
Phylogenomics
Foundations, Methods, and Pathogen Analysis
- 1st Edition - May 17, 2024
- Imprint: Academic Press
- Editors: Igor Mokrousov, Egor Shitikov
- Language: English
- Paperback ISBN:9 7 8 - 0 - 3 2 3 - 9 9 8 8 6 - 4
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 9 1 3 0 9 - 6
Phylogenomics: Foundations, Methods, and Pathogen Analysis offers a deep overview of phylogenomics as a field, compelling recent developments, and detailed methods and approache… Read more

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Request a sales quotePhylogenomics: Foundations, Methods, and Pathogen Analysis offers a deep overview of phylogenomics as a field, compelling recent developments, and detailed methods and approaches for conducting new research. Early chapters introduce phylogenomic analysis of viruses and bacteria, deciphering bacterial outbreaks, and evolution of drug resistance and virulence, with a second section on methods offering instruction in tools for SNP calling and dealing with big datasets, use of Bayesian approach in molecular epidemiology, bacterial evolution modeling and evolutionary reconstruction in the presence of mosaic sequences. Part 3 offers various examples of phylogenomic analysis across medically significant bacteria and viruses, including Yersinia pestis, Salmonella, Mycobacterium tuberculosis, HIV-1, measles virus as well as ancient pathogens research.
- Offers a full overview of phylogenetics and phylogenomics, from its foundations to methods and specialized case studies
- Presents methodologies and algorithms for phylogenomic research studies and analyzes medically significant microorganisms
- Considers examples of phylogenomic analysis across a range of medically significant pathogens
- Includes chapter contributions from leading international experts
- Cover image
- Title page
- Table of Contents
- Copyright
- List of contributors
- Preface
- Part I: General topics and foundations
- Chapter 1. Phylogenomic analysis and the origin and early evolution of viruses
- Abstract
- 1.1 Introduction
- 1.2 Retrodiction
- 1.3 The analytical basis of the phylogenetic framework
- 1.4 Rooting trees
- 1.5 Phylogenomic analysis
- 1.6 Deep evolutionary explorations with alignment-free methods
- 1.7 Untangling the origin and evolution of viruses with structural phylogenomics
- 1.8 Conclusions
- Acknowledgments
- References
- Chapter 2. Application of next-generation sequencing for genetic and phenotypic studies of bacteria
- Abstract
- 2.1 Introduction
- 2.2 Whole genome sequence data
- 2.3 Reference genomes
- 2.4 Pangenome, core genome, and accessory genome
- 2.5 Principles of genotypic classification
- 2.6 Species classification and identification using whole genome sequencing data
- 2.7 Genotyping based on whole genome sequencing data
- 2.8 Genotyping and control of infectious diseases
- 2.9 Genotyping and human genetics of infectious diseases
- 2.10 Conclusion
- References
- Chapter 3. Genomic insights into deciphering bacterial outbreaks
- Abstract
- 3.1 Introduction
- 3.2 Genomes and variation
- 3.3 Sequencing whole genomes
- 3.4 Outbreak delimitation
- 3.5 Forensic analysis of outbreaks and transmissions
- 3.6 Conclusion
- References
- Chapter 4. Drug resistance in bacteria, molecular mechanisms, and evolution
- Abstract
- 4.1 Introduction
- 4.2 What are antibiotics
- 4.3 Mechanisms of bacterial resistance to antibiotics
- 4.4 Evolution of antibiotic resistance
- 4.5 Classes of antibiotics, mechanisms of action and resistance
- 4.6 Disruptors of cell envelope
- 4.7 Other antibiotics
- 4.8 Origin and evolution of bacterial resistance
- 4.9 Newer approaches to deal with antimicrobial resistance
- 4.10 Conclusions
- Acknowledgments
- References
- Chapter 5. Virulence evolution of bacterial species
- Abstract
- 5.1 Introduction
- 5.2 What is virulence?
- 5.3 Models for the evolution of virulence
- 5.4 Molecular infection biology
- 5.5 Virulence factors and mechanisms in Gram-negative pathogens
- 5.6 Virulence factors and mechanisms in Gram-positive bacteria
- 5.7 Acid-fast bacteria
- 5.8 Final remarks
- References
- Part II: Methods in the phylogenomics
- Chapter 6. Modeling evolutionary changes of k-mer patterns of bacterial genomes
- Abstract
- 6.1 Introduction
- 6.2 Estimation of evolutionary distances by comparison of k-mer patterns
- 6.3 Driving forces on the k-mer pattern evolution
- 6.4 Using graph models in investigation of k-mer pattern evolution
- 6.5 Conclusion
- References
- Chapter 7. Clock rates and Bayesian evaluation of temporal signal
- Abstract
- 7.1 Introduction
- 7.2 TMRCAs and mutation rate
- 7.3 Tip-dating and tip randomization
- 7.4 Population changes through time
- 7.5 Case study: Is there a molecular clock in Mycobacterium tuberculosis?
