Evolutionary Biology

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. Haijun Wen
11. Chung-I Wu

• Curated by eLife

  eLife assessment

  This valuable paper reports 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

Insect metamorphosis is regulated differently between sexes by members of a microRNA cluster

1. Chade Li
2. Ki Kei Chan
3. Wenyan Nong
4. ShanShan Chen
5. Wai Lok So
6. Zhe Qu
7. Heidi YC Wu
8. Ho Yin Yip
9. Chi Bun Chan
10. Stephen S Tobe
11. William G Bendena
12. Zhen Peng Kai
13. Jerome HL Hui

• Curated by eLife

  eLife assessment

  This study provides a useful inventory of genes that are up- or down-regulated during the early metamorphic development of male and female larvae and proposes that the microRNA cluster miR-277/34 is involved in the development of sexual differences during early metamorphosis of Drosophila melanogaster, although its precise role remains unclear. The strength of evidence, based on a combination of diverse methods including mRNA and small RNA sequencing, in silico analyses, in vitro assays, and loss-of-function experiments, is incomplete as it lacks a general model and an examination of the potential effects of the miR-277/34 mutations on phenotypes such as morphology or developmental time. This work will be of interest to developmental biologists interested in sexual dimorphism and in the interplay between hormones and microRNAs during development.

Reviewed by eLife

Flexible reproductive seasonality in Africa-dwelling papionins is associated with low environmental productivity and high climatic unpredictability

1. Jules Dezeure
2. Julie Dagorrette
3. Lugdiwine Burtschell
4. Shahrina Chowdhury
5. Dieter Lukas
6. Larissa Swedell
7. Elise Huchard

Reviewed by Peer Community in Ecology

Spatial and temporal distribution of ribosomes in single cells reveals aging differences between old and new daughters of Escherichia coli

1. Lin Chao
2. Chun Kuen Chan
3. Chao Shi
4. Camilla U Rang

• Curated by eLife

  eLife assessment

  This study is a potentially important contribution to the field of protein biosynthesis pathways and their link to aging, especially regarding the thorough analysis of variation in measures expected to correlate with elongation rate in old and new daughter cells derived from old and new mother cells. However, the imaging results, analysis, and methodologies are incomplete, as in its current form several key questions remain unanswered.

Reviewed by eLife

Inversions Can Accumulate Balanced Sexual Antagonism: Evidence from Simulations and Drosophila Experiments

1. Christopher S. McAllester
2. John E. Pool

• Curated by eLife

  eLife assessment

  This study attempts to solve long-standing puzzles about inversion polymorphisms in Drosophila melanogaster by invoking sexually antagonism and negative frequency dependent selection. While the idea developed here is a valuable contribution to the field, the description of the empirical work and the simulations remain incomplete, as they do not provide a full picture of what exactly has been done.

Reviewed by eLife

Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploid Ludwigia grandiflora subsp. hexapetala in western Europe

1. Solenn Stoeckel
2. Ronan Becheler
3. Luis Portillo-Lemus
4. Marilyne Harang
5. Anne-Laure Besnard
6. Gilles Lassalle
7. Romain Causse-Védrines
8. Sophie Michon-Coudouel
9. Daniel J. Park
10. Bernard J. Pope
11. Eric J. Petit
12. Dominique Barloy

Reviewed by Peer Community in Evolutionary Biology

The paradox of extremely fast evolution driven by genetic drift in multi-copy gene systems

1. Xiaopei Wang
2. Yongsen Ruan
3. Lingjie Zhang
4. Xiangnyu Chen
5. Zongkun Shi
6. Haiyu Wang
7. Bingjie Chen
8. Miles E. Tracy
9. Chung-I Wu
10. Haijun Wen

• Curated by eLife

  eLife assessment

  This study attempts to resolve an apparent paradox of rapid evolutionary rates of multi-copy gene systems by using a theoretical model that integrates two classic population models. While the conceptual framework is intuitive and thus useful, the specific model is perplexing and difficult to penetrate for non-specialists. The data analysis of rRNA genes provides inadequate support for the conclusions due to a lack of consideration of technical challenges, mutation rate variation, and the relationship between molecular processes and model parameters.

Reviewed by eLife

Fast evolutionary turnover and overlapping variances of sex-biased gene expression patterns defy a simple binary classification of sexes

1. Chen Xie
2. Sven Künzel
3. Diethard Tautz

• Curated by eLife

  eLife assessment

  This is a useful study on sex differences in gene expression across organs of four mice taxa, although there are some shortcomings in the data analyses and interpretations that should to be better placed in the broader context of the current literature. Hence, the evidence in the current form is incomplete, with several overstated key conclusions.

Reviewed by eLife

Harbouring Starships : The accumulation of large Horizontal Gene Transfers in Domesticated and Pathogenic Fungi

1. Samuel O’Donnell
2. Gabriela Rezende
3. Jean-Philippe Vernadet
4. Alodie Snirc
5. Jeanne Ropars

Reviewed by PREreview

Direct inference of the distribution of fitness effects of spontaneous mutations from recombinant inbred C. elegans mutation accumulation lines

1. Timothy A. Crombie
2. Moein Rajaei
3. Ayush S. Saxena
4. Lindsay M. Johnson
5. Sayran Saber
6. Robyn E. Tanny
7. José Miguel Ponciano
8. Erik C. Andersen
9. Juannan Zhou
10. Charles F. Baer

Reviewed by Arcadia Science