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
Computer Science, Artificial Intelligence
Sumika Chauhan, Manmohan Singh, Ashwani Kumar Aggarwal
Summary: The paper introduces a new Diversity Driven Multi-Parent Evolutionary Algorithm with Adaptive non-uniform mutation to maintain diversity in explored solutions, detect premature convergence, and avoid local optima. The algorithm is driven by population diversity and overcomes the tendency of evolutionary algorithms to get stuck in local optima.
JOURNAL OF EXPERIMENTAL & THEORETICAL ARTIFICIAL INTELLIGENCE
(2021)
Article
Computer Science, Artificial Intelligence
Hao-Gan Huang, Yue-Jiao Gong
Summary: Offline data-driven evolutionary algorithms (DDEAs) have gained attention in the data-driven age. Most studies build surrogate models based on regression methods, which heavily rely on the quality and quantity of offline data. This article proposes an alternative approach using a contrastive learning model based on binary classification to determine the pros and cons between individuals. The proposed model is implemented with a siamese neural network and achieves powerful performance, especially on high-dimensional problems.
IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Nelson Frazao, Isabel Gordo
Summary: Social networks can shape the species composition of the gut microbiome by influencing the ecology of gut bacteria. In an experimental evolution study in mice, it was found that there is a transmission rate of 7% (& PLUSMN;3% 2SE) of E. coli cells per day between hosts living in the same household. The results also showed that hosts with similar diets and habits are expected to have similar microbiome species compositions and evolutionary dynamics.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Elizabeth H. J. Robbins, Steven Kelly
Summary: The chloroplast, evolved from endosymbiosis, has a highly conserved genome organization and a slow rate of molecular evolution. Through analysis of angiosperm plastid genomes, it was found that the distance from the replication origin, amino acid composition, and mRNA abundance are key factors influencing the rate of molecular evolution in plastid genes. These factors account for over 50% of the variation in evolution rate and have constrained the adaptive evolution and evolvability of the chloroplast.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Computer Science, Artificial Intelligence
Zhenzhen Hu, Wenyin Gong, Witold Pedrycz, Yanchi Li
Summary: This paper proposes a DRL-assisted co-evolutionary differential evolution algorithm (CEDE-DRL) that effectively utilizes DRL to help EAs solve constrained optimization problems. The method incorporates co-evolution into the extraction of training data, improves the accuracy of the neural network model through information exchange between multiple populations, and uses multiple constraint handling techniques for offspring selection. DRL is used to evaluate the population state, taking into account feasibility, convergence, and diversity. Additionally, an adaptive operator selection and individual archive elimination mechanism is added to avoid premature convergence and local optima.
SWARM AND EVOLUTIONARY COMPUTATION
(2023)
Article
Computer Science, Artificial Intelligence
Patrick Spettel, Zehao Ba, Dirk V. Arnold
Summary: This paper proposes an active-set evolution strategy for evolutionary black-box optimization with explicit constraints, and experimentally demonstrates its advantage over other algorithms on the problem set.
EVOLUTIONARY COMPUTATION
(2022)
Article
Biotechnology & Applied Microbiology
Peng Gao, Teagen D. Quilichini, Chun Zhai, Li Qin, Kirby T. Nilsen, Qiang Li, Andrew G. Sharpe, Leon Kochian, Jitao Zou, Anireddy S. N. Reddy, Yangdou Wei, Curtis Pozniak, Nii Patterson, C. Stewart Gillmor, Raju Datla, Daoquan Xiang
Summary: Research indicates that there is diversity in the regulation of alternative splicing in polyploid wheat and grass species, not only showing differences in different tissues but also between subgenomes. Analysis of homoeologous triads in polyploid wheat reveals evolutionary divergence in the regulation of embryogenesis between gene-level and transcript-level.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Computer Science, Artificial Intelligence
Hu Peng, Zhenzhen Xu, Jiayao Qian, Xiaogang Dong, Wei Li, Zhijian Wu
Summary: In constrained optimization evolutionary algorithms (COEAs), achieving a balance between the objective function and constraints is crucial. This study proposes a Hybrid Constraint-handling Technique (HCT) that utilizes the information of the population's evolution process to maintain this balance. The proposed ECO-HCT algorithm combines evolutionary algorithms with HCT to solve complex constraint optimization problems (COPs) and has shown competitive performance compared to other advanced methods.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Microbiology
E. Cebrian-Sastre, A. Chiner-Oms, R. Torres-Perez, I. Comas, J. C. Oliveros, J. Blazquez, A. Castaneda-Garcia
Summary: Resistance to rifampicin is a challenge to tuberculosis treatment. This study investigated the mutational landscape of Mycobacterium smegmatis during long-term evolution with increasing concentrations of rifampicin. Antibiotic treatment resulted in increased acquisition of mutations and extinction of wild-type lines, while the noncanonical mismatch repair deficient mutant strain showed high survival and higher levels of rifampicin resistance. The study also identified adaptive genes under positive selection with rifampicin that may be associated with the development of antibiotic resistance.
