The substantial value of modern antibacterial agents is eroded by the inexorable development of antimicrobial resistance (AMR). The discovery and development of antibiotics are central aspects of addressing AMR. Since new drug-resistant mechanisms are continually arising, ways to streamline and accelerate the development of new agents are required. An understanding of dose-exposure-response (D-E-R) relationships (also pharmacokinetic-pharmacodynamic (PK-PD)) provides a means to establish causality, i.e. demonstrating that the new antibiotic acts in a predictable way and ensuring that understanding can be harnessed for therapeutic benefit. D-E-R potentially enables the adequacy of proposed regimens for effectiveness trials to be justified, minimization or replacement of dose-finding studies, selection of regimens in special populations and selection of regimens that minimize the emergence of resistance. Here, we consider the advantages of combining empirical approaches characteristic of modern PK-PD with a mechanistic understanding of drug effect and the emergence of resistance. Conceiving the approach to new dose/schedule selection in this way provides the best chance of designing regimens that are safe and effective, and that result in resistance counterselection. In terms of the latter, regimen intensification, appropriate sequencing of antibiotics and antimicrobial combinations are relevant. This article is part of the Theo Murphy meeting issue 'Evaluating anti-infective drugs'.
Diversity in the ontogeny of physiological systems is a central, too often overlooked tenet of biodiversity. Here, we use intensive screening of the development of heart function in embryos of the gastropod Radix balthica to investigate (i) variability in the physiological development of this system; (ii) how variability is associated with the hierarchical levels of population, egg mass and individual; and (iii) whether such variability links to hatch size. Despite considerable between-individual variability in heart function, a biphasic model was effective in modelling how heart activity changed through time. Heart rate variability analysis revealed marked reduced beat-to-beat variability in the period spanning the second slope of the biphasic pattern. The total number of heartbeats during development was positively correlated with hatch time, suggesting no detectable energetic trade-off between growth and heart function. Variability in the timing of first heart function was greatest at the egg mass level, whereas variation in the timing of the break in the biphasic pattern was greatest within egg masses at the individual level, with the least variability in both traits explained at the level of population, indicating that such physiological diversity is an intrinsic property apparent at every level of biological organization. This article is part of the theme issue 'Embracing variability in comparative physiology: why it matters and what to do with it'.
Treatment of Mycobacterium tuberculosis is uniquely prolonged and complex among bacterial infections due to its unusual propensity for persistence during drug stress. Persisters are subpopulations of organisms tolerant to bactericidal antibiotics and characterized by a slower rate of elimination in the absence of genetic changes associated with resistance. The biological basis of this response is increasingly well understood and novel translational tools have become available that are capable of identifying and characterizing such organisms in vitro and in vivo. Recent in vivo and clinical observations have reaffirmed the existence of multiple subpopulations of organisms during treatment of tuberculosis (TB) but operationalizing this concept in pharmacodynamic modelling and clinical trials has been hampered by the availability of culture-based biomarkers alone. A phenomenological framework, which makes explicit use of the information from new tools, would assist with comparisons between preclinical and clinical data and may be able to support models that quantify the likely size of the pool of persister organisms from which relapses arise, facilitating more accurate predictions of the duration of therapy. Such an approach has the potential for significant translational impact in the development of new treatment regimens for TB. This article is part of the Theo Murphy meeting issue 'Evaluating anti-infective drugs'.
What is the science and practice of collective intelligence at the level of whole systems and at a global scale? How have attempts to organize intelligence at these scales evolved, and how might they evolve in the future? Recent research has attempted to find universal patterns in the organization of intelligence at multiple scales, from atoms and cells to birds and other animals and whole societies. This work offers insights for the design of intelligence at global scales that can support governance, whether for pandemics or climate change, and that can integrate data, models, algorithms, evidence, tacit knowledge, foresight and innovation. This opinion piece argues for analysing common features of intelligence at multiple scales; it describes some important examples of 'intelligence assemblies' in technologies, cities, professions and global initiatives; and it advocates drawing on this framework for understanding intelligence at multiple scales to accelerate both research and design for large-scale intelligence. Questions of macro-cognition design are arguably as important as micro-cognition in terms of potential social impact but they have been less comprehensively researched, partly because they cut across so many disciplinary boundaries. However, a better understanding of these phenomena may be vital for tackling the big global challenges of the twenty-first century and for humanity's future evolution. This article is part of the theme issue 'The evolution of collective intelligence'.
