1. Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins

    This article has 2 authors:
    1. Eric B Zheng
    2. Li Zhao
    This article has been curated by 1 group:
    • Curated by eLife

      Evaluation Summary:

      By integrating in silico predictions and mass-spectrometry, this manuscript tackles the problem of annotating the currently nameless stretches of genomic sequence that actually code for proteins. The hundreds of protein coding fruit fly genes described here offer new inroads for studying some of the very youngest functional elements in genomes, particularly those that have recently emerged from non-coding DNA sequences. To clarify the biological significance of the present study, the authors should both highlight the genes mostly like to encode functional products and conduct a comparison to published datasets that used different methods to identify such genes in fruit flies.

      (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 Arcadia Science, eLife

    This article has 21 evaluationsAppears in 2 listsLatest version Latest activity
  2. Experimental evidence that group size generates divergent benefits of cooperative breeding for male and female ostriches

    This article has 7 authors:
    1. Julian Melgar
    2. Mads F Schou
    3. Maud Bonato
    4. Zanell Brand
    5. Anel Engelbrecht
    6. Schalk WP Cloete
    7. Charlie K Cornwallis
    This article has been curated by 1 group:
    • Curated by eLife

      Evaluation Summary:

      This manuscript is of broad interest to readers in the field of animal behavior and the evolution of cooperation. This work experimentally investigates the effect of differences in group size and group composition on reproductive behavior, by using an impressive sample of semi-wild populations of ostriches. While the paper does not address some aspects of groups, such as relatedness and parentage, overall, this paper is a complete analysis of the breeding ecology of this system and can serve as a blueprint for more of such work in the fields of cooperation, group living and breeding ecology.

      (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

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  3. A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell division numbers

    This article has 3 authors:
    1. Marc de Manuel
    2. Felix L Wu
    3. Molly Przeworski
    This article has been curated by 1 group:
    • Curated by eLife

      Evaluation Summary:

      This paper challenges a fundamental view concerning why males of most animals have a higher germline mutation rate than females. Evidence is provided to show that it is not simply the fact that males have more cell divisions in the germline, but instead, most of the mutations arise from a different balance of DNA damage vs. DNA repair. The case is supported by data from multiple species, from de novo mutation rate estimates from pedigrees, and from fits to a simple heuristic model. This work will be of interest to the broad field of DNA mutations and DNA repair, as well as evolutionary and phylogenomics researchers.

      (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 and Reviewer #2 agreed to share their names with the authors.)

    Reviewed by eLife

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
  4. Eco-evolutionary dynamics of clonal multicellular life cycles

    This article has 3 authors:
    1. Vanessa Ress
    2. Arne Traulsen
    3. Yuriy Pichugin
    This article has been curated by 1 group:
    • Curated by eLife

      Evaluation Summary:

      This manuscript models the evolution of simple multicellular life cycles using evolutionary game theory. The authors discuss natural selection between different life cycles by modeling growth, fragmentation, and interactions between propagules, discovering conditions for selection of a single life cycle or coexistence of multiple ones. Overall, the model is biologically intuitive, the results are rigorous, and the implications for the evolution of multicellularity are interesting.

      (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 #3 agreed to share their name with the authors.)

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  5. Prenatal environmental conditions underlie alternative reproductive tactics that drive the formation of a mixed-kin cooperative society

    This article has 2 authors:
    1. Shailee S. Shah
    2. Dustin R. Rubenstein
    This article has been curated by 1 group:
    • Curated by eLife

      Evaluation Summary:

      This article will be of interest to evolutionary biologists and behavioural ecologists. It aims to quantify the fitness benefits of helping with the breeding attempts of others vs. seeking own breeding attempts via dispersal. It is generally considered that helping is less profitable than breeding, but occurs when superior reproductive options are constrained. Using a long-term dataset of birds, the authors call into question this assumption, and propose that both reproductive tactics can in fact have similar fitness returns, resulting in mixed-kin societies.

      (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 and Reviewer #3 agreed to share their names with the authors.)

