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In the face of ubiquitous threats from parasites, hosts often evolve strategies to resist infection or to altogether avoid contact with parasites. At the microbial scale, bacteria frequently encounter viral parasites, bacteriophages. While bacteria are known to utilize a number of strategies to resist infection by phages, and can physically navigate their environment using complex motility behaviors, it is unknown whether bacteria evolve avoidance of phages. In order to answer this question, we combined experimental evolution and mathematical modeling. Experimental evolution of the bacteriumPseudomonas fluorescensin environments with differing spatial distributions of the phage Phi2 revealed that the host bacteria evolved resistance depending on parasite distribution and infectivity, but did not evolve dispersal to avoid parasite infection. Simulations using parameterized mathematical models of bacterial growth and swimming motility showed that this is a general finding: while increased dispersal is adaptive in the absence of parasites, in the presence of parasites that fitness benefit disappears and resistance becomes adaptive, regardless of the spatial distribution of parasites. Together, these experiments suggest that parasites should rarely, if ever, drive the evolution of bacterial avoidance via dispersal.

Determining how adaptive possibilities do or do not become evolutionary realities is central to understanding the tempo and mode of evolutionary change. Some of the simplest evolutionary landscapes arise from underdominance at a single locus where the fitness valley consists of only one less-fit genotype. Despite their potential for rapid evolutionary change, few such examples have been investigated. We capitalized on an experimental system in which a significant evolutionary shift, the transition from uni-to-multicellularity, was observed in asexual diploid populations of Saccharomyces cerevisiae experimentally selected for increased settling rates. The multicellular phenotype results from recessive single-locus mutations that undergo loss-of-heterozygosity (LOH) events. By reconstructing the necessary heterozygous intermediate steps, we found that the evolution of multicellularity involves a decrease in size during the first steps. Heterozygous genotypes are 20% smaller in size than genotypes with functional alleles. Nevertheless, populations of heterozygotes give rise to multicellular genotypes more readily than unicellular genotypes with two functional alleles, by rapid LOH events. LOH drives adaptation that may enable rapid evolution in diploid yeast. Together these results show discordance between the phenotypic and genotypic multicellular transition. The evolutionary path to multicellularity, and the adaptive benefits of increased size, requires initial size reductions.

Evolution works by adaptation and exaptation. At an organismal level, exaptation and adaptation are seen in the formation of organelles and the advent of multicellularity. At the sub-organismal level, molecular systems such as proteins and RNAs readily undergo adaptation and exaptation. Here we suggest that the concepts of adaptation and exaptation are universal, synergistic, and recursive and apply to small molecules such as metabolites, cofactors, and the building blocks of extant polymers. For example, adenosine has been extensively adapted and exapted throughout biological evolution. Chemical variants of adenosine that are products of adaptation include 2′ deoxyadenosine in DNA and a wide array of modified forms in mRNAs, tRNAs, rRNAs, and viral RNAs. Adenosine and its variants have been extensively exapted for various functions, including informational polymers (RNA, DNA), energy storage (ATP), metabolism (e.g., coenzyme A), and signaling (cyclic AMP). According to Gould, Vrba, and Darwin, exaptation imposes a general constraint on interpretation of history and origins; because of exaptation, extant function should not be used to explain evolutionary history. While this notion is accepted in evolutionary biology, it can also guide the study of the chemical origins of life. We propose that (i) evolutionary theory is broadly applicable from the dawn of life to the present time from molecules to organisms, (ii) exaptation and adaptation were important and simultaneous processes, and (iii) robust origin of life models can be constructed without conflating extant utility with historical basis of origins.

