Evolutionary Biology

eLife assessment

The overarching question of the manuscript is important and the findings inform the patterns and mechanisms of phage-mediated bacterial competition, with implications for microbial evolution and antimicrobial resistance. The evidence in the manuscript is, however, still incomplete and some of the conclusions made are not supported by the data. This manuscript would additionally be strengthened by a clearer narrative, to enable readers to more easily extract the key message this paper wants to convey.

eLife assessment

This study presents a valuable mathematical model for the adaptive dynamics of cancer evolution in response to immune recognition. The mathematical analysis is rigorous and convincing, and overall the framework presented could be used in the future as a solid base for analytically tracking tumor evasion strategies. However additional discussion is needed to clarify certain gaps between the theory and cancer evolution in real systems. The work will be of interest to evolutionary cancer biologists and potentially it may also have implications for the design of clinical interventions.

eLife assessment

This study, of interest to population geneticists and evolutionary biologists alike, aims at investigating temporal variation in patterns of germline mutation during the evolution of human populations. The authors suggest that shifts in mutation spectra occur frequently, over a few thousands of generations, possibly as a consequence of changes in environmental exposure, or of genetic modifiers. There are several important aspects of methodology that need to be clarified, and several additional tests have to be done to confirm that the reported observations are not the result of methodological artifacts. The paper also overstates certain weaknesses of previously published papers on mutation spectrum evolution as well as the generation time hypothesis; correcting these oversimplifications would more accurately capture what the paper's new analyses add to the state of knowledge in these areas.

eLife assessment

This study on snapping shrimp morphological weaponry presents important findings on trade-offs in investment in costly weaponry traits as related to body size and reproduction. Convincing evidence is based on the collection of an exceptional number of fields samples, the inclusion of three shrimp species, and the measurement of numerous morphological and behavioral traits. The evidence shows that there are size-dependent trade-offs, where males and females differ in weapon investment, as weapons are beneficial to males but expensive for females. The findings will be of broad interest to evolutionary biologists and researchers working in the field of animal behavior.

eLife assessment

This manuscript reports valuable findings regarding the evolution of nitrogenases through ancestral sequence reconstruction and resurrection. The results are solid and support the conclusions of the study, and highlight the historical constraints that have been acting on this enzyme. The findings will be of interest for people interested in enzyme evolution in general and particularly for those interested in the evolution of nitrogenases.

eLife assessment

This is an important paper that combines comparative analysis and experimental assays to investigate the role of protein-coding and regulatory changes at TRNP1 in mammalian brain evolution. The evidence supporting a contribution of TRNP1 is convincing, although the link between protein-coding changes and trait evolution is stronger and more readily interpretable than the data on gene regulation. The work will be of interest to researchers in the areas of mammalian evolution, brain evolution, and evolutionary genetics.

eLife assessment

Overall, this manuscript provides fundamental advances to our understanding of the ancestry of insect gustatory and olfactory receptors, by identifying new members of these two related ion channel families in distant species. The approaches to compare protein structure are exceptional and use cutting-edge techniques, going beyond the commonly used approaches. The authors suggest that the family of odorant and gustatory receptors have a common origin and share structural homology in very distant organisms, although the possibility of convergent evolution still exists. This work will serve as a reference for scientists working on insect olfaction and for those working on molecular evolution.

eLife assessment

The authors document an in-depth analysis of introduction patterns of 5 variant waves in Mexico. This is an important analysis and dataset since the genomic epidemiology of SARS-CoV-2 in Mexico is generally understudied, and this paper contributes important missing information. The phylogenetic analyses are solid and well-presented, but the lack of detail regarding the collection of samples across Mexican states makes it difficult to evaluate conclusions about the relationship between observed viral lineages and local case counts. Additionally, in its current form, the manuscript is mostly descriptive, without clear hypotheses tested or discussion of implications.

eLife assessment

This important work advances our understanding of the factors that affect the speed of colour evolution in birds and the resulting diversification patterns. It provides compelling evidence that more complex plumage coloration can lead to rapid colour evolution in kingfishers, and could pave the way for more comprehensive analyses that fully embrace the multidimensional nature of colour variation. Hence, the results will be of broad interest to ornithologists and evolutionary biologists in general, once the authors have streamlined the theoretical framework and explained the novel methodological approaches in more detail.

eLife assessment

The paper provides a valuable, in-depth mathematical analysis of the coevolutionary dynamics resulting from a coupling of players' strategies and (collective) risk, as well as illustrative numerical simulations of the system's trajectories for different starting conditions. It is therefore a solid contribution to our understanding of how cooperation can be sustained when there is feedback between individual decisions and the global risk of disaster. This paper will be of interest to scientists working on mathematical biology/ecology, and more generally various aspects of human decision-making, the interplay between human decisions and the environment, and public goods provision.