Evolutionary Biology

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

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