For micro-organisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether evolution during the free-living stage can be positively pleiotropic to microbial fitness in a host environment. To address this topic, the squid host Euprymna tasmanica and the marine bioluminescent bacterium Vibrio fischeri were utilized. Microbial ecological diversification in static liquid microcosms was used to simulate symbiont evolution during the free-living stage. Thirteen genetically distinct V. fischeri strains from a broad diversity of ecological sources (e.g. squid light organs, fish light organs and seawater) were examined to see if the results were reproducible in many different genetic settings. Genetic backgrounds that are closely related can be predisposed to considerable differences in how they respond to similar selection pressures. For all strains examined, new mutations with striking and facilitating effects on host colonization arose quickly during microbial evolution in the free-living stage, regardless of the ecological context under consideration for a strain's genetic background. Microbial evolution outside a host environment promoted host range expansion, improved host colonization for a micro-organism, and diminished the negative correlation between biofilm formation and motility.

A designed protein complex processively copies one strand of a plasmid with errors to speed up molecular evolution in vivo., Extensive exploration of a protein’s sequence space for improved or new molecular functions requires in vivo evolution with large populations. But disentangling the evolution of a target protein from the rest of the proteome is challenging. Here, we designed a protein complex of a targeted artificial DNA replisome (TADR) that operates in live cells to processively replicate one strand of a plasmid with errors. It enhanced mutation rates of the target plasmid up to 2.3 × 105–fold with only a 78-fold increase in off-target mutagenesis. It was used to evolve itself to increase error rate and increase the efficiency of an efflux pump while simultaneously expanding the substrate repertoire. TADR enables multiple simultaneous substitutions to discover functions inaccessible by accumulating single substitutions, affording potential for solving hard problems in molecular evolution and developing biologic drugs and industrial catalysts.

We draw lessons from microbial experimental evolution and naval warfare to improve the understanding of innovation in financial markets. Major financial innovations often arise without explicit societal planning because novel approaches can be favored by markets, in a manner strikingly parallel to natural selection. We utilize the concept of an adaptive landscape to characterize environments that increase the speed and magnitude of innovation. We apply this adaptive landscape framework to innovation in portfolio management. We create a general taxonomy for understanding and nurturing innovation.

Human behavior (movement, social contacts) plays a central role in the spread of pathogens like SARS- CoV-2. The rapid spread of SARS-CoV-2 was driven by global human movement, and initial lockdown measures aimed to localize movement and contact in order to slow spread. Thus, movement and contact patterns need to be explicitly considered when making reopening decisions, especially regarding return to work. Here, as a case study, we consider the initial stages of resuming research at a large research university, using approaches from movement ecology and contact network epidemiology. First, we develop a dynamical pathogen model describing movement between home and work; we show that limiting social contact, via reduced people or reduced time in the workplace are fairly equivalent strategies to slow pathogen spread. Second, we develop a model based on spatial contact patterns within a specific office and lab building on campus; we show that restricting on-campus activities to labs (rather than labs and offices) could dramatically alter (modularize) contact network structure and thus, potentially reduce pathogen spread by providing a workplace mechanism to reduce contact. Here we argue that explicitly accounting for human movement and contact behavior in the workplace can provide additional strategies to slow pathogen spread that can be used in conjunction with ongoing public health efforts.

Evolution is often deemed irreversible. The evolution of complex traits that require many mutations makes their reversal unlikely. Even in simpler traits, reversals might become less likely as neutral or beneficial mutations, with deleterious effects in the ancestral context, become fixed in the novel background. This is especially true in changes that involve large reorganizations of the organism and its interactions with the environment. The evolution of multicellularity involves the reorganization of previously autonomous cells into a more complex organism; despite the complexity of this change, single cells have repeatedly evolved from multicellular ancestors. These repeated reversals to unicellularity undermine the generality of Dollo's law. In this article, we evaluated the dynamics of reversals to unicellularity from recently evolved multicellular phenotypes of the brewers yeast Saccharomyces cerevisae. Even though multicellularity in this system evolved recently, it involves the evolution of new levels of selection. Strong selective pressures against multicellularity lead to rapid reversibility to single cells in all of our replicate lines, whereas counterselection favoring multicellularity led to minimal reductions to the rates of reversal. History and chance played an important role in the tempo and mode of reversibility, highlighting the interplay of deterministic and stochastic events in evolutionary reversals.

Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic compatibility was recovered rapidly. Extensive computational simulations were performed to assess the role of mutational biases as well as selection for translational efficiency in the engineered phage. Using bacteriophage as a model system, we can begin to unravel the evolutionary processes shaping codon compatibility between viruses and their host.

There have been over 25 independent unicellular to multicellular evolutionary transitions, which have been transformational in the complexity of life. All of these transitions likely occurred in communities numerically dominated by unicellular organisms, mostly bacteria. Hence, it is reasonable to expect that bacteria were involved in generating the ecological conditions that promoted the stability and proliferation of the first multicellular forms as protective units. In this study, we addressed this problem by analyzing the occurrence of multicellularity in an experimental phylogeny of yeasts (Sacharomyces cerevisiae) a model organism that is unicellular but can generate multicellular clusters under some conditions. We exposed a single ancestral population to periodic divergences, coevolving with a cocktail of environmental bacteria that were inoculated to the environment of the ancestor, and compared to a control (no bacteria). We quantified culturable microorganisms to the level of genera, finding up to 20 taxa (all bacteria) that competed with the yeasts during diversification. After 600 generations of coevolution, the yeasts produced two types of multicellular clusters: clonal and aggregative. Whereas clonal clusters were present in both treatments, aggregative clusters were only present under the bacteria treatment and showed significant phylogenetic signal. However, clonal clusters showed different properties if bacteria were present as follows: They were more abundant and significantly smaller than in the control. These results indicate that bacteria are important modulators of the occurrence of multicellularity, providing support to the idea that they generated the ecological conditions‐promoting multicellularity.

Theory indicates that responses to natural selection maximize immediate fitness benefits, leading to adaptations to current environmental conditions and those of the immediate past. Over a century of advances in theory, experiment, and observation have documented innumerable adaptations demonstrating the efficacy of natural selection to finely tune species to their respective environments. However, theory also suggests that natural selection is not a panacea, and that improvements in competitive ability do not necessarily increase long-term survival. Here we show that adaptation in experimental populations of microbes can dramatically reduce population sizes to near extinction levels in a stressful environment. The long-term potential for extinction differed from that identified in short-term ecological observations, but the eventual outcome is consistent with limitations on specific modes of adaptation. These results suggest that additional emphasis on the limitations of adaptation can provide insight on when and how improvements in competitive ability provide longer-term benefits.

Multicellularity provides multiple benefits. Nonetheless, unicellularity is ubiquitous, and there have been multiple cases of evolutionary reversal to a unicellular organization. In this article, we explore some of the costs of multicellularity as well as the possibility and dynamics of evolutionary reversals to unicellularity. We hypothesize that recently evolved multicellular organisms would face a high cost of increased competition for local resources in spatially structured environments because of larger size and increased cell densities. To test this hypothesis we conducted competition assays, computer simulations, and selection experiments using isolates of Saccharomyces cerevisiae that recently evolved multicellularity. In well-mixed environments, multicellular isolates had lower growth rates relative to their unicellular ancestor because of limitations of space and resource acquisition. In structured environments with localized resources, cells in both multicellular and unicellular isolates grew at a similar rate. Despite similar growth, higher local density of cells in multicellular groups led to increased competition and higher fitness costs in spatially structured environments. In structured environments all of the multicellular isolates rapidly evolved a predominantly unicellular life cycle, while in well-mixed environments reversal was more gradual. Taken together, these results suggest that a lack of dispersal, leading to higher local competition, might have been one of the main constraints in the evolution of early multicellular forms.

