Evolutionary Biology

Cell-type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells

1. Ban Wang
2. Alexander L Starr
3. Hunter B Fraser

• Curated by eLife

  eLife assessment

  This is an important study that leverages a human-chimpanzee tetraploid iPSC model to test whether cis-regulatory divergence between species tends to be cell type-specific. The evidence supporting the study's primary conclusions together provide convincing evidence for enrichment of species differences in gene regulation in cell type-specific genes and regulatory elements, motivating future work with larger sample sizes of cell lines. This work will be of broad interest in evolutionary and functional genomics.

Reviewed by eLife

Taste shaped the use of botanical drugs

1. Marco Leonti
2. Joanna Baker
3. Peter Staub
4. Laura Casu
5. Julie Hawkins

• Curated by eLife

  eLife assessment

  This valuable study links the "taste" of botanicals to their application as medicines used by the ancient Greco-Roman society. The authors used phylogenetic linear mixed models in a Bayesian framework to test the relationships between taste qualities, intensities, complexities, and therapeutic use. The evidence supporting the conclusions is solid, although there is a minor weakness concerning the somewhat inconsistent method of botanical preparation and presentation to the taster panelists; subjective bias and robustness of the participants' responses might have been overlooked. The study may be of broad interest to pharmacologists and scientists working on drug discovery, particularly those interested in natural products.

Reviewed by eLife

Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals

1. Jade Castel
2. Florence Pradillon
3. Valérie Cueff
4. Guillaume Leger
5. Claire Daguin-Thiébaut
6. Stéphanie Ruault
7. Jean Mary
8. Stéphane Hourdez
9. Didier Jollivet
10. Thomas Broquet

Reviewed by Peer Community in Evolutionary Biology

Evolutionary dynamics in non-Markovian models of microbial populations

1. Farshid Jafarpour
2. Ethan Levien
3. Ariel Amir

Reviewed by PREreview

Individual differences in developmental trajectory leave a male polyphenic signature in bulb mite populations

1. Jacques A. Deere
2. Isabel M. Smallegange

Reviewed by Peer Community in Evolutionary Biology

Measures of genetic diversification in somatic tissues at bulk and single-cell resolution

1. Marius E Moeller
2. Nathaniel V Mon Père
3. Benjamin Werner
4. Weini Huang

• Curated by eLife

  eLife assessment

  In this paper, the authors introduce fundamental work on mathematical methods for inferring evolutionary parameters of interest from RNA data in healthy tissue and during hematopoiesis. By combining single cell and bulk sequencing analyses, the authors use a stochastic process to inform different aspects of genetic heterogeneity; the strength of evidence in support of the authors' claim is exceptional. The work will be of broad interest to cell biologists and theoretical biologists.

Reviewed by eLife

Comprehensive analysis of gene regulatory dynamics, fitness landscape, and population evolution during sexual reproduction

1. Kenji Okubo
2. Kunihiko Kaneko

Reviewed by PREreview

Efficient estimation for large-scale linkage disequilibrium patterns of the human genome

1. Xin Huang
2. Tian-Neng Zhu
3. Ying-Chao Liu
4. Guo-An Qi
5. Jian-Nan Zhang
6. Guo-Bo Chen

• Curated by eLife

  eLife assessment

  This study presents a valuable new approach for efficient computation of statistics on correlations between genetic variants (linkage disequilibrium, or LD), which the authors apply to quantify the extent of LD across chromosomes. The method appears solid, although the presentation of equations needs clarification and improvement. The authors document that cross-chromosome LD can be substantial, which has implications for geneticists who are interested in population structure and its impact on genetic association studies.

Reviewed by eLife

Repeatability of adaptation in sunflowers reveals that genomic regions harbouring inversions also drive adaptation in species lacking an inversion

1. Shaghayegh Soudi
2. Mojtaba Jahani
3. Marco Todesco
4. Gregory L Owens
5. Natalia Bercovich
6. Loren H Rieseberg
7. Sam Yeaman

• Curated by eLife

  eLife assessment

  This is a valuable comparative study of local adaptation using gene-by-environment and gene-by-phenotype correlations. The analyses seemed still incomplete, as the biological take-home messages were obscured by the statistical approaches used, and it remains unclear how to best interpret the level of genome-wide convergence and in inversions. The repeatability of local adaptation across species, and the role of inversions in local adaptation, are questions of considerable empirical interest.

Reviewed by eLife

A timeline of bacterial and archaeal diversification in the ocean

1. Carolina A Martinez-Gutierrez
2. Josef C Uyeda
3. Frank O Aylward

• Curated by eLife

  eLife assessment

  This important paper addresses the challenging problem of dating the origin of several groups of marine microorganisms. However, while much of the analyses are solid, the lack of robustness analysis in molecular dating component such as using alternative time calibrations, clock models, and input gene sets makes the study incomplete. Despite some concerns, this work is a commendable attempt at an extremely difficult problem and will be of broad interest to microbiologists, geologists, and evolutionary biologists.

Reviewed by eLife