Evolutionary Biology

Whole-genome re-sequencing of the Baikal seal and other phocid seals for a glimpse into their genetic diversity, demographic history, and phylogeny

1. Marcel Nebenführ
2. Ulfur Arnason
3. Axel Janke

• Curated by GigaByte

  Editors Assessment:

  Due to them being found in the landlocked, isolated habitat of Lake Baikal makes the Baikal Seal (Pusa sibirica) unique among all pinnipeds as the only freshwater seal. This paper presents reference-based assemblies of six newly sequenced Baikal seal individuals, one individual of the ringed seal, as well as the first short-read data of the harbor seal and the Caspian seal . This data aiding the study of the genomic diversity of the Baikal seal and to contribute baseline data to the limited genomic data available for seals. Peer review extended the description of the used tools and parameters in the revised manuscript, and provided some more information on the methods..This newly generated sequencing data hopefully now helps to extend the phylogeny of the Phoca/Pusa group on genome-wide data and can also broaden the view into the genetic structure and diversity of the Baikal seal

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Passive accumulation of alkaloids in inconspicuously colored frogs refines the evolutionary paradigm of acquired chemical defenses

1. Rebecca D Tarvin
2. Jeffrey L Coleman
3. David A Donoso
4. Mileidy Betancourth-Cundar
5. Karem López-Hervas
6. Kimberly S Gleason
7. J Ryan Sanders
8. Jacqueline M Smith
9. Santiago R Ron
10. Juan C Santos
11. Brian E Sedio
12. David C Cannatella
13. Richard W Fitch

• Curated by eLife

  eLife Assessment

  This study is important, with the potential to greatly impact future research on the evolution of chemical defense mechanisms in animals. The authors present compelling evidence for the presence of low quantities of alkaloids in amphibians previously thought to lack these toxins. They then integrate these findings with existing literature to propose a four-phase scenario for the evolution of chemical defense in alkaloid-containing poison frogs, emphasizing the role of passive accumulation mechanisms.

Reviewed by eLife

A genomic duplication spanning multiple P450s contributes to insecticide resistance in the dengue mosquito Aedes aegypti

1. Tiphaine Bacot
2. Chloe Haberkorn
3. Joseph Guilliet
4. Julien Cattel
5. Mary Kefi
6. Louis Nadalin
7. Jonathan Filee
8. Frederic Boyer
9. Thierry Gaude
10. Frederic Laporte
11. Jordan Tutagata
12. John Vontas
13. Isabelle Dusfour
14. Jean-Marc Bonneville
15. Jean-Philippe David

Reviewed by Peer Community in Evolutionary Biology

RETRACTED: Biases of Principal Component Analysis (PCA) in Physical Anthropology Studies Require a Reevaluation of Evolutionary Insights

1. Nima Mohseni
2. Eran Elhaik

• Curated by eLife

  eLife Assessment

  The authors present a critique of current usage of principal component analysis in geometric morphometrics, making a compelling case with benchmark data that standard techniques perform poorly. The work is an important contribution to the field and will hopefully lead to a reassessment of the methodology most scientists in morphometrics currently use. This work challenges a very commonly used analytical approach and is bound to raise some controversy in the community, but the authors' critique is based on a well-founded and well-thought out analysis.

Reviewed by eLife

Prey attraction in a generalist microbial predator, Dictyostelium discoideum

1. P. M. Shreenidhi
2. Rachel I. McCabe
3. David C. Queller
4. Joan E. Strassmann

Reviewed by Arcadia Science

Genetic predisposition towards multicellularity in Chlamydomonas reinhardtii

1. I-Chen Kimberly Chen
2. Shania Khatri
3. Matthew D. Herron
4. Frank Rosenzweig

Reviewed by Arcadia Science

A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide

1. Sarah R Mullinax
2. Andrea M Darby
3. Anjali Gupta
4. Patrick Chan
5. Brittny R Smith
6. Robert L Unckless

• Curated by eLife

  eLife Assessment

  This valuable study investigates evolutionary aspects around a single amino acid polymorphism, known to be under long-term balancing selection, in an immune peptide of Drosophila melanogaster. Using alleles with different substitutions, the investigators demonstrate that while one allele provides better survival after systemic infections by a bacterial pathogen, the alternative allele endows its carriers with a longer lifespan under certain conditions. The authors suggest that these contrasting fitness effects of the two alleles contribute to balancing their long-term evolutionary fate. While the work is very interesting, the strength of the provided evidence is still incomplete, and the study would benefit from more rigorous approaches.

Reviewed by eLife

Characterization of cancer-driving nucleotides (CDNs) across genes, cancer types, and patients

1. Lingjie Zhang
2. Tong Deng
3. Zhongqi Liufu
4. Xiangnyu Chen
5. Shijie Wu
6. Xueyu Liu
7. Changhao Shi
8. Bingjie Chen
9. Zheng Hu
10. Qichun Cai
11. Chenli Liu
12. Mengfeng Li
13. Miles E Tracy
14. Xuemei Lu
15. Chung-I Wu
16. Hai-Jun Wen

• Curated by eLife

  eLife Assessment

  This valuable study is a companion to a paper introducing a theoretical framework and methodology for identifying Cancer Driving Nucleotides (CDNs). The evidence that recurrent SNVs or CDNs are common in true cancer driver genes is convincing, with more limited evidence that many more undiscovered cancer driver mutations will have CDNs, and that this approach could identify these undiscovered driver genes with about 100,000 samples.

Reviewed by eLife

The theory of massively repeated evolution and full identifications of cancer-driving nucleotides (CDNs)

1. Lingjie Zhang
2. Tong Deng
3. Zhongqi Liufu
4. Xueyu Liu
5. Bingjie Chen
6. Zheng Hu
7. Chenli Liu
8. Miles E Tracy
9. Xuemei Lu
10. Hai-Jun Wen
11. Chung-I Wu

• Curated by eLife

  eLife Assessment

  This important paper introduces a theoretical framework and methodology for identifying Cancer Driving Nucleotides (CDNs), primarily based on single nucleotide variant (SNV) frequencies. A variety of solid approaches indicate that a mutation recurring three or more times is more likely to reflect selection rather than being the consequence of a mutation hotspot. The method is rigorously quantitative, though the requirement for larger datasets to fully identify all CDNs remains a noted limitation. The work will be of broad interest to cancer geneticists and evolutionary biologists.

Reviewed by eLife

Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense

1. Dario Galanti
2. Jun Hee Jung
3. Caroline Müller
4. Oliver Bossdorf

• Curated by eLife

  eLife Assessment

  This important study presents a significant methodological advance by leveraging previously discarded, unmapped DNA sequence reads to estimate pest infestation loads across plant accessions, and map variation in these apparent pest loads to defense genes. The bioinformatics approach is compelling, and the results should bear broad implications for phenotype-genotype prediction, especially regarding the use of unmapped reads for GWAS.

Reviewed by eLife