Evolutionary Biology

Variation in synonymous nucleotide composition among genomes of sarbecoviruses and consequences for the origin of COVID-19

1. Alexandre Hassanin

Reviewed by ScreenIT

Evolution of brilliant iridescent feather nanostructures

1. Klara Katarina Nordén
2. Chad M Eliason
3. Mary Caswell Stoddard

• Curated by eLife

  Evaluation Summary:

  Nordén et al. examine feather iridescent color diversity across bird species. Their findings show how key modifications in feather melanosomes, pivotal nanophotonic structures, underlie the brilliant colors of iridescent feathers, broadening feather color range approximately twofold. In a next step, the authors evaluate the function of feather melanosomes by performing optical modelling of nanostructure diversity, evaluating up to 4500 distinct nanostructure combinations, which are then contrasted with the observed (color) spectral data from 120 plumage regions across 80 (diverse) bird species. This meticulous integration of diverse methods across a comprehensive dataset will not only inform biologists studying structural color biodiversity, but it may also inspire engineers designing nanophotonic systems.

  (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

Evolutionary footprints of a cold relic in a rapidly warming world

1. Eva Wolf
2. Emmanuel Gaquerel
3. Mathias Scharmann
4. Levi Yant
5. Marcus A Koch

• Curated by eLife

  Evaluation Summary:

  This manuscript has the potential to be of broad interest to scientists seeking to understand the evolutionary dynamics of plants during past periods of rapid climate change. Specifically, within the target genus of Cochlearia, the results indicate increased rates of speciation and diversification in response to pronounced glacial cycles. Future work to establish more direct mechanistic links between the results and conclusions will improve our understanding of adaptation and speciation.

  (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

The roles of history, chance, and natural selection in the evolution of antibiotic resistance

1. Alfonso Santos-Lopez
2. Christopher W Marshall
3. Allison L Haas
4. Caroline Turner
5. Javier Rasero
6. Vaughn S Cooper

• Curated by eLife

  Evaluation Summary:

  This work, which will be of value to evolutionary and clinical microbiologists, uses a well-designed experimental evolution strategy to tease apart contributions of history, chance, and selection on the evolution of antibiotic resistance in A. baumannii, an important microbial pathogen. While relevant, the work will benefit from further clarification regarding some of the concepts and procedures used and revision of some of the interpretations.

  (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

Phylogenetic reconciliation reveals extensive ancestral recombination in Sarbecoviruses and the SARS-CoV-2 lineage

1. Sumaira Zaman
2. Samuel Sledzieski
3. Bonnie Berger
4. Yi-Chieh Wu
5. Mukul S. Bansal

Reviewed by ScreenIT

A simple method for estimating time-irreversible nucleotide substitution rates in the SARS-CoV-2 genome

1. Kazuharu Misawa
2. Ryo Ootsuki

Reviewed by ScreenIT

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