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  6. High-resolution species assignment of Anopheles mosquitoes using k-mer distances on targeted sequences

    This article has 15 authors:
    1. Marilou Boddé
    2. Alex Makunin
    3. Diego Ayala
    4. Lemonde Bouafou
    5. Abdoulaye Diabaté
    6. Uwem Friday Ekpo
    7. Mahamadi Kientega
    8. Gilbert Le Goff
    9. Boris K Makanga
    10. Marc F Ngangue
    11. Olaitan Olamide Omitola
    12. Nil Rahola
    13. Frederic Tripet
    14. Richard Durbin
    15. Mara KN Lawniczak
    This article has been curated by 1 group:
    • Curated by eLife

      Evaluation Summary:

      Boddé et al propose a new approach for species identification in the genus Anopheles. The approach uses an amplicon panel, a kmer-based similarity metric, and a variant auto-encoder to minimize issues of sequence alignment between divergent lineages. The authors provide strong evidence that their approach works well for most samples. The work will be of potential interest to practitioners in the field of parasite carrying mosquitoes.

      (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

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  7. Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows

    This article has 8 authors:
    1. Hyeonsoo Jeong
    2. Nicole M Baran
    3. Dan Sun
    4. Paramita Chatterjee
    5. Thomas S Layman
    6. Christopher N Balakrishnan
    7. Donna L Maney
    8. Soojin V Yi
    This article has been curated by 1 group:
    • Curated by eLife

      Evaluation Summary:

      In this paper, the authors generate and analyze new genome and gene expression data to understand better the evolution of the white-throated sparrow supergene region, which contains 1000 genes and determines whether a bird has a tan or a white stripe. The study nicely illustrates how the cessation of recombination that results from a chromosomal inversion can become a source of evolutionary novelty. The lack of recombination can result in the accumulation of deleterious variation leading to degeneration, but it can also (as here) facilitate genomic diversification and adaptation. The results will be of interest to a broad array of researchers studying genome architecture and phenotypic diversity and evolution.

      (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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  8. Toward a Universal Model for Spatially Structured Populations

    This article has 3 authors:
    1. Loïc Marrec
    2. Irene Lamberti
    3. Anne-Florence Bitbol
    This article has been curated by 1 group:
    • Curated by eLife

      Evaluation Summary:

      This very clear paper, which will be of interest to scientists in the field of evolutionary biology, investigates the effect of population structure on the efficacy of selection on a single locus. The results are based on analytical computations and numerical simulations, conducted in a scientifically rigorous manner. Although the conclusions are currently limited, the paper could serve as a solid basis for a more ambitious investigation.

      (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 and Reviewer #2 agreed to share their names with the authors.)

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  9. Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness

    This article has 3 authors:
    1. Alexandre Laverré
    2. Eric Tannier
    3. Anamaria Necsulea
    This article has been curated by 1 group:
    • Curated by eLife

      Evaluation Summary:

      The paper addresses a subject of potential great interest regarding the evolution of gene regulation and of enhancer landscapes. Available chromatin looping and gene expression data in mouse and human are analyzed to compare diverse properties of genome-wide promoter-centered maps, including associations with gene expression. It is shown that there is conservation of regulatory landscape across the two species, and that the extent of conservation in the TSS-distal landscape is associated with gene expression similarities. These overall results are in agreement with a large body of work in the field.

      (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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  10. Artificial selection methods from evolutionary computing show promise for directed evolution of microbes

    This article has 4 authors:
    1. Alexander Lalejini
    2. Emily Dolson
    3. Anya E Vostinar
    4. Luis Zaman
    This article has been curated by 1 group:
    • Curated by eLife

      Evaluation Summary:

      This paper addresses a very notable gap that exists between evolutionary computing and experimental evolution. While artificial and computational approaches have long been used as an analogy for biological systems (with studies that have produced findings relevant for evolutionary theory), few studies have directly used methods and results from evolutionary computing to directly inform the shape and structure of experimental evolution studies. This study's approach is creative, and its approaches and results may be of use to both computational and experimental audiences. Lastly, this study can spawn future ones that draw even more connections between evolutionary computation/artificial life and evolutionary theory.

      (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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
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