Evolutionary Biology

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. Gail Canning
6. Sabrina J. Ward
7. Naomi Irish
8. Jade Smith
9. Vanessa E. McMillan
10. Jess Hammond
11. Sarah-Jane Osborne
12. Gillian Reynolds
13. Ellie Smith
14. Tania Chancellor
15. David Swarbreck
16. Neil Hall
17. Javier Palma-Guerrero
18. Kim E. Hammond-Kosack
19. Mark McMullan

Reviewed by Review Commons

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

Alternative Splicing Across the Tree of Life: A Comparative Study

1. Rebeca de la Fuente
2. Wladimiro Díaz-Villanueva
3. Vicente Arnau
4. Andrés Moya

• Curated by eLife

  eLife assessment

  The authors examined whether the frequency of alternative splicing across entire genomes correlates with measures of complexities across prokaryotes and eukaryotes. Although the question is very interesting and important for our general understanding of the evolution of life forms, the work is inadequate: the methods, data, and analyses do not support the primary claims. The measure of alternative splicing frequency used by the authors is problematic; the method is inappropriate; the observed correlations may also be explained by known population genetics principles; and parts of the manuscript are difficult to understand.

Reviewed by Arcadia Science, 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