Evolutionary Biology

Phylogeny and Metadata Network Database for Epidemiologic Surveillance

1. Garrick Stott
2. Leke Lyu
3. Gabriella Veytsel
4. Jacky Kuo
5. Ryan Lewis
6. Armand Brown
7. Kayo Fujimoto
8. Justin Bahl

Reviewed by ScreenIT

Diversification dynamics in the Neotropics through time, clades, and biogeographic regions

1. Andrea S Meseguer
2. Alice Michel
3. Pierre-Henri Fabre
4. Oscar A Pérez Escobar
5. Guillaume Chomicki
6. Ricarda Riina
7. Alexandre Antonelli
8. Pierre-Olivier Antoine
9. Frédéric Delsuc
10. Fabien L Condamine

• Curated by eLife

  Evaluation Summary:

  This paper analyzes data from 150 previously published phylogenies of plants and animals from the Neotropics. A range of diversification models is fit in order to characterize patterns of diversification through time and across space. The authors reveal five biogeographic provinces within which long-term diversification has occurred, but they find that contrasting patterns of diversification for lineages are better explained by their phylogenetic relationship than by biogeographic province, such that the observed modern diversity of seed plants and tetrapods is a consequence of the groups' contrasting diversification dynamics. This paper is of potential interest to a broad audience of biologists who are working on the evolution of large-scale biodiversity, diversity hotspots, lineage diversification, and biogeography.

  (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

Functional and structural segregation of overlapping helices in HIV-1

1. Maliheh Safari
2. Bhargavi Jayaraman
3. Henni Zommer
4. Shumin Yang
5. Cynthia Smith
6. Jason D Fernandes
7. Alan D Frankel

• Curated by eLife

  Evaluation Summary:

  This study should be of broad interest to all virologists and many students of molecular genetics. It examines the constraints in a part of the HIV 1 genome that encodes important functional regions of two proteins, Rev and Env, in overlapping reading frames. It is convincingly shown that functional segregation occurs in a part of the overlap region that is critical for both proteins, which has important implications for HIV biology and may aid in the design of future HIV therapies.

  (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

Distinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19

1. Marie Cariou
2. Léa Picard
3. Laurent Guéguen
4. Stéphanie Jacquet
5. Andrea Cimarelli
6. Oliver I. Fregoso
7. Antoine Molaro
8. Vincent Navratil
9. Lucie Etienne

Reviewed by ScreenIT

Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation

1. Austin H Patton
2. Emilie J Richards
3. Katelyn J Gould
4. Logan K Buie
5. Christopher H Martin

• Curated by eLife

  Evaluation Summary:

  This study reports on the inference of the evolutionary trajectory of two specialist species that evolved from one generalist species. The process of speciation is explained as an adaptive process and the changing genetic architecture of the process is analyzed in great detail. The genomic dataset is big and the inference from it solid. The authors reach the conclusion that introgression and de novo mutations, but not standing genetic variation, are the main players in this adaptive process.

  (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

Ancestral reconstruction of duplicated signaling proteins reveals the evolution of signaling specificity

1. Isabel Nocedal
2. Michael T Laub

• Curated by eLife

  Evaluation Summary:

  This manuscript is of interest to protein biochemists, protein engineers, and those interested in molecular evolution. The computation and experiments presented in this paper are very logical and rigorously performed. The results provide an example of how protein interaction specificity can be rewired using a small number of mutations, in the context of ancestral sequence reconstruction.

  (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

Complex fitness landscape shapes variation in a hyperpolymorphic species

1. Anastasia V Stolyarova
2. Tatiana V Neretina
3. Elena A Zvyagina
4. Anna V Fedotova
5. Alexey S Kondrashov
6. Georgii A Bazykin

• Curated by eLife

  Evaluation Summary:

  Stolyarova et al. investigate a highly polymorphic species, the fungus Schizophyllum commune, finding that compared to synonymous mutations, levels of linkage disequilibrium between nonsynonymous mutations are higher within genes than between genes. The authors propose this observation may be explained by compensatory interactions between nonsynonymous alleles, pointing to the presence of positive epistasis. This paper should be of interest to population geneticists and evolutionary biologists studying the role of natural selection.

  (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 evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals

1. Stéphane Peyrégne
2. Janet Kelso
3. Benjamin M Peter
4. Svante Pääbo

• Curated by eLife

  Evaluation Summary:

  Peyregne et al. studied the genes encoding proteins of the spindle apparatus. These genes have an elevated number of nonsynonymous substitutions in modern humans, and by comparison of modern and archaic alleles the authors identify that some Neanderthals had already the modern human haplotype at the KNL1 gene, raising the possibility that Neanderthals acquired it from modern humans. This study will be of interest to evolutionary biologists and anthropologists, because it supports the hypothesis that modern humans and Neanderthals interacted more than once in the past.

  (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

Parasite defensive limb movements enhance acoustic signal attraction in male little torrent frogs

1. Longhui Zhao
2. Jichao Wang
3. Haodi Zhang
4. Tongliang Wang
5. Yue Yang
6. Yezhong Tang
7. Wouter Halfwerk
8. Jianguo Cui

• Curated by eLife

  Evaluation Summary:

  Zhao et al. present an interesting proposal for the evolution of complex multimodal signals based on the analysis of the mating display of small torrent frogs. Combining observational and experimental evidence, they suggest that male limb movements, which are used to swat away blood-sucking midges, have become attractive to female frogs, enhancing the acoustic mating call of these males.

  (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

Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elements

1. David A Murphy
2. Eyal Elyashiv
3. Guy Amster
4. Guy Sella

• Curated by eLife

  Evaluation Summary:

  This paper uses state-of-the-art methods and the latest data to answer the question of whether variation in polymorphism levels along the human genome is mostly driven by linked purifying selection or selective sweeps. It makes a very strong case for the former. The paper is exceptionally well written, and should be of interest to anyone wishing to understand patterns of polymorphism.

  (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