The link between longevity and mitochondrial function has been documented; therefore, we suspect that the evolution of mitochondrial DNA (mtDNA) is linked to the evolution of longevity. We selected 128 fish species with a wide range of longevity and inhabiting habitats with differing temperatures and examined their association with dN/dS ratios of mtDNA genes. Our findings (i) rule out environmental temperature as a primary driver of longevity, (ii) confirm the negative relationship between synonymous substitution rate and longevity for four of the mitochondrial protein coding genes, (iii) reveal a correlation of the fish body length at maturity with the dN/dS ratio for ATP6, ND1 and ND4, and (iv) highlight for the first time to our knowledge, a link between high conservation of the three cytochrome c oxidase (COX) genes and adaptation to temperatures in fishes. By extending conclusions drawn from mtDNA to individual genes, our study opens new avenues for exploring the ageing process. Moreover, the specific link between the evolution of COX genes and habitat temperature confirms the importance of complex IV in temperature adaptation. Our findings also suggest a link between dN/dS in complex I genes and longevity, highlighting the need to examine the functional association between their encoded peptides and lifespan. This article is part of the theme issue 'Evolutionary genetics of mitochondria: on diverse and common evolutionary constraints across eukarya'.
Chemical, biological, radiological and nuclear (CBRN) agents can pose a significant risk to public health. Concerningly, for many of the CBRN threats there are no treatment options available. Conducting pivotal randomized controlled trials (RCTs) usually required for regulatory approval of medicinal products may not be feasible for medical countermeasures (MCM) intended for the treatment of CBRN threats because of the low prevalence and case numbers and ethical concerns on conducting RCTs, considering the potential serious health outcomes associated with CBRN threats. This is concerning, as it hampers the development and availability of new treatments against CBRN threats, which are needed for preparedness to ensure appropriate response to an outbreak. This review outlines alternative, regulatory flexible approaches that were used for the approval under exceptional circumstances of therapeutic MCMs against biological threats in the European Union. Considerations on the requirements of using animal efficacy data as key evidence for inferring efficacy from animals to humans, on using animal pharmacokinetic/pharmacodynamic data including pharmacometric modelling and simulation approaches to predict the human dose and on generating safety data in healthy humans are discussed. Challenges and advantages of this approach are highlighted, including the lessons learned based on the examples of tecovirimat, zanamivir and obiltoxaximab. This article is part of the Theo Murphy meeting issue 'Evaluating anti-infective drugs'.
Human mitochondrial DNA (mtDNA) contains 13 protein-coding subunits of the oxidative phosphorylation pathway, 22 tRNA and two rRNA genes. However, accumulating evidence suggests that mtDNA encodes additional overlapping genetic elements, including mitochondrial-derived peptides (MDPs) and alternative reading frames. Here, we assessed signatures of selection across 66 328 human mtDNAs and studied the potential impact of disease-causing mutation within these mtDNA overlapping sequences. By employing frame-specific dN/dS analysis for the overlapping reading frames, and codon position-specific diversity calculations we found that SHLP6 and SHLP3 (within 16S rRNA) display significant signatures of purifying selection. Mutational asymmetry analysis revealed purifying selection in both frames and strands of GAU/COX1, while other alternative reading frames show asymmetric patterns, supporting negative selection primarily on the encompassing canonical gene. Analysis of mito-ribosome profiling (HEK293 cells) revealed translation initiation signatures only for SHLP6 and ALTND4, providing functional support for their translation in HEK293 cells. Analysis of disease-causing mutations revealed that several such mutations have predicted deleterious effects on both canonical and alternative sequences, though canonical genes tend to be more frequently affected. Taken together, we provide evolutionary and functional evidence supporting biological relevance of certain MDPs and underline the need to re-evaluate the functionality of mutations in such sequences. This article is part of the theme issue 'Evolutionary genetics of mitochondria: on diverse and common evolutionary constraints across eukarya'.
