Evolutionary Biology

Variations and predictability of epistasis on an intragenic fitness landscape

1. Sarvesh Baheti
2. Namratha Raj
3. Supreet Saini

• Curated by eLife

  eLife Assessment

  This paper addresses the important question of quantifying epistasis patterns, which affect the predictability of evolution, by reanalyzing a recently published combinatorial deep mutational scan experiment. The findings are that epistasis is fluid, i.e. strongly background dependent, but that fitness effects of mutations are predictable based on the wild-type phenotype. However, these potentially interesting claims are inadequately supported by the analysis, because measurement noise is not accounted for, arbitrary cutoffs are used, and global nonlinearities are not sufficiently considered. If the results continue to hold after these major improvements in the analysis, they should be of interest to all biologists working in the field of fitness landscapes.

Reviewed by eLife

Magnetotactic Bacteria Optimally Navigate Natural Pore Networks

1. Alexander P. Petroff
2. Julia Hernandez
3. Vladislav Kelin
4. Nina Radchenko-Hannafin

• Curated by eLife

  eLife Assessment

  Combining experiments in microfluidic devices and computer simulation, this study provides a valuable analysis of the relevant parameters that determine the motility of (multicellular) magnetotactic bacteria in sediment-like environments. Despite the limitations imposed by the specific experimental design of the pores, the study presents convincing evidence that there is an optimum in the biological parameters for motile life under such conditions.

Reviewed by eLife

Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

1. Nikesh M. Kumar
2. Taylor L. Cooper
3. Thomas D. Kocher
4. J. Todd Streelman
5. Patrick T. McGrath

• Curated by eLife

  eLife Assessment

  Using several hundreds of samples and cutting-edge genomic methods, including BioNano, PacBio HiFi, and advanced bioinformatic pipelines, the authors identify six large chromosomal inversions segregating in over 100 species of Lake Malawi cichlids. This important study provides compelling evidence for the presence of these six inversions, their differential distribution among populations, and the association of chromosome 10 inversion with a sex-determination locus. This work also provides a starting point for further investigating the role of these inversions with respect to local adaptation, speciation, sex determination, hybridization, and incomplete lineage sorting in cichlids, which represent ~5% of the extant vertebrate species and are one of the most prominent examples of adaptive radiations.

Reviewed by eLife

The potential of inversions to accumulate balanced sexual antagonism is supported by simulations and Drosophila experiments

1. Christopher S McAllester
2. John E Pool

• Curated by eLife

  eLife Assessment

  This study proposes a new model that could solve some long-standing puzzles about inversion polymorphisms in Drosophila melanogaster by invoking sexually antagonism and negative frequency-dependent selection. While the idea developed here is a valuable contribution to the field, the experiment only addresses one element of the hypothesis, so that the empirical evidence in support of the model remains incomplete.

Reviewed by eLife

The Primate Major Histocompatibility Complex: An Illustrative Example of Gene Family Evolution

1. Alyssa Lyn Fortier
2. Jonathan K Pritchard

• Curated by eLife

  eLife Assessment

  This valuable manuscript presents a thorough analysis of the evolution of Major Histocompatibility Complex gene families across Primates. A key strength of this analysis is the use of state-of-the-art phylogenetic methods to estimate rates of gene gain and loss, but estimates of gene loss may suffer from the issue of genes entirely or partially missing from genome assemblies represented in the public databases used, given the notorious difficulty to properly assemble MHC gene genomic regions. Overall the evidence provided is still convincing, but the manuscript may benefit from discussing approaches that can address the issue of entirely or partially missing genes, in particular how the use of long reads to completely re-assemble complex loci might improve the assessment of the complex evolutionary processes at play in MHC gene families.

Reviewed by eLife

Regulatory networks of KRAB zinc finger genes and transposable elements changed during human brain evolution and disease

1. Yao-Chung Chen
2. Arnaud Maupas
3. Katja Nowick

• Curated by eLife

  eLife Assessment

  The authors present new expression analysis software (TEKRABber) to help analyze expression correlations between transposable elements (TEs) and KRAB zinc finger (KRAB-ZNF) genes in experimentaly validated datasets. The authors use this method to decipher the regulatory networks of KRAB-ZNFs and TEs during human brain evolution and in Alzheimer's disease. The direction of the work is important, with potentially significant interest from others looking for a tool for correlative gene expression analysis across individual genomes and species. However, identified biases and shortcomings in the current analysis pipeline could lead to an unacceptable number of false positive and negative signals and thus impact the conclusions, leaving this work in its current form incomplete.

Reviewed by eLife

Fluctuations and the limit of predictability in protein evolution

1. Saverio Rossi
2. Leonardo Di Bari
3. Martin Weigt
4. Francesco Zamponi

Reviewed by Arcadia Science

The population genetics of convergent adaptation in maize and teosinte is not locally restricted

1. Silas Tittes
2. Anne Lorant
3. Sean P McGinty
4. James B Holland
5. Jose de Jesus Sánchez-González
6. Arun Seetharam
7. Maud Tenaillon
8. Jeffrey Ross-Ibarra

• Curated by eLife

  eLife Assessment

  This useful study examines patterns of diversity and divergence in two closely related sub-species of Zea mays, patterns that have bearings on local adaptation in maize and teosinte at intermediate geographic scales. The authors suggest that convergent evolution has been facilitated by both standing variation and gene flow, with independent selective sweeps in the two species. While the data themselves are solid, there are limitations concerning population sampling, false positive rates in sweep detection and integration of phenotypic data, which make it difficult to draw definitive conclusions. The work should in principle be of broad interest to colleagues studying the relationship between domesticated species and their progenitors, as well as those studying instances of parallel evolution.

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, but 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, could be assessed and discussed more. Overall the evidence provided is convincing, and the manuscript may benefit from discussing the future use of more complete assemblies made from long reads to reduce the occurrence of both missing and false TSPs.

Reviewed by eLife

Ectopic gene conversion causing quantitative trait variation

1. Marina Pfalz
2. Seïf-Eddine Naadja
3. Jacqui Anne Shykoff
4. Juergen Kroymann

Reviewed by Arcadia Science