Evolutionary Biology

eLife Assessment

This study provides important insights into the evolution of pesticide resistance, demonstrating that resistance can arise rapidly and repeatedly, which complements prior work on parallel evolution across species. The combination of extensive temporal sampling in the field, experimental evolution, and genomics makes for compelling findings. The authors are to be commended for acknowledging the main limitations of their study in the Discussion. Framing the work in a broader context of resistance beyond arthropod pests would further increase the appeal of the study, which is of relevance for both agronomic practitioners and evolutionary biologists.

eLife Assessment

This important manuscript presents a thorough analysis of trans-specific polymorphism (TSP) in Major Histocompatibility Complex gene families across primates. The analysis makes the most of currently available genomic data and methods to substantially increase the amount and evolutionary time that TSPs can be observed. Both false negative TSPs due to missing genes at the assembly and/or annotation level, as well as false positives due to read mismapping with missing paralogs, are well assessed and discussed. Overall the evidence provided is compelling, and the manuscript clearly delineates the path for future progress on the topic.

eLife Assessment

Tropical single-island endemic bird populations are particularly vulnerable to climate change. The authors investigate genetic evidence of how such species dealt with climate changes in the past as a possible predictor for how they will respond to change in the future, which could provide an important example for the fields of conservation genetics and island biogeography. The authors' integration of genomics and habitat modeling is commendable, but we find that the support for their conclusions is incomplete: at times, the results presented appear to contradict each other, the authors do not fully account for key variables, and the limited taxonomic scope may cause problematic biases for the conclusions.

eLife Assessment

This study provides valuable insights into a new toxin-antidote element in C. elegans, the first naturally occurring unlinked toxin-antidote system where endogenous small RNA pathways post-transcriptionally suppress the toxin. The strength of evidence is solid, using a combination of genomic and experimental methods. Enthusiasm, however, is tempered by its reliance on meta-analysis of existing data sets and limited experimental evaluation.

eLife Assessment

Alignment and sequencing errors are a major concern in molecular evolution, and this valuable study represents a welcome improvement for genome-wide scans of positive selection. This new method seems to perform well and is generally convincing, although the evidence could be made more direct and more complete through additional simulations to determine the extent to which alignment errors are being properly captured.

eLife Assessment

The authors examine the effect of cell-free chromatin particles (cfChPs) derived from human serum or from dying human cells on mouse cells in culture and propose that these cfChPs can serve as vehicles for cell-to-cell active transfer of foreign genetic elements. The work presented in this paper is intriguing and potentially important, but it is incomplete. At this stage, the claim that horizontal gene transfer can occur via cfChPs is not well supported because it is only based on evidence from one type of methodological approach (immunofluorescence and fluorescent in situ hybridization (FISH)) and is not validated by whole genome sequencing.

eLife Assessment

This paper discusses the cognitive implications of potential intentional burial, wall engraving creation, and fire as light source use behaviors by relatively small-brained Homo naledi hominins. The discussion presented in the paper is valuable theoretically in its healthy questioning of prior assumptions concerning the socio-biological constraints of hominin meaning-making behavior. The discussion also contributes practically given that these behaviors have been ascribed to Homo naledi in two associated papers. Still, the strength of evidence in this contribution relies on the validity of the conclusions from the two associated papers, which remain actively questioned. The ultimate assessment of this work will vary among individual readers depending on how they view this debate, but if the conclusions from the associated papers hold up, the conclusions in the current paper can be considered solid.

eLife Assessment

This important study offers a powerful empirical test of a highly influential hypothesis in population genetics. It incorporates a large number of animal genomes spanning a broad phylogenetic spectrum and treats them in a rigorous unified pipeline, providing the convincing negative result that effective population size scales neither with the content of transposable elements nor with overall genome size. These observations demonstrate that there is still no simple, global hypothesis that can explain the observed variation in transposable element content and genome size in animals.

eLife Assessment

This important manuscript by Genzoni et al. reports the striking discovery of a regulatory role for trophic eggs in ant caste determination. Prior to this study, trophic eggs were widely assumed to play only a nutritional role in the colony, but this compelling study shows that trophic eggs can suppress queen development, and therefore regulate caste determination in specific social contexts.

eLife Assessment

Kin selection and inclusive fitness have generated significant controversy. This paper reconsiders the general form of Hamilton's rule in which benefits and costs are defined as regression coefficients, with higher-order coefficients being added to accommodate non-linear interactions. The paper is a landmark contribution to the field with compelling, systematic analysis, giving clarity to long-standing debates.