Humans stand alone in terms of their potential to collectively and cumulatively change their culture in an open-ended manner. This open-endedness provides societies with the ability to continually expand their resources and to increase their capacity to store, transmit and process information at a collective level. Here, we propose that the production of resources arises from the interaction between cultural systems (a society's repertoire of interdependent techniques, artefacts, norms and knowledge) and search spaces (an ensemble of needs, problems and goals facing a society). Starting from this premise, we develop a macro-level model wherein both cultural systems and search spaces are subject to evolutionary dynamics. By manipulating the extent to which these dynamics are characterized by stochastic or selection-like processes, we demonstrate that open-ended growth is extremely rare, historically contingent and only possible when cultural systems and search spaces co-evolve. Here, stochastic factors must be strong enough to continually perturb the dynamics into a far-from-equilibrium state, whereas selection-like factors help maintain effectiveness and ensure the sustained production of resources. Only when this co-evolutionary dynamic maintains effective cultural systems, supports the ongoing expansion of the search space and leads to an increased provision of resources do we observe open-ended cultural evolution. This article is part of the theme issue 'The evolution of collective intelligence'.
The evolution of sexes is closely tied to uniparental inheritance (UPI) of mitochondrial DNA (mtDNA), where only females transmit mtDNA. Unlike nuclear DNA, mtDNA is highly polyploid and never evolved to be part of meiotic sex. Modelling shows that UPI increases mtDNA mutational variance, enhancing selection for high-quality mtDNA and promoting the emergence of sexes from mating types in unicellular eukaryotes. Paternal control of mitochondrial transfer favours some degree of mtDNA leakage, whereas maternal control favours strict UPI, leading to sexual conflict driving turnover in transmission mechanisms. In multicellular organisms, mitotic segregation of mtDNA increases variance in gametes, again facilitating selection. Surprisingly, germline evolution seems to reflect mtDNA mutation rates: plants and sessile metazoans have low rates and produce gametes from somatic cells, while bilaterians and ctenophores with higher rates sequester germlines with restricted cell division. High mtDNA ploidy in oocytes allows early embryonic cell division without replication, reducing mutational variance across tissues and enhancing somatic fitness. Germline mtDNA quality is maintained by mitotic over-proliferation of germ cells and the selective transfer of mtDNA into primordial oocytes linked with massive apoptotic germ-cell atresia. Overall, selection for mtDNA quality elucidates the evolution of sexes and the architecture of the female germline. This article is part of the theme issue 'Evolutionary genetics of mitochondria: on diverse and common evolutionary constraints across eukarya'.
The intensity and frequency of warm events are projected to increase with climate warming, imposing significant challenges for ectothermic species. Daily maximum temperature, or Tmax, in salmonid habitats is exceeding the purported upper temperature limits for these species. Recovery from thermal challenges has been thought to be facilitated by cool daily thermal minima (Tmin), with Tmin above 20°C currently triggering the closure of some recreational fisheries. Here, we sought to investigate the relatively poorly understood effect of Tmax on salmonid metabolic rate and recovery. To this end, we acclimated Brook char (Salvelinus fontinalis) to an ecologically relevant diel thermal cycle with Tmin fixed at 19°C and Tmax set to 24°C for a minimum of one month. We then monitored oxygen consumption rate over 4 days throughout the diel thermal cycle. On the 5th day, Tmax was either 24, 26 or 27 °C, and we continued to monitor oxygen consumption during an 18-h recovery period. After exposure to a Tmax of 26 or 27°C and recovery at 19°C, oxygen consumption rate did not recover to resting levels. Tmax appears to have the potential to adversely affect aerobic metabolism and thus is worth considering in the management of salmonid recreational fisheries. This article is part of the theme issue 'Embracing variability in comparative physiology: why it matters and what to do with it'.
