Evolutionary Biology

Contrasting evolutionary forces of specialization and admixture underlie the genomic and phenotypic diversity of Yarrowia lipolytica

1. Sergio Izquierdo-Gea
2. Javier Vicente
3. Tomás A. Peña
4. Pablo Villarreal
5. Francisco A. Cubillos
6. Cécile Neuvéglise
7. Jorge Barriuso
8. Ignacio Belda
9. Javier Ruiz

Reviewed by Arcadia Science

Identification and comparison of orthologous cell types from primate embryoid bodies shows limits of marker gene transferability

1. Jessica Jocher
2. Philipp Janssen
3. Beate Vieth
4. Fiona C Edenhofer
5. Tamina Dietl
6. Anita Térmeg
7. Paulina Spurk
8. Johanna Geuder
9. Wolfgang Enard
10. Ines Hellmann

• Curated by eLife

  eLife Assessment

  The authors make an important contribution to comparative functional genomics by developing a semi-automated computational pipeline that integrates classification and marker-based cluster annotation to identify orthologous cell types. Using a single-cell RNA-seq dataset of induced pluripotent stem cells and derived embryonic bodies from four primate species: humans, orangutans, cynomolgus macaques, and rhesus macaques, the authors provide convincing evidence that cell type-specific marker genes are substantially less transferable across species than broadly expressed genes, with transferability declining as phylogenetic distance increases. This study establishes a key framework and reference dataset for comparative single-cell analyses and encourages more rigorous evaluation of marker gene transferability across species.

Reviewed by eLife

An interpretable neural network unveils higher-order epistasis in large protein sequence-function relationships

1. Palash Sethi
2. Juannan Zhou

• Curated by eLife

  eLife Assessment

  In this important work, the authors present a new transformer-based neural network designed to isolate and quantify higher-order epistasis in protein sequences. They provide solid evidence that higher-order epistasis can play key roles in protein function. This work will be of interest to the communities interested in modeling biological sequence data and understanding mutational effects.

Reviewed by eLife

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 fundamental study introduces a new biology-informed strategy for deep learning models aiming to predict mutational effects in antibody sequences. It provides convincing 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

The environmental context of the Middle-to-Late Stone Age Transition in eastern Africa: seasonality as a key factor

1. Marianna Fusco
2. Behailu Habte
3. Alice Leplongeon
4. Andrea Manica
5. Enza Elena Spinapolice
6. Michela Leonardi

Reviewed by Peer Community in Archaeology

Constraints on the G1/S transition pathway may favor selection of multicellularity as a passenger phenotype

1. Tom Louis Ducrocq
2. Damien Laporte
3. Bertrand Daignan-Fornier

• Curated by eLife

  eLife Assessment

  This important study implicates that changes in cell regulation may contribute to the evolution of multicellularity. The evidence supporting the conclusions is convincing, with rigorous methods used to test alternative hypotheses. The work will be of broad interest to cell and evolutionary biologists and those studying the cell cycle and cancer.

Reviewed by eLife

Improved genome assembly of whale shark, the world’s biggest fish: revealing “chromocline” in intragenomic heterogeneity

1. Yawako W. Kawaguchi
2. Rui Matsumoto
3. Shigehiro Kuraku

Reviewed by GigaScience

The fate of recessive deleterious or overdominant mutations near mating-type loci under partial selfing

1. Emilie Tezenas
2. Tatiana Giraud
3. Amandine Véber
4. Sylvain Billiard

Reviewed by Peer Community in Evolutionary Biology

Convergent Cellular Adaptation to Freeze-Thaw Stress via a Quiescence-like State in Yeast

1. Charuhansini Tvishamayi
2. Farhan Ali
3. Nandita Chaturvedi
4. Nithila Madhu-Kumar
5. Zeenat Rashida
6. Chandan Muni Reddy
7. Ankita Ray
8. Stephan Herminghaus
9. Shashi Thutupalli

• Curated by eLife

  eLife Assessment

  This study provides valuable insight into stress biology by showing that yeast populations can rapidly evolve a trehalose producing resting state that substantially improves survival and rapid regrowth after freeze-thaw. This finding is consistent with the role of trehalose metabolism as a biophysical adaptation that is broadly relevant to the community working on environmental resilience and dormancy. The evidence is convincing: the authors integrate experimental evolution, cell-level biophysical measurements, and modelling in a mutually reinforcing manner.

Reviewed by eLife

Adaptive variation in avian eggshell structure and gas conductance across elevational gradients?

1. David Ocampo
2. Carlos Daniel Cadena
3. Gustavo A. Londoño

• Curated by eLife

  eLife Assessment

  This important study provides evidence, albeit still incomplete, that high-elevation species lose water at slower rates than low-elevation species. The findings imply that egg physiology may be a factor limiting the distributional range of bird species. While this work reinforces the need for all life stages to be considered when evaluating physiological adjustment to climate change, the analyses as presented by the authors do not clearly highlight the specific impact of species differences in influencing these adjustments.

Reviewed by eLife