Article
Biochemistry & Molecular Biology
Joel T. Nelson, Juan C. Motamayor, Omar E. Cornejo
Summary: This study analyzed the genome of Theobroma cacao and found that most molecular adaptations are not shared among populations, indicating that local selective pressures are more important than regional ones in explaining adaptation across a species' range. It also discovered a high correlation between genes and changes in environmental variables, as well as a significant contribution of disease resistance genes to local adaptations.
Article
Biochemistry & Molecular Biology
Maximilian W. D. Raas, Julien Y. Y. Dutheil
Summary: Through population genomic study, this research provides a detailed characterization of adaptive mutations in protein-coding genes across domesticated and wild populations of Saccharomyces cerevisiae. The study reports a decrease in the effective population size of yeast populations since their divergence with S. paradoxus. The overall contribution of positive selection to S. cerevisiae protein evolution is limited, but there are higher rates of adaptive evolution in wild populations compared to domesticated populations.
Article
Evolutionary Biology
William R. Shoemaker, Daisy Chen, Nandita R. Garud
Summary: Genetic variation in the human gut microbiome plays a crucial role in various phenotypes. However, our understanding of its origins and maintenance is limited. By comparing evolutionary processes across different species, we can identify universal trends and deviations. The human gut microbiome offers unparalleled potential for comparative population genomics studies.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Andres Bendesky, Joseph Brew, Kerel X. Francis, Enrique F. Tello Corbetto, Antonio Gonzalez Ariza, Sergio Nogales Baena, Tsuyoshi Shimmura
Summary: This study sequenced the genomes of geographically diverse gamecocks and nongame chickens, and found that gamecocks have a common origin and genetic distinctions from nonfighting chickens. The gene locus ISPD was identified as the most important in relation to fighting performance.
G3-GENES GENOMES GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Yair E. Gatt, Hanah Margalit
Summary: Within-host adaptation in chronic bacterial infections involves substantial genomic changes. Different species share common adaptive strategies, often driven by the host immune system. The ubiquity of adaptive strategies across species reveals key evolutionary changes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Naima Madi, Daisy Chen, Richard Wolff, B. Jesse Shapiro, Nandita R. Garud
Summary: This study examines the interaction between community assembly, intra-species diversity, and evolutionary change. The results show a positive relationship between community diversity and taxa diversity, consistent with the Diversity Begets Diversity hypothesis. However, this relationship plateaus at high levels of community diversity, suggesting the influence of Ecological Controls. Additionally, higher community diversity predicts gene loss in the future.
Article
Biotechnology & Applied Microbiology
Wei Xu, Di Wu, Tianquan Yang, Chao Sun, Zaiqing Wang, Bing Han, Shibo Wu, Anmin Yu, Mark A. Chapman, Sammy Muraguri, Qing Tan, Wenbo Wang, Zhigui Bao, Aizhong Liu, De-Zhu Li
Summary: This study sheds light on the domestication and genome evolution of castor bean by performing de novo chromosome-level genome assembly of its wild progenitor and analyzing worldwide accessions. Important candidate genes associated with plant architecture and seed size were identified through genome-wide association study and quantitative trait locus analysis. This provides valuable insights for genomics-based breeding of castor bean and potentially other tree-like crops in the future.
Article
Multidisciplinary Sciences
Yulduzkhon Abdullaeva, Binoy Ambika Manirajan, Bernd Honermeier, Sylvia Schnell, Massimiliano Cardinale
Summary: The diversity of seed microbiota was generally higher in cultivated cereals than in wild ancestors, suggesting that domestication lead to a bacterial diversification. On the other hand, more microbe-microbe interactions were detected in wild species, indicating a better-structured, mature community. Typical human-associated taxa, such as Cutibacterium, dominated in cultivated cereals, suggesting an interkingdom transfers of microbes from human to plants during domestication.
JOURNAL OF ADVANCED RESEARCH
(2021)
Editorial Material
Multidisciplinary Sciences
Amber Dance
Summary: Equipped with DNA sequencers and advanced computational tools, archaeogeneticists are now focusing on ancient microbes, highlighting the importance of bacteria in human history.
