Evolutionary Biology

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

1. Angela M Phillips
2. Katherine R Lawrence
3. Alief Moulana
4. Thomas Dupic
5. Jeffrey Chang
6. Milo S Johnson
7. Ivana Cvijovic
8. Thierry Mora
9. Aleksandra M Walczak
10. Michael M Desai

• Curated by eLife

  Evaluation Summary:

  CR6261 and CR9114 are two antibodies that bind to the conserved stem of influenza hemagglutinin (HA) through their VH regions and differ by 14-18 mutations from their inferred germline sequences. The authors constructed large combinatorial libraries containing all combinations of 11 and 16 binding-surface mutations for CR6261 and CR9114. These were used in yeast surface display titrations to infer individual and epistatic contributions to binding diverse HAs and to infer possible evolutionary trajectories going from germline to the mature antibodies. The study provides a wealth of knowledge on amino acid contributions to binding affinity. The study informs our understanding of biochemical epistasis, and could potentially serve as a starting point for a more detailed understanding of antibody affinity maturation more generally.

  (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 names with the authors.)

Reviewed by eLife

Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations

1. Julia M Kreiner
2. George Sandler
3. Aaron J Stern
4. Patrick J Tranel
5. Detlef Weigel
6. John R Stinchcombe
7. Stephen I Wright

• Curated by eLife

  Evaluation Summary:

  This paper studies the evolution of herbicide resistance in Amaranthus tuberculatus, a widespread agricultural weed. By illuminating how adaptive mutations arose and spread in this remarkable example of rapid human-induced adaptation, the study will be of interest to a broad audience, ranging from plant biologists interested in herbicide resistance to evolutionary biologists and population geneticists studying the fundamental factors and processes that govern rapid adaptation. The paper applies innovative population genetic methodology to support its primary finding that resistance mutations have evolved multiple times in parallel.

  (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 names with the authors.)

Reviewed by eLife

A conserved strategy for inducing appendage regeneration in moon jellyfish, Drosophila, and mice

1. Michael J Abrams
2. Fayth Hui Tan
3. Yutian Li
4. Ty Basinger
5. Martin L Heithe
6. Anish Sarma
7. Iris T Lee
8. Zevin J Condiotte
9. Misha Raffiee
10. John O Dabiri
11. David A Gold
12. Lea Goentoro

• Curated by eLife

  Evaluation Summary:

  This paper argues that simple nutritional interventions (L-leucine / insulin / sucrose) can trigger appendage regeneration in species various that do not regenerate appendages in normal conditions. Although the data on Drosophila are not fully convincing and further evidence is needed for this species, in the jellyfish Aurelia and in mice, the results are stunning and provide novel model systems for inducing appendage regeneration in animals and for studying the mechanisms underlying regeneration. These results strengthen an old idea that animals may have an intrinsic capacity to regenerate, which could be revealed by simple (e.g. nutritional) interventions. This paper will be of interest to readers in the field of signaling in regeneration and also in regenerative medicine.

  (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

Tempo and mode of gene expression evolution in the brain across primates

1. Katherine Rickelton
2. Trisha M Zintel
3. Jason Pizzollo
4. Emily Miller
5. John J Ely
6. Mary Ann Raghanti
7. William D Hopkins
8. Patrick R Hof
9. Chet C Sherwood
10. Amy L Bauernfeind
11. Courtney C Babbitt

• Curated by eLife

  Evaluation Summary:

  This paper represents a significant contribution to the study of gene expression and brain evolution in primates, which will be of interest to the evolutionary biology, anthropology, and comparative neuroscience communities. By performing RNA-seq on 18 taxa across the breadth of the extant primate phylogeny, the authors can examine how gene expression levels have changed over the past 70 million years of evolution and attempt to infer genes that contribute to the large amount of variation in brain size across primates. While the data set itself is valuable and exciting, methodological detail is lacking and several opportunities to leverage phylogenetically informed methods to study gene expression and brain size evolution are missed.

  (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

Neural mechanisms of modulations of empathy and altruism by beliefs of others’ pain

1. Taoyu Wu
2. Shihui Han

• Curated by eLife

  Evaluation Summary:

  This article represents a series of behavioral and imaging experiments investigating the effect of cognitive manipulation of beliefs on the explicit perception of other individual's pain and altruistic behavior. The results indicate that manipulations of people's beliefs regarding how much another person suffers alters the way participants rate the pain of others as well as the amount of money participants are willing to donate to the other person. Neuroimaging experiments, using EEG and fMRI, show that manipulating beliefs modulates neural activity in an early time window (P2 component) in response to the emotional expression of the other individual, involving temporo-parietal and medial frontal cortices. While there are some potential concerns about the novelty and implication of these findings, the results are overall clear and consistent throughout the six experiments, integrate with existing data, and are of broad interest to the researchers studying the neurobiology of empathy.

  (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

Understanding patterns of HIV multi-drug resistance through models of temporal and spatial drug heterogeneity

1. Alison F Feder
2. Kristin N Harper
3. Chanson J Brumme
4. Pleuni S Pennings

• Curated by eLife

  Evaluation Summary:

  This study considers how HIV evolutionary dynamics in a multiple drug-treated individual can give rise to the clinical patterns of the accrual of drug resistance mutations, including with understandings of the pharmacokinetics of the drugs in the body to help explain some of the patterns. The subject is of importance both clinically – for the optimal treatment choice for people living with HIV – and scientifically, due to the potential to predict and interpret evolutionary trajectories.

  (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 names with the authors.)

Reviewed by eLife

The infinite alleles model revisited: a Gibbs sampling approach

1. Marc Manceau

Reviewed by ScreenIT

Molecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of selected mutations

1. Patrícia Aline Gröhs Ferrareze
2. Ricardo Ariel Zimerman
3. Vinícius Bonetti Franceschi
4. Gabriel Dickin Caldana
5. Paulo Augusto Netz
6. Claudia Elizabeth Thompson

Reviewed by ScreenIT

ACE2 binding is an ancestral and evolvable trait of sarbecoviruses

1. Tyler N. Starr
2. Samantha K. Zepeda
3. Alexandra C. Walls
4. Allison J. Greaney
5. Sergey Alkhovsky
6. David Veesler
7. Jesse D. Bloom

Reviewed by ScreenIT

Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut

1. Erik Bakkeren
2. Joana Anuschka Herter
3. Jana Sanne Huisman
4. Yves Steiger
5. Ersin Gül
6. Joshua Patrick Mark Newson
7. Alexander Oliver Brachmann
8. Jörn Piel
9. Roland Regoes
10. Sebastian Bonhoeffer
11. Médéric Diard
12. Wolf-Dietrich Hardt

• Curated by eLife

  Evaluation Summary:

  This work describes an important feature of within-host acquisition of antibiotic resistance. This is a follow-up to their recent publication (Bakkeren et al. 2019), and complements their finding of persister cells in the tissues, to show that also chronic, tissue residing bacteria can provide plasmid tissue reservoirs. The experiments the authors performed are elegant and timely. This manuscript will be of interest to readers in the fields of infection biology, plasmid ecology, gut microbiomes, and antimicrobial resistance.

  (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