Article
Biochemistry & Molecular Biology
Lina Kloub, Sean Gosselin, Matthew Fullmer, Joerg Graf, Johann Peter Gogarten, Mukul S. Bansal
Summary: Horizontal gene transfer (HGT) is crucial for prokaryotic evolution, yet little is known about the scale of individual HGT events. A computational framework called HoMer is introduced to infer single-gene HGT events and potential multiple-gene transfers, aiding a better understanding of HGT and microbial evolution on a larger scale through systematic inference of HMGTs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Diego F. Morales-Briones, Nan Lin, Eileen Y. Huang, Dena L. Grossenbacher, James M. Sobel, Caroline D. Gilmore, David C. Tank, Ya Yang
Summary: In this study, phylogenomic datasets using genomes and transcriptomes were used to investigate Monkeyflower (Phrymaceae). The results showed that Phrymaceae exhibited monophyly and gene tree discordance was observed among its tribes. The study also identified potential reticulation events and small-scale genome duplications that may have contributed to the macroevolutionary diversification of Phrymaceae.
AMERICAN JOURNAL OF BOTANY
(2022)
Article
Plant Sciences
Jian Liu, Anders J. Lindstrom, Xun Gong
Summary: Our study explores the plastome characteristics and deep phylogenetic relationships within the Cycas genus. We find that all Cycas plastomes have consistent gene content and structure, with only one gene loss detected in a Philippine species. We identify three plastome regions with high nucleotide variability. Molecular evolutionary analysis reveals purifying selection in most plastid protein-coding genes, except ndhB. Phylogenomic analyses using concatenated and coalescent methods show conflicting topologies at shallow nodes.
Article
Plant Sciences
Fengmao Yang, Jia Ge, Yongjie Guo, Richard Olmstead, Weibang Sun
Summary: This study investigates the evolutionary history of Asian species of the genus Buddleja and reveals 6 hybridization events and several allopolyploid speciation events. The study also corrects earlier misinterpretations and shows that tectonic activity, climate fluctuations, polyploidization, and hybridization contributed to the diversification of this lineage.
Article
Biochemistry & Molecular Biology
Cristian R. Cervantes, Jose-Ruben Montes, Ulises Rosas, Salvador Arias
Summary: This study classified the Mammillaria haageana complex using genomic, morphological, and ecological data. The complex was found to consist of six distinct entities, mainly due to ecological speciation. These species hypotheses can be useful for future extinction risk assessments and conservation strategies.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biology
Jinren Yu, Hong Zhao, Yanting Niu, Yichen You, Russell L. Barrett, Rindra Manasoa Ranaivoson, Romer Narindra Rabarijaona, Gaurav Parmar, Langxing Yuan, Xiaofeng Jin, Pan Li, Jianhua Li, Jun Wen, Zhiduan Chen, Limin Lu
Summary: The genus Causonis serves as a model for exploring different hybridization and polyploidization modes in lineages with contrasting species' distribution ranges. Understanding the specific evolutionary histories and genetic properties of focal species is crucial for conservation strategies.
Article
Microbiology
Nicholas A. T. Irwin, Alexandros A. Pittis, Thomas A. Richards, Patrick J. Keeling
Summary: This study systematically characterized viral-eukaryotic gene exchange, identifying thousands of transfers and revealing their frequency, taxonomic distribution, and predicted functions. The findings highlight the impact of virus-host interactions on evolutionary changes, as well as common strategies employed by viruses to manipulate hosts, such as metabolic reprogramming, proteolytic degradation, and extracellular modification. Additionally, the study implicates genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases impacting a wide range of structures.
NATURE MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Qiong Zhang, Ryan A. Folk, Zhi-Qiong Mo, Hang Ye, Zhao-Yuan Zhang, Hua Peng, Jian-Li Zhao, Shi-Xiong Yang, Xiang-Qin Yu
Summary: Gene tree discordance is an important legacy of biological evolution, with rapid diversification being a major cause of gene tree discordance in the Camellia genus. This study investigated the phylogeny of Camellia and the possible causes of gene tree discordance using transcriptome data from 55 species. The results revealed varying levels of gene tree discordance in the backbone of Camellia and confirmed that none of the proposed sections of Camellia are monophyletic. Integrating all orthologous genes provided the best resolution for the species tree of Camellia.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Minkyu Park, Ali Sarkhosh, Violeta Tsolova, Islam El-Sharkawy
Summary: Horizontally transferred transposable elements play a significant role in plant genome evolution by generating additional TE subfamilies and causing differential proliferation in host genomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Evolutionary Biology
Paul M. Hime, Alan R. Lemmon, Emily C. Moriarty Lemmon, Elizabeth Prendini, Jeremy M. Brown, Robert C. Thomson, Justin D. Kratovil, Brice P. Noonan, R. Alexander Pyron, Pedro L. Peloso, Michelle L. Kortyna, J. Scott Keogh, Stephen C. Donnellan, Rachel Lockridge Mueller, Christopher J. Raxworthy, Krushnamegh Kunte, Santiago R. Ron, Sandeep Das, Nikhil Gaitonde, David M. Green, Jim Labisko, Jing Che, David W. Weisrock
Summary: This study provides a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting conserved exons. It clarifies relationships among amphibians and identifies gene tree-species tree conflict. The results strongly support amphibian monophyly and a sister relationship between frogs and salamanders, with a surprisingly younger timescale for crown and ordinal amphibian diversification.