Review
Geography, Physical
Valeriy Glazko, Boris L. Zybaylov, Yu G. Kosovsky, Galina Glazko, Tatyana T. Glazko
Summary: This paper discusses two universal characteristics of domesticated species compared to their wild ancestors, which are increased socialization and phenotypic variability. The gut microbiome plays a role in the social behavior and diet-related changes in domesticated species, while virome incorporation into the host genome influences evolutionary changes. These findings suggest that changes in microbiome during co-habitation with humans are important in the domestication process.
Article
Plant Sciences
David A. Rasmussen, Niklaus J. Grunwald
Summary: Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. It is particularly useful for understanding the emergence, spread, and evolution of plant pathogens. Phylogeography can provide insights into questions about the origin, native status, and frequency of introductions of pathogens.
Article
Ecology
Melania Vega, Christian Quintero-Corrales, Alicia Mastretta-Yanes, Alejandro Casas, Victorina Lopez-Hilario, Ana Wegier
Summary: By assembling chloroplast genomes of 23 wild, landraces, and breeding lines, we found that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. The Mexican landraces were found to arise from multiple wild populations, and their chloroplast organizations were preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene-introgressed individuals, highlighting the importance of biosecurity and agrobiodiversity conservation.
ECOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Qiuyue Chen, Luis Fernando Samayoa, Chin Jian Yang, Bode A. Olukolu, Alessandra M. York, Jose de Jesus Sanchez-Gonzalez, Wei Xue, Jeffrey C. Glaubitz, Peter J. Bradbury, Maria Cinta Romay, Qi Sun, Edward S. Buckler, James B. Holland, John F. Doebley
Summary: The study found that during maize domestication, additive genetic variance decreased while dominance genetic variance increased. Genetic correlations between traits are moderately conserved between teosinte and maize, but their genetic variance-covariance matrices are significantly different, primarily due to changes in reproductive traits. Long-term selection intensities during domestication were weak, and the G-matrix of teosinte imposed considerable constraint on selection during the early domestication process.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Plant Sciences
Didier Reinhardt, Christophe Roux, Nicolas Corradi, Antonio Di Pietro
Summary: Arbuscular mycorrhizal fungi have long been considered ancient asexuals, but recent genomic studies suggest they may have sexual features. Comparative genomics of conspecific isolates of AMF show unexpected interstrain diversity, indicating a high number of lineage-specific genes, similar to fungal pathogens of plants and humans. These genomic similarities may play a role in AMF adaptation to the environment and symbiotic functioning.
TRENDS IN PLANT SCIENCE
(2021)
Review
Microbiology
JamesW. Marsh, Christian Kirk, Ruth E. Ley
Summary: Genetic manipulation is necessary to study microorganisms in their environments, but many species in the human gut microbiome are not genetically tractable. This review addresses the barriers to genetic techniques for gut microbes and discusses ongoing efforts to develop genetic systems. While there is promise in methods that aim to genetically transform multiple species simultaneously, they still face challenges. Increasing the genetic tractability of gut microbiome species is a top priority for microbiome research and will enable microbiome engineering.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Editorial Material
Immunology
Kristin N. Harper
Editorial Material
Immunology
Kristin N. Harper
Editorial Material
Immunology
Kristin N. Harper
Editorial Material
Immunology
Kristin Nicole Harper
Editorial Material
Immunology
Kristin Nicole Harper
Editorial Material
Immunology
Kristin Nicole Harper
Editorial Material
Immunology
Kristin N. Harper
Editorial Material
Immunology
Kristin N. Harper
Editorial Material
Immunology
Kristin N. Harper
Editorial Material
Immunology
Kristin Nicole Harper
Editorial Material
Immunology
Kirsten Nicole Harper
Editorial Material
Immunology
Kirsten Nicole Harper
Editorial Material
Immunology
Kirsten Nicole Harper
Article
Multidisciplinary Sciences
Lenka Mikalova, Klara Janeckova, Marketa Novakova, Michal Strouhal, Darina Cejkova, Kristin N. Harper, David Smajs
Article
Biology
Alison F. Feder, Kristin N. Harper, Chanson J. Brumme, Pleuni S. Pennings
Summary: Triple-drug therapies have transformed HIV from a fatal condition to a chronic one, significantly reducing the risk of drug resistance evolution, but not eliminating it entirely.