In the SARS-CoV-2 Omicron-variant era, the efficacy of vaccination in preventing viral replication is poorly understood and is further complicated by heterogeneous and hybrid immunity in the population. Here, we analysed by mathematical models the kinetics of both viral load and antibodies in non-human primates with different exposure histories, conferred by infection or vaccination with mono- or bi-valent vaccines. The model describes the control of viral replication by antibodies that accelerate the clearance and reduce the infectivity of viral particles, and suggests that a previous infection leads to a faster elimination of infected cells, which is not mediated by antibodies. Finally, we used the model to simulate natural infections and show that binding, neutralization and exposure history all need to be taken into account to predict risks of infection and transmission. Protection from infection could be reached at binding levels of 3 × 104 AU ml-1 for individuals who received both monovalent and bivalent vaccinations, whereas hybrid immunity (infection followed by bivalent vaccination) could provide complete protection irrespective of antibody levels. These findings highlight the importance of exposure history in shaping immune responses and suggest correlates of protection for future vaccine and monoclonal antibodies strategies. This article is part of the Theo Murphy meeting issue 'Evaluating anti-infective drugs'.
Mitochondrial alternative open reading frames (ORFs) substantially broaden the functional scope traditionally attributed to mitochondrial DNA, encoding peptides and proteins that participate in diverse cellular processes. These newly identified ORFs are embedded within annotated sequences, both coding and non-coding, and reveal layers of overlapping genetic information. We report the discovery of MTALTCO1, a 259 amino-acid protein, the longest mitochondrial alternative protein identified to date, encoded by an ORF located within the human cytochrome oxidase 1 gene, in the +3 reading frame. We confirm the expression and mitochondrial origin of MTALTCO1 through multiple independent lines of evidence, including a custom-designed antibody, mass spectrometry-derived peptides, sequence analysis and inhibitors of mitochondrial expression. Despite encoding AGR codons as arginine, contrary to the prevailing view that these function invariably as stop codons in the vertebrate mitochondrial genetic code, MTALTCO1 shows strong evidence of mitochondrial translation, challenging established models of mitochondrial codon usage and gene expression. Co-immunoprecipitations and pulldown assays delineate MTALTCO1's interaction landscape across major cellular pathways. Finally, we present the first in-depth analysis of conservation for a mitochondrial alternative ORF overlapping a reference protein-coding gene and discuss the results in light of MTALTCO1's suggested role in protein scaffolding. This article is part of the theme issue 'Evolutionary genetics of mitochondria: on diverse and common evolutionary constraints across eukarya'.
Daily temperature fluctuations are a ubiquitous feature of natural environments, yet our understanding of how ectotherms respond to thermal variability remains incomplete. Previous frameworks have predicted that exposure to variable thermal conditions should reduce the temperature sensitivity of physiological rates, thereby enabling ectotherms to maintain stable functions in fluctuating environments. We conducted a comprehensive meta-analysis to test this hypothesis by synthesizing evidence from 26 studies examining the effects of daily temperature variation on ectotherm physiological rates. Our analysis included data on key physiological rates for broad groups of ectotherms. Contrary to expectations, our analysis reveals that daily temperature variability does not systematically reduce the thermal sensitivity of physiological rates in ectotherms. We found some taxonomic differences in thermal sensitivity, with reptiles and fish showing greater sensitivity to temperature variation, potentially exposing these groups to higher vulnerability under fluctuating temperatures. A lack of plasticity in thermal sensitivity suggests either limited capacity or limited need for plastic responses to predictable daily temperature variations. Ectotherms may rely on alternative mechanisms to cope with variable temperatures, including behavioural thermoregulation and acute physiological responses. Our findings challenge current paradigms in thermal biology and highlight potential vulnerabilities of ectotherms to increasing temperature fluctuations under climate change. This article is part of the theme issue 'Embracing variability in comparative physiology: why it matters and what to do with it'.
