Evolutionary Biology

Rescue of Escherichia coli auxotrophy by de novo small proteins

1. Arianne M Babina
2. Serhiy Surkov
3. Weihua Ye
4. Jon Jerlström-Hultqvist
5. Mårten Larsson
6. Erik Holmqvist
7. Per Jemth
8. Dan I Andersson
9. Michael Knopp

• Curated by eLife

  Evaluation Summary:

  This manuscript describes randomly generated small proteins of <50 amino acids that can rescue the growth of an auxotrophic mutant of Escherichia coli. The authors suggest that these proteins function by binding specifically to a regulatory element in the 5' UTR of the his operon RNA, altering RNA structure to increase expression. The study suggests that functional small proteins can evolve de novo and that newly evolved small proteins can function as regulators by binding RNA. This is an exciting idea, but the suggested mechanism involving the binding of the small proteins to RNA requires additional experimental support.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Pre-existing chromosomal polymorphisms in pathogenic E. coli potentiate the evolution of resistance to a last-resort antibiotic

1. Pramod K Jangir
2. Qiue Yang
3. Liam P Shaw
4. Julio Diaz Caballero
5. Lois Ogunlana
6. Rachel Wheatley
7. Timothy Walsh
8. R Craig MacLean

• Curated by eLife

  Evaluation Summary:

  This paper combines evolution experiments with genomic analysis of environmental samples to study the evolution of colistin resistance in E. coli. It highlights the importance of pre-existing genomic variations in clinical strains in driving the evolution of antibiotic resistance. The results presented here are relevant for clinical and non-clinical microbiologists studying antibiotic resistance to last-resort drugs like colistin. The design of the research is simple and elegant, and the genomic data analysis connects the in vitro findings to the real world. However, the authors could better align the experimental and clinical data, and better clarify their experimental design choices.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Evolution of diversity in metabolic strategies

1. Rodrigo Caetano
2. Yaroslav Ispolatov
3. Michael Doebeli

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to scientists within community ecology. The authors present a mathematically solid analysis of how nonlinear constraints influence resource-competition models with trade-offs, with the conclusions being similar to those of previous studies in which trade-offs are not exact.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

Flagellar energy costs across the tree of life

1. Paul E Schavemaker
2. Michael Lynch

• Curated by eLife

  Evaluation Summary:

  This work will be of interest to readers in the fields of cell biology, evolutionary biology, and biophysics. The collected data are of good quality and are properly analysed. The work thus convincingly demonstrates that energetic considerations (building costs versus potential benefit) must be taken into account to understand flagellar evolution.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

Host-parasite coevolution promotes innovation through deformations in fitness landscapes

1. Animesh Gupta
2. Luis Zaman
3. Hannah M Strobel
4. Jenna Gallie
5. Alita R Burmeister
6. Benjamin Kerr
7. Einat S Tamar
8. Roy Kishony
9. Justin R Meyer

• Curated by eLife

  Evaluation Summary:

  This study uses the parlance and framing of the fitness landscape to articulate a co-evolution story between host and parasite. It utilizes a tractable system, bacteriophage λ and E. coli, to ask questions that unite different pillars of evolutionary theory - evolutionary genetics (via the fitness landscape analogy), co-evolution, and host-parasite interactions. The findings will be relevant to a number of audiences, and will likely spawn downstream studies that further interrogate the molecular specifics that underlie host-parasite co-evolution.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Mutational robustness changes during long-term adaptation in laboratory budding yeast populations

1. Milo S Johnson
2. Michael M Desai

• Curated by eLife

  Evaluation Summary:

  Johnson and Desai previously reported "increasing cost epistasis", where mutations tended to have more deleterious effects in higher fitness backgrounds. Here they use the same system as before to investigate adapting populations by introducing a set of 91 mutations at multiple time points. As expected, the mean fitness effect of the mutations does decline in most (but not all) populations as they adapt but the effect is weaker than in the previous work, and in another condition, mean fitness effects of mutations do not change as the populations adapt. They suggest an intriguing interpretation (among others) that the "control coefficient" of selection on growth shifts between different genetic modules over time.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations

1. Anna M Langmüller
2. Jackson Champer
3. Sandra Lapinska
4. Lin Xie
5. Matthew Metzloff
6. Samuel E Champer
7. Jingxian Liu
8. Yineng Xu
9. Jie Du
10. Andrew G Clark
11. Philipp W Messer

• Curated by eLife

  Evaluation Summary:

  The issue of general fitness effects in organisms expressing Cas9 enzymes as part of gene drive genetic control strategies is important, particularly in the emerging field of vector control. This manuscript reports experiments aimed at teasing apart such effects in a Drosophila model system, providing evidence that off-target effects predominate, which may be ameliorated by utilising high-fidelity nucleases, but a more detailed analysis of data and justification for some of the assumptions, especially some direct evidence of off-target cleavage, are still needed to support the authors' inferences. It is currently also not entirely clear how the lines were generated and tested. Finally, additional modelling to include scenarios where the initial frequency of the drive allele is very low (as would be the case for an actual release) would help to strengthen the conclusions.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

A single nucleotide variant in the PPARγ-homolog Eip75B affects fecundity in Drosophila

1. Katja M Hoedjes
2. Hristina Kostic
3. Thomas Flatt
4. Laurent Keller

• Curated by eLife

  Evaluation Summary:

  Hoedjes et al. examine how a single nucleotide variant in a regulatory region upstream of the Eip75B gene influences key aspects of life history in Drosophila, using RNAi knockdowns, inbred lines and CRISPR/Cas9 allele replacement at the endogenous locus. This study represents one of the very few examples in animals where the effect of a naturally segregating single nucleotide variant on a complex trait is carefully quantified.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Lung evolution in vertebrates and the water-to-land transition

1. Camila Cupello
2. Tatsuya Hirasawa
3. Norifumi Tatsumi
4. Yoshitaka Yabumoto
5. Pierre Gueriau
6. Sumio Isogai
7. Ryoko Matsumoto
8. Toshiro Saruwatari
9. Andrew King
10. Masato Hoshino
11. Kentaro Uesugi
12. Masataka Okabe
13. Paulo M Brito

• Curated by eLife

  Evaluation Summary:

  This study used valuable materials from five osteichthyan vertebrate species and investigated their lung morphology in them. The comparison of the observations suggest an origin of the lung as an unpaired organ, with the present-day paired forms in amniotes being a result of secondary modification. The sound morphological comparison presented provides valuable insight into the evolution of the lung. The work will be of interest to colleagues studying vertebrate evolution.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern

1. Mahan Ghafari
2. Qihan Liu
3. Arushi Dhillon
4. Aris Katzourakis
5. Daniel B. Weissman

Reviewed by ScreenIT