MICROBIOLOGY SPECTRUM
(2023)
Review
Ecology
Angela McGaughran, Rebecca Laver, Ceridwen Fraser
Summary: In the current Anthropocene epoch, human activities are driving new climatic trajectories, leading to hotter conditions and a range of impacts on the biosphere. Organisms may respond to these changes with acclimation, adaptation, relocation, or extinction, as new abiotic gradients are established. Temperature changes may lead to extirpations, extinctions, and range shifts, but can also prompt phenotypic or behavioral plasticity as species adapt to new conditions. Recent genomic research suggests that some species can evolve rapidly in response to environmental change, offering insights into how temperature might accelerate evolution in the Anthropocene.
TRENDS IN ECOLOGY & EVOLUTION
(2021)
Review
Microbiology
James P. R. Connolly, Andrew J. Roe, Nicky O'Boyle
Summary: Studying the adaptive evolutionary trajectories in bacteria has contributed to a better understanding of stress responses, revealed important insights into microbial physiology, facilitated the production of highly optimized strains for biotechnology, and enhanced our understanding of genomic plasticity in chronic infections.
CRITICAL REVIEWS IN MICROBIOLOGY
(2021)
Article
Computer Science, Artificial Intelligence
Kangjia Qiao, Jing Liang, Kunjie Yu, Minghua Yuan, Boyang Qu, Caitong Yue
Summary: The paper introduces a self-adaptive resources allocation-based differential evolution (SRADE) to balance diversity, convergence, constraints, and objective function in addressing constrained optimization problems. By dynamically assigning different mutation strategies to individuals based on their performance feedback, the method effectively improves search efficiency under limited resources by focusing on the most efficient strategy.
KNOWLEDGE-BASED SYSTEMS
(2022)
Article
Environmental Sciences
Edward J. Calabrese, Dima Yazji Shamoun, Evgenios Agathokleous
Summary: This paper suggests that the origin of the LNT concept for ionizing radiation was based on a lack of understanding of evolution, leading to the establishment of the linear no threshold dose response model. However, modern advancements in repair mechanisms have shown that the historical foundations of LNT were flawed.
ENVIRONMENTAL POLLUTION
(2022)
Article
Computer Science, Artificial Intelligence
Sumika Chauhan, Manmohan Singh, Ashwani Kumar Aggarwal
Summary: This work presents an evolutionary algorithm approach with different mutation schemes to address the problems of premature convergence and local optima in evolutionary algorithms. The mutation process is adaptive, using fitness variance and space aggregation concept. Multiple mutation methods, including wavelet mutation, Levy flight, particle swarm optimization-based mutation, chaotic mutation, and non-uniform mutation, are employed. Experimental results are evaluated in terms of standard deviation and average, and the effectiveness is tested using the Wilcoxon's rank-sum test. The best mutation method is compared with other optimization techniques, and further applied to the area coverage optimization problem of WSN.