In order to investigate the contribution of the physical environment to variation in multicellular development of Myxococcus xanthus, phenotypes developed by different genotypes in a gradient of substrate stiffness conditions were quantitatively characterized. Statistical analysis showed that plastic phenotypes result from the genotype, the substrate conditions and the interaction between them. Also, phenotypes were expressed in two distinguishable scales, the individual and the population levels, and the interaction with the environment showed scale and trait specificity. Overall, our results highlight the constructive role of the physical context in the development of microbial multicellularity, with both ecological and evolutionary implications.

Models are universal in science, both as theoretical formulations of reality and as model systems, representatives of other organisms. A recent paper on how scientists view the world divides our work into the mind, the lab, and the field and suggests that models must not be conflated with reality. But in practice, these distinctions are blurred. For example, are flour beetles a model system for other insects when their natural habitat is the same as the way they live in the lab? In addition, models can become restrictive when they are viewed as archetypes, making us overgeneralize about the world and ignoring meaningful variation. The study of sexual conflict in insects illustrates some of the pitfalls of relying on Drosophila as a model system for sexual selection. Microbes can be used as models for populations and communities and are essential parts of larger biological systems. Finally, some models are not meant to replicate the world but are worlds unto themselves in which diverse possibilities can be directly observed.

Adaptive radiations are major contributors to species diversity. Although the underlying mechanisms of adaptive radiations, specialization and trade-offs, are relatively well understood, the tempo and repeatability of adaptive radiations remain elusive. Ecological specialization can occur through the expansion into novel niches or through partitioning of an existing niche. To test how the mode of resource specialization affects the tempo and repeatability of adaptive radiations, we selected replicate bacterial populations in environments that promoted the evolution of diversity either through niche expansion or through niche partitioning, and in a third low-quality single-resource environment, in which diversity was not expected to evolve. Colony size diversity evolved equally fast in environments that provided ecological opportunities regardless of the mode of resource specialization. In the low-quality environments, diversity did not consistently evolve. We observed the largest fitness improvement in the low-quality environment and the smallest the glucose-limited environment. We did not observe a change in the rate of evolutionary change in either trait or environment, suggesting that the pool of beneficial mutations was not exhausted. Overall, the mode of resource specialization did not affect the tempo or repeatability of adaptive radiations. These results demonstrate the limitations of eco-evolutionary feedbacks to affect evolutionary outcomes.

Wendell Minckley had just graduated from college in 1957, and his love was aquatic environments and wildlife management. After his first fortuitous trip to Cuatro Cienegas Basin (CCB) in 1958, his life changed and devoted his career to understand this amazing oasis. In 1997 Minckley, by then a well-established professor at Arizona State University, brought along a new colleague, Jim Elser, a limnologist interested in the basic stoichiometric composition of life. Jim was fascinated by the abundance of stromatolites and microbial mats as the base of the aquatic food web, just as in the early Cambrian sea. What made CCB so special was its extremely low phosphorus and the unbalanced stoichiometry; those were the ancient conditions of the sea in the Precambrian. Jim got the Astrobiology Institute of NASA interested, but they needed Mexican scientists involved as well as experts in microbiology and evolution. Valeria Souza and Luis Eguiarte visited the CCB in 1999, and this chapter is about the fascination that they felt at the mysteries behind the enormous microbial biodiversity in the blue-eye ponds (locally called pozas). However, this lost world that had survived eons did not give its secrets lightly, and the hardships to study it are many, so they needed more and more colleagues to join into the task. In the last decade, the now large scientific team has been trying to understand why there are so many species in a place without food, and trying to describe as much as possible and as fast as possible. They all feel this sense of urgency since they are working against the implacable clock of ecosystem degradation. Paradise was disappearing fast given the unsustainable use of water from the deep aquifer to irrigate thirsty alfalfa cultivars in the desert. The decision to save CCB and its amazing biota required to transform a sleepy rural society by translating science to the public and more importantly to give scientific tools to the kids of the owners of the land. Bright-eyed children became conscious about the ecosystem through art, and teenagers are taking actions by discovering that they are the stewards of the biodiversity they are describing in the lab of their high school using molecular tools. There is a revolution occurring in this oasis: science is the tool; kids are the drivers.

