Evolutionary Biology

eLife Assessment

The focus of this manuscript is a computational procedure to reveal signatures of selection on transcription factor binding sites through assessing changes in predicted binding affinity, setting out to avoid biases inherent in previous tests. The general approach could become a valuable resource for the community that can also be used for a broader range of questions. However, in its current implementation, the methods are inadequate to sufficiently support the primary claims.

eLife Assessment

This paper presents important findings on how the shapes of leaves might be biased towards simpler shapes due to biases in how variation is generated by developmental processes rather than selection. The authors present solid evidence that combines image analysis of a herbarium dataset and computational analysis of a model of leaf development. The paper should be of interest to diverse researchers, ranging from plant development to the evolution of complexity more broadly.

eLife Assessment

This valuable study advances our understanding of genes contributing to Drosophila resistance to octanoic acid, a primary toxin present in Morinda fruit, which is the natural host plant for Drosophila sechellia, a species that has become a model for understanding evolutionary specialization. The authors provide solid results from an original combination of experimental evolution and cell-based CRISPR screens. This work will be of interest to the Drosophila community and researchers interested in the genetic basis of polygenic traits.

eLife Assessment

In this important theoretical contribution, the authors study the evolution of large microbial populations competing for resources in the challenging and relevant regime of overlapping ecological and evolutionary timescales. The modeling approach is overall convincing, anlthough its presentation would benefit from clarifications, e.g. on assumptions and approximations. The results will be of broad interest to researchers in evolutionary biology, ecology and microbiology.

eLife Assessment

Tropical single-island endemic bird populations are particularly vulnerable to climate change. This study investigates genetic evidence of how such species dealt with climate change in the past as a possible predictor of how they will respond 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 currently inadequate: some model parameter choices do not seem to reflect the biology of the studied species or to be well founded, which can cause misalignment of modeled dynamics with glaciation windows crucial for interpreting the study's results against its claims.

eLife Assessment

This important study identifies a new toxin/antidote (T/A) system in the model nematode C. elegans. These results suggest there are alternative mechanisms to neutralize selfish genetic elements. The authors present solid data that robustly support their central conclusion. This work will be of broad interest to investigators in evolutionary biology and reproductive biology.

eLife Assessment

This important study used whole-genome data to investigate Beefalo ancestry for the first time, providing insight into the genetics of Beefalo cattle and challenging the long-held claim of 37.5% bison ancestry reported by the American Beefalo Association. Despite some limitations regarding sequencing depth and sampling, the expert use of a comprehensive set of population-genomic methods allowed the authors to demonstrate convincingly that Beefalo and bison hybrid ancestry profiles are consistent with repeated backcrossing to either parental species. The work will be of significant interest to evolutionary biologists, population geneticists, animal breeders, and those involved in the conservation genetics of bovine species.

eLife Assessment

In this manuscript, the authors investigate programmed DNA elimination (PDE) across nematodes using a large-scale cytological approach. This work is potentially significant because it expands PDE beyond a few known nematodes to a much broader set of Rhabditidae species, providing an important resource for investigating PDE's evolutionary origins and functions. The strength of evidence, however, is incomplete; the technique used to evaluate PDE is insufficient to provide unambiguous support for the phenomenon, so additional methods, such as genomic sequencing from a few species spanning the range of elimination levels, would be required to confirm these findings. This research would be of interest to geneticists, evolutionary biologists, and those working on the regulation of genome integrity.

eLife Assessment

This important study implicates that changes in cell regulation may contribute to the evolution of multicellularity. The evidence supporting the conclusions is convincing, with rigorous methods used to test alternative hypotheses. The work will be of broad interest to cell and evolutionary biologists and those studying the cell cycle and cancer.

eLife Assessment

This manuscript applies a theoretical analysis to two published datasets on yeast and bacterial evolution to compare different ways of quantifying fitness. It makes an important advance by clarifying how discrepancies can arise by using different approaches and provides recommendations for best practices. Overall, this is an impressive and highly beneficial study that is based on convincing evidence and has the potential of setting standards in this rapidly growing field.