Evolutionary Biology

Parallel HIV-1 fitness landscapes shape viral dynamics in humans and macaques that develop broadly neutralizing antibodies

1. Kai S Shimagaki
2. Rebecca M Lynch
3. John P Barton

• Curated by eLife

  eLife Assessment

  In this important quantitative study of HIV-1 evolution in humans and rhesus macaques, selection coefficients are inferred at scale over the HIV genome. Selection coefficients are similar in humans and macaques, providing compelling evidence that these coefficients are representative of the fitness landscapes of these viruses within hosts. This work will be of interest to the community working on quantitative evolution and fitness landscape inference, and the finding that rapid fitness gains in the HIV population predict bNAb emergence has significant implications for HIV vaccine design.

Reviewed by eLife

G protein-coupled receptor diversity and evolution in the closest living relatives of Metazoa

1. Alain Garcia De Las Bayonas
2. Nicole King

• Curated by eLife

  eLife Assessment

  This important study fills a gap in our knowledge of the evolution of GPCRs in holozoans, as well as the phylogeny of associated signaling pathway components such as G proteins, GRKs, and RIC8 proteins. The evidence supporting the conclusions is compelling, with the analysis of extensive new genomic data from choanoflagellates and other non-animal holozoans. Overall, the study is thorough and well-executed. It will be a resource for researchers interested in both the comparative genomics of multicellularity and GPCR biology more broadly, especially given the importance of GPCRs as highly druggable targets

Reviewed by eLife

The holocephalan ratfish endoskeleton shares trabecular and areolar mineralization patterns, but not tesserae, with elasmobranchs little skate and catshark, and appears paedomorphic

1. Oghenevwogaga J Atake
2. Fidji Berio
3. Melanie Debiais-Thibaud
4. B Frank Eames

• Curated by eLife

  eLife Assessment

  This important study significantly advances our understanding of the skeleton of cartilaginous fishes by using a range of state of the art and complementary approaches to compare the skeleton amongst three cartilagenous fishes (catshark, little skate and ratfish). The evidence presented is compelling and likely to impact several fields of study.

Reviewed by eLife

Alternative Splicing Across the Tree of Life: A Comparative Study

1. Rebeca de la Fuente
2. Wladimiro Díaz-Villanueva
3. Vicente Arnau
4. Andrés Moya

• Curated by eLife

  eLife Assessment

  The authors examined the frequency of alternative splicing across prokaryotes and eukaryotes and found that the rate of alternative splicing varies with taxonomic groups and genome coding content. This solid work, based on nearly 1,500 high-quality genome assemblies, relies on a novel genome-scale metric that enables cross-species comparisons and that quantifies the extent to which coding sequences generate multiple mRNA transcripts via alternative splicing. This timely study provides an important basis for improving our general understanding of genome architecture and the evolution of life forms.

Reviewed by eLife, Arcadia Science

Host and antibiotic jointly select for greater virulence in Staphylococcus aureus

1. Michelle Su
2. Kim L Hoang
3. McKenna Penley
4. Michelle H Davis
5. Jennifer D Gresham
6. Levi T Morran
7. Timothy D Read

• Curated by eLife

  eLife Assessment

  This important study examines the evolution of virulence and antibiotic resistance in Staphylococcus aureus under multiple selection pressures. The evidence presented is convincing, with rigorous data that characterizes the outcomes of the evolution experiments. However, the manuscript's primary weakness is in its presentation, as claims about the causal relationship between genotypes and phenotypes are based on correlational evidence. The manuscript needs to be revised to address these limitations, clarify the implications of the experimental design, and adjust the overall narrative to better reflect the nature of the findings.

Reviewed by eLife

Determinants of mutation load in birds

1. Fidel Botero-Castro
2. Jochen B. W. Wolf

Reviewed by Arcadia Science

On the utility of Deep Learning for model classification and parameter estimation on complex diversification scenarios

1. P.G. Peña
2. G. Iglesias
3. E. Talavera
4. AS. Meseguer
5. I. Sanmartín

Reviewed by Arcadia Science

Forecasting protein evolution by integrating birth-death population models with structurally constrained substitution models

1. David Ferreiro
2. Luis Daniel González-Vázquez
3. Ana Prado-Comesaña
4. Miguel Arenas

• Curated by eLife

  eLife Assessment

  This manuscript introduces a useful protein-stability-based fitness model for simulating protein evolution and unifying non-neutral models of molecular evolution with phylogenetic models. The model is applied to five viral proteins that are of structural and functional importance. While the general modelling approach is solid, and effectively preserves folding stability, the evidence for the model's predictive power remains limited, since it shows little improvement over neutral models in predicting protein evolution. The work should be of interest to researchers developing theoretical models of molecular evolution.

Reviewed by eLife

Whole genome sequencing and assembly of the house sparrow, Passer domesticus

1. Vikas Kumar
2. Gopesh Sharma
3. Sankalp Sharma
4. Samvrutha Prasad
5. Shailesh Desai
6. Toral Vaishnani
7. Dalia Vishnudasan
8. Gopinathan Maheswaran
9. Kaomud Tyagi
10. Inderjeet Tyagi
11. Polavarapu B Kavi Kishor
12. Gyaneshwer Chaubey
13. Prashanth Suravajhala

• Curated by GigaByte

  Editors Assessment:

  This paper presents present the genome sequencing of the house sparrow (Passer domesticus) carrying out genome assembly and annotation using in silico approaches with tools that could be a valuable resource for understanding passerine evolution, biology, ethnology, geography, and demography. The final genome assembly was generated using short read sequencing and a computational workflow that included Shovill, SPAdes, MaSuRCA, and BUSCO benchmarking. Producing a 922 MB reference genome with 24,152 genes. The first draft was significantly smaller than this but peer review provided suggestions on how to improve the assembly quality. And after a few attempts and assembly with a reasonable size and BUSCO score was achieved. This openly available data potentially serving as a valuable resource for checking adaptation, divergence, and speciation of birds.

  This evaluation refers to version 2 of the preprint

Reviewed by GigaByte

Graph Neural Networks for Likelihood-Free Inference in Diversification Models

1. Amélie Leroy
2. Ismaël Lajaaiti
3. Sophia Lambert
4. Jakub Voznica
5. Maximilian Pichler
6. Hélène Morlon
7. Florian Hartig
8. Laurent Jacob

Reviewed by Arcadia Science