Evolutionary Biology

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

CLOCK evolved in cnidaria to synchronize internal rhythms with diel environmental cues

1. Raphael Aguillon
2. Mieka Rinsky
3. Noa Simon-Blecher
4. Tirza Doniger
5. Lior Appelbaum
6. Oren Levy

• Curated by eLife

  eLife assessment

  This fundamental study for the first time defines genetically the role of the Clock gene in basal metazoa, using the cnidarian Nematostella vectensis. With convincing evidence, the study provides insight into the early evolution of circadian clocks. Clock in this species is necessary for daily rhythms under constant conditions, but not under a rhythmic light/dark cycle, suggesting that the major role of the circadian oscillator in this species could be a stabilizing function under non-rhythmic environmental conditions.

Reviewed by eLife

Gene family expansions underpin context-dependency of the oldest mycorrhizal symbiosis

1. Damian J. Hernandez
2. Gwendolyn B. Pohlmann
3. Michelle E. Afkhami

Reviewed by Arcadia Science

Experimental evolution for the recovery of growth loss due to genome reduction

1. Kenya Hitomi
2. Yoichiro Ishii
3. Bei-Wen Ying

• Curated by eLife

  eLife assessment

  This is an important study of the recovery of genome-reduced bacterial cells in laboratory evolution experiments, to understand how they regain their fitness. Through the analysis of gene expression and a series of tests, the authors present convincing evidence indicating distinct molecular changes in the evolved bacterial strains, although the precise mechanisms remain uncharacterized. These findings imply that diverse mechanisms are employed to offset the effects of a reduced genome, offering intriguing insights into genome evolution.

Reviewed by eLife

Genomic signatures associated with the evolutionary loss of egg yolk in parasitoid wasps

1. Xianxin Zhao
2. Yuanyuan Liu
3. Bo Yuan
4. Zhichao Cao
5. Yi Yang
6. Chun He
7. Kevin C. Chan
8. Shan Xiao
9. Haiwei Lin
10. Qi Fang
11. Gongyin Ye
12. Xinhai Ye

Reviewed by Arcadia Science

CAnDI: a new tool to investigate conflict in homologous gene trees and explain convergent trait evolution

1. Holly M Robertson
2. Joseph F Walker
3. Edwige Moyroud

Reviewed by Arcadia Science

Evolutionary trade-offs in dormancy phenology

1. Théo Constant
2. F Stephen Dobson
3. Caroline Habold
4. Sylvain Giroud

• Curated by eLife

  eLife assessment

  This valuable and ambitious review examines seasonal dormancy in various species, including hibernating mammals (excluding bats and bears) and ectotherms. It provides a solid test of hypotheses on dormancy timing, considering energetic constraints and life history as alternative drivers. The review will be of interest to evolutionary biologists.

Reviewed by eLife

Environmentally regulated clonal-aggregative multicellularity in a choanoflagellate

1. Núria Ros-Rocher
2. Josean Reyes-Rivera
3. Uzuki Horo
4. Chantal Combredet
5. Yeganeh Foroughijabbari
6. Ben T. Larson
7. Maxwell C. Coyle
8. Erik A.T. Houtepen
9. Mark J. A. Vermeij
10. Jacob L. Steenwyk
11. Thibaut Brunet

Reviewed by Arcadia Science