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Scientists have grappled with reconciling biological evolution 1 , 2 with the immutable laws of the Universe defined by physics. These laws underpin life’s origin, evolution and the development of human culture and technology, yet they do not predict the emergence of these phenomena. Evolutionary theory explains why some things exist and others do not through the lens of selection. To comprehend how diverse, open-ended forms can emerge from physics without an inherent design blueprint, a new approach to understanding and quantifying selection is necessary 3 – 5 . We present assembly theory (AT) as a framework that does not alter the laws of physics, but redefines the concept of an ‘object’ on which these laws act. AT conceptualizes objects not as point particles, but as entities defined by their possible formation histories. This allows objects to show evidence of selection, within well-defined boundaries of individuals or selected units. We introduce a measure called assembly ( A ), capturing the degree of causation required to produce a given ensemble of objects. This approach enables us to incorporate novelty generation and selection into the physics of complex objects. It explains how these objects can be characterized through a forward dynamical process considering their assembly. By reimagining the concept of matter within assembly spaces, AT provides a powerful interface between physics and biology. It discloses a new aspect of physics emerging at the chemical scale, whereby history and causal contingency influence what exists. Assembly theory conceptualizes objects as entities defined by their possible formation histories, allowing a unified language for describing selection, evolution and the generation of novelty.

Strategic interactions arise in all domains of life. This form of competition often plays out in dynamically changing environments. The strategies employed in a population may alter the state of the environment, which may in turn feedback to change the incentive structure of strategic interactions. Feedbacks between strategies and the environment are common in social-ecological systems, evolutionary-ecological systems, and even psychological-economic systems. Here we develop a framework of ‘eco-evolutionary game theory’ that enables the study of strategic and environmental dynamics with feedbacks. We consider environments governed either by intrinsic growth, decay, or tipping points. We show how the joint dynamics of strategies and the environment depend on the incentives for individuals to lead or follow behavioral changes, and on the relative speed of environmental versus strategic change. Our analysis unites dynamical phenomena that occur in settings as diverse as human decision-making, plant nutrient acquisition, and resource harvesting. We discuss implications in fields ranging from ecology to economics. Strategic game payoffs often depend on the state of the environment, which in turn can be influenced by game strategies. Here, Tilman et al. develop a general framework for modeling strategic games with environmental feedbacks and analyze case studies from decision-making, ecology, and economics.

Communities that are very rich in species could persist thanks to the stabilizing role of higher-order interactions, in which the presence of a species influences the interaction between other species. High order interactions maintain species diversity How the tremendous biodiversity observed in nature is maintained is a central question in ecology. Simple models of interacting competitors fail to reproduce the stable persistence of very large ecological communities, while neutral models in which species do not interact and diversity is maintained by immigration and speciation yield unrealistically small fluctuations in population abundance. Using competitive network models, Stefano Allesina and colleagues show that higher order interactions, whereby the presence of one species influences the interaction between other species, allow highly diverse communities to persist in closed systems with a fixed number and identity of species and in more realistic open systems, which gain new species through immigration and speciation. Ecologists have long sought a way to explain how the remarkable biodiversity observed in nature is maintained. On the one hand, simple models of interacting competitors cannot produce the stable persistence of very large ecological communities 1 , 2 , 3 , 4 , 5 . On the other hand, neutral models 6 , 7 , 8 , 9 , in which species do not interact and diversity is maintained by immigration and speciation, yield unrealistically small fluctuations in population abundance 10 , and a strong positive correlation between a species’ abundance and its age 11 , contrary to empirical evidence. Models allowing for the robust persistence of large communities of interacting competitors are lacking. Here we show that very diverse communities could persist thanks to the stabilizing role of higher-order interactions 12 , 13 , in which the presence of a species influences the interaction between other species. Although higher-order interactions have been studied for decades 14 , 15 , 16 , their role in shaping ecological communities is still unclear 5 . The inclusion of higher-order interactions in competitive network models stabilizes dynamics, making species coexistence robust to the perturbation of both population abundance and parameter values. We show that higher-order interactions have strong effects in models of closed ecological communities, as well as of open communities in which new species are constantly introduced. In our framework, higher-order interactions are completely defined by pairwise interactions, facilitating empirical parameterization and validation of our models.

