Predicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive ‘wrinkly spreader’ (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects.

Atmospheric oxygen is thought to have played a vital role in the evolution of large, complex multicellular organisms. Challenging the prevailing theory, we show that the transition from an anaerobic to an aerobic world can strongly suppress the evolution of macroscopic multicellularity. Here we select for increased size in multicellular ‘snowflake’ yeast across a range of metabolically-available O₂ levels. While yeast under anaerobic and high-O₂ conditions evolved to be considerably larger, intermediate O₂ constrained the evolution of large size. Through sequencing and synthetic strain construction, we confirm that this is due to O₂-mediated divergent selection acting on organism size. We show via mathematical modeling that our results stem from nearly universal evolutionary and biophysical trade-offs, and thus should apply broadly. These results highlight the fact that oxygen is a double-edged sword: while it provides significant metabolic advantages, selection for efficient use of this resource may paradoxically suppress the evolution of macroscopic multicellular organisms.

It has been argued that the historical nature of evolution makes it a highly path-dependent process. Under this view, the outcome of evolutionary dynamics could have resulted in organisms with different forms and functions. At the same time, there is ample evidence that convergence and constraints strongly limit the domain of the potential design principles that evolution can achieve. Are these limitations relevant in shaping the fabric of the possible? Here, we argue that fundamental constraints are associated with the logic of living matter. We illustrate this idea by considering the thermodynamic properties of living systems, the linear nature of molecular information, the cellular nature of the building blocks of life, multicellularity and development, the threshold nature of computations in cognitive systems and the discrete nature of the architecture of ecosystems. In all these examples, we present available evidence and suggest potential avenues towards a well-defined theoretical formulation.

Syntrophy allows a microbial community as a whole to survive in an environment, even though individual microbes cannot. The metabolic interdependence typical of syntrophy is thought to arise from the accumulation of degenerative mutations during the sustained co-evolution of initially self-sufficient organisms. An alternative and underexplored possibility is that syntrophy can emerge spontaneously in communities of organisms that did not co-evolve. Here, we study this de novo origin of syntrophy using experimentally validated computational techniques to predict an organism’s viability from its metabolic reactions. We show that pairs of metabolisms that are randomly sampled from a large space of possible metabolism and viable on specific primary carbon sources often become viable on new carbon sources by exchanging metabolites. The same biochemical reactions that are required for viability on primary carbon sources also confer viability on novel carbon sources. Our observations highlight a new and important avenue for the emergence of metabolic adaptations and novel ecological interactions. By exchanging resources, the members of a microbial community can survive in environments where individual species cannot. Despite the abundance of such syntrophy, little is known about its evolutionary origin. The predominant hypothesis is that syntrophy arises when originally independent organisms in the same community become interdependent by accumulating mutations. In this view, syntrophy arises when organisms co-evolve. In sharp contrast we find that different metabolism can interact syntrophically without a shared evolutionary history. We show that syntrophy is an inherent and emergent property of the complex chemical reaction networks that constitute metabolism.

In the search for life beyond Earth, distinguishing the living from the non-living is paramount. However, this distinction is often elusive, as the origin of life is likely a stepwise evolutionary process, not a singular event. Regardless of the favored origin of life model, an inherent “grayness” blurs the theorized threshold defining life. Here, we explore the ambiguities between the biotic and the abiotic at the origin of life. The role of grayness extends into later transitions as well. By recognizing the limitations posed by grayness, life detection researchers will be better able to develop methods sensitive to prebiotic chemical systems and life with alternative biochemistries.