Review
Food Science & Technology
Anton E. Shikov, Iuliia A. Savina, Anton A. Nizhnikov, Kirill S. Antonets
Summary: Bacterial organisms have undergone homologous recombination and horizontal gene transfer multiple times, resulting in enhanced adaptation to new environments, specialization, the emergence of new species, and changes in virulence. Analysis of genomic studies of bacterial species in the past 30 years reveals that these genetic exchanges are associated with ecological diversification, pathogenesis, and symbiosis.
Review
Microbiology
Jeronimo Rodriguez-Beltran, Javier DelaFuente, Ricardo Leon-Sampedro, R. Craig MacLean, Alvaro San Millan
Summary: Plasmids play a vital role in bacterial ecology and evolution by mobilizing accessory genes through horizontal gene transfer. Recent studies show that plasmids, kept at multiple copies per cell, create islands of polyploidy in bacterial genomes, leading to evolution governed by different rules than those affecting chromosomal genes. Plasmids may accelerate bacterial evolution by promoting the evolution of plasmid-encoded genes and enhancing the adaptation of their host chromosomes.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Biology
Xavier Didelot, Julian Parkhill
Summary: In recent years, the practicality of sequencing whole genomes from a large number of bacterial isolates has increased significantly, providing new insights into the evolution and epidemiology of bacterial pathogens. This article presents a step-by-step approach for large-scale genomic epidemiology analyses, focusing on the construction and application of dated phylogenies. The key advantage of this approach is its computational scalability, allowing for the analysis of hundreds or thousands of genomes within a short period of time.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Giovanni Pascarella, Chung Chau Hon, Kosuke Hashimoto, Annika Busch, Joachim Luginbuhl, Callum Parr, Wing Hin Yip, Kazumi Abe, Anton Kratz, Alessandro Bonetti, Federico Agostini, Jessica Severin, Shigeo Murayama, Yutaka Suzuki, Stefano Gustincich, Martin Frith, Piero Carninci
Summary: This study reveals the somatic recombination of repeat elements, such as Alu and L1, in the human genome. It also identifies tissue-specific non-allelic homologous recombination hallmarks and retroelements as potential recombination hotspots. The study further shows that neuron-specific recombination of repeat elements accompanies chromatin changes during cell-fate determination. Moreover, somatic recombination profiles are altered in Parkinson's and Alzheimer's disease, indicating a link between retroelement recombination and genomic instability in neurodegeneration.
Review
Ecology
Isaiah Paolo A. Lee, Omar Tonsi Eldakar, J. Peter Gogarten, Cheryl P. Andam
Summary: Cooperation exists at all levels of biological organization, with bacteria cooperating by secreting beneficial molecules for the whole population. Recent findings show that mobile genetic elements promote bacterial cooperation through horizontal gene transfer (HGT), and cooperation can facilitate more frequent HGT. HGT itself can be considered as a form of cooperation and serves as an important enforcement mechanism in bacterial populations.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Biology
Michael Sheinman, Ksenia Arkhipova, Peter F. Arndt, Bas E. Dutilh, Rutger Hermsen, Florian Massip
Summary: Horizontal gene transfer (HGT) is a key force in microbial evolution, with long-distance HGT being frequent. The function of sequences strongly impacts their transfer rate, varying significantly between different functional categories. This study provides a comprehensive view of HGT and its role in driving bacterial evolution.
Article
Multidisciplinary Sciences
Parithi Balachandran, Isha A. Walawalkar, Jacob Flores, Jacob N. Dayton, Peter A. Audano, Christine R. Beck
Summary: Transposable element-mediated rearrangements impact more than 500 kbp of an average human genome, are a source of individual variation, a substrate for evolutionary change, and can occur through diverse mechanisms.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Celia P. F. Domingues, Joao S. Rebelo, Francisco Dionisio, Teresa Nogueira
Summary: Antimicrobial resistance is a significant threat to public health, as excessive use of antibiotics leads to the emergence of multi-drug resistance. Our large-scale analysis of bacterial genomes revealed that over 95% of the genomes contain genes associated with resistance to various antimicrobial classes. Additionally, we found unexpected co-occurrences of resistance genes in plasmids, increasing the potential for resistance dissemination.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Evolutionary Biology
Christina L. Burch, Artur Romanchuk, Michael Kelly, Yingfang Wu, Corbin D. Jones
Summary: Horizontal gene transfer (HGT) plays a significant role in bacterial genome evolution, leading to phenotypic diversity and the emergence of new traits and species. The likelihood of gene transfer varies depending on the connectivity of genes, which can be explained by the complexity hypothesis and the balance hypothesis.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Kamil S. Jaron, Darren J. Parker, Yoann Anselmetti, Patrick Tran Van, Jens Bast, Zoe Dumas, Emeric Figuet, Clementine M. Francois, Keith Hayward, Victor Rossier, Paul Simion, Marc Robinson-Rechavi, Nicolas Galtier, Tanja Schwander
Summary: This study investigated the genome evolution of parthenogenetic species in the stick insect genus Timema and found that parthenogenesis leads to a significant reduction in heterozygosity and often results in genetically uniform populations. Additionally, the study revealed that parthenogenetic species experience less effective positive selection, indicating that sex is prevalent in natural populations due to its facilitation of rapid adaptation. The study also observed no increased accumulation of transposable elements in parthenogenetic species, likely due to the low TE activity in the genus. Overall, these findings provide empirical support for the negative consequences of parthenogenesis as predicted by theory.
