Evolutionary Biology

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

Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein

1. Jordan D. Zehr
2. Sergei L. Kosakovsky Pond
3. Darren P. Martin
4. Kristina Ceres
5. Gary R. Whittaker
6. Jean K. Millet
7. Laura B. Goodman
8. Michael J. Stanhope

Reviewed by ScreenIT

Global Mutational Sweep of SARS-CoV-2: From Chaos to Order

1. Xin Wang
2. Mingda Hu
3. Yuan Jin
4. Boqian Wang
5. Yunxiang Zhao
6. Long Liang
7. Junjie Yue
8. Hongguang Ren

Reviewed by ScreenIT

Differential use of multiple genetic sex determination systems in divergent ecomorphs of an African crater lake cichlid

1. Hannah Munby
2. Tyler Linderoth
3. Bettina Fischer
4. Mingliu Du
5. Grégoire Vernaz
6. Alexandra M. Tyers
7. Benjamin P. Ngatunga
8. Asilatu Shechonge
9. Hubert Denise
10. Shane A. McCarthy
11. Iliana Bista
12. Eric A. Miska
13. M. Emília Santos
14. Martin J. Genner
15. George F. Turner
16. Richard Durbin

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to evolutionary biologists and geneticists, particularly those interested in the evolution of sex determination and sexual conflicts. It provides an unprecedented dataset that enables the authors to show convincingly the presence of three different Y-chromosomes segregating within a species, differential presence of the Ys among ecomorphs, and identifies candidate sex determination genes on the different Ys. Examination of the impact of genetic sex on a male fitness proxy in ecological context provides a compelling case study to explain the stable maintenance of multiple genetic sex determination systems in a species.

  (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

Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals

1. Omaya Dudin
2. Sébastien Wielgoss
3. Aaron M. New
4. Iñaki Ruiz-Trillo

Reviewed by Review Commons

Evolution of host-microbe cell adherence by receptor domain shuffling

1. EmilyClare P Baker
2. Ryan Sayegh
3. Kristin M Kohler
4. Wyatt Borman
5. Claire K Goodfellow
6. Eden R Brush
7. Matthew F Barber

• Curated by eLife

  Evaluation Summary:

  Baker et al. investigates the molecular evolution in primates of one protein family, the CEACAMs, that are a recurrent target of bacterial surface adhesions at epithelial surfaces. They show that multiple members of this gene family have experienced repeated episodes of positive selection in primates, especially in the N-terminal domains that are associated with protein binding and go on to evaluate the functional consequences of these evolutionary changes.

  (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 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife