Evolutionary Biology

eLife assessment

This is an important paper that proposes a novel evolutionary mechanism by which copy-number mutations can slow down the accumulation of point mutations in populations evolving in certain environments. The authors use an evolution experiment in bacteria equipped with a clever reporter system to provide solid evidence that this mechanism indeed operates. This paper will be of broad interest to readers in evolutionary biology and related fields.

eLife assessment

This valuable study combines phenotypic analysis, quantitative genetics and population genomics to propose that multiple genes underlie adaptive divergence in a marine midge system linked to tidal rhythm. Genes with a plausible role in perceiving and responding to lunar information are among the loci that most highly differentiate populations with distinct behaviors, but how much of this might be due to demography remains unclear. The evidence from quantitative trait locus is also deemed incomplete at this point.

eLife assessment

This valuable study provides solid evidence for a new intervention, exposure to male vs. female olfactory cues, with an impact on female mouse lifespan. This is interesting to the field of aging research, especially since most described pro-longevity interventions to date tend to work better in male mice. Although the data broadly support the claims, additional analyses showing all probed phenotypes are needed to support all claims.

eLife assessment

Neverov and colleagues analyze patterns of correlated changes of amino acids in the SARS-CoV-2 spike protein to identify networks of interacting positions using an improved version of the previously validated method. Identifying such patterns of co-evolution is important for a better understanding of spike-protein evolution. The evidence for the identified co-evolving pairs is solid, though the degree of certainty varies among the different identified groups of potentially interacting positions.

eLife assessment

The authors re-analyzed a previously published dataset and identify patterns suggestive of increased bacterial biodiversity in the gut may creating new niches that lead to gene loss in a focal species and promote generation of more diversity. Two limitations are (i) that sequencing depth may not be sufficient to analyze strain-level diversity and (ii) that the evidence is exclusively based on correlations, and the observed patterns could also be explained by other eco-evolutionary processes. The claims should be supported by a more detailed analysis, and alternative hypotheses that the results do not fully exclude should be discussed. Understanding drivers of diversity in natural microbial communities is an important question that is of central interest to biomedically oriented microbiome scientists, microbial ecologists and evolutionary biologists.

eLife assessment

The authors investigate the cost and benefits of maintaining seemingly redundant multiple copies of the translation machinery components. The authors demonstrate that while redundant multiple copies are beneficial in a nutrient-rich environment, maintaining these extra copies is costly and deleterious in a nutrient-poor environment. This explains why copy numbers of translation machinery genes are under selection according to the environmental niche an organism occupies. The work is very important and the findings exciting and supported by compelling evidence. In particular, the fitness gain upon deletion of translation genes in poor conditions is an insightful observation.

eLife assessment

This study reports an interesting analysis of evolutionary variation in forelimb/hand bone shapes in relation to functional and developmental variation along the proximo-distal axis. The authors found expected and compelling patterns of evolutionary shape variation along the proximo-distal axis but less expected, yet equally compelling, patterns of shape integration. This paper will be of interest to researchers working on macroevolutionary patterns and sources of morphological diversity.

eLife assessment

The manuscript makes a fundamental contribution to our understanding of sugar release by symbiotic dinoflagellates, and is of broad interest for the fields of ecology, marine biology, and cell biology. The experiments, which combine algal culture with targeted metabolomics, transcriptomics and the application of inhibitors, provide substantial, though not entirely complete evidence for an acidic environment mimicking conditions reported for the intracellular organelle that hosts the symbiotic algae, leading to upregulation of algal cellulases, which in turn degrade the algal cell wall and thereby releasing glucose and galactose that can be used as a source of food by the coral host. This is a new idea and could significantly contribute to our understanding of photosymbiosis.

eLife assessment

This study addresses a fundamental question about the origin and evolution of selfish genetic elements, focusing on the paradoxical abundance of toxin-antidote elements in selfing Caenorhabditis species. The authors propose for the C. elegans peel-1 zeel-1 locus fitness advantages; if these the findings can be supported with additional data, they will be of considerable interest to the field due to their wider implications for the evolution of such systems.

eLife assessment

This manuscript provides an improved version of the little skate genome, which will be of great interest to the field of comparative genomics and evolutionary biology. The authors use the genome to compare gene expression and chromatin accessibility profiles in motor neurons of the little skate and other species (mouse, chicken), aiming to predict conserved and divergent gene regulatory mechanisms underlying motor neuron development. While the manuscript contributes a valuable resource to the field, more rigorous analyses and experimental validation are needed to support the major claims of this study.