Evolutionary Biology

Functionally important residues from graph analysis of coevolved dynamic couplings

1. Manming Xu
2. Sarath Chandra Dantu
3. James A Garnett
4. Robert A Bonomo
5. Alessandro Pandini
6. Shozeb Haider

• Curated by eLife

  eLife Assessment

  This paper reports the analysis of coevolutionary patterns and dynamical information for identifying functionally relevant sites. These findings are considered important due to the broad utility of the unified framework and network analysis capable of revealing communities of key residues that go beyond the residue-pair concept. The data are solid and the results are clearly presented.

Reviewed by eLife

Parallel HIV-1 fitness landscapes shape viral dynamics in humans and macaques that develop broadly neutralizing antibodies

1. Kai S Shimagaki
2. Rebecca M Lynch
3. John P Barton

• Curated by eLife

  eLife Assessment

  In this important quantitative study of HIV-1 evolution in humans and rhesus macaques, selection coefficients are inferred at scale over the HIV genome. Selection coefficients are similar in humans and macaques, providing convincing evidence that these coefficients are representative of the fitness landscapes of these viruses within hosts. This work should be of interest to the community working on quantitative evolution and fitness landscape inference, and the finding that rapid fitness gains in the HIV population predict bNAb emergence has implications for HIV vaccine design.

Reviewed by eLife

Ancestral sequence reconstruction of the Mic60 Mitofilin domain reveals residues supporting respiration in yeast

1. Friederike M. C. Benning
2. Tristan A. Bell
3. Tran H. Nguyen
4. Della Syau
5. Louise B. Connell
6. Yi-Ting Liao
7. Matthew P. Keating
8. Margaret Coughlin
9. Anja E. H. Nordstrom
10. Maria Ericsson
11. Corrie J. B. daCosta
12. Luke H. Chao

Reviewed by preLights

Social and environmental predictors of gut microbiome age in wild baboons

1. Mauna R Dasari
2. Kimberly E Roche
3. David Jansen
4. Jordan Anderson
5. Susan C Alberts
6. Jenny Tung
7. Jack A Gilbert
8. Ran Blekhman
9. Sayan Mukherjee
10. Elizabeth A Archie

• Curated by eLife

  eLife Assessment

  This study leverages an impressive and comprehensive longitudinal 16S rRNA gut microbiome dataset from baboons to provide important insight regarding the use of a microbiome-based clock to predict biological age. The evidence for age-associated microbiome features and environmental and social variables that impact microbiome aging is convincing. This study of microbiomes as markers of host age will fuel inquiries and studies and interest a broad range of researchers, especially those interested in alternatives to measuring biological aging.

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 study makes the important finding that pleiotropy is positively associated with parallelism of evolutionary responses in gene expression. This finding, if true, runs counter to current expectations in the field. The analysis uses state-of-the art experimental evolution approach to study the genetic basis of adaptation of Drosophila simulans to a hot environment. Although the experimental results are convincing, the theoretical model is incomplete, due to several unusual assumptions. It remains to be seen whether the main conclusion can be replicated in other contexts.

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 Tracy
9. Liying Huang
10. Chung-I Wu
11. Haijun Wen

• Curated by eLife

  eLife Assessment

  This study presents a useful theoretical model of molecular evolution of multi-copy gene systems by extending the classic Haldane model and applies the model to explain the surprisingly rapid evolution of rRNA genes. Although the conceptual model is intuitive and provides a new perspective for contextualizing this problem, the model presented does not adequately consider plausible biological constraints on the molecular and genetic processes. The lack of such constraints in the model, along with technical issues in the data analysis, provide incomplete support for the conclusion that the genetic variation patterns of rRNA genes in mouse is compatible with neutral evolution.

Reviewed by eLife

The Generalized Haldane (GH) model tracking population size changes and resolving paradoxes of genetic drift

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

• Curated by eLife

  eLife Assessment

  This study presents a useful model of genetic drift by incorporating variance in reproductive success, aiming to address several apparent paradoxes in molecular evolution. However, some of the apparent paradoxes only arise in the most basic version of standard models and have been reconciled in more advanced models. Nonetheless, this paper offers intuitive explanations for these apparent paradoxes, by adopting a new perspective and solid modeling and analysis. More broadly, the proposed model provides an alternative framework to address puzzling observations in molecular evolution, which will be of interest to evolutionary and population geneticists.

Reviewed by eLife

Rafting a waterfall: Artificial selection for 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 compelling. 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

No evidence for a trade-off between reproduction and survival in a meta-analysis across birds

1. Lucy A Winder
2. Mirre JP Simons
3. Terry Burke

• Curated by eLife

  eLife Assessment

  This important study challenges conventional life-history theory by demonstrating that reproductive-survival trade-offs are minimal in birds, except when reproductive effort is experimentally exaggerated. The evidence is solid, drawing from a meta-analysis of over 30 bird species, and effectively separates the effects of individual quality from reproductive costs. The findings will be of broad interest to evolutionary biologists and ecologists studying life-history trade-offs and reproductive strategies.

Reviewed by eLife

The adaptive landscapes of three global Escherichia coli transcriptional regulators

1. Cauã Antunes Westmann
2. Leander Goldbach
3. Andreas Wagner

• Curated by eLife

  eLife Assessment

  This study maps the genotype-phenotype landscapes of three E. coli transcription factors and the topographical features of these landscapes. It shows that ruggedness and epistasis do not hinder the evolution of strong transcription factor binding sites. These convincing findings contribute valuable insights into fitness landscape theories and highlight the role of chance, contingency, and evolutionary biases in gene regulation. The authors then study the topographical features of these landscapes, especially the number and distribution of local maxima, as well as the statistical properties of evolutionary paths on these landscapes.

Reviewed by eLife