Evolutionary Biology

Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic

1. Jesse D Bloom

Reviewed by ScreenIT

APOE4 is associated with elevated blood lipids and lower levels of innate immune biomarkers in a tropical Amerindian subsistence population

1. Angela R Garcia
2. Caleb Finch
3. Margaret Gatz
4. Thomas Kraft
5. Daniel Eid Rodriguez
6. Daniel Cummings
7. Mia Charifson
8. Kenneth Buetow
9. Bret A Beheim
10. Hooman Allayee
11. Gregory S Thomas
12. Jonathan Stieglitz
13. Michael D Gurven
14. Hillard Kaplan
15. Benjamin C Trumble

• Curated by eLife

  Evaluation Summary:

  The authors ask why the APOE4 allele has persisted, often at high frequencies, in human populations despite its associations to heart disease and Alzheimer's disease. They consider the hypothesis that APOE4 may be advantageous in a high pathogen and high physical environment settings (as opposed to a low pathogen industrial lifestyle) through an in-depth characterization of the Tsimane in Bolivia. The study is of broad interest with an insightful dataset; the conclusions are somewhat limited by the nature and current description and treatment of the data.

  (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

Highly contiguous assemblies of 101 drosophilid genomes

1. Bernard Y Kim
2. Jeremy R Wang
3. Danny E Miller
4. Olga Barmina
5. Emily Delaney
6. Ammon Thompson
7. Aaron A Comeault
8. David Peede
9. Emmanuel RR D'Agostino
10. Julianne Pelaez
11. Jessica M Aguilar
12. Diler Haji
13. Teruyuki Matsunaga
14. Ellie E Armstrong
15. Molly Zych
16. Yoshitaka Ogawa
17. Marina Stamenković-Radak
18. Mihailo Jelić
19. Marija Savić Veselinović
20. Marija Tanasković
21. Pavle Erić
22. Jian-Jun Gao
23. Takehiro K Katoh
24. Masanori J Toda
25. Hideaki Watabe
26. Masayoshi Watada
27. Jeremy S Davis
28. Leonie C Moyle
29. Giulia Manoli
30. Enrico Bertolini
31. Vladimír Košťál
32. R Scott Hawley
33. Aya Takahashi
34. Corbin D Jones
35. Donald K Price
36. Noah Whiteman
37. Artyom Kopp
38. Daniel R Matute
39. Dmitri A Petrov

• Curated by eLife

  Evaluation Summary:

  Drosophila species have long served as an important model system for genetics and genomics. The authors have developed an important community resource of high standard genomes for many species across the Drosophila clade. This resource will serve to empower the next generation of Drosophila research and provides an important road map for similar efforts in other groups of organisms.

  (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

Stronger net selection on males across animals

1. Lennart Winkler
2. Maria Moiron
3. Edward H Morrow
4. Tim Janicke

• Curated by eLife

  Evaluation Summary:

  This study addresses an interesting and important question in evolutionary biology: how does the variance in fitness (components) vary between the sexes? In particular, it aims to evaluate whether there is a larger sex difference in systems with strong sexual selection. This study will be of considerable interest to researchers working on sexual coevolution and the role of sexual selection in promoting adaptation. However, there are some concerns regarding the limitations of the data and methods in support of the conclusions.

  (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 #3 agreed to share their name with the authors.)

Reviewed by eLife

Evolution of irreversible somatic differentiation

1. Yuanxiao Gao
2. Hye Jin Park
3. Arne Traulsen
4. Yuriy Pichugin

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to researchers working on a broad range of questions in evolutionary biology, from the evolution of multicellularity to senescence and cancer. With their model, the authors study an often-neglected aspect of cellular differentiation and division of labour. While the model is relatively simple, the premise and the findings are thought-provoking and this study can potentially provide the groundwork for further investigation.

  (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

Novel neuroanatomical integration and scaling define avian brain shape evolution and development

1. Akinobu Watanabe
2. Amy M Balanoff
3. Paul M Gignac
4. M Eugenia L Gold
5. Mark A Norell

• Curated by eLife

  Evaluation Summary:

  Watanabe and colleagues analyse endocasts from extant (and some fossil) material to identify the distinct evolutionary and developmental patterns governing the growth and scaling relationships found in avian brains. The use of sophisticated geometric morphometrics, high-quality digital endocasts, and a suite of multivariate statistical tests robustly support the findings asserted in the paper, namely that crown birds exhibit a distinct allometric relationship that dictates their brain evolution and development. This paper is of broad interest to those working in comparative and evolutionary neuroanatomy as well as vertebrate paleontology.

  (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

Cis-regulatory variants affect gene expression dynamics in yeast

1. Ching-Hua Shih
2. Justin Fay

• Curated by eLife

  Evaluation Summary:

  The authors use RNAseq in yeast hybrids to study the effect of cis-variation on evolutionary divergence in gene expression and expression dynamics. Importantly, some of the findings are further confirmed using reporter assays. This is a clever and efficient approach that allows obtaining a genome-wide view of how cis-sequence variation affects expression. What sets this study apart from previous work is that the authors use hybrids across different genetic distances, separate expression levels and dynamics by sampling across different time points during an environmental shift, and also investigate 3' sequences. The main conclusions confirm that SNPs and InDels both affect gene expression as well as dynamics, and that on average, InDels have larger effects compared to SNPs, especially on expression dynamics. Moreover, the results also reflect negative selection on expression levels, with the effect of some cis mutations compensated by other cis variation, which ultimately results in complex interactions between the different cis-acting polymorphisms. Together, the results further our understanding of how cis sequence variation supports divergence in gene expression levels and dynamics.

  (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

Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2

1. Haibo Wu
2. Na Xing
3. Kaiwen Meng
4. Beibei Fu
5. Weiwei Xue
6. Pan Dong
7. Wanyan Tang
8. Yang Xiao
9. Gexin Liu
10. Haitao Luo
11. Wenzhuang Zhu
12. Xiaoyuan Lin
13. Geng Meng
14. Zhenglin Zhu

Reviewed by ScreenIT

Identification of evolutionary trajectories shared across human betacoronaviruses

1. Marina Escalera-Zamudio
2. Sergei L. Kosakovsky Pond
3. Natalia Martínez de la Viña
4. Bernardo Gutiérrez
5. Rhys P. D. Inward
6. Julien Thézé
7. Lucy van Dorp
8. Hugo G. Castelán-Sánchez
9. Thomas A. Bowden
10. Oliver G. Pybus
11. Ruben J.G. Hulswit

Reviewed by ScreenIT

SARS-CoV-2 convergent evolution as a guide to explore adaptive advantage

1. Jiří Zahradník
2. Jaroslav Nunvar
3. Gideon Schreiber

Reviewed by ScreenIT