Evolutionary Biology

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

Cnidarian hair cell development illuminates an ancient role for the class IV POU transcription factor in defining mechanoreceptor identity

1. Ethan Ozment
2. Arianna N Tamvacakis
3. Jianhong Zhou
4. Pablo Yamild Rosiles-Loeza
5. Esteban Elías Escobar-Hernandez
6. Selene L Fernandez-Valverde
7. Nagayasu Nakanishi

• Curated by eLife

  Evaluation Summary:

  This manuscript focusses on a little studied, but highly interesting presumptive mechanosensory cell type in cnidarians, the 'hair cell'. The work shows that the POU-IV transcription factor is required for the maturation of this cell type in the sea anemone Nematostella vectensis. Because POU-IV transcription factors also play essential roles in the differentiation of mechanoreceptors in many bilaterian phyla, this suggests an evolutionarily ancient role of POU-IV in regulating mechanosensory identity. This study will hence be of great interest to developmental biologists and evolutionary biologists who are interested in the developmental evolution of neuronal cell types.

  (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

Genetic basis and dual adaptive role of floral pigmentation in sunflowers

1. Marco Todesco
2. Natalia Bercovich
3. Amy Kim
4. Ivana Imerovski
5. Gregory L Owens
6. Óscar Dorado Ruiz
7. Srinidhi V Holalu
8. Lufiani L Madilao
9. Mojtaba Jahani
10. Jean-Sébastien Légaré
11. Benjamin K Blackman
12. Loren H Rieseberg

• Curated by eLife

  Evaluation Summary:

  This work identifies the primary genetic mechanism underlying UV-absorbance variation across the geographic range of sunflower (Helianthus annuus) and provides evidence that suggests that abiotic variables, rather than pollinators, may maintain this variation in H. annuus and perhaps Helianthus broadly. While claims about direct links to fitness in natural population remain untested, the authors synthesize an ambitious amount of work from an impressive breadth of methods (from transgenics to ecology) that will be of high interest to ecologists and evolutionary biologists.

  (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

An estimate of the deepest branches of the tree of life from ancient vertically evolving genes

1. Edmund RR Moody
2. Tara A Mahendrarajah
3. Nina Dombrowski
4. James W Clark
5. Celine Petitjean
6. Pierre Offre
7. Gergely J Szöllősi
8. Anja Spang
9. Tom A Williams

• Curated by eLife

  Evaluation Summary:

  This contribution is of interest to molecular phylogeny scientists in particular and to a broad public interested in early evolution in general, as it confirms the long-standing (but recently challenged) assumption that bacteria and archaea are separated by a long branch. It elegantly rebuts a recent study claiming that one of the common markers used for molecular evolution, ribosomal proteins, are actually ill-suited for deep phylogenies and that archaea and bacteria are much closer to each other than previously thought.

  (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