SYSTEMATIC BIOLOGY
(2021)
Article
Biology
Nico Bremer, Michael Knopp, William F. Martin, Fernando D. K. Tria
Summary: The accuracy of T:D estimates obtained by tree reconciliations has not been compared to estimates obtained by independent means. The root inferences using ALE are strongly dependent upon T:D and gene duplications have a far greater impact on ALE's preferences for phylogenetic root placement than gene transfers or gene losses do. Obtaining reliable species tree roots with ALE is only possible when gene duplications are abundant in the data and the number of falsely inferred gene duplications is low.
Article
Biochemistry & Molecular Biology
Cheng-Kuo Lai, Yi-Chien Lee, Huei-Mien Ke, Min R. Lu, Wei-An Liu, Hsin-Han Lee, Yu-Ching Liu, Toyoshi Yoshiga, Taisei Kikuchi, Peichen J. Chen, Isheng Jason Tsai
Summary: In this study, the genomes of six Aphelenchoides species, including four strains of the A. besseyi species complex, were analyzed. The systematic identification of horizontal gene transfer (HGT) genes revealed that these genes were mostly acquired from bacteria, fungi, and plants. This study provides a comprehensive understanding of HGT in nematodes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Xinyi Guo, Terezie Mandakova, Karolina Trachtova, Baris Ozudogru, Jianquan Liu, Martin A. Lysak
Summary: This study reveals the complex genomic history of the mustard family tribe Biscutelleae, showing contentious relationships within this plant family. Genome evolution in Biscutelleae was influenced by pervasive hybridizations and subsequent genome duplications, leading to a complex pattern of relationships among the genera.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Rebeca Hernandez-Gutierrez, Cassio van den Berg, Carolina Granados Mendoza, Marcia Penafiel Cevallos, M. Efrain Freire, Emily Moriarty Lemmon, Alan R. Lemmon, Susana Magallon
Summary: This study aims to generate a phylogenetic hypothesis of the cotton and cacao family using nuclear genes, and analyzes the discordance among different methods and gene histories.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Richard G. J. Hodel, Elizabeth A. Zimmer, Bin-Bin Liu, Jun Wen
Summary: Plant biologists have resolved the long-standing mystery of the origin of the apple tribe through genomic data analysis. They have also discovered conflicts between nuclear gene trees and species trees in other nodes of the Amygdaloideae subfamily of Rosaceae.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Ecology
Gemma G. R. Murray, Fang Wang, Ewan M. Harrison, Gavin K. Paterson, Alison E. Mather, Simon R. Harris, Mark A. Holmes, Andrew Rambaut, John J. Welch
METHODS IN ECOLOGY AND EVOLUTION
(2016)
Article
Multidisciplinary Sciences
Gemma G. R. Murray, Andre E. R. Soares, Ben J. Novak, Nathan K. Schaefer, James A. Cahill, Allan J. Baker, John R. Demboski, Andrew Doll, Rute R. Da Fonseca, Tara L. Fulton, M. Thomas P. Gilbert, Peter D. Heintzman, Brandon Letts, George McIntosh, Brendan L. O'Connell, Mark Peck, Marie-Lorraine Pipes, Edward S. Rice, Kathryn M. Santos, A. Gregory Sohrweide, Samuel H. Vohr, Russell B. Corbett-Detig, Richard E. Green, Beth Shapiro
Article
Genetics & Heredity
Darko D. Cotoras, Gemma G. R. Murray, Joshua Kapp, Rosemary G. Gillespie, Charles Griswold, W. Brian Simison, Richard E. Green, Beth Shapiro
Article
Paleontology
Jelmer W. Eerkens, Ruth Nichols, Gemma G. R. Murray, Katherine Perez, Engel Murga, Phil Kaijankoski, Jeffrey S. Rosenthal, Laurel Engbring, Beth Shapiro
INTERNATIONAL JOURNAL OF PALEOPATHOLOGY
(2018)
Review
Biochemistry & Molecular Biology
Marta Matuszewska, Gemma G. R. Murray, Ewan M. Harrison, Mark A. Holmes, Lucy A. Weinert
TRENDS IN MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Gemma G. R. Murray, Jane Charlesworth, Eric L. Miller, Michael J. Casey, Catrin T. Lloyd, Marcelo Gottschalk, Alexander W. (Dan) Tucker, John J. Welch, Lucy A. Weinert
Summary: The study shows that genome reduction is consistently associated with pathogenicity in bacteria.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Geography, Physical
Juliette Funck, Peter D. Heintzman, Gemma G. R. Murray, Beth Shapiro, Holly McKinney, Jean-Bernard Huchet, Nancy Bigelow, Patrick Druckenmiller, Matthew J. Wooller
QUATERNARY SCIENCE REVIEWS
(2020)
Article
Biology
Nazreen F. Hadjirin, Eric L. Miller, Gemma G. R. Murray, Phung L. K. Yen, Ho D. Phuc, Thomas M. Wileman, Juan Hernandez-Garcia, Susanna M. Williamson, Julian Parkhill, Duncan J. Maskell, Rui Zhou, Nahuel Fittipaldi, Marcelo Gottschalk, A. W. (Dan) Tucker, Ngo Thi Hoa, John J. Welch, Lucy A. Weinert
Summary: AMR poses a serious threat to human health and food security worldwide. This study focused on characterising AMR in Streptococcus suis in pigs, revealing differences in resistance levels between countries and the potential for resistance transmission between pigs and humans. Genomic data can be valuable in combating AMR.
