Evolutionary Biology

Evolution of host-microbe cell adherence by receptor domain shuffling

1. EmilyClare P Baker
2. Ryan Sayegh
3. Kristin M Kohler
4. Wyatt Borman
5. Claire K Goodfellow
6. Eden R Brush
7. Matthew F Barber

• Curated by eLife

  Evaluation Summary:

  Baker et al. investigates the molecular evolution in primates of one protein family, the CEACAMs, that are a recurrent target of bacterial surface adhesions at epithelial surfaces. They show that multiple members of this gene family have experienced repeated episodes of positive selection in primates, especially in the N-terminal domains that are associated with protein binding and go on to evaluate the functional consequences of these evolutionary changes.

  (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 names with the authors.)

Reviewed by eLife

Protein-coding potential of RNAs measured by potentially translated island scores

1. Yusuke Suenaga
2. Mamoru Kato
3. Momoko Nagai
4. Kazuma Nakatani
5. Hiroyuki Kogashi
6. Miho Kobatake
7. Takashi Makino

Reviewed by Review Commons

Sequence and structural conservation reveal fingerprint residues in TRP channels

1. Deny Cabezas-Bratesco
2. Francisco A Mcgee
3. Charlotte K Colenso
4. Kattina Zavala
5. Daniele Granata
6. Vincenzo Carnevale
7. Juan C Opazo
8. Sebastian E Brauchi

• Curated by eLife

  Evaluation Summary:

  Transient Receptor Potential (TRP) cation channels, related to voltage-gated channels, appeared before plants and animals diverged in evolution and expanded in vertebrates into seven major subfamilies and took multiple essential physiological functions encoding chemical and physical information into electrical signals. In this manuscript, Deny Cabezas-Bratesco and co-workers draw from multiple sequence alignments and available structural information to identify highly conserved features in the transmembrane domains across several major TRP subfamilies in vertebrate and invertebrate animals and even in unicellular organisms. By systematically analyzing their findings, the authors propose a structural framework hinting at common mechanisms utilized by TRP channels to integrate stimuli into electric signals, which has major implications for a wide range of biological processes where TRP channels play a role.

  (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

Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis

1. Michal Motyka
2. Dominik Kusy
3. Matej Bocek
4. Renata Bilkova
5. Ladislav Bocak

• Curated by eLife

  Evaluation Summary:

  This manuscript provides some clear ideas on the use of next-generation sequencing data to rapidly increase biodiversity inventories and set the basis for future research. The principal objective of this study is to demonstrate how biodiversity information for a hyperdiverse tropical group can be rapidly expanded via targeted field research and large-scale sequencing. The authors use a comprehensive sampling for a tribe of beetles with complicated morphological characters, highlight the existence of multiple undescribed taxa. The database of sequences could set a benchmark for the spatiotemporal evaluation of biodiversity, would support evidence-based conservation planning, and would provide a robust framework for systematic, biogeographic, and evolutionary studies.

  (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

δ1 variant of SARS-COV-2 acquires spike V1176F and yields a highly mutated subvariant in Europe

1. Xiang-Jiao Yang

Reviewed by ScreenIT

SARS-COV-2 C.1.2 variant is highly mutated but may possess reduced affinity for ACE2 receptor

1. Xiang-Jiao Yang

Reviewed by ScreenIT

SARS-COV-2 γ variant acquires spike P681H or P681R for improved viral fitness

1. Xiang-Jiao Yang

Reviewed by ScreenIT

A kinetic error filtering mechanism for enzyme-free copying of nucleic acid sequences

1. Tobias Göppel
2. Benedikt Obermayer
3. Irene A. Chen
4. Ulrich Gerland

• Curated by eLife

  Evaluation Summary:

  How was it possible for prebiotic RNA or DNA molecules to reliably self-replicate, in the absence of sophisticated enzymes capable of error correction? This paper proposes a novel mechanism for error correction in templated copying, and is therefore of interest for cell and evolutionary biologists, biophysicists and readers in the field of origin-of-life science. The kinetic error filtering proposed here does not require sophisticated machinery but reduces errors significantly while retaining a reasonable yield rate. Crucial to this mechanism is a cyclically varying environment, such as might exist in hydrothermal vents. The plausibility of the mechanism is supported by thoughtful and rigourous calculations rooted in an experimentally-grounded model.

  (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

Unconventional conservation reveals structure-function relationships in the synaptonemal complex

1. Lisa E Kursel
2. Henry D Cope
3. Ofer Rog

• Curated by eLife

  Evaluation Summary:

  Although the synaptonemal complex (SC) is an essential, deeply conserved structure that holds meiotic chromosomes together, the constituent proteins evolve exceptionally rapidly. This rapid evolution in turn has hindered the identification of SC proteins based solely on sequence homology. This manuscript overcomes this challenge by developing and validating a clever protein structure-based approach that leverages sequence divergence - rather than sequence conservation - to identify novel SC components.

  (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

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

1. Nicolás Mongiardino Koch
2. Jeffrey R Thompson
3. Avery S Hiley
4. Marina F McCowin
5. A Frances Armstrong
6. Simon E Coppard
7. Felipe Aguilera
8. Omri Bronstein
9. Andreas Kroh
10. Rich Mooi
11. Greg W Rouse

• Curated by eLife

  Evaluation Summary:

  The study by Koch et al presents new phylogenomic and molecular clock analyses of echinoids. The study uses state of the art phylogenetic approaches and includes 17 newly sequenced genomes and transcriptomes, which are used to estimate the tree topology and divergence times of major groups of echinoids. The molecular clock-estimated times of origin of particular echinoid lineages predate the lineages' appearance on the fossil record by tens of millions of years, prompting re-evaluation of the early evolution of echinoid diversity.

  (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