Article
Ecology
Jason Bertram, Joanna Masel
Article
Genetics & Heredity
Scott G. Foy, Benjamin A. Wilson, Jason Bertram, Matthew H. J. Cordes, Joanna Masel
Article
Genetics & Heredity
Jason Bertram, Joanna Masel
Article
Evolutionary Biology
Kendra M. Meer, Paul G. Nelson, Kun Xiong, Joanna Masel
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Evolutionary Biology
Karina Zile, Christophe Dessimoz, Yannick Wurm, Joanna Masel
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Biology
Kevin Gomez, Jason Bertram, Joanna Masel
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Biology
Jennifer E. James, Sara M. Willis, Paul G. Nelson, Catherine Weibel, Luke J. Kosinski, Joanna Masel
Summary: The study found that the reduction in hydrophobic clustering is universal across lineages, while only young animal domains tend to have higher structural disorder. Trends in amino acid composition among ancient domains reflect the order of recruitment into the genetic code, indicating that the composition of contemporary descendants of ancient sequences reflects amino acid availability during the earliest stages of life.
Article
Genetics & Heredity
Kun Xiong, Mark Gerstein, Joanna Masel
Summary: Transcriptional regulatory networks (TRNs) exhibit certain motifs, with type 1 incoherent feed-forward loops (I1FFLs) and negative feedback loops (NFBLs) being common solutions. The evolution of these motifs is influenced by selection conditions, with I1FFLs generally evolving more frequently than NFBLs. The evolutionary accessibility and not just relative functionality shape motif evolution in TRNs, with the expression levels of specific genes playing a crucial role.
Article
Evolutionary Biology
Cuong Cao Dang, Bui Quang Minh, Hanon McShea, Joanna Masel, Jennifer Eleanor James, Le Sy Vinh, Robert Lanfear
Summary: This study introduces a new maximum likelihood method, nQMaker, that can estimate time nonreversible amino acid substitution models and rooted phylogenetic trees. The results show that the nonreversible models estimated with nQMaker are a better fit to empirical alignments than pre-existing reversible models, and the improvements in model fit scale with the size of the data set.
SYSTEMATIC BIOLOGY
(2022)
Article
Ecology
Thomas Bataillon, Thomas H. G. Ezard, Michael Kopp, Joanna Masel
Article
Evolutionary Biology
Luke J. Kosinski, Nathan R. Aviles, Kevin Gomez, Joanna Masel
Summary: Proteins, as the workhorses of the cell, can cause harm through misfolding and aggregation. However, sometimes proteins can be born from noncoding DNA without harm. By studying the fitness of different Escherichia coli lineages expressing unique random peptides, researchers found that simple amino acid frequencies, rather than the ordering of amino acids, predicted lineage fitness. Smaller amino acids that promote intrinsic structural disorder had less harmful effects on fitness. These amino acids were also enriched in young animal proteins.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Jennifer E. James, Paul G. Nelson, Joanna Masel
Summary: Protein domains that emerged recently have higher disorder and clustering of hydrophobic residues. There is a hypothesis that different levels of selection affect the retention probabilities of domains with different properties. Loss rates were inferred for animal Pfam domains and were found to depend on disorder and clustering trait values. The results support the hypothesis that domain loss slowly eliminates domains with suboptimal disorder and clustering levels, affecting proteome composition.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Public, Environmental & Occupational Health
Joanna Masel, James Ian Mackie Petrie, Jason Bay, Wolfgang Ebbers, Aalekh Sharan, Scott Michael Leibrand, Andreas Gebhard, Samuel Zimmerman
Summary: Digital contact tracing and notification have not lived up to expectations in combating the COVID-19 pandemic due to multiple points of failure. Research indicates that achieving a significant reduction in transmission risk requires high success rates in technology adoption, contact detection, prompt diagnosis and notification, and behavior change. Recommendations include emphasizing user autonomy, integrating tracing/notification apps with testing, manual contact tracing, and scientific data collection.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2023)
Article
Multidisciplinary Sciences
James Petrie, Joanna Masel
Summary: Targeted quarantine and social distancing measures should be implemented based on current disease prevalence to achieve the optimal balance between controlling transmission and minimizing total social isolation. The value of a quarantine policy increases with lower case counts, is less affected by vaccination unless exemptions are in place, and is greatly enhanced by more information on individual infectiousness risk.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2021)