Evolutionary Biology

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

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

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

1. Joshua L Cherry

• Curated by eLife

  eLife Assessment

  The is a valuable evaluation of a previously published simulation model on the role of heterozygote advantage in shaping MHC diversity, showing that the conclusions from this model hold only within a narrow parameter range that might be unrealistic. The author presents an alternative model, in which MHC homozygotes with duplicated MHC genes outperform heterozygotes with single genes, thereby challenging the explanation that heterozygote advantage will lead to high allelic variation at a given MHC gene. The topic is highly relevant for eco-immunology and evolutionary genetics, but several major aspects of the author's claim need to be clarified to make the model interpretable. While the work has the potential to improve our understanding of the question of how the extraordinary diversity at the MHC locus evolves, without this addition, the conclusions remain incomplete.

Reviewed by eLife

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