Evolutionary Biology

Rapid expansion of SARS-CoV-2 variants of concern is a result of adaptive epistasis

1. Michael R. Garvin
2. Erica T. Prates
3. Jonathon Romero
4. Ashley Cliff
5. Joao Gabriel Felipe Machado Gazolla
6. Monica Pickholz
7. Mirko Pavicic
8. Daniel Jacobson

Reviewed by ScreenIT

Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations

1. Christopher W Bakerlee
2. Angela M Phillips
3. Alex N Nguyen Ba
4. Michael M Desai

• Curated by eLife

  Evaluation Summary:

  The pleiotropic effects of beneficial mutations have been characterized in various settings, but it is less clear whether and how these pleiotropic patterns change over the course of evolution. Using a technically innovative and intensive experimental design with evolving yeast populations, the authors show that patterns of pleiotropy depend on the evolution environment and can change and vary substantially over relatively short timescales. They also find a surprising amount of variation among replicate populations that increases over time, so generalism or specialism is not deterministic. These technical and conceptual strengths were diminished by insufficient focus on the details of certain treatments that are demonstrative of these broader findings, making the take-home message somewhat unclear.

  (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

Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region

1. Yatish Turkahia
2. Bryan Thornlow
3. Angie Hinrichs
4. Jakob McBroome
5. Nicolas Ayala
6. Cheng Ye
7. Nicola De Maio
8. David Haussler
9. Robert Lanfear
10. Russell Corbett-Detig

Reviewed by ScreenIT

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