Article
Multidisciplinary Sciences
Mark Pagel, Ciara O'Donovan, Andrew Meade
Summary: Macroevolution poses challenges to evolutionary theory due to abrupt changes and long stagnation periods. This study introduces a statistical model that considers directional changes and evolvability changes to account for this uneven evolutionary landscape. In mammals, both processes independently contribute to macroevolution, with increased evolvability being more common than reduced evolutionary potentials. Large or sudden phenotypic changes can be statistically explained as biased random walks, bridging the gap between macroevolution and gradualist microevolution. This study emphasizes the importance of considering multiple evolutionary processes simultaneously.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Quinn Langdon, Daniel Powell, Bernard Kim, Shreya Banerjee, Cheyenne Payne, Tristram Dodge, Ben Moran, Paola Fascinetto-Zago, Molly Schumer
Summary: This study analyzes the drivers of variation in local ancestry across the genome in hybridization events between two species pairs of swordtail fish and finds unexpectedly high levels of repeatability. The analysis also identifies regions of the genome where minor parent ancestry is unusually low or high across species pairs, indicating shared selection sites and mechanisms.
Article
Multidisciplinary Sciences
Sarah Kronheim, Ethan Solomon, Louis Ho, Michelle Glossop, Alan R. Davidson, Karen L. Maxwell
Summary: This study presents the genomic and biological characterization of twelve Streptomyces phages. Genome analyses reveal genetic relatedness among these phages, while experimental approaches demonstrate their broad host ranges, early infection during the Streptomyces lifecycle, and induction of secondary metabolite production and sporulation in some Streptomyces species. This work expands the knowledge of Streptomyces phages and improves our understanding of their dynamics with their hosts.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Xingyang Cui, Dasong Xia, Xinyi Huang, Yue Sun, Mang Shi, Jianqiang Zhang, Ganwu Li, Yongbo Yang, Haiwei Wang, Xuehui Cai, Tongqing An
Summary: In this study, the genomic sequences of PRRSV-2 from 1991 to 2021 were analyzed, revealing the temporal and geographical distribution of recombinant PRRSVs and the location of recombination hot spots. It was found that recombinant PRRSVs based on the L1 backbone had higher replication capacity. These findings provide new insights into PRRSV recombination and the mechanism behind it.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Hannah Trost, Arianna Merkell, Felicia Wednesday Lopezcolorado, Jeremy M. Stark
Summary: Repeat-mediated deletions (RMDs) are chromosomal rearrangements that result in the loss of sequences between homologous repeats. The mechanisms of RMD suppression and resolution of sequence divergence are poorly understood. In this study, we identified MLH1 as a suppressor of RMDs with sequence divergence, acting in the same pathway as MSH2 and MSH6. We also found that MLH1 promotes directional resolution of sequence divergence in the RMD product, and this polarity is influenced by the MLH1-PMS2 endonuclease.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Evolutionary Biology
Rohan Maddamsetti, Philip J. Hatcher, Anna G. Green, Barry L. Williams, Debora S. Marks, Richard E. Lenski
GENOME BIOLOGY AND EVOLUTION
(2017)
Review
Multidisciplinary Sciences
Zachary D. Blount, Richard E. Lenski, Jonathan B. Losos
Article
Microbiology
Otmane Lamrabet, Mikael Martin, Richard E. Lenski, Dominique Schneider
Article
Biochemistry & Molecular Biology
Kyle J. Card, Thomas LaBar, Jasper B. Gomez, Richard E. Lenski
Article
Microbiology
Esha Atolia, Spencer Cesar, Heidi A. Arjes, Manohary Rajendram, Handuo Shi, Benjamin D. Knapp, Somya Khare, Andres Aranda-Diaz, Richard E. Lenski, Kerwyn Casey Huang
Article
Multidisciplinary Sciences
Kyle J. Card, Misty D. Thomas, Joseph L. Graves, Jeffrey E. Barrick, Richard E. Lenski
Summary: Antibiotic resistance is a growing health concern, with epistatic interactions between mutations complicating the ability to predict evolution. Differences in genetic backgrounds can lead to idiosyncratic responses in the evolvability of resistance, with lineages founded by different genotypes taking parallel or divergent mutational paths. Historical contingency can alter both genotypic and phenotypic pathways to antibiotic resistance, as evidenced by differences in mutation patterns among different genetic starting points.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Ecology
Kyle J. Card, Jalin A. Jordan, Richard E. Lenski
Summary: The study found that the fitness costs of antibiotic resistance are not always correlated with the phenotypic level of resistance or the underlying genetic changes, but are instead influenced by specific resistance mutations and the genetic backgrounds in which they occur.
