Evolutionary Biology

An evolutionary model identifies the main selective pressures for the evolution of genome-replication profiles

1. Rossana Droghetti
2. Nicolas Agier
3. Gilles Fischer
4. Marco Gherardi
5. Marco Cosentino Lagomarsino

• Curated by eLife

  Summary: The reviewers appreciate that the manuscript presents a simple but compelling model that explains the dynamics of replication origin birth and death, which enhances our understanding of the selection pressures that have shaped the distribution of replication origins. However, both reviewers had a series of concerns.

Reviewed by eLife

Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk

1. Juan Manuel Vazquez
2. Vincent J. Lynch

Reviewed by eLife

Mitochondrial copper and phosphate transporter specificity was defined early in the evolution of eukaryotes

1. Xinyu Zhu
2. Aren Boulet
3. Katherine M. Buckley
4. Casey B. Phillips
5. Micah G. Gammon
6. Laura E. Oldfather
7. Stanley A. Moore
8. Scot C. Leary
9. Paul A. Cobine

Reviewed by eLife

High-quality carnivore genomes from roadkill samples enable species delimitation in aardwolf and bat-eared fox

1. Rémi Allio
2. Marie-Ka Tilak
3. Céline Scornavacca
4. Nico L. Avenant
5. Erwan Corre
6. Benoit Nabholz
7. Frédéric Delsuc

• Curated by eLife

  Summary: Collectively, we liked a lot about your paper and we would accordingly like to encourage its continued evolution. However, we felt that the approximately equal balance at present between the roadkill genomics assembly pipeline and the phylogenetic and genetic diversity results was not justified, and we requested a shift accordingly as described below. Second, we require several analytical updates to the manuscript to ensure robustness of the main genetic diversity results.

Reviewed by eLife

Adaptive evolution of nontransitive fitness in yeast

1. Sean W Buskirk
2. Alecia B Rokes
3. Gregory I Lang

• Curated by eLife

  Summary: The findings presented in this manuscript are interesting. They show that selection is happening at multiple scales - among viruses within a cell - and between their host cells within a population. The conflict between these levels of selection results in evolved populations that are less fit than the ancestors. This work demonstrates that evolution may not be a simple linear march of progress. Rather, progress over short time scales can sometimes lead to a reduction of fitness over the longer time scale due to the evolution of ecological interactions.

Reviewed by eLife

Evolutionary dynamics of transposable elements in bdelloid rotifers

1. Reuben W. Nowell
2. Christopher G. Wilson
3. Pedro Almeida
4. Philipp H. Schiffer
5. Diego Fontaneto
6. Lutz Becks
7. Fernando Rodriguez
8. Irina R. Arkhipova
9. Timothy G. Barraclough

• Curated by eLife

  Summary: Nowell et. al. present an analysis of transposable elements (TEs) in bdelloid rotifers and compare their dynamics to those in related species. Through this comparative analysis, the authors test various evolutionary hypotheses about asexual genomes, as well as recent suggestions that these ancient asexual organisms may not actually be asexual. Nowell et. al. find no evidence supporting the presence of recombination (and thus, sex) in bdelloid rotifers, and no strong predicted evolutionary signatures of asexuality in TE dynamics in these species. Additionally, they find evidence for expansion of RNAi-related genes, which may play a role in countering the expected TE dynamics in asexual species. Overall, this work is substantial, thorough, and presents some answers to long-standing questions about the genome evolution of long-term asexual species.

Reviewed by eLife

Migration without interbreeding: evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes

1. Christoph Stritt
2. Elena L. Gimmi
3. Michele Wyler
4. Abdelmonaim H. Bakali
5. Aleksandra Skalska
6. Robert Hasterok
7. Luis A. J. Mur
8. Nicola Pecchioni
9. Anne C. Roulin

• Curated by eLife

  Summary: This paper has several strengths. It addresses Brachypodium distachyon population genetics and demography to help understand phenomena that have been investigated in less data-rich papers before. The authors do so with whole-genome sequencing of both a pre-existing global collection and additional "gap-filling" sampling. Analyses have been conducted using best practices, and most of the conclusions reflect the data and analyses presented.

  Major findings include the existence of large-scale population structure with three distinct lineages, discordance between geographical occurrence and genetic relatedness (clades within the lineages), and at shorter geographic scales, signs of dispersal without interbreeding. These patterns are explained by a combination of near-complete selfing and seed dispersal.

  The work attempts to cover a lot of ground, including selfing, seed dispersal, coalescence theory, microevolution, plasticity and frequency dependent selection, all mentioned in the abstract. The presentation would probably benefit from focusing on one or two aspects and making a stronger case for them.

  The reviewers noted that studies of this kind will often be descriptive due to the largely untestable nature of complex hypotheses of historical dispersal and evolution. Direct empirical testing of some of the hypotheses put forward here would require substantial experimental work (e.g. measuring the fitness of artificial hybrids to demonstrate post-zygotic reproductive isolation). As a first pass, simulations would likely suffice to test whether processes such as drift, selfing, and founder effects are sufficient to explain the population structure, or whether more complex processes such as frequency-dependent selection or reproductive isolation need to be invoked.

Reviewed by eLife

Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

1. Alejandro Berrio
2. Valerie Gartner
3. Gregory A Wray

Reviewed by PeerJ, ScreenIT

The Population Genetics of Collateral Resistance and Sensitivity

1. Sarah M. Ardell
2. Sergey Kryazhimskiy

Reviewed by eLife

On the Emergence of P-Loop NTPase and Rossmann Enzymes from a Beta-Alpha-Beta Ancestral Fragment

1. Liam M. Longo
2. Jagoda Jabłońska
3. Pratik Vyas
4. Manil Kanade
5. Rachel Kolodny
6. Nir Ben-Tal
7. Dan S. Tawfik

Reviewed by Review Commons