Article
Ecology
Lindi M. Wahl, Mark M. Tanaka
Summary: The cost of sexual reproduction provides a significant advantage for derived asexual organisms, but their phylogenetic distribution suggests a higher risk of extinction compared to those engaging in sexual reproduction. Bacteria and archaea, on the other hand, have been able to persist for billions of years without sexual reproduction due to their large population sizes. However, asexual populations undergoing selective sweeps may still lose genetic variation and experience a reduction in effective population size, ultimately increasing the risk of extinction.
AMERICAN NATURALIST
(2022)
Article
Biochemistry & Molecular Biology
Hussein A. Hejase, Ziyi Mo, Leonardo Campagna, Adam Siepel
Summary: A novel method called SIA was developed to detect and quantify positive selection using the ancestral recombination graph and deep learning. Extensive benchmarking showed its effectiveness in simulations and real data, revealing novel signals of selection in European populations and confirming selection signals in genes related to human phenotypes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Hanqing Zhao, Matthijs Souilljee, Pavlos Pavlidis, Nikolaos Alachiotis
Summary: ASDEC is a neural network-based framework that can scan whole genomes for selective sweeps. It achieves similar classification performance to other convolutional neural network-based classifiers, but is trained and classifies genomic regions much faster by inferring region characteristics from raw sequence data. Using ASDEC for genomic scans resulted in higher sensitivity, success rates, and detection accuracy compared to state-of-the-art methods.
Article
Biochemistry & Molecular Biology
Limei Zhong, Youlin Zhu, Kenneth M. Olsen
Summary: This study used genome scans to uncover selection marks of hard and soft sweeps in domesticated soybeans, revealing that hard sweeps are mainly present in domesticated soybeans, while soft sweeps are more common in wild ancestors. The results contribute to a better understanding of genetic characteristics of domestication traits in soybeans.
Article
Multidisciplinary Sciences
Laura Boyle, Sofia Hletko, Jenny Huang, June Lee, Gaurav Pallod, Hwai-Ray Tung, Richard Durrett
Summary: The main mathematical result of this paper is that the change of variables in the ordinary differential equation for the competition of two infections in an SIR model can be transformed into a logistic differential equation, which accurately predicts the rapid turnover of dominant variants. The fitting of the logistic equation to data shows sensible estimates of the increase in infectivity. These arguments can be applied to any epidemic modeled by SIR equations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Quentin Rougemont, Barbara Huber, Simon H. Martin, Annabel Whibley, Catalina Estrada, Darha Solano, Robert Orpet, W. Owen McMillan, Brigitte Frerot, Mathieu Joron
Summary: By studying the speciation process of Heliconius butterflies, it is found that wing pattern divergence may play a role in speciation and be associated with hybridization and reproductive isolation.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Agronomy
Ryuji Uesugi, Akiya Jouraku, Suprada Sukonthabhirom Na Pattalung, Norihide Hinomoto, Seigo Kuwazaki, Hiroyuki Kanamori, Yuichi Katayose, Shoji Sonoda
Summary: The study revealed that the G4946E mutation plays a key role in resistance and has multiple origins across east and southeast Asia, despite geographical barriers. Field populations showed partial recovery in resistance levels during winter, with the frequency of the resistant allele decreasing. Regions that do not experience overwintering have significantly lower frequencies of the E4946 allele compared to overwintering regions.
PEST MANAGEMENT SCIENCE
(2021)
Article
Entomology
Wen-Ting Dai, Jin Li, Li-Ping Ban
Summary: In this study, we analyzed resequencing data of two resistant and one susceptible strains of codling moth and identified several genes potentially involved in insecticide resistance. Our results highlight the complexity of the insecticide resistance mechanism in codling moth and provide valuable insights for developing effective resistance management strategies.
Article
Physics, Multidisciplinary
Michael Kordell II, Rainer J. Fries, Che Ming Ko
Summary: The isotropic 3-dimensional harmonic oscillator potential is an approximate description of various systems in different branches of physics, and it has interesting applications in studying the binding of two particles into angular momentum eigenstates. In this study, we compute the probabilities for the coalescence of two distinguishable particles into bound states in this potential, using wave packets and the phase-space formulation. We also derive a general formula for expanding angular momentum eigenstates based on 1-dimensional harmonic oscillator eigenstates.
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
Chemistry, Multidisciplinary
Huahai Yu, Ying Piao, Yifan Zhang, Jiajia Xiang, Shiqun Shao, Jianbin Tang, Zhuxian Zhou, Youqing Shen
Summary: This study reports a nanocarrier based on OPDEA that can hitchhike on red blood cells and preferentially release at the infection site. The nanocarrier achieves selective hitchhiking and release through its affinity with both red blood cell membrane and bacteria cell wall, enabling efficient drug delivery and improved penetration in biofilm.
Review
Ecology
Brian Charlesworth, Jeffrey D. Jensen
Summary: Genetic variations and evolution patterns at a given site in a genome are strongly influenced by selection at genetically linked sites, with recombination rates correlating with within-population genetic variability. Different population genetic processes like selective sweeps, background selection, and associative overdominance lead to varying patterns of variability, while interaction between selective and demographic processes significantly impacts variability patterns within genomes.
ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 52, 2021
(2021)
Article
Ecology
Madeline A. Chase, Hans Ellegren, Carina F. Mugal
Summary: The debate in population genomics surrounding patterns of genomic differentiation between closely related species suggests that both shared and lineage-specific species differentiation patterns may be influenced by selective sweeps and recombination dynamics.
Article
Biochemical Research Methods
Irena Jenickova, Petr Kasparek, Silvia Petrezselyova, Jan Elias, Jan Prochazka, Jana Kopkanova, Michal Navratil, Cyril Barinka, Radislav Sedlacek
Summary: The Cre-loxP recombination system is a powerful tool for genome engineering, with one application being the induction of Cre recombination in genetic mouse models. A technique of delivering Cre protein into mouse zygotes by electroporation is described as simple, affordable, and highly efficient, resulting in faster generation of desired models. Additionally, it is shown that the method is suitable for allelic conversion in primary cells derived from conditional mouse models.
Article
Engineering, Chemical
M. H. Kandemir, K. Mohan, R. M. Wagterveld, D. R. Yntema, K. J. Keesman
Summary: The study investigated and demonstrated the application of frequency-sweep dynamic acoustic fields for size-selective particle filtration on centimeter scale, showing that the filtration performance is largely affected by the sweep period and the outlet flow rate. Lab experiments and simulations were used to explore these effects and demonstrate the prototype's selective filtration performance.
SEPARATION AND PURIFICATION TECHNOLOGY
(2021)