In this chapter we will explore whether the niche concept is useful to understand microbes, since we believe that this key concept in ecology is particularly useful in the investigation of microbial biodiversity. On the one hand, with microbes we can conduct experiments to analyze in detail all the aspects of the Grinnellian niche, in a way that cannot be done in other organisms. On the other hand, even if complicated, we can develop different experiments and observations to start analyzing the Eltonian aspects of the niche. Here we develop our ideas on how to study the niche components in microbial systems and describe our advances in analyzing these components in a particular group of organisms in the Cuatro Cienegas Basin (CCB). In this oasis, the distinctive oligotrophic conditions of several freshwater systems in CCB promote unique microbial interactions in order to cope with nutrient stress, where antagonist and synergic effects influence bacterial diversity structure, modifying the nature and intensity of biotic interactions. For example, Bacillus has few antagonistic interactions among strains of a given sampling site but strong antagonisms when competing against strains from different sites. Interestingly, antagonistic strains belonged to two genetically close species, and their targets belonged to taxonomically separate groups. Even more so, the same Bacillus strains showed great diversity in the dependence of the different strains on other community members. While antagonistic strains were in general prototrophs, a large proportion of sensitive and resistant strains exhibited auxotrophy suggesting that they need their community in order to survive. At CCB we believe that the cohesion of the community through these positive interactions is paramount to explain survival in such a harsh environment. As a result, the multidimensional space where the theater of life plays in CCB is very rich and full of actors, which shifts constantly, as virus and other process “chop the head” of the dominant species and former “underdogs” of the rare biosphere take their roles. Finally, since this play of “life at the edge” has been continued in the same site for a very long time with coevolving communities, here the “conversations and negotiations” between microscopic actors seem to be the reason why this stage has persisted for such a long time.

Developmental evolution has frequently been identified as a mode for rapid adaptation, but direct observations of the selective benefits and associated mechanisms of developmental evolution are necessarily challenging to obtain. Here we show rapid evolution of greatly increased rates of dispersal by developmental changes when populations experience stringent selection. Replicate populations of the filamentous fungus Trichoderma citrinoviride underwent 85 serial transfers, under conditions initially favoring growth but not dispersal. T. citrinoviride populations shifted away from multicellular growth toward increased dispersal by producing one thousand times more single-celled asexual conidial spores, three times sooner than the ancestral genotype. Conidia of selected lines also germinated fifty percent faster. Gene expression changed substantially between the ancestral and selected fungi, especially for spore production and growth, demonstrating rapid evolution of tight regulatory control for down-regulation of growth and up-regulation of conidia production between 18 and 24 hours of growth. These changes involved both developmentally fixed and plastic changes in gene expression, showing that complex developmental changes can serve as a mechanism for rapid adaptation.

No abstract available Keywords: antagonistic interactions; cheating; conflict; consortia; cooperation; diversity; mutualistic interactions; spatial structure.

The origin and evolution of multicellularity was directly investigated using experimental evolution. Using settling selection, multicellularity evolved quickly and repeatedly from a common unicellular ancestor, Baker’s yeast. The transition occurred by persistent adhesion of daughter cells following cell replication. The resulting multicellular individuals had a morphology reminiscent of snowflakes, with many characteristics of extant multicellular species, including cell–cell attachment, a single-cell bottleneck, and juvenile and adult life history stages. Cellular division of labor by apoptosis evolved in large snowflake clusters, ameliorating the effects of a trade-off between snowflake settling and growth rate. Continued settling selection led to additional adaptation, such as a more hydrodynamic cluster shape. The majority of the developmental changes that evolved after the transition to multicellularity were contingent on this transition and even on the specific mode of cluster formation. The origin and subsequent evolution of multicellular complexity in snowflake yeast can be directly attributed to natural selection.

