Evolutionary Biology

Mutational robustness changes during long-term adaptation in laboratory budding yeast populations

1. Milo S Johnson
2. Michael M Desai

• Curated by eLife

  Evaluation Summary:

  Johnson and Desai previously reported "increasing cost epistasis", where mutations tended to have more deleterious effects in higher fitness backgrounds. Here they use the same system as before to investigate adapting populations by introducing a set of 91 mutations at multiple time points. As expected, the mean fitness effect of the mutations does decline in most (but not all) populations as they adapt but the effect is weaker than in the previous work, and in another condition, mean fitness effects of mutations do not change as the populations adapt. They suggest an intriguing interpretation (among others) that the "control coefficient" of selection on growth shifts between different genetic modules over 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 #2 agreed to share their name with the authors.)

Reviewed by eLife

Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations

1. Anna M Langmüller
2. Jackson Champer
3. Sandra Lapinska
4. Lin Xie
5. Matthew Metzloff
6. Samuel E Champer
7. Jingxian Liu
8. Yineng Xu
9. Jie Du
10. Andrew G Clark
11. Philipp W Messer

• Curated by eLife

  Evaluation Summary:

  The issue of general fitness effects in organisms expressing Cas9 enzymes as part of gene drive genetic control strategies is important, particularly in the emerging field of vector control. This manuscript reports experiments aimed at teasing apart such effects in a Drosophila model system, providing evidence that off-target effects predominate, which may be ameliorated by utilising high-fidelity nucleases, but a more detailed analysis of data and justification for some of the assumptions, especially some direct evidence of off-target cleavage, are still needed to support the authors' inferences. It is currently also not entirely clear how the lines were generated and tested. Finally, additional modelling to include scenarios where the initial frequency of the drive allele is very low (as would be the case for an actual release) would help to strengthen the conclusions.

  (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 single nucleotide variant in the PPARγ-homolog Eip75B affects fecundity in Drosophila

1. Katja M Hoedjes
2. Hristina Kostic
3. Thomas Flatt
4. Laurent Keller

• Curated by eLife

  Evaluation Summary:

  Hoedjes et al. examine how a single nucleotide variant in a regulatory region upstream of the Eip75B gene influences key aspects of life history in Drosophila, using RNAi knockdowns, inbred lines and CRISPR/Cas9 allele replacement at the endogenous locus. This study represents one of the very few examples in animals where the effect of a naturally segregating single nucleotide variant on a complex trait is carefully quantified.

  (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

Lung evolution in vertebrates and the water-to-land transition

1. Camila Cupello
2. Tatsuya Hirasawa
3. Norifumi Tatsumi
4. Yoshitaka Yabumoto
5. Pierre Gueriau
6. Sumio Isogai
7. Ryoko Matsumoto
8. Toshiro Saruwatari
9. Andrew King
10. Masato Hoshino
11. Kentaro Uesugi
12. Masataka Okabe
13. Paulo M Brito

• Curated by eLife

  Evaluation Summary:

  This study used valuable materials from five osteichthyan vertebrate species and investigated their lung morphology in them. The comparison of the observations suggest an origin of the lung as an unpaired organ, with the present-day paired forms in amniotes being a result of secondary modification. The sound morphological comparison presented provides valuable insight into the evolution of the lung. The work will be of interest to colleagues studying vertebrate 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 #2 and Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern

1. Mahan Ghafari
2. Qihan Liu
3. Arushi Dhillon
4. Aris Katzourakis
5. Daniel B. Weissman

Reviewed by ScreenIT

Admixture of evolutionary rates across a butterfly hybrid zone

1. Tianzhu Xiong
2. Xueyan Li
3. Masaya Yago
4. James Mallet

• Curated by eLife

  Evaluation Summary:

  The authors leverage theory, simulations, and empirical population genomics to evaluate what are the consequences of differences in substitution rates in hybridizing species. This is a largely overlooked phenomenon. This study highlights the issue and demonstrates that two hybridizing species of Papilio have differences in their substitution rates. The work will be of interest to a large group of evolutionary biologists, especially those studying evolution at the whole-genome level.

  (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

Widespread introgression across a phylogeny of 155 Drosophila genomes

1. Anton Suvorov
2. Bernard Y. Kim
3. Jeremy Wang
4. Ellie E. Armstrong
5. David Peede
6. Emmanuel R.R. D’Agostino
7. Donald K. Price
8. Peter J. Waddell
9. Michael Lang
10. Virginie Courtier-Orgogozo
11. Jean R. David
12. Dmitri Petrov
13. Daniel R. Matute
14. Daniel R. Schrider
15. Aaron A. Comeault

• Curated by eLife

  Evaluation Summary:

  The authors present an impressive view of introgression across the Drosophila clade. There is strong support for signals of introgression along numerous branches of the phylogeny. However, the placement of these introgression events on the phylogeny and their impact on genome-wide patterns of relatedness are less 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 agreed to share their name with the authors.)

Reviewed by eLife

The spatiotemporal patterns of major human admixture events during the European Holocene

1. Manjusha Chintalapati
2. Nick Patterson
3. Priya Moorjani

• Curated by eLife

  Evaluation Summary:

  This manuscript presents DATES, a method to infer the timing of admixture events using genetic data from present-day or ancient individuals. This is a robust method that is useful in the field of paleogenomics and outperforms existing methods. In this manuscript, DATES is applied to >1000 ancient human genomes to characterize major admixture events during the European Holocene. This work will be of interest to scholars in the fields of population genetics, paleogenomics, archeology, biological anthropology, and history.

  (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

Convergent mosaic brain evolution is associated with the evolution of novel electrosensory systems in teleost fishes

1. Erika L Schumacher
2. Bruce A Carlson

• Curated by eLife

  Evaluation Summary:

  This ms examines changes in brain region size in several groups of weakly electric fishes, the Mormyroidea, and the Gymnotiformes and weakly electric catfishes (Synodontis spp.), which evolved electroreception independently of mormyrids. These are an interesting group for examination of mosaic growth. Many analyses are thoughtful and well executed, but there is some concern about whether the observed volumetric decreases are a consequence of the method.

  (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

Squamation and scale morphology at the root of jawed vertebrates

1. Yajing Wang
2. Min Zhu

• Curated by eLife

  Evaluation Summary:

  This manuscript will be of strong interest to scientists studying the development of early jawed vertebrates, in particular the extent and structure of their dermal skeleton, but it will also interest a broader audience, given how it connects modern-day morphological techniques to paleobiology. The authors provide the most complete account to date of the body scales of an antiarch stem-group gnathostome; this is the first work to model in 3-D the entire scale cover of such a fossil fish. The authors show that the body scales are varied in form, regionalized and that they comprise two main tissue layers. Based on this they argue that these conditions are plesiomorphic for antiarchs and the gnathostome crown group.

  (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