Evolutionary Biology

Contingency and chance erase necessity in the experimental evolution of ancestral proteins

1. Victoria Cochran Xie
2. Jinyue Pu
3. Brian P.H. Metzger
4. Joseph W. Thornton
5. Bryan C. Dickinson

• Curated by eLife

  Evaluation Summary:

  This manuscript, which will be of interest to students of evolution and anybody interested in protein function, uses an original, clever, high throughput, and rapid experimental protein evolution method to assess the roles and contributions of contingency, chance, and necessity in the evolution of protein-protein interactions. The authors focus on the animal BCL-2 protein family and on the evolution of their binding properties to two proteins, NOXA and BID. Using several replicates and several starting points, they found little predictability between replicates of single starting points and among those from multiple starting points, indicating that there is no single pathway through sequence space to the selected function, and that historical contingency is the primary cause of protein evolution here. The presented results convincingly illustrate the potential of this novel technology for future work in directed protein evolution.

  (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 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics

1. Peijun Ma
2. Lorrie L He
3. Alejandro Pironti
4. Hannah H Laibinis
5. Christoph M Ernst
6. Abigail L Manson
7. Roby P Bhattacharyya
8. Ashlee M Earl
9. Jonathan Livny
10. Deborah T Hung

• Curated by eLife

  Evaluation Summary:

  This manuscript is of interest to several fields in biology and medicine including evolutionary genomics and antibiotic stewardship. Ma et al. sought to investigate the breadth of genetic mechanisms for evolution of carbapenem resistance across various lineages of the bacterial pathogen Klebsiella pneumoniae. The authors performed systematic and thorough bioinformatic and genetic analyses to identify how transposon activity and CRISPR-Cas systems facilitate the evolution of antibiotic resistance and restriction of horizontally acquired genetic elements, respectively. The study's results emphasize the importance of additional factors, other than MIC values, such as genetic background, plasmid/transposon activity, and drug identity and choice in determining the rate at which resistance can evolve in K. pneumoniae.

  (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 #2 agreed to share their name with the authors.)

Reviewed by eLife

Local adaptation and archaic introgression shape global diversity at human structural variant loci

1. Stephanie M Yan
2. Rachel M Sherman
3. Dylan J Taylor
4. Divya R Nair
5. Andrew N Bortvin
6. Michael C Schatz
7. Rajiv C McCoy

• Curated by eLife

  Evaluation Summary:

  The technical challenges of identifying and quantifying the frequency of structural variants (SV) on a population scale has been a major limitation to the study of recent human adaptation. This manuscript applies a recent graph-based genotyping method that leverages a library of SVs identified by long-read sequencing to identify SVs in large short-read based cohorts. This is a sensible and powerful approach that highlights several examples of likely adaptive SV evolution in different human populations. The key findings and examples are well supported by the data and methods used. However, the manuscript would benefit from further comparisons and context from previous studies, and deeper exploration of the biological significance. In addition to providing novel examples of adaptive SV evolution, this analysis may serve as a template for future analyses that merge long-read and short-read datasets.

  (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

High rates of evolution preceded shifts to sex-biased gene expression in Leucadendron, the most sexually dimorphic angiosperms

1. Mathias Scharmann
2. Anthony G Rebelo
3. John R Pannell

• Curated by eLife

  Evaluation Summary:

  This is one of the first studies to investigate sex-biased gene expresion in a broad phylogenetic context, and the first in a plant genus. The findings go against the classical view that sex-biased gene expression is driven by sex-specific selection for sexual dimorphism, and instead suggests that sex-bias preverentially evolved in genes that already had the highest expression variance to begin with. It will broadly appeal to researchers interested in the evolution of sexual dimorphism.

  (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

A meta-analysis of the association between male dimorphism and fitness outcomes in humans

1. Linda H Lidborg
2. Catharine Penelope Cross
3. Lynda G Boothroyd

• Curated by eLife

  Evaluation Summary:

  This work evaluates the strength of the evidence that human sexual dimorphism is the product of sexual selection. As a meta-analysis of studies that connect various measures of masculinity to various measures of reproductive success, this paper represents a synthesis of what this vast literature can show thus far. The work will be of general interest to evolutionary social scientists from a variety of disciplines, and it does a good job of clearly and concisely presenting the current state of sexual selection research on human males. The data are well presented, but the interpretation of the results is currently limited by some gaps in the theoretical framework guiding the manuscript.

  (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 #1-4 agreed to share their names with the authors.)

Reviewed by eLife

Tachykinin signaling inhibits task-specific behavioral responsiveness in honeybee workers

1. Bin Han
2. Qiaohong Wei
3. Fan Wu
4. Han Hu
5. Chuan Ma
6. Lifeng Meng
7. Xufeng Zhang
8. Mao Feng
9. Yu Fang
10. Olav Rueppell
11. Jianke Li

• Curated by eLife

  Evaluation Summary:

  The authors provide convincing evidence that tachykinin signaling is involved in regulating response thresholds of task-specific stimuli only in the respective behavioral specialist. For example tachykinin signaling affects responses to pollen in pollen foragers and responses to larval chemical cues only in nurse bees. The study highlights the importance of peptide signaling in social behaviors in insects for the first time.

  (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 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

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