Evolutionary Biology

The biogeography of evolutionary radiations on oceanic archipelagos

1. Baptiste Brée
2. Thomas J. Matthews
3. José María Fernández-Palacios
4. Christian Paroissin
5. Kostas A. Triantis
6. Robert J. Whittaker
7. François Rigal

Reviewed by Peer Community in Ecology

Iridescent structural coloration in a crested Cretaceous enantiornithine bird from the Jehol Biota

1. Zhiheng Li
2. Jinsheng Hu
3. Thomas A Stidham
4. Mao Ye
5. Min Wang
6. Yanhong Pan
7. Tao Zhao
8. Jingshu Li
9. Zhonghe Zhou
10. Julia A Clarke

• Curated by eLife

  eLife Assessment

  This study presents a potentially fundamental analysis of a fossil feather from a 125-million-year-old enantiornithine bird. Using sophisticated 3D microscopic and numerical methods, the authors conclude that the feather was iridescent and brightly colored, possibly indicating that this was a male bird that used its crest in sexual displays. At present, the strength of evidence supporting the conclusions is considered incomplete based on methodological shortcomings and questions about taphonomy.

Reviewed by eLife

Weak evidence for heritable changes in response to selection by aphids in Arabidopsis accessions

1. Marc W Schmid
2. Klara Kropivšek
3. Samuel E Wuest
4. Bernhard Schmid
5. Ueli Grossniklaus

• Curated by eLife

  eLife Assessment

  This paper examines selection on induced epigenetic variation ("Lamarckian evolution") in response to herbivory in Arabidopsis thaliana. The authors find weak evidence for such adaptation, which contrasts with a recently published study that reported extensive heritable variation induced by the environment. The authors convincingly demonstrate that the findings of the previous study were confounded by mix-ups of genetically distinct material, so that standing genetic variation was mistaken for acquired (epigenetic) variation. Given the controversy surrounding the influence of heritable epigenetic variation on phenotypic variation and adaptation, this study is an important, clarifying contribution; it serves as a timely reminder that sequence-based verification of genetic material should be prioritized when either genetic identity or divergence is of importance to the conclusions.

Reviewed by eLife

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. The evidence presented by the authors is convincing 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

Refining the resolution of the yeast genotype–phenotype map using single-cell RNA-sequencing

1. Arnaud N'Guessan
2. Wen Yuan Tong
3. Hamed Heydari
4. Alex N Nguyen Ba

• Curated by eLife

  eLife Assessment

  This useful study describes expression profiling by scRNA-seq of thousands of cells of recombinant yeast genotypes from a system that models natural genetic variation. The rigorous new method presented here shows promise for improving the efficiency of genotype-to-phenotype mapping in yeast, providing convincing evidence for its efficacy. This manuscript focuses on overcoming technical challenges with this approach and identifies several new biological insights that build upon the field of genotype-to-phenotype mapping, a central question of interest to geneticists and evolutionary biologists.

Reviewed by eLife

Recurrent mutations drive the rapid evolution of pesticide resistance in the two-spotted spider mite Tetranychus urticae

1. Li-Jun Cao
2. Jin-Cui Chen
3. Joshua A Thia
4. Thomas L Schmidt
5. Richard Ffrench-Constant
6. Lin-Xi Zhang
7. Yu Yang
8. Meng-Chu Yuan
9. Jia-Yue Zhang
10. Xiao-Yang Zhang
11. Qiong Yang
12. Ya-Jun Gong
13. Hu Li
14. Xuexin Chen
15. Ary A Hoffmann
16. Shu-Jun Wei

• Curated by eLife

  eLife Assessment

  This study provides important insights into the evolution of pesticide resistance, demonstrating that resistance can arise rapidly and repeatedly, which complements prior work on parallel evolution across species. The combination of extensive temporal sampling in the field, experimental evolution, and genomics makes for compelling findings. The authors are to be commended for acknowledging the main limitations of their study in the Discussion. Framing the work in a broader context of resistance beyond arthropod pests would further increase the appeal of the study, which is of relevance for both agronomic practitioners and evolutionary biologists.

Reviewed by eLife

Ancient trans-species polymorphism at the Major Histocompatibility Complex in primates

1. Alyssa Lyn Fortier
2. Jonathan K Pritchard

• Curated by eLife

  eLife Assessment

  This important manuscript presents a thorough analysis of trans-specific polymorphism (TSP) in Major Histocompatibility Complex gene families across primates. The analysis makes the most of currently available genomic data and methods to substantially increase the amount and evolutionary time that TSPs can be observed. Both false negative TSPs due to missing genes at the assembly and/or annotation level, as well as false positives due to read mismapping with missing paralogs, are well assessed and discussed. Overall the evidence provided is compelling, and the manuscript clearly delineates the path for future progress on the topic.

Reviewed by eLife

Species biology and demographic history determines species vulnerability to climate change in tropical island endemic birds

1. Ratnesh Karjee
2. Vikram Iyer
3. Durbadal Chatterjee
4. Rajasri Ray
5. Kritika M Garg
6. Balaji Chattopadhyay

• Curated by eLife

  eLife Assessment

  Tropical single-island endemic bird populations are particularly vulnerable to climate change. The authors investigate genetic evidence of how such species dealt with climate changes in the past as a possible predictor for how they will respond to change in the future, which could provide an important example for the fields of conservation genetics and island biogeography. The authors' integration of genomics and habitat modeling is commendable, but we find that the support for their conclusions is incomplete: at times, the results presented appear to contradict each other, the authors do not fully account for key variables, and the limited taxonomic scope may cause problematic biases for the conclusions.

Reviewed by eLife

Divergent C. elegans toxin alleles are suppressed by distinct mechanisms

1. Stefan Zdraljevic
2. Laura Walter-McNeill
3. Giancarlo N Bruni
4. Joshua S Bloom
5. Daniel HW Leighton
6. JB Collins
7. Heriberto Marquez
8. Noah Alexander
9. Leonid Kruglyak

• Curated by eLife

  eLife Assessment

  This study provides valuable insights into a new toxin-antidote element in C. elegans, the first naturally occurring unlinked toxin-antidote system where endogenous small RNA pathways post-transcriptionally suppress the toxin. The strength of evidence is solid, using a combination of genomic and experimental methods. Enthusiasm, however, is tempered by its reliance on meta-analysis of existing data sets and limited experimental evaluation.

Reviewed by eLife

Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors

1. Avery Selberg
2. Nathan L Clark
3. Timothy B Sackton
4. Spencer V Muse
5. Alexander G Lucaci
6. Steven Weaver
7. Anton Nekrutenko
8. Maria Chikina
9. Sergei L Kosakovsky Pond

• Curated by eLife

  eLife Assessment

  Alignment and sequencing errors are a major concern in molecular evolution, and this valuable study represents a welcome improvement for genome-wide scans of positive selection. This new method seems to perform well and is generally convincing, although the evidence could be made more direct and more complete through additional simulations to determine the extent to which alignment errors are being properly captured.

Reviewed by eLife