Evolutionary Biology

Loss of a morph is associated with asymmetric character release in a radiation of woodland salamanders

1. Brian P. Waldron
2. Maggie M. Hantak
3. Emily F. Watts
4. Josef C. Uyeda
5. Alan R. Lemmon
6. Emily Moriarty Lemmon
7. Robert P. Guralnick
8. David C. Blackburn
9. Shawn R. Kuchta

Reviewed by preLights

The effect of gene tree dependence on summary methods for species tree inference

1. Wanting He
2. Celine Scornavacca
3. Yao-ban Chan

Reviewed by Peer Community in Evolutionary Biology

Rapid evolution of fine-scale recombination during domestication: a perspective from population genomics

1. Zheng-Xi Liu
2. Ming Li
3. Xue-Hai Ge
4. Kun Wang
5. Si Si
6. Chang-Rong Ge
7. Jian-Hai Chen
8. Li-Rong Hu
9. Min-Sheng Peng
10. Ting-Ting Yin
11. Ali Esmailizadeh
12. Chang Zhang
13. Lu-Jiang Qu
14. Xue-Mei Lu
15. Jian-Lin Han
16. Ya-Ping Zhang
17. Ming-Shan Wang

• Curated by eLife

  eLife Assessment

  This paper addresses valuable questions about the evolution of recombination landscape under domestication by examining recombination maps in domesticated chickens and their wild ancestor. However, despite employing a state-of-the-art deep learning method for recombination map inference, the lack of systematic benchmarking and presence of some unexpected patterns raise concerns about the reliability of the inferred maps, thus providing incomplete support for rapid evolution of recombination landscapes. Additionally, due to methodological limitations in testing for intra-genome correlations between evolutionary processes, the current evidence is inadequate to support the associations of recombination with selection and/or introgression in domesticated chickens.

Reviewed by eLife

Evolutionary basis of intermale sexual behavior by multiple pheromone switches in Drosophila

1. Youcef Ouadah
2. Thomas H. Naragon
3. Hayley Smihula
4. Emily L. Behrman
5. Mohammed A. Khallaf
6. Yun Ding
7. David L. Stern
8. Joseph Parker
9. David J. Anderson

Reviewed by Arcadia Science

Separating selection from mutation in antibody language models

1. Frederick A Matsen
2. Will Dumm
3. Kevin Sung
4. Mackenzie M Johnson
5. David Rich
6. Tyler Starr
7. Yun S Song
8. Julia Fukuyama
9. Hugh K Haddox

• Curated by eLife

  eLife Assessment

  This important study introduces a new biology-informed strategy for deep learning models aiming to predict mutational effects in antibody sequences. It provides solid evidence that separating selection from the nucleotide-level mutation process improves performance over the objectives of protein language models inspired by natural language processing. This paper should be of interest to computational immunologists, but also to the broader community interested in deep learning for biological sequence data and evolution.

Reviewed by eLife

Ancestral Protein Reconstruction of a membrane trafficking GTPase uncovers unanticipated properties of the ancestral protein and of modern Arf1 GTPases

1. Marine Alves
2. Mandeep Sivia
3. Kristína Záhonová
4. Catherine L. Jackson
5. Joel B. Dacks

Reviewed by Arcadia Science

Structural constraints acting on the SARS-CoV-2 spike protein reveal limited space for viral adaptation

1. James C Herzig
2. Michael L Magwira
3. Simon C Lovell

Reviewed by PREreview

The effects of host phylogenetic coverage and congruence metric on Monte Carlo-based null models of phylosymbiosis

1. James G. DuBose

Reviewed by Peer Community in Evolutionary Biology

Kinematics and morphological correlates of descent strategies in arboreal mammals suggest early upright postures in euprimates

1. Séverine LD Toussaint
2. Dionisios Youlatos
3. John A Nyakatura

• Curated by eLife

  eLife Assessment

  This valuable study examines how mammals descend effectively and securely along vertical substrates. The conclusions from comparative analyses based on behavioral data and morphological measurements collected from 21 species across a wide range of taxa are convincing, making the work of interest to all biologists studying animal locomotion.

Reviewed by eLife

Pre-Cambrian origin of envelope-carrying retrotransposons in metazoans

1. Shashank Chary
2. Rippei Hayashi

• Curated by eLife

  eLife Assessment

  This important study provides convincing evidence that envelope-carrying Ty3/gypsy retrotransposons (errantiviruses) are ancient, widespread, and actively expanding across nearly all major animal phyla. Using comprehensive phylogenetic and AlphaFold2-based structural analyses, the authors show that these elements independently acquired membrane fusion proteins early in metazoan evolution, likely predating the bilaterian-non-bilaterian split. While some aspects could be more clearly contextualized and explained better, the work offers insights into the deep evolutionary roots of retroelement-envelope associations and the origins of retroviruses.

Reviewed by eLife