Article
Genetics & Heredity
Nandita R. Garud, Philipp W. Messer, Dmitri A. Petrov
Summary: The debate over whether hard sweeps or soft sweeps dominate adaptation has continued, with the authors proposing that soft sweeps are prevalent in North American Drosophila melanogaster. Another study by Harris et al. has raised doubts about the reliability of soft sweeps detected, instead suggesting that hard sweeps may be more likely. However, upon reanalysis, the authors confirm that soft sweeps are the dominant mode of adaptation in North American Drosophila melanogaster.
Article
Biochemistry & Molecular Biology
Leo Speidel, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, Simon R. Myers
Summary: The study introduces a fast and scalable approach, Colate, for inferring ancestral relationships between low-coverage genomes without requiring phasing or imputation. The method leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. By applying this approach to modern and ancient DNA samples, the research identifies dynamic population structure and gene flow between early farmers and European hunter-gatherer groups.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Emmanuel Tergemina, Ahmed F. Elfarargi, Paulina Flis, Andrea Fulgione, Mehmet Goektay, Celia Neto, Marleen Scholle, Padraic J. Flood, Sophie-Asako Xerri, Johan Zicola, Nina Doering, Herculano Dinis, Ute Kraemer, David E. Salt, Angela M. Hancock
Summary: This study demonstrates a two-step evolutionary process in which nutrient homeostasis was rewired to adapt to extremely low soil manganese conditions. A variant disrupting the iron uptake transporter gene quickly became fixed in the population, increasing manganese but limiting iron in the leaves. Multiple independent gene duplications then compensated for the loss of the iron transporter gene, improving iron homeostasis. This research provides a clear example of a multilocus adaptive walk and sheds light on how genetic variants reshape phenotypes and spread over space and time.
Article
Biochemistry & Molecular Biology
M. J. Shepherd, J. S. Horton, T. B. Taylor
Summary: This study reveals the importance of genomic features in facilitating the formation of mutational hotspots, including genomic location, local nucleotide sequence, gene strandedness, and the presence of mismatch repair proteins.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Matt J. Thorstensen, Melinda R. Baerwald, Ken M. Jeffries
Summary: The study compared mRNA and microsatellite data sets of two populations of a minnow species in the San Francisco Estuary, finding that mRNA sequencing revealed patterns of population structure similar to microsatellites but with lower genetic variation. Phenotypic plasticity and signatures of selection were mostly mutually exclusive within individual genes.
Article
Entomology
Jinyu Li, Longqing Shi, Wei Chen, Yi Mao, Liette Vasseur, Geoff Gurr, Minsheng You, Shijun You
Summary: The study on the tea green leafhopper found that climatic differences play a significant role in the subpopulation differentiation of the leafhopper, which explains the observed increase in outbreak frequency under climate change. This study also demonstrates the usefulness of molecular genetic approaches in studying the effects of environmental heterogeneity on natural population genetic variation.
ENTOMOLOGIA GENERALIS
(2023)
Article
Genetics & Heredity
Melanie B. Abrams, Claire A. Dubin, Faisal AlZaben, Juan Bravo, Pierre M. Joubert, Carly Weiss, Rachel B. Brem
Summary: This study used the thermotolerance growth advantage of yeast to explore how species-defining traits evolve, identifying positive selection at genes promoting thermotolerance, with a focus on the ESP1 gene. Experimental results showed that genetic divergence in the ESP1 coding region leads to differences in thermotolerance growth.
G3-GENES GENOMES GENETICS
(2021)
Review
Genetics & Heredity
Jianzhi Zhang
Summary: Genomics, a interdisciplinary field of biology, has revolutionized various subdisciplines of life sciences by providing large amount of data, introducing high-throughput technologies, and offering new approaches to biology. In this review, the author describes what they have learned from genomics, mainly focusing on variation, interaction, and selection, which are central topics in evolutionary biology. The author expects that the most important contributions of genomics to evolutionary biology in the future will include providing genome sequences of almost all known species on Earth, facilitating high-throughput phenotyping of natural variants and mutants, and assisting in the determination of causality in evolutionary processes using experimental evolution.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Evolutionary Biology
Samuel D. Payet, Morgan S. Pratchett, Pablo Saenz-Agudelo, Michael L. Berumen, Joseph D. DiBattista, Hugo B. Harrison
Summary: This study compares the population genomics and demographic histories of the common coral grouper in the Coral Sea and the Great Barrier Reef and finds low genetic connectivity between the two regions. The results suggest that the Coral Sea population was founded by a small number of individuals from the Great Barrier Reef and has experienced a long period of isolation, leading to lower genetic diversity in the Coral Sea.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jianglin Zhou, Xuejun Wang, Zhe Zhou, Shengqi Wang
Summary: The exceptional outbreak of monkeypox in 100 non-endemic countries since 2022 poses a major public health concern. Analysis of codon usage patterns in the 2022 outbreak strains of monkeypox virus revealed unique evolutionary features, with codon usage bias predominantly determined by mutation pressure. The virus also showed adaptation to various primate hosts, including humans, indicating the importance of sustained monitoring.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ulas Isildak, Alessandro Stella, Matteo Fumagalli
Summary: Balancing selection is an important adaptive mechanism for a wide range of phenotypes, but its detection from genomic data is challenging. In this study, two deep neural networks were developed and implemented to accurately predict loci under recent selection, with convolutional neural network (CNN) outperforming artificial neural network (ANN). The trained networks successfully identified loci under recent selection in European populations and within the MEFV gene region, highlighting the potential functional relevance of common variants predicted to be under incomplete sweep.