Sexual reproduction is a widely spread feature of eukaryotes and was already present in the last eukaryotic common ancestor. While most extant eukaryotes inherit mitochondria from a single parent, the mechanisms enforcing uniparental inheritance vary widely. The first eukaryotes likely would not have evolved such mechanisms yet, so cellular fusion would have led to mitochondrial mixing (biparental inheritance). Here, we explore the evolutionary consequences of biparental inheritance of endosymbionts during host-symbiont coevolution using a multi-level, individual-based model of endosymbiosis. Our results show that biparental inheritance introduces evolutionary conflict, as it facilitates the spread of fast-replicating symbionts, which can drive host populations to extinction. However, in a diverse environment, proto-eukaryotes diversify and adapt to distinct niches, protecting the population from total collapse caused by selfish symbionts. Moreover, this conflict can be resolved through the evolution of signalling mechanisms that allow hosts to regulate symbiont cell cycles. In many cases, sexually reproducing populations not only survive but also outperform their asexual counterparts. We conclude that sexual reproduction could have appeared early during eukaryogenesis and may have facilitated the evolution of host control over the endosymbiont cell cycle. This article is part of the theme issue 'Evolutionary genetics of mitochondria: on diverse and common evolutionary constraints across eukarya'.
Quantifying therapeutic responses in clinical malaria is easier than for most other infections as the intraerythrocytic parasites can be counted by microscopy or estimated using quantitative PCR. In treating the blood-stage of malaria, between 107 and 1013 parasites undergo a first-order decline in densities at a rate determined by the concentrations and potency of the antimalarial drug. A simple conceptual framework based on total intravascular parasite biomass and standard sigmoid concentration-effect relationships for parasite killing explains most, but not all, aspects of antimalarial therapeutic responses, and it has proved very useful in designing chemoprevention and treatment regimens and in understanding the selection and spread of resistance. Drugs acting on younger circulating ring-stage asexual parasites (artemisinins, cipargamin, ganaplacide) provide rapid parasite clearance, which translates into faster clinical recoveries and a life-saving benefit in severe malaria. Artemisinin-sensitive Plasmodium falciparum densities decline with a half-life (PC1/2) of usually less than 5 h. Many antimalarial drugs are eliminated slowly and provide protracted exposures, which allows full treatment to be administered in 3 days, and also provides chemosuppression of newly acquired infections for 1 month. Greater availability of drug measurement in malaria-endemic areas would facilitate the field assessment of antimalarial drugs. This article is part of the Theo Murphy meeting issue 'Evaluating anti-infective drugs'.
Body size is a key trait that influences ecological processes such as metabolism, abundance and species interactions. While the metabolic theory of ecology (MTE) proposes a universal scaling of metabolic rate with body mass, recent evidence shows that this relationship is not fixed. Environmental factors like temperature and predation can alter the metabolic scaling exponent, potentially reshaping size distributions. However, most research has examined these patterns within individual species, leaving open questions about how environmental drivers affect scaling at the community level. To address this, we performed a mesocosm experiment manipulating both temperature and fish predator presence in freshwater macroinvertebrate communities. We found that warming altered metabolic rates in a predation-dependent way: without fish, metabolic rates increased in large individuals but decreased in small individuals, whereas the opposite occurred with fish present. This suggests that larger individuals reduce their baseline metabolic rates under predation risk, especially at higher temperatures. Interestingly, the slope of the community size distribution remained stable across treatments, indicating that shifts in metabolic scaling occurred independently of changes in size structure. Together, these findings highlight the environmental sensitivity of metabolic scaling and suggest that links between metabolism scaling and size distributions may be more complex than MTE predicts. This article is part of the theme issue 'Embracing variability in comparative physiology: why it matters and what to do with it'.
Conventional ecological and conservation approaches often rely on average-based strategies, which obscure the complexity of biological systems. This article revisits the concept of the 'Tyranny of the Golden Mean' to argue that variability and plasticity are not sources of disorder, but essential components of ecological robustness, particularly in the Amazon. The Amazon's extraordinary heterogeneity shapes physiological, biochemical and genetic diversity. At genetic, biochemical and physiological levels, Amazonian aquatic species exhibit resilience, enabled by traits like low oxygen tolerance, metabolic flexibility and microanatomical adaptations. Examples span to amphibians, reptiles, aquatic insects and floodplain trees, illustrating that such adaptive strategies are widespread across taxa. These responses are context-specific and often missed by average values. As environmental changes intensify, conservation strategies based on means become insufficient. Recognizing variability is essential, as it underpins resilience to rapid environmental changes. We advocate for adaptive management, in which biological variability is recognized as a source of strength rather than noise. This approach enables the identification of critical thresholds and tipping points, enhancing the capacity to anticipate and respond to disruption. Ultimately, embracing variability improves conservation effectiveness and aligns with the evolutionary and ecological realities of the Amazon. This article is part of the theme issue 'Embracing variability in comparative physiology: why it matters and what to do with it'.