The authors derive a condition for how natural selection chooses between two competing strategies on any graph for weak selection, elucidating which population structures promote certain behaviours, such as cooperation. Evolution, the great game Evolution is a game that anyone can play. The traits that evolve in a population depend on how the players interact. Students are familiar with toy populations in which every member of the population can interact equally with any other, but as W. S. Gilbert wrote, “When everyone is somebody, then no one's anybody”. In the real world, the numbers and identities of the players can change, and realistic simulations of evolution have proven exceedingly hard to create. Recent models have worked only in special cases in which all individuals have the same number of neighbours. Benjamin Allen and colleagues have now devised a model that works for any number of neighbours, providing that natural selection is weak. They simulate how small changes in population structure can affect evolutionary outcomes, and that cooperation flourishes most in populations with strong ties between pairs of individuals. Evolution occurs in populations of reproducing individuals. The structure of a population can affect which traits evolve 1 , 2 . Understanding evolutionary game dynamics in structured populations remains difficult. Mathematical results are known for special structures in which all individuals have the same number of neighbours 3 , 4 , 5 , 6 , 7 , 8 . The general case, in which the number of neighbours can vary, has remained open. For arbitrary selection intensity, the problem is in a computational complexity class that suggests there is no efficient algorithm 9 . Whether a simple solution for weak selection exists has remained unanswered. Here we provide a solution for weak selection that applies to any graph or network. Our method relies on calculating the coalescence times 10 , 11 of random walks 12 . We evaluate large numbers of diverse population structures for their propensity to favour cooperation. We study how small changes in population structure—graph surgery—affect evolutionary outcomes. We find that cooperation flourishes most in societies that are based on strong pairwise ties.

The Azores, Madeira, Selvagens, Canary Islands and Cabo Verde are commonly united under the term “Macaronesia”. This study investigates the coherency and validity of Macaronesia as a biogeographic unit using six marine groups with very different dispersal abilities: coastal fishes, echinoderms, gastropod molluscs, brachyuran decapod crustaceans, polychaete annelids, and macroalgae. We found no support for the current concept of Macaronesia as a coherent marine biogeographic unit. All marine groups studied suggest the exclusion of Cabo Verde from the remaining Macaronesian archipelagos and thus, Cabo Verde should be given the status of a biogeographic subprovince within the West African Transition province. We propose to redefine the Lusitanian biogeographical province, in which we include four ecoregions: the South European Atlantic Shelf, the Saharan Upwelling, the Azores, and a new ecoregion herein named Webbnesia, which comprises the archipelagos of Madeira, Selvagens and the Canary Islands.

Social dilemmas occur when incentives for individuals are misaligned with group interests 1 – 7 . According to the ‘tragedy of the commons’, these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9 – 15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16 – 19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment—either naturally occurring or designed—help to overcome social dilemmas. Cooperation is more likely to evolve in a public-goods-distribution game when payoffs can change between rounds so that the stakes increase when players cooperate and decrease when players defect.

Key Points The Archaea was recognized as a third domain of life 40 years ago. Molecular evidence soon suggested that the Eukarya represented a sister group to the Archaea or that eukaryotes descended from archaea. Culture-independent genomics has revealed the vast diversity existing among the Archaea, including the recently described Asgard superphylum. Phylogenomic analyses have placed the Asgard archaea as the closest prokaryotic relatives of eukaryotes. Comparative genomic analyses have reconstructed a complex last eukaryotic common ancestor. However, how and in which order these complex eukaryotic features evolved in an Asgard archaea-related ancestor remains largely unclear. Genomic investigation of Asgard archaea showed that they carry several genes formerly believed to be eukaryotic specific, illuminating early events during eukaryogenesis. Fully understanding the process of eukaryogenesis requires finding answers to several challenging and intertwined questions. Although we have seemingly answered some of these questions, others remain fiercely debated, and new questions continue to arise. The Archaea was recognized as a third domain of life 40 years ago. In this Review, Eme et al . outline a brief history of the changing shape of the tree of life and examine how the recent discovery of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of the eukaryotic cell. Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor.

