Evolutionary Biology

Fluidity and Predictability of Epistasis on an Intragenic Fitness Landscape

1. Sarvesh Baheti
2. Namratha Raj
3. Supreet Saini

• Curated by eLife

  eLife Assessment

  This paper addresses the significant question of quantifying epistasis patterns, which affect the predictability of evolution, by reanalyzing a recently published combinatorial deep mutational scan experiment. The findings are useful, showing that epistasis is fluid, i.e. strongly background dependent, but that fitness effects of mutations are statistically predictable based on the background fitness. While the general approach appears solid, some claims remain incompletely supported by the analysis, as arbitrary cutoffs are used and the description of methods lacks specifics. This analysis should be of interest to the community working on fitness landscapes.

Reviewed by eLife

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. Gytis Dudas
8. Placide Mbala-Kingebeni
9. Marc A. Suchard
10. Andrew Rambaut

Reviewed by PREreview

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 time-course RNA-seq data from four tree species in natural environments and analyzed seasonal patterns of gene expression. This fundamental study substantially advances our understanding of how seasonal environments shape gene expression. The evolutionary effects of seasonal environments on gene expression are rarely studied at this scale and the dataset is extensive. The evidence supporting the conclusions is compelling, with caveats and limitations clearly described. The work will be of broad interest to colleagues studying evolution and gene expression.

Reviewed by eLife

There and back again: the dynamic evolution of panarthropod germ cell specification mechanisms

1. Jonchee A. Kao
2. Emily L. Rivard
3. Rishabh R. Kapoor
4. Cassandra G. Extavour

Reviewed by preLights

The primate Major Histocompatibility Complex as a case study of gene family evolution

1. Alyssa Lyn Fortier
2. Jonathan K Pritchard

• Curated by eLife

  eLife Assessment

  This important manuscript presents a thorough analysis of the evolution of Major Histocompatibility Complex gene families across primates. A key strength of this analysis is the use of state-of-the-art phylogenetic methods to estimate rates of gene gain and loss, accounting for the notorious difficulty to properly assemble MHC genomic regions. Overall the evidence for the authors' conclusions – that there is considerable diversity in how MHC diversity is deployed across species – is compelling.

Reviewed by eLife

Coalescence and Translation: A Language Model for Population Genetics

1. Kevin Korfmann
2. Nathaniel S. Pope
3. Melinda Meleghy
4. Aurélien Tellier
5. Andrew D. Kern

Reviewed by Arcadia Science

Tandem duplication of serpin genes yields functional variation and snake venom inhibitors

1. Meilyn S. Ward
2. Matthew L. Holding
3. Laura M. Haynes
4. David Ginsburg

Reviewed by preLights

Evolutionary Adaptations of IRG1 Refines Itaconate Synthesis and Mitigates Innate Immunometabolism Trade-offs

1. Richard V Szeligowski
2. Francois Miros
3. Andres Saez
4. Marisa DeCiucis
5. Gunter P Wagner
6. Hongying Shen

• Curated by eLife

  eLife Assessment

  This important study addresses the timely and interesting question of how itaconate generation emerged in evolution, using taxonomic analysis of the gene and enzyme cis-aconitate decarboxylase (CAD). The authors provide solid evidence identifying three CAD branches in metazoans and showing that the early metazoan paleo-form indeed generates aconitate and is already linked to innate immunity. They further provide limited evidence suggesting that taxonomic differences in subcellular localisation of this enzyme may allow for innate immune signalling without compromising cellular energetics. The implications of the study will be of high interest to the field of innate host defence and immunometabolism.

Reviewed by eLife

Convergent iridescence and divergent chemical signals in sympatric sister-species of Amazonian butterflies

1. Joséphine Ledamoisel
2. Bruno Buatois
3. Rémi Mauxion
4. Christine Andraud
5. Melanie McClure
6. Vincent Debat
7. Violaine Llaurens

• Curated by eLife

  eLife Assessment

  This study presents a valuable assessment of and solid evidence for increased similarity in visual appearance combined with increased chemical differences between two butterfly species in sympatry compared with differences between three populations of one of the two species in allopatry. The similarity in visual appearance hints to an evolutionary response to shared predators (but alternative explanations are possible). Thus, the difference in chemical signaling likely helps to avoid between-species mating in sympatry.

Reviewed by eLife

Importance of higher-order epistasis in 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