Evolutionary Biology

The rise and fall of SARS-CoV-2 variants and the mutational profile of Omicron

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

Reviewed by ScreenIT

Genomic epidemiological models describe pathogen evolution across fitness valleys

1. Pablo Cárdenas
2. Vladimir Corredor
3. Mauricio Santos-Vega

Reviewed by ScreenIT

Genomic determinants of Furin cleavage in diverse European SARS-related bat coronaviruses

1. Anna-Lena Sander
2. Andres Moreira-Soto
3. Stoian Yordanov
4. Ivan Toplak
5. Andrea Balboni
6. Ramón Seage Ameneiros
7. Victor Corman
8. Christian Drosten
9. Jan Felix Drexler

Reviewed by ScreenIT

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

1. Changshuo Wei
2. Ke-Jia Shan
3. Weiguang Wang
4. Shuya Zhang
5. Qing Huan
6. Wenfeng Qian

Reviewed by ScreenIT

Connexins evolved after early chordates lost innexin diversity

1. Georg Welzel
2. Stefan Schuster

• Curated by eLife

  Evaluation Summary:

  This paper addresses the question of why invertebrates use innexins and vertebrates connexins to form gap junctions. The authors survey genomic data across animal diversity to search for innexins and connexins and analyse the distribution of glycosylation sites in the extracellular loops of these proteins. The reported data support the hypothesis that connexins replaced innexins in chordate gap junctions due to an evolutionary bottle neck. Overall, the data were properly analyzed, but could be improved with respect to the sequence data for some phyla and the discussion from the results obtained.

  (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

The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

1. Lucie A Bergeron
2. Søren Besenbacher
3. Tychele Turner
4. Cyril J Versoza
5. Richard J Wang
6. Alivia Lee Price
7. Ellie Armstrong
8. Meritxell Riera
9. Jedidiah Carlson
10. Hwei-yen Chen
11. Matthew W Hahn
12. Kelley Harris
13. April Snøfrid Kleppe
14. Elora H López-Nandam
15. Priya Moorjani
16. Susanne P Pfeifer
17. George P Tiley
18. Anne D Yoder
19. Guojie Zhang
20. Mikkel H Schierup

• Curated by eLife

  Evaluation Summary:

  Bergeron et al show that mutation rate independently estimated by several teams with a same pedigree dataset can be different due the methods and approaches used to identify de novo mutations. This result is of primary importance because it shows the necessity to have standard mutation identification method and the difficulties to compare mutation rates from different studies.

  (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

Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes

1. Juan Rodriguez-Rivas
2. Giancarlo Croce
3. Maureen Muscat
4. Martin Weigt

Reviewed by ScreenIT

Getting out of a mammalian egg: the egg tooth and caruncle of the echidna

1. Jane C. Fenelon
2. Abbie Bennetts
3. Neal Anthwal
4. Michael Pyne
5. Stephen D. Johnston
6. Alistair R. Evans
7. Abigail S. Tucker
8. Marilyn B. Renfree

• Curated by eLife

  Evaluation Summary:

  This paper addresses the development, fate and homology of the egg tooth and caruncle of the short-beaked echidna (Tachyglossus aculeatus) and will be of broad interest to workers in the fields of vertebrate evolutionary/developmental biology, comparative anatomy and palaeontology. This manuscript features high quality histological and tomographic data from an unprecedented developmental series of pre- and post-hatching echidna stages. The study is well-organised and clearly reported, though additional image data would strengthen the authors' 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 #1 and Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy

1. Katelyn Mika
2. Camilla M Whittington
3. Bronwyn M McAllan
4. Vincent J Lynch

• Curated by eLife

  Evaluation Summary:

  Mika and colleagues reconstruct the evolution of uterine endometrial transcriptomes during pregnancy from 23 diverse species of mammals that differ with respect to their degree of placental invasiveness. Through this analysis the authors infer that the eutherian mammal ancestor had an invasive mode of placentation and that the degree of invasiveness of placentation is reflected on uterine endometrial gene expression during pregnancy. Thus, phylogenetic analysis of gene expression profiles of different mammals groups them on the basis of degree of placental invasiveness, a quite striking finding.

  (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

Mutation saturation for fitness effects at human CpG sites

1. Ipsita Agarwal
2. Molly Przeworski

• Curated by eLife

  Evaluation Summary:

  Diminishing returns on sampling new variable sites with increasing samples sizes is a classic limitation of population genomics and one that limits the power of population genomic approaches to make site-specific inferences of natural selection. This timely study demonstrates that methylated CpG sites, which have a mutation rate an order of magnitude higher than other sites in the genome, are saturated with polymorphisms in modern human genomic datasets. They can thus serve as a starting point for understanding the effects of natural selection at the resolution of single nucleotide sites. The manuscript is a clearly written presentation of the state of the field and the claims are supported by a variety of thoughtful analyses. Additional work will be needed to take full advantage of the insights from this study.

  (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