Disentangling individual selection from kin selection is one of the greatest challenges of evolutionary biology. Even solitary organisms that do not interact directly with conspecifics may interact indirectly with them through competition for resources. As a result, traits that appear to affect individual fitness alone can also modify the fitness of relatives nearby and thus may evolve partially through these cryptic indirect fitness effects. Here we develop a method to quantitatively separate direct and indirect fitness consequences when some microbes become dormant, while neighbors of the same genotype remain active. Dormant microbes typically survive stresses that kill metabolically active cells, but dormancy also has a social side effect, sparing resources that may be used by nondormant individuals for growth. In structured populations, spared resources may be preferentially consumed by nondormant clonemates, providing an indirect benefit. Without population structure, however, exploitation by a never-dormant competitor imposes an indirect fitness cost on dormant cells. Cryptic indirect fitness effects may play a significant role in the evolution of many ostensibly asocial traits.

Multicellular complexity is a central topic in biology, but the evolutionary processes underlying its origin are difficult to study and remain poorly understood. Here we use experimental evolution to investigate the tempo and mode of multicellular adaptation during a de novo evolutionary transition to multicellularity. Multicelled "snowflake" yeast evolved from a unicellular ancestor after 7 days of selection for faster settling through liquid media. Over the next 220 days, snowflake yeast evolved to settle 44% more quickly. Throughout the experiment the clusters evolved faster settling by three distinct modes. The number of cells per cluster increased from a mean of 42 cells after 7 days of selection to 114 cells after 227 days. Between days 28 and 65, larger clusters evolved via a twofold increase in the mass of individual cells. By day 227, snowflake yeast evolved to form more hydrodynamic clusters that settle more quickly for their size than ancestral strains. The timing and nature of adaptation in our experiment suggests that costs associated with large cluster size favor novel multicellular adaptations, increasing organismal complexity.

Model organisms are central to contemporary biology and studies of embryogenesis in particular. Biologists utilize only a small number of species to experimentally elucidate the phenomena and mechanisms of development. Critics have questioned whether these experimental models are good representatives of their targets because of the inherent biases involved in their selection (e.g., rapid development and short generation time). A standard response is that the manipulative molecular techniques available for experimental analysis mitigate, if not counterbalance, this concern. But the most powerful investigative techniques and molecular methods are applicable to single-celled organisms (‘microbes’). Why not use unicellular rather than multicellular model organisms, which are the standard for developmental biology? To claim that microbes are not good representatives takes us back to the original criticism leveled against model organisms. Using empirical case studies of microbes modeling ontogeny, we break out of this circle of reasoning by showing: (a) that the criterion of representation is more complex than earlier discussions have emphasized; and, (b) that different aspects of manipulability are comparable in importance to representation when deciding if a model organism is a good model. These aspects of manipulability harbor the prospect of enhancing representation. The result is a better understanding of how developmental biologists conceptualize research using experimental models and suggestions for underappreciated avenues of inquiry using microbes. More generally, it demonstrates how the practical aspects of experimental biology must be scrutinized in order to understand the associated scientific reasoning.