Article
Genetics & Heredity
Gemma G. R. Murray, Andrew Balmer, Josephine Herbert, Nazreen W. Hadijirin, Caroline Kemp, Marta A. Matuszewska, Sebastian Bruchmann, A. S. Md. Mukarram P. Hossain, Marcelo Gottschalk, Alexander P. Tucker, Eric Miller, Lucy P. Weinert
Summary: Mutation rates vary greatly within and between bacterial species, and understanding the factors that drive this variation is crucial for understanding the evolutionary dynamics of bacterial populations. This study focused on investigating the impact of ecology and genome size on mutation rates, using Streptococcus suis as a model. The results showed that invasive disease isolates consistently had higher mutation rates compared to carriage isolates, regardless of their genome sizes, and displayed a bias towards G/C to A/T mutations, particularly in populations with smaller genomes and higher AT content. These findings suggest that ecology plays a stronger role in influencing mutation rates than genome size over certain timescales, and transitions to invasive disease are consistently associated with rapid increases in mutation rates, highlighting the importance of ecological factors in the adaptive potential of bacterial pathogens.
Article
Biology
Marta Matuszewska, Gemma G. R. Murray, Xiaoliang Ba, Rhiannon Wood, Mark A. Holmes, Lucy A. Weinert, Daniel J. Wilson
Summary: The transmission of MRSA from livestock to humans results in a faster adaptation to the human host than the loss of antibiotic resistance. Additionally, the stable inheritance of resistance-associated MGEs suggests that the impact of reducing antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to occur.
Article
Ecology
Ming-Shan Wang, Gemma G. R. Murray, Daniel Mann, Pamela Groves, Alisa O. Vershinina, Megan A. Supple, Joshua D. Kapp, Russell Corbett-Detig, Sarah E. Crump, Ian Stirling, Kristin L. Laidre, Michael Kunz, Love Dalen, Richard E. Green, Beth Shapiro
Summary: This study reveals a massive admixture event between polar bears and brown bears approximately 100,000 years ago, during a period of climate change-induced overlap in their ranges. The gene flow was largely unidirectional, with polar bear genes being incorporated into the genomes of brown bears. These findings highlight the complex reticulate paths that evolution can take within a regime of radically shifting climate.
NATURE ECOLOGY & EVOLUTION
(2022)
Editorial Material
Microbiology
Gemma G. R. Murray, Chrispin Chaguza
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Simen Fredriksen, Suzanne D. E. Ruijten, Gemma G. R. Murray, Maria Juanpere-Borras, Peter van Baarlen, Jos Boekhorst, Jerry M. Wells
Summary: Streptococcus suis can colonize the upper respiratory tract of healthy pigs but can also cause disease. This study compared the gene expression of pathogenic and commensal strains of S. suis and found that although there is genomic divergence, the transcriptomes remain conserved when grown in active porcine serum. However, key pathways showed variation in regulation and expression.
MICROBIAL GENOMICS
(2023)
Article
Multidisciplinary Sciences
Christopher Ruis, Aaron Weimann, Gerry Tonkin-Hill, Arun Prasad Pandurangan, Marta Matuszewska, Gemma G. R. Murray, Roger C. Levesque, Tom L. Blundell, R. Andres Floto, Julian Parkhill
Summary: The study reveals that mutagens and defects in DNA repair can generate context-specific mutational signatures in bacteria, similar to the findings in cancer cells. By reconstructing mutational spectra and analyzing bacterial lineages, the researchers identified mutational patterns associated with DNA repair defects and niche-specific mutagens. These mutational signatures were found to be influenced by both bacterial phylogeny and replication niche. The results suggest that mutational spectra can be used to infer transmission routes for bacterial pathogens.
NATURE COMMUNICATIONS
(2023)