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

    This article has 3 authors:
    1. Bing Guo
    2. Shannon Takala-Harrison
    3. Timothy D O’Connor
    This article has been curated by 1 group:
    • 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

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  2. Refining the resolution of the yeast genotype-phenotype map using single-cell RNA-sequencing

    This article has 4 authors:
    1. Arnaud N’Guessan
    2. Wen Yuan Tong
    3. Hamed Heydari
    4. Alex N Nguyen Ba
    This article has been curated by 1 group:
    • 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

    This article has 15 evaluationsAppears in 1 listLatest version Latest activity
  3. G protein-coupled receptor diversity and evolution in the closest living relatives of Metazoa

    This article has 2 authors:
    1. Alain Garcia De Las Bayonas
    2. Nicole King
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study fills an gap in our knowledge of the evolution of GPCRs in holozoans, as well as the phylogeny of associated signaling pathway components such as G proteins, GRKs, and RIC8 proteins. The evidence supporting the conclusions is compelling, with the analysis of extensive new genomic data from choanoflagellates and other non-animal holozoans. Overall, the study is thorough and well-executed. It will be a resource for researchers interested in both the comparative genomics of multicellularity and GPCR biology more broadly, especially given the importance of GPCRs as highly druggable targets.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  4. Recurrent Mutations Drive the Rapid Evolution of Pesticide Resistance in the Two-spotted Spider Mite Tetranychus urticae

    This article has 16 authors:
    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. Xue-Xin Chen
    15. Ary A Hoffmann
    16. Shu-Jun Wei
    This article has been curated by 1 group:
    • 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

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  5. The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference

    This article has 7 authors:
    1. Mahboobeh Behruznia
    2. Maximillian Marin
    3. Daniel Whiley
    4. Maha Farhat
    5. Jonathan C Thomas
    6. Maria Rosa Domingo-Sananes
    7. Conor J Meehan
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This useful study analyzed 335 Mycobacterium tuberculosis Complex genomes and found that MTBC has a closed pangenome with few accessory genes. The research provides solid evidence for gene presence-absence patterns which support the appending conclusions.

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  6. Ancient Trans-Species Polymorphism at the Major Histocompatibility Complex in Primates

    This article has 2 authors:
    1. Alyssa Lyn Fortier
    2. Jonathan K Pritchard
    This article has been curated by 1 group:
    • 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

    This article has 11 evaluationsAppears in 1 listLatest version Latest activity
  7. Species biology and demographic history determines species vulnerability to climate change in tropical island endemic birds

    This article has 6 authors:
    1. Ratnesh Karjee
    2. Vikram Iyer
    3. Durbadal Chatterjee
    4. Rajasri Ray
    5. Kritika M Garg
    6. Balaji Chattopadhyay
    This article has been curated by 1 group:
    • 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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  8. Divergent C. elegans toxin alleles are suppressed by distinct mechanisms

    This article has 9 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  9. Adaptations in wing morphology rather than wingbeat kinematics enable flight in small hoverfly species

    This article has 4 authors:
    1. Camille Le Roy
    2. Nina Tervelde
    3. Thomas Engels
    4. Florian T Muijres
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study addresses how wing morphology and kinematics change across hoverflies of different body sizes. The authors provide convincing evidence that there is no significant correlation between body size and wing kinematics across 28 species and instead argue that non-trivial changes in wing size and shape evolved to support flight across the size range. Overall, this paper illustrates the power and beauty of an integrative approach to animal biomechanics and will be of broad interest to biologists, physicists and engineers.

    Reviewed by eLife

    This article has 10 evaluationsAppears in 1 listLatest version Latest activity
  10. Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors

    This article has 9 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
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