Evolutionary Biology

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

Horizontally transferred cell-free chromatin particles function as autonomous ‘satellite genomes’ and vehicles for transposable elements within host cells

1. Soumita Banerjee
2. Soniya Sanjay Shende
3. Laxmi Kata
4. Relestina Simon Lopes
5. Swathika Praveen
6. Ruchi Joshi
7. Naveen Kumar Khare
8. Gorantla V Raghuram
9. Snehal Shabrish
10. Indraneel Mittra

• Curated by eLife

  eLife Assessment

  The authors examine the effect of cell-free chromatin particles (cfChPs) derived from human serum or from dying human cells on mouse cells in culture and propose that these cfChPs can serve as vehicles for cell-to-cell active transfer of foreign genetic elements. The work presented in this paper is intriguing and potentially important, but it is incomplete. At this stage, the claim that horizontal gene transfer can occur via cfChPs is not well supported because it is only based on evidence from one type of methodological approach (immunofluorescence and fluorescent in situ hybridization (FISH)) and is not validated by whole genome sequencing.

Reviewed by eLife

Meaning-making behavior in a small-brained hominin, Homo naledi, from the late Pleistocene: contexts and evolutionary implications

1. Agustín Fuentes
2. Marc Kissel
3. Penny Spikins
4. Keneiloe Molopyane
5. John Hawks
6. Lee R Berger

• Curated by eLife

  eLife Assessment

  This paper discusses the cognitive implications of potential intentional burial, wall engraving creation, and fire as light source use behaviors by relatively small-brained Homo naledi hominins. The discussion presented in the paper is valuable theoretically in its healthy questioning of prior assumptions concerning the socio-biological constraints of hominin meaning-making behavior. The discussion also contributes practically given that these behaviors have been ascribed to Homo naledi in two associated papers. Still, the strength of evidence in this contribution relies on the validity of the conclusions from the two associated papers, which remain actively questioned. The ultimate assessment of this work will vary among individual readers depending on how they view this debate, but if the conclusions from the associated papers hold up, the conclusions in the current paper can be considered solid.

Reviewed by eLife

Effective population size does not explain long-term variation in genome size and transposable element content in animals

1. Alba Marino
2. Gautier Debaecker
3. Anna-Sophie Fiston-Lavier
4. Annabelle Haudry
5. Benoit Nabholz

• Curated by eLife

  eLife Assessment

  This important study offers a powerful empirical test of a highly influential hypothesis in population genetics. It incorporates a large number of animal genomes spanning a broad phylogenetic spectrum and treats them in a rigorous unified pipeline, providing the convincing negative result that effective population size scales neither with the content of transposable elements nor with overall genome size. These observations demonstrate that there is still no simple, global hypothesis that can explain the observed variation in transposable element content and genome size in animals.

Reviewed by eLife

Trophic eggs affect caste determination in the ant Pogonomyrmex rugosus

1. Eléonore Genzoni
2. Tanja Schwander
3. Laurent Keller

• Curated by eLife

  eLife Assessment

  This important manuscript by Genzoni et al. reports the striking discovery of a regulatory role for trophic eggs in ant caste determination. Prior to this study, trophic eggs were widely assumed to play only a nutritional role in the colony, but this compelling study shows that trophic eggs can suppress queen development, and therefore regulate caste determination in specific social contexts.

Reviewed by eLife

The general version of Hamilton’s rule

1. Matthijs van Veelen

• Curated by eLife

  eLife Assessment

  Kin selection and inclusive fitness have generated significant controversy. This paper reconsiders the general form of Hamilton's rule in which benefits and costs are defined as regression coefficients, with higher-order coefficients being added to accommodate non-linear interactions. The paper is a landmark contribution to the field with compelling, systematic analysis, giving clarity to long-standing debates.

Reviewed by eLife

Performance evaluation of adaptive introgression classification methods

1. Jules Romieu
2. Ghislain Camarata
3. Pierre-André Crochet
4. Miguel de Navascués
5. Raphaël Leblois
6. François Rousset

Reviewed by Peer Community in Evolutionary Biology

Learning the Shape of Evolutionary Landscapes: Geometric Deep Learning Reveals Hidden Structure in Phenotype-to-Fitness Maps

1. Manuel Razo-Mejia
2. Madhav Mani
3. Dmitri A. Petrov

Reviewed by Arcadia Science

Divergent organelle allocation in the evolution of sperm gigantism revealed from subcellular quantification of nematode sperm with electron microscopy

1. Rebecca Schalkowski
2. Asher D Cutter

Reviewed by Arcadia Science

An initial report of circa 241,000- to 335,000-year-old rock engravings and their relation to Homo naledi in the Rising Star cave system, South Africa

1. Lee R Berger
2. John Hawks
3. Agustín Fuentes
4. Dirk Van Rooyen
5. Mathabela Tsikoane
6. Maropeng Mpete
7. Samuel Nkwe
8. Keneiloe Molopyane

• Curated by eLife

  eLife Assessment

  This paper presents important information about potential Homo naledi-associated markings discovered on the walls of the Hill Antechamber of the Rising Star Cave system, South Africa. If confirmed, the antiquity, intentionality, and authorship of the reported markings will have profound archaeological implications, as such behaviors are otherwise widely considered to be unique to our species, Homo sapiens. This report concerns preliminary findings and as it stands the study is incomplete, with further work needed in the future to support the claims about the anthropogenic nature, age, and author of the engravings.

Reviewed by eLife