Evolutionary Biology

Single Cell Sequencing Provides Clues about the Developmental Genetic Basis of Evolutionary Adaptations in Syngnathid Fishes

1. Hope M. Healey
2. Hayden B. Penn
3. Clayton M. Small
4. Susan Bassham
5. Vithika Goyal
6. Micah A. Woods
7. William A. Cresko

• Curated by eLife

  eLife assessment

  This study provides a single-cell atlas for syngnathid fishes (seahorses, pipefishes, and seadragons), a valuable new resource to investigate the molecular basis of the many unique characters that define the pipefish embryo. The findings are generally supported by solid arguments, but whereas the single-cell RNA-sequencing analysis appears to be of good quality, the spatiotemporal expression data only incompletely support the authors' arguments. Additional computational analyses on cell identity and developmental trajectories would allow a deeper examination of the current data from these unconventional model organisms, to provide new insights into understanding the extraordinary adaptations of the Syngnathidae family. If appropriately improved, the work could be of broad interest for evolutionary developmental biology, particularly for fishes.

Reviewed by eLife

Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

1. Gemma I. Martínez-Redondo
2. Israel Barrios-Núñez
3. Marçal Vázquez-Valls
4. Ana M. Rojas
5. Rosa Fernández

Reviewed by Arcadia Science

Artificial selection for microbial collective composition can succeed or fail depending on the initial and target values

1. Juhee Lee
2. Wenying Shou
3. Hye Jin Park

• Curated by eLife

  eLife assessment

  This important study of artificial selection in microbial communities shows that the possibility of selecting a desired fraction of slow and fast-growing types is impacted by their initial fractions. The evidence, which relies on mathematical analysis and simulations of a stochastic model, is convincing. It highlights the tension between selection at the strain and the community level. This study should be of interest to researchers interested in ecology, both theoretical and experimental.

Reviewed by eLife

Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genus Gaeumannomyces

1. Rowena Hill
2. Michelle Grey
3. Mariano Olivera Fedi
4. Daniel Smith
5. Sabrina J. Ward
6. Gail Canning
7. Naomi Irish
8. Jade Smith
9. Vanessa E. McMillan
10. Jess Hammond
11. Sarah-Jane Osborne
12. Tania Chancellor
13. David Swarbreck
14. Neil Hall
15. Javier Palma-Guerrero
16. Kim E. Hammond-Kosack
17. Mark McMullan

Reviewed by Review Commons

Extant cartilaginous fishes share trabecular and areolar mineralization patterns, but not tesserae, and evidence for a paedomorphic chimaera skeleton

1. Oghenevwogaga J. Atake
2. Fidji Berio
3. Melanie Debiais-Thibaud
4. B. Frank Eames

• Curated by eLife

  eLife assessment

  This study presents valuable research comparing three different species of extant cartilaginous fishes and describes new data on ratfish. The methods are convincing although the reviewers noted that standardized methods are essential when comparing numerical datasets. This study would be of interest to skeletal biologists working on the evolution of chondrichthyan skeletons.

Reviewed by eLife

Sex-biased regulatory changes in the placenta of native highlanders contribute to adaptive fetal development

1. Tian Yue
2. Yongbo Guo
3. Xuebin Qi
4. Wangshan Zheng
5. Hui Zhang
6. Bin Wang
7. Kai Liu
8. Bin Zhou
9. Xuerui Zeng
10. Ouzhuluobu
11. Yaoxi He
12. Bing Su

• Curated by eLife

  eLife assessment

  This fundamental study reports differential expression of key genes in full-term placenta between Tibetans and Han Chinese at high elevations, which are more pronounced in the placenta of male fetus than in female fetus. The gene expression data were collected and analyzed using solid and validated methodology, although there is limited support for hypoxia-specific responses due to a lack of low-altitude samples. Several of the placental genes found in this study have been previously reported to show signatures of positive selection in Tibetans, pointing to a potential mechanism of how human populations adapt to high elevation by mitigating the negative effects of low oxygen on fetal growth. The work will be of interest to evolutionary and population geneticists as well as researchers working on human hypoxic response.

Reviewed by eLife

Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific

1. Remy Gatins
2. Carlos F. Arias
3. Carlos Sánchez
4. Giacomo Bernardi
5. Luis F. De León

• Curated by GigaByte

  Editors Assessment:

  The King Angelfish (Holacanthus passer) is a great example of a Holacanthus angelfish that are some of the most iconic marine fishes of the Tropical Eastern Pacific. However, very limited genomic resources currently exist for the genus and these authors have assembled and annotated the nuclear genome of the species, and used it examine the demographic history of the fish. Using nanopore long reads to assemble a compact 583 Mb reference with a contig N50 of 5.7 Mb, and 97.5% BUSCOs score. Scruitinising the data, the BUSCO score was high compared to the initial N50’s, providing some useful lessons learned on how to get the most out of ONT data. The analysis suggests that the demographic history in H. passer was likely shaped by historical events associated with the closure of the Isthmus of Panama, rather than by the more recent last glacial maximum. This data provides a genomic resource to improve our understanding of the evolution of Holacanthus angelfishes, and facilitating research into local adaptation, speciation, and introgression of marine fishes. In addition, this genome can help improve the understanding of the evolutionary history and population dynamics of marine species in the Tropical Eastern Pacific.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Reversions mask the contribution of adaptive evolution in microbiomes

1. Paul A Torrillo
2. Tami D Lieberman

• Curated by eLife

  eLife assessment

  This valuable study addresses the interpretation of patterns of synonymous and nonsynonymous diversity in microbial genomes. The authors present solid theoretical and computational evidence that adaptive mutations that revert the amino acids to an earlier state can significantly impact the observed ratios of synonymous and nonsynonymous mutations in human commensal bacteria. This paper will be of interest to microbiologists with a background in evolution.

Reviewed by eLife

Pervasive relaxed selection on spermatogenesis genes coincident with the evolution of polygyny in gorillas

1. Jacob D. Bowman
2. Neide Silva
3. Erik Schüftan
4. Joana M. Almeida
5. Rion Brattig-Correia
6. Raquel A. Oliveira
7. Frank Tüttelmann
8. David Enard
9. Paulo Navarro-Costa
10. Vincent J. Lynch

• Curated by eLife

  eLife assessment

  This important work reports that genome-wide patterns of relaxed purifying selection on genes involved in male fertility may represent a response to the reduced sperm competition in the gorillas' mating system. However, the evidence supporting the conclusion is incomplete and needs to be strengthened. This work will be of interest to researchers working on evolution and reproductive biology.

Reviewed by eLife

mirror determines the far posterior domain in butterfly wings

1. Martik Chatterjee
2. Xin Y. Yu
3. Noah K. Brady
4. Gabriel C. Hatto
5. Robert D. Reed

• Curated by eLife

  eLife assessment

  This article is a valuable addition to the growing literature on the developmental patterning of insect wings. Using CRISPR mutagenesis and localization of mRNA, the authors present solid evidence that the transcription factor Mirror is necessary for specifying the morphological identity of the most posterior regions of butterfly wings. The manuscript would benefit from more careful use of terminology and appropriate citation of related Drosophila literature, and there are also some concerns about whether the phenotype represents transformation or loss which might be clarified through a closer look at ultrastructure. With a clearer presentation of terminology, this paper would be of general interest to developmental and evolutionary biologists.

Reviewed by eLife