Evolutionary Biology

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

The need for high-quality oocyte mitochondria at extreme ploidy dictates mammalian germline development

1. Marco Colnaghi
2. Andrew Pomiankowski
3. Nick Lane

• Curated by eLife

  Evaluation Summary:

  Non-nuclear genomes, such as those of mitochondria, contribute to many aspects of cellular function, organismal function, and fitness. Understanding their biology and evolutionary dynamics is thus an essential component eukaryotic evolution. The manuscript addresses an important and complex problem regarding the relationship between mitochondrial mutations, their impacts on gamete function, and the attendant evolutionary processes. The authors present a computational approach to distinguish between three hypotheses about the level of selection most likely to explain the distribution of mitochondrial mutations in human populations. They propose that selection among mitochondria is the most likely process to match empirical, clinical data, for mitochondrial mutation loads. There is, however, currently a mismatch between the fact that the data are derived from numerous different species whose biology is not always comparable, the model, and the title of the paper.

  (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

Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

1. Katelyn Mika
2. Mirna Marinić
3. Manvendra Singh
4. Joanne Muter
5. Jan Joris Brosens
6. Vincent J Lynch

• Curated by eLife

  Evaluation Summary:

  The study by Mika and colleagues uses a comparative transcriptomics approach to identify changes in the expression of genes that specifically occurred during the evolution of the human endometrium. The authors find that hundreds of genes gained or lost endometrial expression in the human lineage and that several of these genes are potentially implicated in the pathophysiology of human pregnancy. The study contributes to ongoing interest in the effect of human evolution on the pathophysiology of human pregnancy, and has the potential to serve as a model of how to study the evolution of pregnancy-associated genomic changes in particular species and tissues.

  (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, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Mutation signatures inform the natural host of SARS-CoV-2

1. Shanjun Deng
2. Ke Xing
3. Xionglei He

Reviewed by ScreenIT

Increased frequency of recurrent in-frame deletions in new expanding lineages of SARS CoV-2 reflects immune selective pressure

1. Arghavan Alisoltani
2. Lukasz Jaroszewski
3. Mallika Iyer
4. Arash Iranzadeh
5. Adam Godzik

Reviewed by ScreenIT

One viral sequence for each host? – The neglected within-host diversity as the main stage of SARS-CoV-2 evolution

1. Yongsen Ruan
2. Mei Hou
3. Jiarui Li
4. Yangzi Song
5. Hurng-YI Wang
6. Xionglei He
7. Hui Zeng
8. Jian Lu
9. Haijun Wen
10. Chen Chen
11. Chung-I Wu

Reviewed by ScreenIT