopia, changes specifically linked to the availability of human casualties of war. We found that the spotted hyena scats contained primarily domestic livestock at both the battle and control sites. Human hair was prevalent in hyena scats from battle sites but was absent in scats collected from the control sites.

Species interactions play a crucial role in shaping biodiversity, species coexistence, population dynamics, community stability and ecosystem functioning. Our understanding of the role of the diversity of species interactions driving these species, community and ecosystem features is limited because current approaches often focus only on trophic interactions. This is why a new modelling framework that includes a greater diversity of interactions between species is crucially needed. We developed a modular, user‐friendly, and extensible Julia package that delivers the core functionality of the bio‐energetic food web model. Moreover, it embeds several ecological interaction types alongside the capacity to manipulate external drivers of ecological dynamics. These new features represent important processes known to influence biodiversity, coexistence, functioning and stability in natural communities. Specifically, they include: (a) an explicit multiple nutrient intake model for producers, (b) competition among producers, (c) temperature dependence implemented via the Boltzmann‐Arhennius rule, and (d) the ability to model several non‐trophic interactions including competition for space, plant facilitation, predator interference and refuge provisioning. The inclusion of the various features provides users with the ability to ask questions about multiple simultaneous processes and stressor impacts, and thus develop theory relevant to real world scenarios facing complex ecological communities in the Anthropocene. It will allow researchers to quantify the relative importance of different mechanisms to stability and functioning of complex communities. The package was build for theoreticians seeking to explore the effects of different types of species interactions on the dynamics of complex ecological communities, but also for empiricists seeking to confront their empirical findings with theoretical expectations. The package provides a straightforward framework to model explicitly complex ecological communities or provide tools to generate those communities from few parameters.

Food webs, the networks of feeding links between species, are central to our understanding of ecosystem structure, stability, and function. One of the key aspects of food web structure is complexity, or connectance, the number of links expressed as a proportion of the total possible number of links. Connectance (complexity) is linked to the stability of webs and is a key parameter in recent models of other aspects of web structure. However, there is still no fundamental biological explanation for connectance in food webs. Here, we propose that constraints on diet breadth, driven by optimal foraging, provide such an explanation. We show that a simple diet breadth model predicts highly constrained values of connectance as an emergent consequence of individual foraging behavior. When combined with features of real food web data, such as taxonomic and trophic aggregation and cumulative sampling of diets, the model predicts well the levels of connectance and scaling of connectance with species richness, seen in real food webs. This result is a previously undescribed synthesis of foraging theory and food web theory, in which network properties emerge from the behavior of individuals and, as such, provides a mechanistic explanation of connectance currently lacking in food web models.

Harnessing science‐based policy is key to addressing global challenges like the biodiversity and climate crises. Open research principles underpin effective science‐based policy, but the uptake of these principles is likely constrained by the politicisation, commoditisation and conflicting motives of stakeholders in the research landscape. Here, using the mission and vision statements from 129 stakeholders from across the research landscape, we explore alignment in open research principles between stakeholders. We find poor alignment between stakeholders, largely focussed around journals, societies and funders, all of which have low open research language‐use. We argue that this poor alignment stifles knowledge flow within the research landscape, ultimately limiting the mobilisation of impactful science‐based policy. We offer recommendations on how the research landscape could embrace open research principles to accelerate societies' ability to solve global challenges. Open research principles underpin the effective science‐based policy key to tackling global challenges; however, the uptake of these principles is likely constrained by the politicisation, commoditisation and conflicting motives of stakeholders in the research landscape. Here, using the mission and vision statements from 129 stakeholders from across the research landscape, we explore alignment in open research principles. We find that poor alignment between different stakeholders stifles knowledge flow within the research landscape, ultimately limiting the mobilisation of impactful science‐based policy.