Evolutionary Biology

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. The strength of evidence is solid, using well-executed genomic analyses to identify differences in heterozygosity between females and diploid males, though not yet functional validation of the candidate locus.

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 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

Structural evolution of nitrogenase enzymes over geologic time

1. Bruno Cuevas-Zuviría
2. Franka Detemple
3. Kaustubh Amritkar
4. Amanda K Garcia
5. Lance C Seefeldt
6. Oliver Einsle
7. Betül Kaçar

• Curated by eLife

  eLife Assessment

  This valuable study presents computational analyses of over 5,000 predicted extant and ancestral nitrogenase structures. The data analyses are convincing, it offers unique insights into the relationship between structural evolution and environmental and biological phenotypes. The data generated in this study provide a vast resource that can serve as a starting point for studies of reconstructed and extant nitrogenases.

Reviewed by eLife

The evolution of gene expression in seasonal environments

1. Shuichi N Kudo
2. Yuka Ikezaki
3. Junko Kusumi
4. Hideki Hirakawa
5. Sachiko Isobe
6. Akiko Satake

• Curated by eLife

  eLife Assessment

  The authors collected valuable time-course RNA-seq data from four tree species in natural environments and analyzed seasonal patterns of gene expression. The genome assemblies and gene expression data across multiple species and tissues are convincing, but the overarching conclusions are inadequately supported due to weaknesses in the study design, which encompasses three different environments and two distinct time periods. This makes it impossible to disentangle genetic effects - which are critical for evolutionary inferences - from environmental influences on gene expression.

Reviewed by eLife

Comparative genomics of Rickettsiella bacteria reveal variable metabolic pathways potentially involved in symbiotic interactions with arthropods

1. Anna M. Floriano
2. Adil El-Filali
3. Julien Amoros
4. Marie Buysse
5. Hélène Jourdan-Pineau
6. Hein Sprong
7. Robert Kohl
8. Ron P. Dirks
9. Peter Schaap
10. Jasper Koehorst
11. Bart Nijsse
12. Didier Bouchon
13. Vincent Daubin
14. Fabrice Vavre
15. Olivier Duron

Reviewed by Peer Community in Evolutionary Biology

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