Evolutionary Biology

Parallel evolution of Pseudomonas aeruginosa phage resistance and virulence loss in response to phage treatment in vivo and in vitro

1. Meaghan Castledine
2. Daniel Padfield
3. Pawel Sierocinski
4. Jesica Soria Pascual
5. Adam Hughes
6. Lotta Mäkinen
7. Ville-Petri Friman
8. Jean-Paul Pirnay
9. Maya Merabishvili
10. Daniel de Vos
11. Angus Buckling

• Curated by eLife

  Evaluation Summary:

  With the increased interest in phage therapy to treat antibiotic resistant infections, there are questions about the ease at which bacteria evolve phage resistance. To examine this, Castledine et al. cultured a set of bacterial isolates from a patient pre- and during phage therapy and also experimentally evolved a mixture of the bacterial isolates from the patient in the absence or presence of phage in vitro. Overall, the authors observed similarities between the evolutionary outcomes (genomic and phenotypic) in the patient and in vitro.

  (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

Does the evolution of division of labour require accelerating returns from individual specialisation?

1. Guy Alexander Cooper
2. Hadleigh Frost
3. Ming Liu
4. Stuart Andrew West

• Curated by eLife

  Evaluation Summary:

  This is a strong and concise paper using mathematical modelling to explore the conditions under which reproductive division of labour can evolve. It clarifies open questions regarding scenarios where specialising individuals experience diminishing returns from engaging in division of labour. The authors provide a comprehensive set of analyses highlighting when division of labour can evolve under such conditions and when not. The paper's primary claims are supported by the analysis provided, and the paper is likely of interest to evolutionary biologists, ecologists, computational biologists, and microbiologists.

  (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

Computation of Antigenicity Predicts SARS-CoV-2 Vaccine Breakthrough Variants

1. Ye-Fan Hu
2. Jing-Chu Hu
3. Hua-Rui Gong
4. Antoine Danchin
5. Ren Sun
6. Hin Chu
7. Ivan Fan-Ngai Hung
8. Kwok Yung Yuen
9. Kelvin Kai-Wang To
10. Bao-Zhong Zhang
11. Thomas Yau
12. Jian-Dong Huang

Reviewed by ScreenIT

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

1. Darren P Martin
2. Spyros Lytras
3. Alexander G Lucaci
4. Wolfgang Maier
5. Björn Grüning
6. Stephen D Shank
7. Steven Weaver
8. Oscar A MacLean
9. Richard J Orton
10. Philippe Lemey
11. Maciej F Boni
12. Houriiyah Tegally
13. Gordon Harkins
14. Cathrine Scheepers
15. Jinal N Bhiman
16. Josie Everatt
17. Daniel G Amoako
18. James Emmanuel San
19. Jennifer Giandhari
20. Alex Sigal
21. NGS-SA
22. Carolyn Williamson
23. Nei-yuan Hsiao
24. Anne von Gottberg
25. Arne De Klerk
26. Robert W Shafer
27. David L Robertson
28. Robert J Wilkinson
29. B Trevor Sewell
30. Richard Lessells
31. Anton Nekrutenko
32. Allison J. Greaney
33. Tyler N. Starr
34. Jesse D. Bloom
35. Ben Murrell
36. Eduan Wilkinson
37. Ravindra K Gupta
38. Tulio de Oliveira
39. Sergei L Kosakovsky Pond

Reviewed by ScreenIT

matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2

1. Cheng Ye
2. Bryan Thornlow
3. Angie Hinrichs
4. Alexander Kramer
5. Cade Mirchandani
6. Devika Torvi
7. Robert Lanfear
8. Russell Corbett-Detig
9. Yatish Turakhia

Reviewed by ScreenIT

Modeling the spatiotemporal spread of beneficial alleles using ancient genomes

1. Rasa A Muktupavela
2. Martin Petr
3. Laure Ségurel
4. Thorfinn Korneliussen
5. John Novembre
6. Fernando Racimo

• Curated by eLife

  Evaluation Summary:

  This manuscript is of broad interest for evolutionary biologists who seek to understand the dynamics of strongly advantageous mutations across time and space. It presents an elegant framework for inferring the strength of natural selection and spread of adaptive variants that accounts for spatially and temporal patterns of genetic variation. The authors extend a previously developed statistical inference method, performs some tests of the performance of their method on simulated data and apply the method to two well-known targets of selection. The development of the method is timely given the growing availability of ancient DNA collections, which have the power to largely increase the accuracy of selection inferences and parameter estimates.

  (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 name with the authors.)

Reviewed by eLife

Covariant Fitness Clusters Reveal Structural Evolution of SARS-CoV-2 Polymerase Across the Human Population

1. Chao Wang
2. Nadia Elghobashi-Meinhardt
3. William E. Balch

Reviewed by ScreenIT

The Runaway Evolution of SARS-CoV-2 Leading to the Highly Evolved Delta Strain

1. Yongsen Ruan
2. Mei Hou
3. Xiaolu Tang
4. Xionglei He
5. Xuemei Lu
6. Jian Lu
7. Chung-I Wu
8. Haijun Wen

Reviewed by ScreenIT

Novel multicellular prokaryote discovered next to an underground stream

1. Kouhei Mizuno
2. Mais Maree
3. Toshihiko Nagamura
4. Akihiro Koga
5. Satoru Hirayama
6. Soichi Furukawa
7. Kenji Tanaka
8. Kazuya Morikawa

• Curated by eLife

  Evaluation Summary:

  This is a fascinating article on the discovery of an unusual form of bacterial multicellularity: an organism that can exist in dense, filamentous multicellular structures and clusters of coccobacillus daughter cells. Experiments that mimic the periodic immersion that the bacteria experience in their natural cave environment suggest that water immersion plays a role in this life-cycle dynamics. This work, while rather qualitative, will nevertheless likely attract great interest from a diverse range of scientists working on multicellularity, the biophysics of cell packing, and geobiological problems.

  (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

Pyruvate:ferredoxin oxidoreductase and low abundant ferredoxins support aerobic photomixotrophic growth in cyanobacteria

1. Yingying Wang
2. Xi Chen
3. Katharina Spengler
4. Karoline Terberger
5. Marko Boehm
6. Jens Appel
7. Thomas Barske
8. Stefan Timm
9. Natalia Battchikova
10. Martin Hagemann
11. Kirstin Gutekunst

• Curated by eLife

  Evaluation Summary:

  The work supports the hypothesis that novel specific enymes evolved to modify metabolic pathways, allowing phototrophs to shift from growth under photoautotrophic and photomixotrophic growth conditions.

  (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 name with the authors.)

Reviewed by eLife