Evolutionary Biology

Experimental bleaching of photosymbiotic amoeba revealed strain-dependent differences in algal symbiosis ability

1. Daisuke Yamagishi
2. Ryo Onuma
3. Sachihiro Matsunaga
4. Shin-ya Miyagishima
5. Shinichiro Maruyama

Reviewed by Arcadia Science

Improved inference of population histories by integrating genomic and epigenomic data

1. Thibaut Sellinger
2. Frank Johannes
3. Aurélien Tellier

• Curated by eLife

  eLife assessment

  This important study extends existing sequentially Markovian coalescent approaches to include the combined use of SNPs and hypervariable loci such as epimutations. This is an intriguing addition to infer population size history in the recent past, and the authors provide solid validation of their methods via simulation and analysis of empirical data in Arabidopsis thaliana. Given the increasing availability of such data, this work is a timely contribution and represents a foundation for further developments to explore when and where these methods will be best used.

Reviewed by eLife

Convergent evolution in silico reveals shape and dynamic principles of directed locomotion

1. Renata B Biazzi
2. André Fujita
3. Daniel Y Takahashi

• Curated by eLife

  eLife assessment

  This study provides an important, original framework to study locomotion on the ground with physics-based simulations. Through numerical simulations, the authors propose that intermediate numbers of body modules and high body symmetry enhance speed. The current way discussions and conclusions are written is overly broad: evidence that evolution may favour bilateral symmetry and modularity for efficient directed locomotion is still incomplete as further performance metrics and a more accurate description of the dynamics in water are needed.

Reviewed by eLife

Template switching during DNA replication is a prevalent source of adaptive gene amplification

1. Julie Chuong
2. Nadav Ben Nun
3. Ina Suresh
4. Julia Matthews
5. Titir De
6. Grace Avecilla
7. Farah Abdul-Rahman
8. Nathan Brandt
9. Yoav Ram
10. David Gresham

• Curated by eLife

  eLife assessment

  This study provides important new insights into the contribution of local DNA features to the molecular mechanisms and dynamics of copy number variation (CNV) formation during adaptive evolution. While limited to a single CNV, the experiments are carefully controlled and present convincing evidence that supports the conclusions. This work will be of general interest to those studying genome architecture and evolution from yeast biologists to cancer researchers.

Reviewed by eLife

Passive accumulation of alkaloids in non-toxic frogs challenges paradigms of the origins 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 Fitch

• Curated by eLife

  eLife assessment

  This important study sheds light on how poison frogs gain their toxins, with surprising new data on low levels of toxins in previously non-toxic frogs. The authors propose a new theory for evolution of toxicity based on convincing evidence, but the manuscript needs restructuring to be clearer. While the manuscript will benefit from improved presentation, this research has the potential to greatly impact our understanding of animal defense mechanisms.

Reviewed by eLife

Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands

1. Joannes A. A. Dekker
2. Dorothea Mylopotamitaki
3. Annemieke Verbaas
4. Virginie Sinet-Mathiot
5. Samantha Presslee
6. Morgan L. McCarthy
7. Morten Tange Olsen
8. Jesper V. Olsen
9. Youri van den Hurk
10. Joris Brattinga
11. Frido Welker

Reviewed by Peer Community in Archaeology

The integrated WF-Haldane (WFH) model of genetic drift resolving the many paradoxes of molecular evolution

1. Yongsen Ruan
2. Xiaopei Wang
3. Mei Hou
4. Wenjie Diao
5. Miles E. Tracy
6. Shuhua Xu
7. Zhongqi Liufu
8. Haijun Wen
9. Chung-I Wu

• Curated by eLife

  eLife assessment

  This study presents a useful modification of a standard model of genetic drift by incorporating variance in offspring numbers, claiming to address several paradoxes in molecular evolution. It is unfortunate that the study fails to engage prior literature that has extensively examined the impact of variance in offspring number, implying that some of the paradoxes presented might be resolved within existing frameworks. In addition, while the modified model yields intriguing theoretical predictions, the simulations and empirical analyses are incomplete to support the authors' claims.

Reviewed by eLife

Distinguishing mutants that resist drugs via different mechanisms by examining fitness tradeoffs

1. Kara Schmidlin
2. Sam Apodaca
3. Daphne Newell
4. Alexander Sastokas
5. Grant Kinsler
6. Kerry Geiler-Samerotte

• Curated by eLife

  eLife assessment

  This study provides valuable new insights into the trade-offs associated with the evolution of drug resistance in the yeast S. cerevisiae, based on a solid approach to evolving and phenotyping hundreds of independent strains. The authors identify distinct phenotypic clusters, defined by their growth across defined conditions, which suggest that tradeoffs are diverse but at the same time could be limited to a few classes according to the underlying resistance mechanisms. The methodologies used align with the current state-of-the-art, and the data and analysis are solid as they broadly support the claims, with only a few minor weaknesses remaining after revision. This work will interest molecular biologists working on the evolution of new phenotypes and microbiologists studying multi-drug therapy.

Reviewed by eLife

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses

1. Renan Maestri
2. Benoît Perez-Lamarque
3. Anna Zhukova
4. Hélène Morlon

• Curated by eLife

  eLife assessment

  Maestri et al report the absence of phylogenetic evidence supporting codiversification of mammalian coronaviruses and their hosts, leading to the important conclusion that the evolutionary history of the virus and its hosts are decoupled through frequent host switches. The evidence for frequent host switching, derived from state-of-the-art probabilistic modeling of co-evolution, is convincing. The study adds a new perspective to the ongoing debate over the timescale of coronavirus evolution.

Reviewed by eLife

Artificial selection improves pollutant degradation by bacterial communities

1. Flor I. Arias-Sánchez
2. Björn Vessman
3. Alice Haym
4. Géraldine Alberti
5. Sara Mitri

Reviewed by Arcadia Science