MOLECULAR ECOLOGY RESOURCES
(2021)
Review
Biology
Alejandro V. Cano, Bryan L. Gitschlag, Hana Rozhonova, Arlin Stoltzfus, David M. McCandlish, Joshua L. Payne
Summary: Predicting evolutionary outcomes is crucial, and current focus is on adaptive processes mainly through selection. However, adaptive processes rely on new mutations, which are influenced by predictable biases. This article provides an overview of existing theory and evidence for mutation-biased adaptation, discussing its implications for prediction in various fields. The authors argue that with improving knowledge on mutational biases, short-term prediction challenges can be addressed effectively.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Remi Matthey-Doret
Summary: SimBit is a high-performance population genetics simulator that can simulate various selection, demographic and mating scenarios, track QTLs and model ecological relationships among multiple species. It comes with a convenient R wrapper for project management and outperforms other simulators in most benchmarks.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Olivier Cotto, Troy Daya
Summary: This study reveals that inferring the underlying genotype-fitness map from observed DFEs is challenging, as many different maps can produce the same DFE. The research also suggests that a random genotype-fitness map would result in the DFE with the largest information entropy, which matches empirical DFEs well.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Kelsey E. Johnson, Christopher J. Adams, Benjamin F. Voight
Summary: Researchers have discovered that the analysis of genetic variation in a population often assumes that rare variants are inherited from a single common ancestral event. However, this assumption may not hold true due to genetic and technical processes such as recurrent mutations, gene conversions, and genotyping errors. By using a Bayesian hierarchical model and Gibbs sampling, researchers can accurately distinguish rare variants consistent and inconsistent with a simple inheritance model. The findings suggest that inconsistent variants are correlated with higher local mutation rates and genomic features, providing insights into recent mutations in human populations.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Arlin Stoltzfus, Ryan W. Norris
MOLECULAR BIOLOGY AND EVOLUTION
(2016)
Editorial Material
Multidisciplinary Sciences
Arlin Stoltzfus, David M. McCandlish
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Fisheries
Jiri Zahradnik, Lucie Kolarova, Hana Parizkova, Petr Kolenko, Bohdan Schneider
FISH & SHELLFISH IMMUNOLOGY
(2018)
Article
Biotechnology & Applied Microbiology
Jiri Zahradnik, Jaroslav Nunvar, Hana Parizkova, Lucie Kolarova, Andrea Palyzova, Helena Maresova, Michal Grulich, Eva Kyslikova, Pavel Kyslik
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2018)
Article
Mathematics, Applied
A. V. Cano, M. G. Cosenza
Article
Biochemical Research Methods
Alejandro V. Cano, Joshua L. Payne
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Mathematics, Interdisciplinary Applications
M. G. Cosenza, O. Alvarez-Llamoza, A. V. Cano
Summary: In this study, we demonstrate the emergence of dynamic clustering and chimera states in networks of globally coupled robust-chaos oscillators. Through statistical analysis, we characterize the collective behavior of these systems in terms of synchronization, incoherence, and the presence of clusters and chimeras. Additionally, we find that the dynamics of robust chaos does not limit the formation of these states in coupled networks, contrary to previous conjectures.
Article
Biochemistry & Molecular Biology
Hana Rozhonova, Joshua L. Payne
Summary: This paper discusses the controversy about whether the genetic code is optimized for resource conservation, with the authors arguing that the standard genetic code is not optimized for resource conservation.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Biology
Susanna Manrubia, Jose A. Cuesta, Jacobo Aguirre, Sebastian E. Ahnert, Lee Altenberg, Alejandro V. Cano, Pablo Catalan, Ramon Diaz-Uriarte, Santiago F. Elena, Juan Antonio Garcia-Martin, Paulien Hogeweg, Bhavin S. Khatri, Joachim Krug, Ard A. Louis, Nora S. Martin, Joshua L. Payne, Matthew J. Tarnowski, Marcel Weiss
Summary: This article discusses the knowledge of how genotypes map onto molecular phenotypes and organismal functions, and explores theoretical and empirical approaches to broaden and improve this understanding, aiming to derive an updated picture of evolutionary processes.
PHYSICS OF LIFE REVIEWS
(2021)
Review
Biology
Alejandro V. Cano, Bryan L. Gitschlag, Hana Rozhonova, Arlin Stoltzfus, David M. McCandlish, Joshua L. Payne
Summary: Predicting evolutionary outcomes is crucial, and current focus is on adaptive processes mainly through selection. However, adaptive processes rely on new mutations, which are influenced by predictable biases. This article provides an overview of existing theory and evidence for mutation-biased adaptation, discussing its implications for prediction in various fields. The authors argue that with improving knowledge on mutational biases, short-term prediction challenges can be addressed effectively.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Review
Evolutionary Biology
Van D. Nguyen, Thanh H. Nguyen, Abu Saleh Md Tayeen, H. Dail Laughinghouse, Luna L. Sanchez-Reyes, Jodie Wiggins, Enrico Pontelli, Dmitry Mozzherin, Brian O'Meara, Arlin Stoltzfus
EVOLUTIONARY BIOINFORMATICS
(2020)
Article
Physics, Fluids & Plasmas
A. V. Cano, M. G. Cosenza