The origin of eukaryotic cells remains a highly contested problem. While eukaryotes arose from the merger of a bacterial and an archaeal partner giving rise to mitochondria and the cell proper, the order of steps is not known, nor is it understood why it was a singular event. Prokaryotes engage in various cooperative interactions everywhere, yet there is no evidence that they could establish stable endosymbiotic relationships on their own. Many assume that mitochondria came first, and their critical presence and features enabled the complex cellular architecture, including the nucleus. Here we find support for the alternative, claiming that a nuclear compartment was a prerequisite for successful stable endosymbiosis. We review independent lines of evidence suggesting that the pre-existence of a nuclear membrane or equivalent mechanism to separate translation from transcription may have been essential to limit genetic inference owing to extensive horizontal gene transfer in the wake of pre-mitochondrial (endo)symbionts and to stabilize the host genome against foreign DNA, especially from (endo)symbiotic partners. We claim that an asymmetry in control potential between partners is required for successful integration of an endosymbiont. This would explain why there are no further prokaryotic endosymbioses known to us (extant or extinct). We propose predictions that can be tested to support the hypothesis. This article is part of the theme issue 'Evolutionary genetics of mitochondria: on diverse and common evolutionary constraints across eukarya'.
Mismatches between interacting mitochondrial and nuclear gene products in hybrids have been proposed to disproportionately contribute to early species boundaries. Under this model, genetic incompatibilities emerge when mitochondrial haplotypes are in a cellular context without their coevolved nuclear-encoded mitochondrial (n-mt) proteins. Some case studies have shown that such disruptions in mitonuclear coevolution can contribute to reproductive isolation, but whether mitonuclear incompatibilities generate selection that impacts multiple n-mt loci and/or causes broad, genome-wide contributions to speciation is unclear. Here, we leverage a system with several hybridizing species pairs (Xiphophorus fishes) that have known mitonuclear incompatibilities of large effect. We divided nuclear-encoded genes into three classes based on level of interaction with mitochondrial gene products. We found only inconsistent statistical support for a difference between these classes in the degree of positive covariation in mitonuclear ancestry. We discuss evidence that these analyses are sensitive to the amount of non-synonymous divergence between parent species in interacting n-mt genes or the age of the hybridization event. Overall, our results imply that genome-wide scans focused on enrichment of broad functional gene classes may often be insufficient for detecting a history of mitonuclear coevolution, even when strong selection is acting on mitonuclear incompatibilities at multiple loci. This article is part of the theme issue 'Evolutionary genetics of mitochondria: on diverse and common evolutionary constraints across eukarya'.
Analyses of vertebrate locomotion have frequently revealed variations in locomotor energetics and movement both among individuals and through time within an individual. This variation is often collapsed into mean values for broad comparative analyses of function. However, kinematic patterns of locomotion, even when animals move at a near-constant mean speed, frequently vary with both the physical and biological context. Here, we demonstrate, using analyses of fish locomotion and energetics, how variation among individuals in kinematic gaits can manifest as changes in dynamics of metabolic rate (estimated from oxygen uptake). We present kinematic data from a small school of giant danio (Devario aequipinnatus) to show that fishes within a school frequently modulate their kinematics and change position, even when the school moves at an overall constant mean speed. We show that rainbow trout (Oncorhynchus mykiss), swimming over a range of speeds, exhibit considerable variation in tail beat frequency and metabolic rate among speeds. By experimentally altering the fluid dynamic environment, we demonstrate that brook trout (Salvelinus fontinalis) show correlated modulation of both kinematics and metabolic rate. Simultaneous measurement of energetic and biomechanical characteristics can unveil the physiological, biomechanical and fluid dynamic mechanisms that underlie dynamic changes in vertebrate locomotor gaits. This article is part of the theme issue 'Embracing variability in comparative physiology: why it matters and what to do with it'.