Evolutionary Biology

Global epistasis emerges from a generic model of a complex trait

1. Gautam Reddy
2. Michael M Desai

• Curated by eLife

  Evaluation Summary:

  The authors consider Darwinian evolution for large systems, with a main focus on how adaptation changes over time. Frequently observed patterns of declining adaptability for a population in a new environment are discussed, i.e., that fitness tends to increase fast initially and then at a slower rate. Another topic is historical contingency in adaptation. A condition for minimal contingency is provided, and a new model (the connectedness model, or CN model) is introduced accordingly. The manuscript is innovative, conceptually interesting, and provides quantitative precision beyond most related studies in the field. However, the presentation currently does not work well for a general audience.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewers #1, #2, and #3 agreed to share their names with the authors.)

Reviewed by eLife

Genetic integration of behavioural and endocrine components of the stress response

1. Thomas M Houslay
2. Ryan L Earley
3. Stephen J White
4. Wiebke Lammers
5. Andrew J Grimmer
6. Laura M Travers
7. Elizabeth L Johnson
8. Andrew J Young
9. Alastair Wilson

• Curated by eLife

  Evaluation Summary:

  This is a timely paper on the genetic integration of behavioral and physiological components of the stress response in guppies. Using evolutionary quantitative genetic approaches, the authors show that genetic variation in the cortisol stress response is associated with genetic variation in stress-related behaviors. This result suggests that physiological and behavioral responses to stress should show correlated evolution in response to natural selection, which is of interest to evolutionary biologists and for animal welfare. The reviewers pointed out several conceptual and methodological issues with the definition of the phenotypes under study and and with the definition strong genetic integration.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae

1. Pengyao Jiang
2. Anja R Ollodart
3. Vidha Sudhesh
4. Alan J Herr
5. Maitreya J Dunham
6. Kelley Harris

Reviewed by Review Commons

Ploidy and recombination proficiency shape the evolutionary adaptation to constitutive DNA replication stress

1. Marco Fumasoni
2. Andrew W. Murray

Reviewed by Review Commons

Morphological and genomic shifts in mole-rat ‘queens’ increase fecundity but reduce skeletal integrity

1. Rachel A Johnston
2. Philippe Vullioud
3. Jack Thorley
4. Henry Kirveslahti
5. Leyao Shen
6. Sayan Mukherjee
7. Courtney M Karner
8. Tim Clutton-Brock
9. Jenny Tung

• Curated by eLife

  Evaluation Summary:

  This manuscript takes a deep dive into the skeletal effects of burrowing and eusocial Damaraland mole rats. By exploring the genetic and skeletal consequences of breeding restricted to a single queen with multiple and closely-timed pregnancies and lactation, this study offers a compelling story that will bolster textbooks on skeletal biology, mammalian evolution, and ethology. The results show the molecular mechanisms driving adaptive plasticity within the unusually expanded lumbar spine and thin limb bones of queens are an adaptive consequence of breeding status.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

An evolutionary model identifies the main evolutionary biases for the evolution of genome-replication profiles

1. Rossana Droghetti
2. Nicolas Agier
3. Gilles Fischer
4. Marco Gherardi
5. Marco Cosentino Lagomarsino

• Curated by eLife

  Summary: The reviewers appreciate that the manuscript presents a simple but compelling model that explains the dynamics of replication origin birth and death, which enhances our understanding of the selection pressures that have shaped the distribution of replication origins. However, both reviewers had a series of concerns.

Reviewed by eLife

Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk

1. Juan M Vazquez
2. Vincent J Lynch

Reviewed by eLife

Mitochondrial copper and phosphate transporter specificity was defined early in the evolution of eukaryotes

1. Xinyu Zhu
2. Aren Boulet
3. Katherine M Buckley
4. Casey B Phillips
5. Micah G Gammon
6. Laura E Oldfather
7. Stanley A Moore
8. Scot C Leary
9. Paul A Cobine

Reviewed by eLife

High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox

1. Rémi Allio
2. Marie-Ka Tilak
3. Celine Scornavacca
4. Nico L Avenant
5. Andrew C Kitchener
6. Erwan Corre
7. Benoit Nabholz
8. Frédéric Delsuc

• Curated by eLife

  Summary: Collectively, we liked a lot about your paper and we would accordingly like to encourage its continued evolution. However, we felt that the approximately equal balance at present between the roadkill genomics assembly pipeline and the phylogenetic and genetic diversity results was not justified, and we requested a shift accordingly as described below. Second, we require several analytical updates to the manuscript to ensure robustness of the main genetic diversity results.

Reviewed by eLife

Adaptive evolution of nontransitive fitness in yeast

1. Sean W Buskirk
2. Alecia B Rokes
3. Gregory I Lang

• Curated by eLife

  Summary: The findings presented in this manuscript are interesting. They show that selection is happening at multiple scales - among viruses within a cell - and between their host cells within a population. The conflict between these levels of selection results in evolved populations that are less fit than the ancestors. This work demonstrates that evolution may not be a simple linear march of progress. Rather, progress over short time scales can sometimes lead to a reduction of fitness over the longer time scale due to the evolution of ecological interactions.

Reviewed by eLife