Evolutionary Biology

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

Viral population genomics reveals host and infectivity impact on SARS-CoV-2 adaptive landscape

1. Kaitlyn Gayvert
2. Richard Copin
3. Sheldon McKay
4. Ian Setliff
5. Wei Keat Lim
6. Alina Baum
7. Christos A. Kyratsous
8. Gurinder S. Atwal

Reviewed by ScreenIT

Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins

1. Muhammad Hasan
2. Zhouyi He
3. Mengqi Jia
4. Alvin C.F. Leung
5. Kathiresan Natarajan
6. Wentao Xu
7. Shanqi Yap
8. Feng Zhou
9. Shihong Chen
10. Hailei Su
11. Kaicheng Zhu
12. Haibin Su

Reviewed by ScreenIT

Rapid longitudinal SARS-CoV-2 intra-host emergence of novel haplotypes regardless of immune deficiencies

1. Laura Manuto
2. Marco Grazioli
3. Andrea Spitaleri
4. Paolo Fontana
5. Luca Bianco
6. Luigi Bertolotti
7. Martina Bado
8. Giorgia Mazzotti
9. Federico Bianca
10. Francesco Onelia
11. Giovanni Lorenzin
12. Fabio Simeoni
13. Dejan Lazarevic
14. Elisa Franchin
15. Claudia Del Vecchio
16. Ilaria Dorigatti
17. Giovanni Tonon
18. Daniela Cirillo
19. Enrico Lavezzo
20. Andrea Crisanti
21. Stefano Toppo

Reviewed by ScreenIT