Understanding the relationship between phylogeny and predicted traits is important to uncover the dimension of the predictive power of a microbial composition approach. Numerous works have addressed the taxonomic composition of bacteria in communities, but little is known about trait heterogeneity in closely related bacteria that co-occur in communities. We evaluated a sample of 467 isolates from the Churince water system of the Cuatro Cienegas Basin (CCB), enriched for Bacillus spp. The 16S rRNA gene revealed a random distribution of taxonomic groups within this genus among 11 sampling sites. A subsample of 141 Bacillus spp. isolates from sediment, with seven well-represented species was chosen to evaluate the heterogeneity and the phylogenetic signal of phenotypic traits that are known to diverge within small clades, such as substrate utilization, and traits that are conserved deep in the lineage, such as prototrophy, swarming and biofilm formation. We were especially interested in evaluating social traits, such as swarming and biofilm formation, for which cooperation is needed to accomplish a multicellular behavior and for which there is little information from natural communities. The phylogenetic distribution of traits, evaluated by the Purvis and Fritz's D statistics approached a Brownian model of evolution. Analysis of the phylogenetic relatedness of the clusters of members sharing the trait using consenTRAIT algorithm, revealed more clustering and deeper phylogenetic signal for prototrophy, biofilm and swimming compared to the data obtained for substrate utilization. The explanation to the observed Brownian evolution of social traits could be either loss due to complete dispensability or to compensated trait loss due to the availability of public goods. Since many of the evaluated traits can be considered to be collective action traits, such as swarming, motility and biofilm formation, the observed microdiversity within taxonomic groups might be explained by distributed functions in structured communities.

The most evident aspect of biodiversity is the variety of complex forms and behaviors among organisms, both living and extinct. Comparative molecular and physiological studies show that the evolution of complex phenotypic traits involves multiple levels of biological organization (i.e. genes, chromosomes, organelles, cells, individual organisms, species, etc.). Regardless of the specific molecular mechanisms and details, the evolution of different complex biological organizations share a commonality: cooperation and conflict among the parts of the biological unit under study. The potential for conflict among parts is abundant. How then do complex systems persist, given the necessity of cooperative behavior for their maintenance, when the potential for conflict occurs across all levels of biological organization? In this Research Topic and eBook we present ideas and work on the question, how coexistence of biological components at different levels of organization persists in the face of antagonistic, conflicting or even exploitative behavior of the parts? The goal of this topic is in presenting examples of cooperation and conflict at different levels of biological organization to discuss the consequences that this “tension” have had in the diversification and emergence of novel phenotypic traits. Exemplary cases are studies investigating: the evolution of genomes, formation of colonial aggregates of cells, biofilms, the origin and maintenance of multicellular organisms, and the stable coexistence of multispecies consortia producing a cooperative product. Altogether, we hope that the contributions to this Research Topic build towards mechanistic knowledge of the biological phenomenon of coexistence in the face of conflict. We believe that knowledge on the mechanisms of the origin and evolutionary maintenance of cooperation has implications beyond evolutionary biology such as novel approaches in controlling microbial infections in medicine and the modes by studies in synthetic biology are conducted when designing economically important microbial consortia.The most evident aspect of biodiversity is the variety of complex forms and behaviors among organisms, both living and extinct. Comparative molecular and physiological studies show that the evolution of complex phenotypic traits involves multiple levels of biological organization (i.e. genes, chromosomes, organelles, cells, individual organisms, species, etc.). Regardless of the specific molecular mechanisms and details, the evolution of different complex biological organizations share a commonality: cooperation and conflict among the parts of the biological unit under study. The potential for conflict among parts is abundant. How then do complex systems persist, given the necessity of cooperative behavior for their maintenance, when the potential for conflict occurs across all levels of biological organization? In this Research Topic and eBook we present ideas and work on the question, how coexistence of biological components at different levels of organization persists in the face of antagonistic, conflicting or even exploitative behavior of the parts? The goal of this topic is in presenting examples of cooperation and conflict at different levels of biological organization to discuss the consequences that this “tension” have had in the diversification and emergence of novel phenotypic traits. Exemplary cases are studies investigating: the evolution of genomes, formation of colonial aggregates of cells, biofilms, the origin and maintenance of multicellular organisms, and the stable coexistence of multispecies consortia producing a cooperative product. Altogether, we hope that the contributions to this Research Topic build towards mechanistic knowledge of the biological phenomenon of coexistence in the face of conflict. We believe that knowledge on the mechanisms of the origin and evolutionary maintenance of cooperation has implications beyond evolutionary biology such as novel approaches in controlling microbial infections in medicine and the modes by studies in synthetic biology are conducted when designing economically important microbial consortia.