Evolutionary Biology

DNA methylation enables recurrent endogenization of giant viruses in an animal relative

1. Luke A. Sarre
2. Iana V. Kim
3. Vladimir Ovchinnikov
4. Marine Olivetta
5. Hiroshi Suga
6. Omaya Dudin
7. Arnau Sebé-Pedrós
8. Alex de Mendoza

Reviewed by preLights

A critical reexamination of recovered SARS-CoV-2 sequencing data

1. F. Débarre
2. Z. Hensel

Reviewed by Arcadia Science

The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role

1. Robert Horvath
2. Nikolaos Minadakis
3. Yann Bourgeois
4. Anne C Roulin

• Curated by eLife

  eLife assessment

  This valuable study seeks to disentangle the different selective forces shaping the evolutionary dynamics of transposable elements (TEs) in the wild grass Brachypodium distachyon. Using haplotype-length metrics, and genetic and environmental differentiation tests, the authors present convincing evidence that positive selection on TE polymorphisms is rare and that the distribution of TE ages points to purifying selection being the main force acting on TE evolution in this species. This study will be relevant for anyone interested in the role of TEs in evolution and adaptation.

Reviewed by eLife

Exploring the effects of ecological parameters on the spatial structure of genetic tree sequences

1. Mariadaria K. Ianni-Ravn
2. Martin Petr
3. Fernando Racimo

Reviewed by Peer Community in Evolutionary Biology

Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans

1. Florian Bénitière
2. Anamaria Necsulea
3. Laurent Duret

• Curated by eLife

  eLife assessment

  This fundamental study evaluates the evolutionary significance of variations in the accuracy of the intron-splicing process across vertebrates and insects. Using a powerful combination of comparative and population genomics approaches, the authors present convincing evidence that higher rates of alternative splicing tend to be observed in species with lower effective population size, a key prediction of the drift-barrier hypothesis. The analysis is carefully conducted and has broad implications beyond the studied species. As such, it will strongly appeal to anyone interested in the evolution of genome architecture and the optimisation of genetic systems.

Reviewed by eLife, Peer Community in Evolutionary Biology

The molecular mechanism and evolutionary divergence of caspase 3/7-regulated gasdermin E activation

1. Hang Xu
2. Zihao Yuan
3. Kunpeng Qin
4. Shuai Jiang
5. Li Sun

• Curated by eLife

  eLife assessment

  This important study elucidates the molecular divergence of caspase 3 and 7 in the vertebrate lineage. Convincing biochemical and mutational data provide evidence that in humans, caspase 7 has lost the ability to cleave gasdermin E due to changes in a key residue, S234. The diversification and specialization of gasdermins such as gasdermin E in humans compared to early vertebrates such as teleosts may enable each human gasdermin molecule to have more restricted and tightly regulated physiological functions in different cell death pathways.

Reviewed by eLife

How did UGA codon translation as tryptophan evolve in certain ciliates? A critique of Kachale et al. 2023 Nature

1. Estienne Carl Swart
2. Christiane Emmerich
3. Kwee Boon Brandon Seah
4. Minakshi Singh
5. Yekaterina Shulgina
6. Aditi Singh

• Curated by eLife

  eLife assessment

  The manuscript explores the ways in which the genetic code evolves, specifically how stop codons are reassigned to become sense codons. The authors present phylogenetic data showing that mutations at position 67 of the termination factor are present in organisms that nevertheless use the UGA codon as a stop codon, thereby questioning the importance of this position in the reassignment of stop codons. Alternative models on the role of eRF1 would reflect a more balanced view of the data. Overall, the data are solid and these findings will be valuable to the genomic/evolution fields.

Reviewed by eLife

Evolutionary rate covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions

1. Jordan Little
2. Maria Chikina
3. Nathan L Clark

• Curated by eLife

  eLife assessment

  This useful study seeks to address the importance of physical interaction between proteins in higher-order complexes for covariation of evolutionary rates at different sites in these interacting proteins. Following up on a previous analysis with a smaller dataset, the authors provide compelling evidence that the exact contribution of physical interactions, if any, remains difficult to quantify. The work will be of relevance to anyone interested in protein evolution.

Reviewed by eLife

Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure

1. Jun Ishigohoka
2. Karen Bascón-Cardozo
3. Andrea Bours
4. Janina Fuß
5. Arang Rhie
6. Jacquelyn Mountcastle
7. Bettina Haase
8. William Chow
9. Joanna Collins
10. Kerstin Howe
11. Marcela Uliano-Silva
12. Olivier Fedrigo
13. Erich D Jarvis
14. Javier Pérez-Tris
15. Juan Carlos Illera
16. Miriam Liedvogel

Reviewed by Peer Community in Evolutionary Biology

How to survive the mutational meltdown: lessons from plant RNA viruses

1. Guillaume Lafforgue
2. Marie Lefebvre
3. Thierry Michon
4. Santiago F. Elena

Reviewed by Peer Community in Evolutionary Biology