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

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

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