Evolutionary Biology

Chromosome-level genome assembly of the lemon sole, Microstomus kitt (Pleuronectiformes: Pleuronectidae)

1. Marcel Nebenführ
2. David Prochotta
3. Maria A. Nilsson
4. Menno J. de Jong
5. Tunca D. Yazici
6. Fabienne Langefeld
7. Malambo Muloongo
8. Helena Woköck
9. Jakob Jilg
10. Sina C. Bender
11. Marvin M. Zangl
12. Juan-Manuel Ortega Guatame
13. Kimberley Williams
14. Moritz Sonnewald
15. Axel Janke

• Curated by GigaByte

  Editors Assessment:

  This Data Release paper presents the first genome assembly of the lemon sole (Microstomus kitt), a commercially important flatfish found in European coastal waters. It is also interesting that this work was carried out in a University course setting involving the students. The resulting chromosome-level genome was assembled using long-read PacBio HiFi sequencing and the Hi-C technique. The 628 Mbp reference (which is consistent with other Pleuronectidae fish species) is assembled into 24 chromosome-length scaffolds with high completeness, achieving a scaffold N50 of 27.2 Mbp. Peer review and data curation made the author clarify a few points and share all of the data and results in an open and well curated manner. The annotated genome of the lemon sole, with its high continuity, should therefore provide important reference data for future population genetic analyses and conservation strategies of this organism.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely related Drosophila species

1. David W. J. McQuarrie
2. Frannie H. S. Stephens
3. Alexander D. Ferguson
4. Roland Arnold
5. Alberto Civetta
6. Matthias Soller

Reviewed by Review Commons

High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains

1. Caroline Kikawa
2. Andrea N. Loes
3. John Huddleston
4. Marlin D. Figgins
5. Philippa Steinberg
6. Tachianna Griffiths
7. Elizabeth M. Drapeau
8. Heidi Peck
9. Ian G. Barr
10. Janet A. Englund
11. Scott E. Hensley
12. Trevor Bedford
13. Jesse D. Bloom

• Curated by eLife

  eLife Assessment

  This important study advances our understanding of population-level immune responses to influenza in both children and adults. The strength of the evidence supporting the conclusions is compelling, with high-throughput profiling assays and mathematical modeling. The work will be of interest to immunologists, virologists, vaccine developers, and those working on mathematical modeling of infectious diseases.

Reviewed by eLife

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

1. David Ferreiro
2. Luis Daniel González-Vázquez
3. Ana Prado-Comesaña
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