Evolutionary Biology

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

Using General Algebra to Model the Directed Evolution of an Asexual Population

1. Kangbien Park

Reviewed by Arcadia Science

High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains

1. Caroline Kikawa
2. Andrea N Loes
3. John Huddleston
4. Marlin D Figgins
5. Philippa Steinberg
6. Tachianna Griffiths
7. Elizabeth M Drapeau
8. Heidi Peck
9. Ian G Barr
10. Janet A Englund
11. Scott E Hensley
12. Trevor Bedford
13. Jesse D Bloom

• Curated by eLife

  eLife Assessment

  This important study advances our understanding of population-level immune responses to influenza in both children and adults. The strength of the evidence supporting the conclusions is compelling, with high-throughput profiling assays and mathematical modeling. The work will be of interest to immunologists, virologists, vaccine developers, and those working on mathematical modeling of infectious diseases.

Reviewed by eLife

Heterogeneity of genetic sequence within quasi-species of influenza virus revealed by single-molecule sequencing

1. Kenji Tamao
2. Hiroyuki Noji
3. Kazuhito Tabata

• Curated by eLife

  eLife Assessment

  This study is an important contribution to the field of viral sequencing, providing methods for more accurate characterization of viral genetic diversity using long-read sequencing and unique molecular identifiers (UMIs). Although it is a small pilot study, it shows promise as a convincing, validated methodology with broad applicability.

Reviewed by eLife