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Rather than using genome sequence data to make conclusions about how an organism lives, the reverse approach can be adopted — using gene networks generated for a group of related organisms with similar lifestyles to infer the gene content of another member of the group.

Understanding how evolution of antimicrobial resistance increases resistance to other drugs is of key importance. Here, Lazar et al. build a map of cross-resistance interactions between antibiotics in Escherichia coliand show that chemical and genomic similarities are good predictors of bacterial cross-resistance.

Moculus is a virtual reality headset for mice that allows realistic display of three-dimensional environments. The system improves performance in visual-learning tasks and can be combined with various microscopes to study neural circuitry.

Balázs Papp and colleagues construct a genetic interaction map of yeast metabolism and use a genome-scale systems biology model to examine the structure of the metabolic network. They use an automated machine-learning method to reconcile differences between the experimental and computational genetic interaction maps. In contrast to previous studies, they do not find evidence for prevalent positive interactions in essential metabolic genes.

Antimicrobial peptide resistance genes are found to be widespread in the gut microbiome but are exchanged at lower rates compared to antibiotic resistance genes, with functional compatibility between bacteria being important for gene exchange.

A fundamental question in evolutionary biology is how complex innovations requiring multiple genetic changes arise. Here the authors provide lines of evidence that changing environments facilitate the adaptive evolution of complex metabolic innovations via stepwise acquisition of single reactions.

An acousto-optic two-photon microscope with continuous three-dimensional trajectory and random-access scanning modes can scan near-cubic-millimeter volumes of tissue at sub-millisecond temporal resolution in vivo. The system can be used to image both sub-cellular as well as network-scale neuronal activity.

An extensive experimental analysis of resistance to antibiotics in development or introduced post-2017 in ESKAPE bacteria reveals the dynamics of resistance acquisition, mutational targets and the presence of mutations in clinical and environmental isolates.

This Review describes the successful efforts of modelling approaches that combine evolutionary theory, systems biology and molecular data to interpret past evolution and, crucially, to predict evolutionary processes at the molecular and network levels.

Manczinger and colleagues define ‘promiscuity’ as a feature of HLA-I alleles representing peptide repertoire breadth; promiscuous alleles may promote a more tolerant tumor microenvironment and negatively impact tumor immune surveillance.

This study shows that only those dual-targeting antibiotics limit resistance in Gram-negative pathogens that also target the membrane of the bacteria. This mechanism provides a basis for designing future antibiotics with reduced resistance potential.

Multidrug-resistant Escherichia coli have a high frequency of collateral sensitivity to antimicrobial peptides, which may arise from changes in lipopolysaccharide regulation.

In this Opinion article, the authors highlight the potential of genome engineering for the study of evolution and focus on microbial systems. They discuss the prospects and problems of the emerging field of evolutionary genome engineering, and pinpoint how a combination of genome engineering and laboratory evolution can shed light on evolutionary forces.

Application of reprogrammed bacteriophage to functional metagenomics in clinically relevant bacterial strains improves identification of antibiotic resistance genes, including those against recently developed or approved antibiotics.

The role of compensatory mutations in phenotypic evolution is unclear. Here the authors use experimental evolution to show that gene loss followed by compensatory evolution contributes to the rapid emergence of new cellular and multicellular morphologies in the budding yeast.

In vivo, in vitro and in silico experiments demonstrate that interface residues of homomeric proteins are enriched toward protein C termini to avoid premature assembly and aggregation.

The authors use single-nucleus RNA-seq to identify 10 GABAergic interneuron subtypes in human cortex layer 1. Molecular, morphological, and physiological evidence points to an emerging human cell type, the rosehip cell, not found in other species.

The genetics underlying bacterial susceptibility to antimicrobial peptides (AMPs) remain unclear. Here, using a genome-wide chemical-genetic approach, the authors map the diversity of resistance determinants across AMPs in Escherichia coli and provide evidence that cross-resistance is prevalent only between AMPs with similar modes of action.

Antimicrobial peptides (AMPs) are emerging as drug candidates, but the risk of pathogen resistance is not well understood. Here, the authors investigate AMP resistance evolution in E. coli, finding physicochemical features that make AMPs less prone to resistance and no cross- or horizontally-acquired resistance.

Microglia undergo rapid phenotype changes in response to tissue disturbances but the impact of these changes on neuronal networks is unclear. Here, the authors show that microglia contribute to neuronal synchrony in acute brain slices, while their marked phenotypic transformation is influenced by injury-related focal ATP events.

In European Neolithic populations, the arrival of farmers prompted admixture with local hunter-gatherers over many centuries, resulting in distinct signatures in each region due to a complex series of interactions.

Calcium-activated chloride currents are thought to amplify the olfactory signal during the transduction process. Here the authors identify Ano2 as the critical channel in both main olfactory epithelium and in the vomeronasal organ. Surprisingly, disruption of Ano2 did not reduce performance in an olfactory behavioral task, suggesting that olfaction does not actually depend on these channels.

Many factors other than protein structure and function affect the rate of protein evolution. Advances in genomics make it possible to assess the contribution of all these factors and move towards a more integrated view of how proteins evolve.

The adenosine–adenosine receptor system has a key role in regulating glucose homeostasis and in the pathophysiology of type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM). In this Review, the authors discuss the role of the adenosinergic system in regulating both the onset and progression of T1DM and T2DM, and the potential of manipulating this system as an approach to manage T1DM, T2DM and their associated complications.

The evolution of complex adaptations poses conceptual challenges. Here, the authors discuss adaptive and non-adaptive scenarios in the evolution of complex adaptations and propose molecular mechanisms that provide access to new adaptive paths.