Article
Microbiology
Nkrumah A. Grant, Ali Abdel Magid, Joshua Franklin, Yann Dufour, Richard E. Lenski
Summary: The study demonstrates that bacteria evolve larger cells in experimental environments, confirming the ability of cell morphology to evolve and diversify with substantial heterogeneity across replicate lines. Across 50,000 generations, cell size and fitness remain correlated, indicating the beneficial aspect of larger cells and partial compensation for less favorable surface area-to-volume ratios.
JOURNAL OF BACTERIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Ruth Rodriguez-Pastor, Yarden Shafran, Nadav Knossow, Ricardo Gutierrez, Shimon Harrus, Luis Zaman, Richard E. Lenski, Jeffrey E. Barrick, Hadas Hawlena
Summary: This article introduces laboratory experiments on the evolution of blood-borne parasitic microbes in animal hosts, offering guidelines for designing such experiments. The importance of selecting appropriate ancestral genotypes, treatments, replicates, controls, variables, covariates, and timing for checkpoints is emphasized, along with recommended preliminary experiments for quantification and transmission methods. Despite their technical nature, these methodological considerations also have conceptual implications.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Dustin J. Marshall, Martino Malerba, Thomas Lines, Aysha L. Sezmis, Chowdhury M. Hasan, Richard E. Lenski, Michael J. McDonald
Summary: Body size and population dynamics are correlated across different domains of life, and there may be fundamental constraints on the coevolution of size and demography imposed by metabolism. Experimental observations confirm the prediction of metabolic theory that larger cells have higher metabolic rates but lower metabolic rates relative to their size. Additionally, populations of larger cells achieved lower maximum densities but higher maximum biomasses than populations of smaller cells, contradicting the assumption that the costs of building new individuals should directly scale with their size. This finding challenges existing theories and necessitates a reevaluation of the evolutionary drivers and ecological consequences of biological size.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Infectious Diseases
Jalin A. Jordan, Richard E. Lenski, Kyle J. Card
Summary: Antibiotic resistance is an increasing concern, and this study focuses on the fitness and cost of resistance in ampicillin-resistant mutants. The findings highlight the importance of comparative studies and reveal the nuanced processes behind antibiotic resistance phenotypes.
Review
Ecology
Make Ni Leathlobhair, Richard E. Lenski
Summary: Cancer cell populations undergo the same core evolutionary processes as asexually reproducing unicellular organisms. Transmissible cancers are exceptional examples of these processes, with mechanisms influenced by population genetic theory.
NATURE ECOLOGY & EVOLUTION
(2022)
Review
Biochemistry & Molecular Biology
Richard E. Lenski
Summary: The long-term evolution experiment (LTEE) with Escherichia coli started in 1988 and has reached 75,000 generations, exploring questions about phenotypic and genetic evolution dynamics and repeatability. The experimental design, including culture regime, growth medium, ancestral strain, and statistical replication, has contributed to the stability and success of LTEE. Challenges associated with a long-running project, such as handling procedural errors and managing frozen samples, have been overcome. The simplicity of the experimental design and procedures, with the support of evolving genomic technologies, has allowed for unexpected discoveries and contributions beyond initial expectations.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Ecology
Richard E. Lenski
AMERICAN NATURALIST
(2017)