Evolutionary Biology

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

Digital restoration of the pectoral girdles of two Early Cretaceous birds and implications for early-flight evolution

1. Shiying Wang
2. Yubo Ma
3. Qian Wu
4. Min Wang
5. Dongyu Hu
6. Corwin Sullivan
7. Xing Xu

• Curated by eLife

  Evaluation Summary:

  The authors provide new 3D fossil findings in Sapeornis, an avialan which lived during the early Cretaceous period, a key node in our understanding of the evolution of avian flight. The functional reconstruction of two critical skeletal elements of the avian flight apparatus, the scapula and coracoid, enable the authors to hypothesize how the evolution of the scapula and coracoid enabled the modern avian wing stroke. The new 3D morphological reconstruction enables future integrative studies of Sapeornis flight performance based on biomechanical, muscle physiological and aerodynamic principles and is thus a key building block to inform our general understanding of the evolution of avian flight.

  (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

Genome size evolution in the diverse insect order Trichoptera

1. Jacqueline Heckenhauer
2. Paul B Frandsen
3. John S Sproul
4. Zheng Li
5. Juraj Paule
6. Amanda M Larracuente
7. Peter J Maughan
8. Michael S Barker
9. Julio V Schneider
10. Russell J Stewart
11. Steffen U Pauls

Reviewed by GigaScience

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

1. Lucie A. Bergeron
2. Søren Besenbacher
3. Jaco Bakker
4. Jiao Zheng
5. Panyi Li
6. George Pacheco
7. Mikkel-Holger S. Sinding
8. Maria Kamilari
9. M. Thomas P. Gilbert
10. Mikkel H. Schierup
11. Guojie Zhang

Reviewed by GigaScience