Evolutionary Biology

Evidence of latency reshapes our understanding of Ebola virus reservoir dynamics

1. John T. McCrone
2. Guy Baele
3. Ifeanyi F. Omah
4. Eddy Kinganda-Lusamaki
5. Joseph A. Brew
6. Luiz M. Carvalho
7. Nicola F. Müller
8. Gytis Dudas
9. Placide Mbala-Kingebeni
10. Marc A. Suchard
11. Andrew Rambaut

Reviewed by Rapid Reviews Infectious Diseases, PREreview

The population structure of invasive Lantana camara is shaped by its mating system

1. P Praveen
2. Rajesh Gopal
3. Uma Ramakrishnan

• Curated by eLife

  eLife Assessment

  The submission by Praveen et al. reports important findings describing the structure of genetic and colour variation in its native range for the globally invasive weed Lantana camara. Whilst the importance of the research question and the scale of the sampling is appreciated, the analysis, which is currently incomplete, requires further tests to support the claims made by the authors.

Reviewed by eLife

Heterozygote advantage cannot explain MHC diversity, but MHC diversity can explain heterozygote advantage

1. Joshua L Cherry

• Curated by eLife

  eLife Assessment

  This valuable study re-evaluates a published simulation model on the role of heterozygote advantage in shaping MHC diversity. By modifying key modeling assumptions, the author argues that the original conclusions depend on a narrow and potentially unrealistic parameter range. While the work is in principle solid, the robustness of this claim is viewed differently by the reviewers. The manuscript further proposes an alternative modeling framework in which expansion of the MHC gene family allows homozygotes to outperform heterozygotes, thereby challenging the idea that heterozygote advantage alone can account for high allelic diversity at MHC loci. The topic is highly relevant for eco-immunology and evolutionary genetics, although it is not clear yet how well the model generalizes to other genes with different patterns of haplotype diversity in the population and different degrees of heterozygous advantage.

Reviewed by eLife

Ecological specialization and admixture drive the genomic and phenotypic diversity in 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 H Rich
6. Tyler N 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

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