In human societies, individuals who violate social norms may be punished by third-party observers who have not been harmed by the violator; this study suggests that a reason why the observers are willing to punish is to be seen as more trustworthy by the community. Punishing schedule denotes trustworthiness Human societies appear to be unique in that individuals may be punished for violating social norms — even if the violator has not harmed the punisher and the punishment exerts a cost. Explaining the reasons why this behaviour has evolved has been problematic. These authors offer a model showing that 'third-party punishment' can be an honest signal of trustworthiness. Those who incur a cost by punishing wrongdoers are seen as trustworthy by the community, and behave in a more trustworthy way. But there's a catch: this signal becomes weaker when a more informative signalling mechanism is introduced. That is, when potential punishers have the chance to engage in costly helping, they are less likely to punish, and punishment is perceived as a weaker sign of trustworthiness. Either way, the costs of punishment may be recouped by the long-term reputational benefit of appearing to be trustworthy. Third-party punishment (TPP) 1 , 2 , 3 , 4 , 5 , 6 , 7 , in which unaffected observers punish selfishness, promotes cooperation by deterring defection. But why should individuals choose to bear the costs of punishing? We present a game theoretic model of TPP as a costly signal 8 , 9 , 10 of trustworthiness. Our model is based on individual differences in the costs and/or benefits of being trustworthy. We argue that individuals for whom trustworthiness is payoff-maximizing will find TPP to be less net costly (for example, because mechanisms 11 that incentivize some individuals to be trustworthy also create benefits for deterring selfishness via TPP). We show that because of this relationship, it can be advantageous for individuals to punish selfishness in order to signal that they are not selfish themselves. We then empirically validate our model using economic game experiments. We show that TPP is indeed a signal of trustworthiness: third-party punishers are trusted more, and actually behave in a more trustworthy way, than non-punishers. Furthermore, as predicted by our model, introducing a more informative signal—the opportunity to help directly—attenuates these signalling effects. When potential punishers have the chance to help, they are less likely to punish, and punishment is perceived as, and actually is, a weaker signal of trustworthiness. Costly helping, in contrast, is a strong and highly used signal even when TPP is also possible. Together, our model and experiments provide a formal reputational account of TPP, and demonstrate how the costs of punishing may be recouped by the long-run benefits of signalling one’s trustworthiness.

Despite decades of surveillance and pharmaceutical and non-pharmaceutical interventions, seasonal influenza viruses continue to cause epidemics around the world each year. The key process underlying these recurrent epidemics is the evolution of the viruses to escape the immunity that is induced by prior infection or vaccination. Although we are beginning to understand the processes that underlie the evolutionary dynamics of seasonal influenza viruses, the timing and nature of emergence of new virus strains remain mostly unpredictable. In this Review, we discuss recent advances in understanding the molecular determinants of influenza virus immune escape, sources of evolutionary selection pressure, population dynamics of influenza viruses and prospects for better influenza virus control.

A study of more than 2,000 bird species shows that diversity in bill shape expands towards extreme morphologies early in avian evolution in a series of major jumps, before switching to a second phase in which bills repeatedly evolve similar shapes by subdividing increasingly tight regions of already occupied niche space. The evolution of bird bill shape What shapes biological diversity? A study of more than 2,000 bird species shows that diversity in bill shape expands early in avian evolution before settling down to a more sedate phase, tapping wedges into Darwin's canonical barrel. The surprise, though, is that this pattern is decoupled from temporal variation. Early evolution is no faster than evolution later on. In addition, the authors identify a few occurrences of rapid increases in rate along single branches, leading to clades with extreme morphologies but few species The origin and expansion of biological diversity is regulated by both developmental trajectories 1 , 2 and limits on available ecological niches 3 , 4 , 5 , 6 , 7 . As lineages diversify, an early and often rapid phase of species and trait proliferation gives way to evolutionary slow-downs as new species pack into ever more densely occupied regions of ecological niche space 6 , 8 . Small clades such as Darwin’s finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear 9 . Here we address this problem on a global scale by analysing a crowdsourced dataset of three-dimensional scanned bill morphology from more than 2,000 species. We find that bill diversity expanded early in extant avian evolutionary history, before transitioning to a phase dominated by packing of morphological space. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare, but major, discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill-shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian 9 and Simpsonian 4 ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks.