Evolutionary Biology

Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen

1. Oscar A. MacLean
2. Spyros Lytras
3. Steven Weaver
4. Joshua B. Singer
5. Maciej F. Boni
6. Philippe Lemey
7. Sergei L. Kosakovsky Pond
8. David L. Robertson

Reviewed by ScreenIT

Natural Selection is Unlikely to Explain Why Species Get a Thin Slice of π

1. Vince Buffalo

• Curated by eLife

  Evaluation Summary:

  The manuscript revisits an enduring and central question in population genetics known as Lewontin's paradox: that in contrast to the prediction of the field's null model, which suggests that levels of neutral genetic diversity should be proportional to the census population size, in reality, census population sizes span several orders of magnitude more than the approximately three orders of magnitude spanned by levels of genetic diversity. The manuscript provides a nice review of previous work as well as thought-provoking novel analyses. There are also several issues that make it difficult to interpret the new results.

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

Reviewed by eLife

Understanding the evolution of multiple drug resistance in structured populations

1. David V McLeod
2. Sylvain Gandon

• Curated by eLife

  Evaluation Summary:

  This paper addresses the important question of multidrug resistance evolution, which is of both theoretical and applied interest. The authors efforts to carefully distinguish population and metapopulation linkage disequilibrium and to develop a framework to rigorously analyze the relationship between the two has promise, although we have noted concerns about the modeling framework used and results interpretation. If these concerns can be sufficiently addressed, then this paper has the potential to represent a clear advance in our understanding of microbial population dynamics.

  (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

Rampant tooth loss across 200 million years of frog evolution

1. Daniel J Paluh
2. Karina Riddell
3. Catherine M Early
4. Maggie M Hantak
5. Gregory FM Jongsma
6. Rachel M Keeffe
7. Fernanda Magalhães Silva
8. Stuart V Nielsen
9. María Camila Vallejo-Pareja
10. Edward L Stanley
11. David C Blackburn

• Curated by eLife

  Evaluation Summary:

  This manuscript will find a broad audience in the fields of evolutionary and developmental biology, especially herpetology, systematics, and those interested in the evolutionary history of vertebrate teeth. The expansive dataset presented by the authors has allowed for rigorous computational analyses yielding new insight into the evolutionary history of teeth in frogs, which is a topic that has received little attention from the scientific community. The resulting data largely support the key claims of 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. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Glycan-based shaping of the microbiota during primate evolution

1. Sumnima Singh
2. Patricia Bastos-Amador
3. Jessica Ann Thompson
4. Mauro Truglio
5. Bahtiyar Yilmaz
6. Silvia Cardoso
7. Daniel Sobral
8. Miguel P Soares

• Curated by eLife

  Evaluation Summary:

  30 million years ago the ancestors of Old World primates lost the ability to produce alpha-gal due to the fixation of several loss-of-function mutations in the GGTA1 gene. The evolutionary advantage of such loss remains elusive. Here, the authors provide additional insights into the pleiotropic role of ggta1 in shaping the gut microbiota, immune function, susceptibility to sepsis, and eventual fitness advantage.

  (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, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers

1. Kai He
2. Triston G Eastman
3. Hannah Czolacz
4. Shuhao Li
5. Akio Shinohara
6. Shin-ichiro Kawada
7. Mark S Springer
8. Michael Berenbrink
9. Kevin L Campbell

• Curated by eLife

  Evaluation Summary:

  This study, based on an elaborated animal sample collection, reconstructs a comprehensive tree of Eulipotyphla, especially concentrating on Talpidae (moles), and infers the transitions of their lifestyles. It also models myoglobin structure and calculate electrophoretic mobility, demonstrating that semiaquatic eulipotyphlans have a higher net surface charge than fossorial, semifossorial, and terrestrial relatives. This variable myoglobin property indicates convergent shifts to a semi-aquatic lifestyle in multiple independent lineages including three separate times by ‘water shrews’, the smallest endothermic divers.

  (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

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