Evolutionary Biology

Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

1. Richard G Dorrell
2. Alan Kuo
3. Zoltan Füssy
4. Elisabeth H Richardson
5. Asaf Salamov
6. Nikola Zarevski
7. Nastasia J Freyria
8. Federico M Ibarbalz
9. Jerry Jenkins
10. Juan Jose Pierella Karlusich
11. Andrei Stecca Steindorff
12. Robyn E Edgar
13. Lori Handley
14. Kathleen Lail
15. Anna Lipzen
16. Vincent Lombard
17. John McFarlane
18. Charlotte Nef
19. Anna MG Novák Vanclová
20. Yi Peng
21. Chris Plott
22. Marianne Potvin
23. Fabio Rocha Jimenez Vieira
24. Kerrie Barry
25. Colomban de Vargas
26. Bernard Henrissat
27. Eric Pelletier
28. Jeremy Schmutz
29. Patrick Wincker
30. Joel B Dacks
31. Chris Bowler
32. Igor V Grigoriev
33. Connie Lovejoy

Reviewed by Review Commons

Selection and the direction of phenotypic evolution

1. François Mallard
2. Bruno Afonso
3. Henrique Teotónio

• Curated by eLife

  eLife assessment

  This is a potentially important paper that takes advantage of an unusually comprehensive evolutionary genetic dataset to tease apart the relationship between genetic variation and phenotypic divergence over the ~medium term (50 generations). The questions addressed have broad relevance across evolution, conservation, and agricultural fields, and this paper will particularly appeal to evolutionary biologists. Nonetheless, the strength of evidence is incomplete for the major results and conclusions reported.

Reviewed by eLife

Sweepstakes reproductive success via pervasive and recurrent selective sweeps

1. Einar Árnason
2. Jere Koskela
3. Katrín Halldórsdóttir
4. Bjarki Eldon

• Curated by eLife

  Evaluation Summary:

  Analysis of molecular data from genome sequencing provides crucial information on the diversity of biological and evolutionary processes that shape genetic diversity. However, the models of genetic evolution used to make these inferences sometimes oversimplify important aspects of species biology. This study shows that accounting for high variance in reproductive success in models can better explain the genetic diversity of an extremely fecund marine species, the Atlantic cod. The manuscript is scientifically sound and provides careful statistical analyses of alternative evolutionary models. It concludes that pervasive selection, rather than demographic changes or sweepstakes reproduction, is one of the main drivers of genetic diversity in Atlantic cod.

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

Reviewed by eLife

Evolution of genome fragility enables microbial division of labor

1. Enrico Sandro Colizzi
2. Bram van Dijk
3. Roeland M H Merks
4. Daniel E Rozen
5. Renske M A Vroomans

Reviewed by Review Commons

Desiccation resistance differences in Drosophila species can be largely explained by variations in cuticular hydrocarbons

1. Zinan Wang
2. Joseph P Receveur
3. Jian Pu
4. Haosu Cong
5. Cole Richards
6. Muxuan Liang
7. Henry Chung

• Curated by eLife

  Evaluation Summary:

  This paper is an extensive analysis of the underlying basis of desiccation resistance in 50 Drosophila species from diverse habitats. The work suggests that the longer methyl-branched alkanes (mbCHC) of the cuticular hydrocarbons are critical for this resistance. The study, which informs on the evolution of desiccation resistance in flies, is well done, although the main hypothesis is currently only partially supported by coating experiments, which presently lack controls and would be greatly strengthened by "replacement" experiments to add mbCHCs to flies without CHCs. The work is of relevance to evolutionary biologists in general.

  (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

Evolutionary rescue of phosphomannomutase deficiency in yeast models of human disease

1. Ryan C Vignogna
2. Mariateresa Allocca
3. Maria Monticelli
4. Joy W Norris
5. Richard Steet
6. Ethan O Perlstein
7. Giuseppina Andreotti
8. Gregory I Lang

• Curated by eLife

  Evaluation Summary:

  Vignogna et al. used yeast genetics, experimental evolution and biochemistry to investigate human congenital disorders of glycosylation, often caused by mutations in PMM2. They took advantage of the observation that the budding yeast gene SEC53 is almost identical to human PMM2, and used experimental evolution to find interactors of SEC53/PMM2. Mutations in genes corresponding to other human CDG genes, including PGM1, were overrepresented. The mechanisms of how reduced pgm1 activity could compensate for defects of sec53 are not yet clear.

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

Reviewed by eLife

Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes

1. Yi Feng
2. Rafik Neme
3. Leslie Y Beh
4. Xiao Chen
5. Jasper Braun
6. Michael W Lu
7. Laura F Landweber

Reviewed by Review Commons

Most cancers carry a substantial deleterious load due to Hill-Robertson interference

1. Susanne Tilk
2. Svyatoslav Tkachenko
3. Christina Curtis
4. Dmitri A Petrov
5. Christopher D McFarland

• Curated by eLife

  Evaluation Summary:

  Cancers have frequently been found to show little evidence for purifying selection in their patterns of mutations. The key observation here is that tumors with low mutation burden show compelling evidence of efficient selection, but that tumors with high mutation burden do not. This is an important finding. The broader implication is that high mutation load tumors carry a substantial deleterious mutation load and may use common strategies to tolerate them, possibly providing a therapeutic target. Overall this work makes important observational and conceptual contributions to cancer genomics.

  (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 name with the authors.)

Reviewed by eLife

The evolution of manipulative cheating

1. Ming Liu
2. Stuart Andrew West
3. Geoff Wild

• Curated by eLife

  Evaluation Summary:

  The authors use theoretical models to examine the joint evolution of different cheating strategies: selfish cheating (not contributing to a common good), and manipulative cheating (inducing a competitor to preferentially provide benefits to the cheat). The models seem well formulated and the results robust. That said, improvements could be made to the presentation to clarify the assumptions and wider applicability of the model. An improved article would provide a better understanding of the mechanisms behind cheating, which would be of interest to readers working on the evolution of cooperation, potentially opening up new directions for theoretical and empirical work.

  (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

Balancing selection on genomic deletion polymorphisms in humans

1. Alber Aqil
2. Leo Speidel
3. Pavlos Pavlidis
4. Omer Gokcumen

• Curated by eLife

  Evaluation Summary:

  Detecting and quantifying balancing selection is a notoriously difficult challenge. In this study, the authors use both empirical analyses and simulations to characterize the amount of balancing selection in the human genome, focusing specifically on the contribution of polymorphic deletions. These results will be of interest to population and human geneticists. Although the presented evidence supports some degree of balancing selection among shared ancient polymorphisms, these findings primarily rely on the elimination of alternative explanations rather than a direct estimation of the extent of balancing selection. The conclusions are also based on simulations of a single demographic model without testing the robustness to other plausible model parameters.

  (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