Evolutionary Biology

Variational Phylodynamic Inference Using Pandemic-scale Data

1. Caleb Ki
2. Jonathan Terhorst

Reviewed by ScreenIT

The rise and fall of SARS-CoV-2 variants and the emergence of competing Omicron lineages

1. Tanner Wiegand
2. Aidan McVey
3. Anna Nemudraia
4. Artem Nemudryi
5. Blake Wiedenheft

Reviewed by ScreenIT

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

1. William W Hannon
2. Pavitra Roychoudhury
3. Hong Xie
4. Lasata Shrestha
5. Amin Addetia
6. Keith R Jerome
7. Alexander L Greninger
8. Jesse D Bloom

Reviewed by ScreenIT

In vivo intraoral waterflow quantification reveals hidden mechanisms of suction feeding in fish

1. Pauline Provini
2. Alexandre Brunet
3. Andréa Filippo
4. Sam Van Wassenbergh

• Curated by eLife

  Evaluation Summary:

  How do fish suck food underwater? Using new artificial food particles that are radio opaque and naturally buoyant, Provini et al. imaged the roller-coaster ride that food particles make being sucked-in from outside to inside the fish, using 3D stereo high-speed fluoroscopy. The recordings show fish to have an intriguing ability to generate flows that center the food particles as they enter the buccal cavity that carries them from the outside to the center of the digestive tract. Remarkably, the flow patterns in the mouth that accomplish this seem to differ between the two species of fish studied, although samples sizes are small at present. These new insights will interest biologists working on suction feeding mechanisms ranging from millimeter-sized carnivorous water plants, tadpoles and fish larvae, to large fish and marine mammals, and even gigantic whales. Bioinspired engineers designing rapid underwater suction apparatuses may benefit from harnessing the new insights to elegantly center items of interest.

  (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

Late-life fitness gains and reproductive death in Cardiocondyla obscurior ants

1. Luisa Maria Jaimes-Nino
2. Jürgen Heinze
3. Jan Oettler

• Curated by eLife

  Evaluation Summary:

  Evolution of ageing remains only partially understood, and this research will be of interest to evolutionary biologists, entomologists, or anyone intrigued by senescence. The authors focus on following a large number of ant (C. obscurior) colonies and provide intriguing data in relation to age-specific mortality and reproduction. The gist of their argument is that the mortality is decreasing with age while reproduction (production of sexuals) is increasing with age, such that there is little evidence of ageing in this species. The experimental design is elegant and the data collection thorough, providing insight into the rarely observed final stages of an ant colonies life. The analyses are mostly sound, but the conclusions would benefit from a broader exploration of the structure and constraints inherent to ant societies.

  (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

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