Evolutionary Biology

Adaptive convergent evolution of genome proofreading in SARS-CoV2: insights into the Eigen’s paradox

1. Keerthic Aswin
2. Srinivasan Ramachandran
3. Vivek T Natarajan

Reviewed by ScreenIT

Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

1. Kathryn E. Kistler
2. John Huddleston
3. Trevor Bedford

Reviewed by ScreenIT

Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level

1. David Laloum
2. Marc Robinson-Rechavi

Reviewed by Review Commons

Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes)

1. Zsolt Merényi
2. Máté Virágh
3. Emile Gluck-Thaler
4. Jason C Slot
5. Brigitta Kiss
6. Torda Varga
7. András Geösel
8. Botond Hegedüs
9. Balázs Bálint
10. László G Nagy

• Curated by eLife

  Evaluation Summary:

  This manuscript provides a deep characterization of transcriptional regulation and conservation across key stages of complex multicellular development during mushroom formation. The authors present evidence for extensive allele-specific expression that includes many developmentally regulated genes that appear to have evolved recently. These findings help underscore how the tuning of gene expression and gains of new genes, the function of which will need to be unraveled in future, are likely the basis for the evolution of complex morphologies in fungi. This work should be of broad interest to evolutionary biologists, and especially to those studying the evolution of gene regulation.

  (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 #4 agreed to share their names with the authors.)

Reviewed by eLife

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