Evolutionary Biology

Benchmarking and Optimization of Methods for the Detection of Identity-By-Descent in High-Recombining Plasmodium falciparum Genomes

1. Bing Guo
2. Shannon Takala-Harrison
3. Timothy D. O’Connor

• Curated by eLife

  eLife Assessment

  This important study presents an evaluation of several tools used for detecting Identity-By-Descent (IBD) segments in highly recombining genomes, using simulated data to replicate the high recombination and low marker density of Plasmodium falciparum, the parasite responsible for malaria. Most of the evidence presented by the authors is solid demonstrating that users should be cautious calling IBD when SNP density is low and recombination rate is high. This study will be of interest to scientists working in the field of genome evolution and infectious diseases.

Reviewed by eLife

Human genetic ancestry, Mycobacterium tuberculosis diversity and tuberculosis disease severity in Dar es Salaam, Tanzania

1. Michaela Zwyer
2. Zhi Ming Xu
3. Amanda Ross
4. Jerry Hella
5. Mohamed Sasamalo
6. Maxime Rotival
7. Hellen Hiza
8. Liliana K. Rutaihwa
9. Sonia Borrell
10. Klaus Reither
11. Jacques Fellay
12. Damien Portevin
13. Lluis Quintana-Murci
14. Sebastien Gagneux
15. Daniela Brites

• Curated by eLife

  eLife Assessment

  This useful observational study was conducted in Dar es Salaam, Tanzania, to investigate potential associations between genetic variation in Mycobacterium tuberculosis and human host vs. disease severity. The authors conclude that human genetic ancestry did not contribute to tuberculosis severity, but the evidence for this conclusion is currently incomplete, as the analysis did not fully leverage the genome-wide data available in a human-strain association study, and there was no comparison group from the general population (or household controls), to which the ancestry findings could be compared. The findings have significance for the understanding of the influence of host / bacillary genetics on tuberculosis disease.

Reviewed by eLife

On the variation of structural divergence among residues in enzyme evolution

1. Julian Echave
2. Mathilde Carpentier

Reviewed by Arcadia Science

On the nature of the earliest known lifeforms

1. Dheeraj Kanaparthi
2. Frances Westall
3. Marko Lampe
4. Baoli Zhu
5. Thomas Boesen
6. Bettina Scheu
7. Andreas Klingl
8. Petra Schwille
9. Tillmann Lueders

• Curated by eLife

  eLife Assessment

  This provocative manuscript presents important comparisons of the morphologies of Archaean bacterial microfossils to those of microbes transformed under environmental conditions that mimic those present on Earth during the same Eon. The evidence in support of the conclusions is solid. The authors' environmental condition selection for their experiment is justified.

Reviewed by eLife

Recurrent Evolutionary Innovations in Rodent and Primate Schlafen Genes

1. Joris Mordier
2. Marine Fraisse
3. Michel Cohen-Tannoudji
4. Antoine Molaro

Reviewed by Review Commons

Recombination shapes the diversification of the wtf meiotic drivers

1. Yan Wang
2. Hao Xu
3. Qinliu He
4. Zhiwei Wu
5. Zhen Gong
6. Guan-Zhu Han

• Curated by eLife

  eLife Assessment

  This important study provides one mechanism that can explain the rapid diversification of poison-antidote pairs in fission yeast: recombination between existing pairs. The evidence is largely solid, but the study can benefit from demonstrating that the novel poison-antidote constructed by the authors can serve as a meiotic driver. The work is of interest to colleagues studying genetic incompatibilities.

Reviewed by eLife

An evolutionarily conserved Hox-Gbx segmentation code in the rice coral Montipora capitata

1. Shuonan He
2. Emma Rangel-Huerta
3. Eric Hill
4. Lacey Ellington
5. Shiyuan (Cynthia) Chen
6. Sofia Robb
7. Eva Majerová
8. Crawford Drury
9. Matthew C Gibson

• Curated by eLife

  eLife Assessment

  The authors studied the development of mesentery borders in the rice coral Montipora, a new experimental system, to complement existing data from the sea anemone Nematostella. They make a solid case that in Montipora, there is a sequence of Hox-Gbx genes whose staggered expression in the unsegmented larva is suggestive of their role in subdividing the gastric cavity into repeated units bordered by mesenteries, as in the sea anemone Nematostella. Pharmacological experiments also point to the involvement of the BMP pathway in this process, but additional experiments validating this are necessary. This is a valuable contribution to the field of cnidarian evolution, suggesting that BMP- and "Hox-Gbx code"-dependent patterning of the directive axis was ancestral for Anthozoa.

Reviewed by eLife

Template switching during DNA replication is a prevalent source of adaptive gene amplification

1. Julie N Chuong
2. Nadav Ben Nun
3. Ina Suresh
4. Julia Cano Matthews
5. Titir De
6. Grace Avecilla
7. Farah Abdul-Rahman
8. Nathan Brandt
9. Yoav Ram
10. David Gresham

• Curated by eLife

  eLife Assessment

  This study provides important new insights into the contributions of local DNA features to the complex molecular mechanisms and dynamics of copy number variation (CNV) formation during adaptive evolution. While limited to a single CNV of interest, the study is well-designed and carefully controlled, presenting compelling evidence that supports the conclusions. This work will be of general interest to those studying genome architecture and evolution from yeast biologists to cancer researchers.

Reviewed by eLife

Quantifying microbial fitness in high-throughput experiments

1. Justus Wilhelm Fink
2. Michael Manhart

• Curated by eLife

  eLife Assessment

  This manuscript applies a theoretical analysis to two published datasets on yeast and bacterial evolution to compare different ways of quantifying fitness. It makes an important advance by clarifying how discrepancies can arise by using different approaches and provides recommendations for best practices. While the evidence is solid, some improvements in the presentation of the data and a greater focus on the causes of the discrepancies between the various fitness estimates would strengthen the paper further.

Reviewed by eLife

Genotypic and phenotypic consequences of domestication in dogs

1. Sweetalana
2. Shirin Nataneli
3. Shengmiao Huang
4. Jazlyn A Mooney
5. Zachary A Szpiech

Reviewed by Arcadia Science