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 valuable new resource to investigate the molecular basis of the particular features characterizing the pipefish embryo. The authors found both unique and shared gene expression patterns in pipefish organs compared with other teleost fishes. The solid data collected in this unconventional model organism will give new insights into understanding the extraordinary adaptations of the Syngnathidae family and will be of interest in the domain of evolution of fish development.

Reviewed by eLife

The integrated WF-Haldane (WFH) model of genetic drift resolving the many paradoxes of molecular evolution

1. Yongsen Ruan
2. Xiaopei Wang
3. Mei Hou
4. Wenjie Diao
5. Miles E. Tracy
6. Shuhua Xu
7. Zhongqi Liufu
8. Haijun Wen
9. Chung-I Wu

• Curated by eLife

  eLife Assessment

  This study presents a useful modification of a standard model of genetic drift by incorporating variance in reproductive success, claiming to address several paradoxes in molecular evolution. However, some of the claimed "paradoxes" seem to be overstatements, as previous literature has pointed out the limitations of the standard model and proposed more advanced models to address those limitations. While the modified model presented in this paper yields some intriguing theoretical predictions, the analysis and simulations presented are incomplete to support the authors' strong claims, and it is unclear how much the model helps explain empirical observations.

Reviewed by eLife

Pleiotropy increases parallel selection signatures during adaptation from standing genetic variation

1. Wei-Yun Lai
2. Sheng-Kai Hsu
3. Andreas Futschik
4. Christian Schlötterer

• Curated by eLife

  eLife Assessment

  This is a study that makes the important finding that pleiotropy is positively associated with parallelism of evolutionary responses in gene expression, while theory would predict the opposite. The analysis uses a state-of-the-art experimental evolution approach to study the genetic basis of adaptation of Drosophila simulans to a hot environment. The experimental data is relevant and its analysis is robust, however, this paper appears to conflate gene expression variation and its underlying causative variation, in both its data interpretation and theoretical framework. This leads to incomplete conclusions on the causal link between pleiotropy and genetic variation and their role during adaptation.

Reviewed by eLife

Whole-genome re-sequencing of the Baikal seal and other phocid seals for a glimpse into their genetic diversity, demographic history, and phylogeny

1. Marcel Nebenführ
2. Ulfur Arnason
3. Axel Janke

• Curated by GigaByte

  Editors Assessment:

  Due to them being found in the landlocked, isolated habitat of Lake Baikal makes the Baikal Seal (Pusa sibirica) unique among all pinnipeds as the only freshwater seal. This paper presents reference-based assemblies of six newly sequenced Baikal seal individuals, one individual of the ringed seal, as well as the first short-read data of the harbor seal and the Caspian seal . This data aiding the study of the genomic diversity of the Baikal seal and to contribute baseline data to the limited genomic data available for seals. Peer review extended the description of the used tools and parameters in the revised manuscript, and provided some more information on the methods..This newly generated sequencing data hopefully now helps to extend the phylogeny of the Phoca/Pusa group on genome-wide data and can also broaden the view into the genetic structure and diversity of the Baikal seal

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Passive accumulation of alkaloids in inconspicuously colored frogs refines the evolutionary paradigm of acquired chemical defenses

1. Rebecca D Tarvin
2. Jeffrey L Coleman
3. David A Donoso
4. Mileidy Betancourth-Cundar
5. Karem López-Hervas
6. Kimberly S Gleason
7. J Ryan Sanders
8. Jacqueline M Smith
9. Santiago R Ron
10. Juan C Santos
11. Brian E Sedio
12. David C Cannatella
13. Richard Fitch

• Curated by eLife

  eLife Assessment

  This study is important, with the potential to greatly impact future research on the evolution of chemical defense mechanisms in animals. The authors present compelling evidence for the presence of low quantities of alkaloids in amphibians previously thought to lack these toxins. They then integrate these findings with existing literature to propose a four-phase scenario for the evolution of chemical defense in alkaloid-containing poison frogs, emphasizing the role of passive accumulation mechanisms.

