Evolutionary Biology

A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations

1. Ruth Charlotte Eccleston
2. Emilia Manko
3. Susana Campino
4. Taane G Clark
5. Nicholas Furnham

• Curated by eLife

  eLife assessment

  This report is a useful demonstration of how to predict the mutational pathways to antimicrobial resistance (AMR) emergence, particularly in the enzyme DHFR (dihydrofolate reductase). The methodology is overall solid but some of the claims are only partially supported. The work will be of interest to microbiologists and evolutionary biologists interested in antimicrobial resistance and its population genetics dynamic.

Reviewed by eLife

TRPA5 encodes a thermosensitive ankyrin ion channel receptor in a triatomine insect

1. Marjorie A. Liénard
2. David Baez-Nieto
3. Cheng-Chia Tsai
4. Wendy A. Valencia-Montoya
5. Balder Werin
6. Urban Johanson
7. Jean-Marc Lassance
8. Jen Q. Pan
9. Nanfang Yu
10. Naomi E. Pierce

Reviewed by Arcadia Science

Reconstructing cell type evolution across species through cell phylogenies of single-cell RNAseq data

1. Jasmine L. Mah
2. Casey W. Dunn

Reviewed by Arcadia Science

Gene expression plasticity followed by genetic change during colonization in a high-elevation environment

1. Huishang She
2. Yan Hao
3. Gang Song
4. Xu Luo
5. Fumin Lei
6. Weiwei Zhai
7. Yanhua Qu

• Curated by eLife

  eLife assessment

  This study provides useful information on the evolution of gene expression levels and plasticity in tissues impacted by hypoxia during colonization of a high-altitude environment. Unfortunately, the evidence for the conclusions is incomplete because of the low sample size available.

Reviewed by eLife

Divergent functions of two clades of flavodoxin in diatoms mitigate oxidative stress and iron limitation

1. Shiri Graff van Creveld
2. Sacha N Coesel
3. Stephen Blaskowski
4. Ryan D Groussman
5. Megan J Schatz
6. E Virginia Armbrust

• Curated by eLife

  eLife assessment

  This study presents valuable findings regarding the functional diversification of flavodoxins from diatoms, a protein initially described as an Fe-sparing substitute for ferredoxin in Fe-poor open ocean environments. The evidence supporting the claims of the authors is solid, although the study could be strengthened by using a wider gradient of oxidative stress in the experiments and using Fe limitation methodology, which allows more certain differentiation between a low Fe and oxidative stress response.

Reviewed by eLife

Fight Not Flight: Parasites Drive the Bacterial Evolution of Resistance, Not Escape

1. Michael Blazanin
2. Jeremy Moore
3. Sydney Olsen
4. Michael Travisano

Reviewed by Arcadia Science

Selection on many loci drove the origin and spread of a key innovation

1. Sean Stankowski
2. Zuzanna B. Zagrodzka
3. Martin D. Garlovsky
4. Arka Pal
5. Daria Shipilina
6. Diego Garcia Castillo
7. Alan Le Moan
8. Erica Leder
9. James Reeve
10. Kerstin Johannesson
11. Anja M. Westram
12. Roger K. Butlin

Reviewed by Arcadia Science

New hypotheses of cell type diversity and novelty from orthology-driven comparative single cell and nuclei transcriptomics in echinoderms

1. Anne Meyer
2. Carolyn Ku
3. William L Hatleberg
4. Cheryl A Telmer
5. Veronica Hinman

• Curated by eLife

  eLife assessment

  This study is an excellent example of how one can use high-throughput technologies to address animal evolution from a cell-type perspective. The authors present a beautiful analysis of single-nucleus RNA-seq data from three embryonic stages in a sea star; this is the first single-cell data from this large group of echinoderms and the first single-nucleus transcriptomic study in any echinoderm. The authors demonstrate the presence of unique as well as previously unnoticed homologous cell types between a sea star and a sea urchin, discovery very intriguing to echinoderm developmental biologists, which will also be of great interest to scientists in the broad fields of evolution and development.

Reviewed by eLife

Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks

1. Arturo Torres Ortiz
2. Michelle Kendall
3. Nathaniel Storey
4. James Hatcher
5. Helen Dunn
6. Sunando Roy
7. Rachel Williams
8. Charlotte Williams
9. Richard A Goldstein
10. Xavier Didelot
11. Kathryn Harris
12. Judith Breuer
13. Louis Grandjean

• Curated by eLife

  eLife assessment

  This valuable study presents a novel and theoretically interesting model to account for viral diversity within hosts in evolutionary and genomic analyses of pathogens. The simulation results presented are solid, although there are some aspects of the methodology that require further investigation in order to establish their validity. The application to SARS-CoV-2 shows promise, but would benefit from further evaluation.

Reviewed by eLife

Evolution of an extreme hemoglobin phenotype contributed to the sub-Arctic specialization of extinct Steller’s sea cows

1. Anthony V Signore
2. Phillip R Morrison
3. Colin J Brauner
4. Angela Fago
5. Roy E Weber
6. Kevin L Campbell

• Curated by eLife

  eLife assessment

  This important study functionally characterizes hemoglobin from Steller's sea cow, a cold-water adapted sirenian that went extinct ~250 years ago. Using ancestral sequence reconstruction, site-directed mutagenesis and biochemical assays to compare Steller's hemoglobin to those from (sub)tropical extant sea cows (all of which are proficient divers despite lacking massive muscle oxygen storage), the authors build a solid case for the molecular basis of cold adaptation, centered around an increased solubility and higher oxygen carrying capacity. Remarkably, a single amino acid replacement would explain most of the distinctive functional features of this hemoglobin, which include a hitherto unknown resistance to DPG. Overall, this work will be of interest to evolutionary biologists, physiologists, and biochemists, as well as an enjoyable and informative read for the general public.

Reviewed by eLife