Evolutionary Biology

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

The wtf meiotic driver gene family has unexpectedly persisted for over 100 million years

1. Mickaël De Carvalho
2. Guo-Song Jia
3. Ananya Nidamangala Srinivasa
4. R Blake Billmyre
5. Yan-Hui Xu
6. Jeffrey J Lange
7. Ibrahim M Sabbarini
8. Li-Lin Du
9. Sarah E Zanders

• Curated by eLife

  Evaluation Summary:

  This paper's central findings - that wtf genes are old, rapidly evolving, and often meiotic drivers - are important and of broad interest to evolutionary biologists and geneticists. The study's main claims are supported by convincing evidence from comparative genomic data, phylogenetic analyses, and functional experiments. However, support for the verbal model of wtf persistence is currently incomplete.

  (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

Mandrill mothers associate with infants who look like their own offspring using phenotype matching

1. Marie JE Charpentier
2. Clémence Poirotte
3. Berta Roura-Torres
4. Paul Amblard-Rambert
5. Eric Willaume
6. Peter M Kappeler
7. François Rousset
8. Julien P Renoult

• Curated by eLife

  Evaluation Summary:

  This article is of potential interest to researchers working on primate social behaviour, as it presents a novel mechanism for how an association with non-relatives can be favoured under kin selection. In a wild mandrill population, mothers are observed to preferentially lead offspring to associate with paternal half-sibs, a potential mechanism for encouraging nepotistic interactions between their offspring and other members of their group. The authors' explanation for their results was considered to be only partially supported by the data and a more measured and nuanced presentation would be appropriate.

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

Reviewed by eLife

Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins

1. Eric B Zheng
2. Li Zhao

• Curated by eLife

  Evaluation Summary:

  By integrating in silico predictions and mass-spectrometry, this manuscript tackles the problem of annotating the currently nameless stretches of genomic sequence that actually code for proteins. The hundreds of protein coding fruit fly genes described here offer new inroads for studying some of the very youngest functional elements in genomes, particularly those that have recently emerged from non-coding DNA sequences. To clarify the biological significance of the present study, the authors should both highlight the genes mostly like to encode functional products and conduct a comparison to published datasets that used different methods to identify such genes in fruit flies.

  (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 Arcadia Science, eLife

Experimental evidence that group size generates divergent benefits of cooperative breeding for male and female ostriches

1. Julian Melgar
2. Mads F Schou
3. Maud Bonato
4. Zanell Brand
5. Anel Engelbrecht
6. Schalk WP Cloete
7. Charlie K Cornwallis

• Curated by eLife

  Evaluation Summary:

  This manuscript is of broad interest to readers in the field of animal behavior and the evolution of cooperation. This work experimentally investigates the effect of differences in group size and group composition on reproductive behavior, by using an impressive sample of semi-wild populations of ostriches. While the paper does not address some aspects of groups, such as relatedness and parentage, overall, this paper is a complete analysis of the breeding ecology of this system and can serve as a blueprint for more of such work in the fields of cooperation, group living and breeding ecology.

  (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

A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell division numbers

1. Marc de Manuel
2. Felix L Wu
3. Molly Przeworski

• Curated by eLife

  Evaluation Summary:

  This paper challenges a fundamental view concerning why males of most animals have a higher germline mutation rate than females. Evidence is provided to show that it is not simply the fact that males have more cell divisions in the germline, but instead, most of the mutations arise from a different balance of DNA damage vs. DNA repair. The case is supported by data from multiple species, from de novo mutation rate estimates from pedigrees, and from fits to a simple heuristic model. This work will be of interest to the broad field of DNA mutations and DNA repair, as well as evolutionary and phylogenomics researchers.

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

Reviewed by eLife