Reviewed by eLife

A genomic duplication spanning multiple P450s contributes to insecticide resistance in the dengue mosquito Aedes aegypti

1. Tiphaine Bacot
2. Chloe Haberkorn
3. Joseph Guilliet
4. Julien Cattel
5. Mary Kefi
6. Louis Nadalin
7. Jonathan Filee
8. Frederic Boyer
9. Thierry Gaude
10. Frederic Laporte
11. Jordan Tutagata
12. John Vontas
13. Isabelle Dusfour
14. Jean-Marc Bonneville
15. Jean-Philippe David

Reviewed by Peer Community in Evolutionary Biology

Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice

1. Jenny Chen
2. Phoebe R Richardson
3. Christopher Kirby
4. Sean R Eddy
5. Hopi E Hoekstra

• Curated by eLife

  eLife Assessment

  This important study identifies species- and sex-specific neuronal cell types and gene expression in the medial preoptic area (MPOA) to help understand the evolutionary divergence of social behaviors. The evidence from single-nucleus RNA sequencing and immunostaining is convincing and suggests that cellular differences in the MPOA may contribute to behavioral variations such as mating and parental care that are apparent in two closely related deer mouse species. These rich observations provide an entry point for future hypothesis-driven experiments to demonstrate a causal role for these populations in sex- or species-variable behaviors in vertebrates. These data will be a resource that is of value to behavioral neuroscientists.

Reviewed by eLife

The paradox of extremely fast evolution driven by genetic drift in multi-copy gene systems

1. Xiaopei Wang
2. Yongsen Ruan
3. Lingjie Zhang
4. Xiangnyu Chen
5. Zongkun Shi
6. Haiyu Wang
7. Bingjie Chen
8. Miles E Tracy
9. Chung-I Wu
10. Haijun Wen

• Curated by eLife

  eLife Assessment

  This study presents a useful theoretical model of molecular evolution and attempts to use it to resolve the paradox of rapid evolution of ribosomal RNA genes. While intuitive, the model's underlying issue is grouping many factors under "variance in reproductive success" without explicitly modeling the molecular processes. This limitation, along with insufficient consideration of technical challenges in alignment and variants calling, provides incomplete support for the authors' claim that the observed paradoxical patterns in rRNA genes can largely be explained by homogenizing processes, such as gene conversion, unequal crossover and replication slippage.

Reviewed by eLife

Biases of Principal Component Analysis (PCA) in Physical Anthropology Studies Require a Reevaluation of Evolutionary Insights

1. Nima Mohseni
2. Eran Elhaik

• Curated by eLife

  eLife Assessment

  The authors present a critique of current usage of principal component analysis in geometric morphometrics, making a compelling case with benchmark data that standard techniques perform poorly. The work is an important contribution to the field and will hopefully lead to a reassessment of the methodology most scientists in morphometrics currently use. This work challenges a very commonly used analytical approach and is bound to raise some controversy in the community, but the authors' critique is based on a well-founded and well-thought out analysis.

Reviewed by eLife

Seasonal and comparative evidence of adaptive gene expression in mammalian brain size plasticity

1. William R Thomas
2. Troy Richter
3. Erin T O’Neil
4. Cecilia Baldoni
5. Angelique P Corthals
6. Dominik von Elverfeldt
7. John Nieland
8. Dina KN Dechmann
9. Richard G Hunter
10. Liliana M Dávalos

• Curated by eLife

  eLife Assessment

  This study presents valuable findings related to seasonal brain size plasticity in the Eurasian common shrew (Sorex araneus), which is an excellent model system for these studies. The evidence supporting the authors' claims is convincing. However, the authors should be careful when applying the term adaptive to the gene expression changes they observe; it would be challenging to demonstrate the differential fitness effects of these gene expression changes. The work will be of interest to biologists working on neuroscience, plasticity, and evolution.

Reviewed by eLife