Evolutionary Biology

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

Cancer–immune coevolution dictated by antigenic mutation accumulation

1. Long Wang
2. Christo Morison
3. Weini Huang

• Curated by eLife

  eLife Assessment

  This important work presents a stochastic branching process model of tumour-immune coevolution, incorporating stochastic antigenic mutation accumulation and escape within the cancer cell population. They then used this model to investigate how tumour-immune interactions influence tumour outcome and the summary statistics of sequencing data of bulk and single-cell sequencing of a tumour. The evidence is compelling and the work will be of interest to cancer-immune biology fields.

Reviewed by eLife

Heterozygosity at a conserved candidate sex determination locus is associated with female development in the clonal raider ant (Ooceraea biroi)

1. Kip D Lacy
2. Jina Lee
3. Kathryn Rozen-Gagnon
4. Wei Wang
5. Thomas S Carroll
6. Daniel JC Kronauer

• Curated by eLife

  eLife Assessment

  This study provides valuable insights into the evolutionary conservation of sex determination mechanisms in ants by identifying a candidate sex-determining region in a parthenogenetic species. It uses solid, well-executed genomic analyses based on differences in heterozygosity between females and diploid males. While the candidate locus awaits functional validation in this species, the study provides convincing support for the ancient origin of a non-coding locus implicated in sex determination.

Reviewed by eLife

The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference

1. Mahboobeh Behruznia
2. Maximillian Marin
3. Daniel J Whiley
4. Maha Reda Farhat
5. Jonathan C Thomas
6. Maria Rosa Domingo-Sananes
7. Conor J Meehan

• Curated by eLife

  eLife Assessment

  This useful study analyzed 335 Mycobacterium tuberculosis Complex genomes and found that MTBC has a closed pangenome with few accessory genes. The research provides solid evidence for gene presence-absence patterns which support the appending conclusions however, the main criticism regarding the dominance of genome reduction remains.

Reviewed by eLife

Regulatory networks of KRAB zinc finger genes and transposable elements changed during human brain evolution and disease

1. Yao-Chung Chen
2. Arnaud Maupas
3. Katja Nowick

• Curated by eLife

  eLife Assessment

  The authors present a software (TEKRABber) to analyze how expression of transposable elements (TEs) and TE silencing factors KRAB zinc finger (KRAB-ZNF) genes are correlated in experimentally validated datasets. TEKRABber is used to reconstruct regulatory networks of KRAB-ZNFs and TEs during human brain evolution and in Alzheimer's disease. The direction of the work is important, with potentially significant interest from others looking for a tool for correlative gene expression analysis across individual genomes and species. However, the reviews identified biases and shortcomings in the pipeline that could lead to an unacceptable number of false positive and negative signals and thus impact the conclusions, leaving the work in its current form incomplete.

Reviewed by eLife

Malaria shaped human spatial organisation for the last 74 thousand years

1. Margherita Colucci
2. Michela Leonardi
3. James Blinkhorn
4. Seth R. Irish
5. Cecilia Padilla-Iglesias
6. Stefanie Kaboth-Bar
7. William D. Gosling
8. Robert W. Snow
9. Andrea Manica
10. Eleanor M.L. Scerri

Reviewed by preLights