Evolutionary Biology

Forecasting protein evolution by integrating birth-death population models with structurally constrained substitution models

1. David Ferreiro
2. Luis Daniel Gonzalez-Vazquez
3. Ana Prado-Comesana
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 four viral proteins that are of structural and functional importance. The justification of some hypotheses regarding fitness is incomplete, as well as the evidence for the model's predictive power, since it shows little improvement over neutral models in predicting protein evolution.

Reviewed by eLife

Sending mixed signals: 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 increased similarity in visual appearance combined with an increased chemical difference between two butterfly species in sympatry compared with differences between three populations of one of the two species in allopatry. While the evidence is solid, its interpretation in terms of evolutionary responses to shared predators (visual signals) and avoiding between-species mating (chemical signals) is overstated due to the lack of direct experimental evidence.

Reviewed by eLife

Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

1. Nikesh M Kumar
2. Taylor L Cooper
3. Thomas D Kocher
4. J Todd Streelman
5. Patrick T McGrath

• Curated by eLife

  eLife Assessment

  Using several hundreds of samples and cutting-edge genomic methods, including BioNano, PacBio, HiFi, and advanced bioinformatic pipelines, the authors identify six large chromosomal inversions segregating in over 100 species of Lake Malawi cichlids. This important study provides compelling evidence for the presence of these six inversions, their differential distribution among populations, and the association of chromosome 10 inversion with a sex-determination locus. This work also provides a starting point for further investigating the role of these inversions with respect to local adaptation, speciation, sex determination, hybridization, and ILS in cichlids, which represent ~5% of the extant vertebrate species and are one of the most prominent examples of adaptive radiations.

Reviewed by eLife

Refining the resolution of the yeast genotype-phenotype map using single-cell RNA-sequencing

1. Arnaud N’Guessan
2. Wen Yuan Tong
3. Hamed Heydari
4. Alex N Nguyen Ba

• Curated by eLife

  eLife Assessment

  This useful study describes expression profiling by scRNA-seq of thousands of cells of recombinant yeast genotypes from a system that models natural genetic variation. The rigorous new method presented here shows promise for improving the efficiency of genotype-to-phenotype mapping in yeast, providing convincing evidence for its efficacy. This manuscript focuses on overcoming technical challenges with this approach and identifies several new biological insights that build upon the field of genotype-to-phenotype mapping, a central question of interest to geneticists and evolutionary biologists.

Reviewed by eLife

Population structure and genetic diversity of the Critically Endangered bowmouth guitarfish ( Rhina ancylostomus ) in the Northwest Indian Ocean

1. Marja J. Kipperman
2. Rima W. Jabado
3. Alifa Bintha Haque
4. Daniel Fernando
5. P.A.D.L Anjani
6. Julia L.Y. Spaet
7. Emily Humble

Reviewed by Peer Community in Evolutionary Biology

Upstream open reading frames buffer translational variability during Drosophila evolution and development

1. Yuanqiang Sun
2. Yuange Duan
3. Peixiang Gao
4. Chenlu Liu
5. Kaichun Jin
6. Shengqian Dou
7. Wenxiong Tang
8. Hong Zhang
9. Jian Lu

• Curated by eLife

  eLife Assessment

  This study reveals the important role of upstream open reading frames (uORFs) in limiting the translational variability of downstream coding sequences. Through a combination of computational simulations, comparative analyses of translation efficiency across different developmental stages in two closely related Drosophila species, and manipulative, experimental validation of translation buffering by an uORF for a gene, the authors provide convincing evidence supporting their conclusions. This work will be of broad interest to molecular biologists and geneticists.

Reviewed by eLife

DateBack, an evolving open-access repository of Phoenix archaeobotanical data supporting new perspectives on the history of date palm cultivation

1. Margot Besseiche
2. Elora Chambraud
3. Vladimir Dabrowski
4. Elisa Brandstatt
5. François Sabot
6. Charlène Bouchaud
7. Muriel Gros-Balthazard

Reviewed by Peer Community in Archaeology

Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals

1. Oliver Voigt
2. Magdalena V. Wilde
3. Thomas Fröhlich
4. Benedetta Fradusco
5. Sergio Vargas
6. Gert Wörheide

• Curated by eLife

  eLife Assessment

  This important paper reports the discovery of calcarins, a protein family that seems to be involved in calcification in the calcareous sponge Sycon ciliatum, significantly enhancing our understanding of the molecular and cellular mechanisms underlying spicule formation in sponges and the evolution of carbonate biomineralization. The conclusions are supported by compelling evidence based on an integrated analysis that combines transcriptomics, genomics, proteomics, and precise in situ hybridization. These findings will be of broad interest to cell biologists, biochemists, and evolutionary biologists.

Reviewed by eLife

mirror determines the far posterior domain in butterfly wings

1. Martik Chatterjee
2. Xin Yi Yu
3. Noah K Brady
4. Connor Amendola
5. Gabriel C Hatto
6. Robert D Reed

• Curated by eLife

  eLife Assessment

  This important study provides evidence of a deeply conserved role for the gene Mirror in providing positional identity in the posterior part of butterfly and fly wings, despite increased morphological complexity of butterfly wings. The findings are solid for the field of evo-devo. However, the tools in butterflies are more limited than in Drosophila and it is more difficult to determine which specific cells are mutant and whether the effect of mutation is cell-intrinsic. The work will be of interest to evolutionary and developmental biologists working on insect wing evolution and the evolution of patterning more generally.

Reviewed by eLife

Magnetotactic Bacteria Optimally Navigate Natural Pore Networks

1. Alexander P Petroff
2. Julia Hernandez
3. Vladislav Kelin
4. Nina Radchenko-Hannafin

• Curated by eLife

  eLife Assessment

  Combining experiments in microfluidic devices and computer simulation, this study provides a valuable analysis of the relevant parameters that determine the motility of (multicellular) magnetotactic bacteria in sediment-like environments. The study presents convincing evidence that there is an optimum in the biological parameters for motile life under such conditions.

Reviewed by eLife