- 7.6 Models limits and sensitivity
- 7.7 Fluctuating mutation rates
- 7.8 The rise of fine-tuned phyloepidemiology models
- 7.9 Conclusion and perspectives
- Acknowledgments
- References
- Chapter 8. Microbial evolutionary reconstruction in the presence of mosaic sequences
- Abstract
- 8.1 Introduction
- 8.2 Biological processes giving rise to viral and bacterial mosaic sequences
- 8.3 Mosaic sequence and structure detection methods
- 8.4 Potential impacts of mixed evolutionary signals on traditional phylogenetic reconstruction
- 8.5 Tree-based approaches to dealing with mosaic sequences and mixed evolutionary signals
- 8.6 Network-based approaches to reconstructing an entangled evolutionary history
- 8.7 Final remarks
- Acknowledgments
- References
- Chapter 9. Tools for short variant calling and the way to deal with big datasets
- Abstract
- 9.1 Introduction
- 9.2 Types of whole genome sequencing data
- 9.3 Pretreatment of data
- 9.4 Calling of short variants
- 9.5 Postprocessing of variants
- 9.6 Large datasets and computational solutions to deal with them
- 9.7 All-in-one pipelines
- 9.8 Conclusion
- Funding
- Acknowledgments
- References
- Part III: Phylogenomics of specific pathogens
- Chapter 10. Phylogenomics of Yersinia pestis
- Abstract
- 10.1 Introduction
- 10.2 Phylogeny and geographic distribution of extant Yersinia pestis populations
- 10.3 Origin and transmission pattern of three historic pandemics
- 10.4 Characters of evolutionary dynamics
- 10.5 Conclusions
- References
- Chapter 11. Salmonella phylogenomics
- Abstract
- 11.1 Introduction
- 11.2 Materials and methods
- 11.3 Results
- 11.4 Discussion
- References
- Chapter 12. The phylogenomics of Shigella spp.
- Abstract
- 12.1 Shigella and shigellosis
- 12.2 The evolution of Shigella from Escherichia coli
- 12.3 The phylogenomics of individual Shigella spp
- 12.4 Interactions with the accessory genome
- 12.5 Outlook for Shigella phylogenomics
- References
- Chapter 13. Phylogenomic diversity within Corynebacterium diphtheriae, a reemerging threat to global public health
- Abstract
- 13.1 Introduction
- 13.2 Biochemical characteristics
- 13.3 Global epidemiology
- 13.4 Phylogenomic diversity
- 13.5 Corynephages and tox gene diversity
- 13.6 Other virulence genes
- 13.7 Antibiotic resistance
- 13.8 Conclusion
- References
- Chapter 14. Phylogenomics of the East Asian lineage of Mycobacterium tuberculosis
- Abstract
- 14.1 Introduction
- 14.2 An overview of L2 genotyping methods
- 14.3 Single nucleotide polymorphism-based L2 population structure
- 14.4 Genomic features of L2 at the level of regions of differences and IS6110
- 14.5 Concluding considerations
- Acknowledgments
- References
- Chapter 15. Population genomics of Mycobacterium kansasii
- Abstract
- 15.1 Background
- 15.2 Taxonomy and genomic diversity of Mycobacterium kansasii complex
- 15.3 Recombination driving speciation and diversification of the Mycobacterium kansasii complex
- 15.4 Genetic evidence of environmental source of clinical infections
- 15.5 Genes potentially contributing to the success of Mycobacterium kansasii
- 15.6 Within host adaptive evolution of Mycobacterium kansasii
- 15.7 Summary
- References
- Chapter 16. Taxonomy and phylogenomics of Leptospira
- Abstract
- 16.1 Taxonomy/phylogeny
- 16.2 Genome architecture and gene repertoire
- 16.3 General features
- 16.4 Gene repertoire across Leptospira species
- 16.5 Concluding remarks
- References
- Chapter 17. Phylogenomics and evolution of measles virus
- Abstract
- 17.1 Measles virus as a reemerging threat
- 17.2 Current status
- 17.3 Genome organization
- 17.4 Understanding phylogenomic diversity and evolution of MeV: data-led approach
- 17.5 Data sources for MeV: MeaNS, GenBank, UniProt, genome, PDB, IEDB
- 17.6 Analytical approaches: data to knowledge
- 17.7 Data curation and binning
- 17.8 Multiple sequence alignment
- 17.9 Named strain mapping
- 17.10 Recombination detection
- 17.11 Phylogenetic inference
- 17.12 Estimation of nucleotide substitution rate
- 17.13 Population stratification
- 17.14 Selection pressure
- 17.15 Genotype–phenotype correlation
- 17.16 Knowledge to translation
- Acknowledgments
- References
- Chapter 18. Phylogenomics of human immunodeficiency virus type 1 (HIV-1)
- Abstract
- 18.1 Introduction
- 18.2 Laboratory and analytical methods for genotyping human immunodeficiency virus type 1
- 18.3 Application of human immunodeficiency virus type 1 genotyping to clinical and phylogenomic investigations
- 18.4 Conclusions
- References
- Chapter 19. Respiratory syncytial viruses
- Abstract
- Abbreviations
- 19.1 Introduction
- 19.2 Respiratory syncytial virus phylogeny
- 19.3 Phylodynamics of the respiratory syncytial virus fusion protein
- 19.4 Selective pressure in the respiratory syncytial virus F gene/protein
- 19.5 Relationships among antigen, conformational epitope, and reinfection in the respiratory syncytial virus F protein
- 19.6 Perspective
- Acknowledgments
- Data availability statement
- Conflicts of interest
- References
- Chapter 20. The phylogenomics of flaviviruses
- Abstract
- 20.1 Introduction
- 20.2 Dengue virus
- 20.3 Zika virus
- 20.4 West Nile virus
- 20.5 Japanese encephalitis virus
- 20.6 Yellow fever virus
- 20.7 Tick-borne encephalitis virus
- References
- Chapter 21. How clonal is Staphylococcus aureus?
- Abstract
- 21.1 Introduction
- 21.2 Why is the concept of clonality so relevant?
- 21.3 What are the specificities of the predominant clonal evolution* model?
- 21.4 Staphylococcus aureus and the predominant clonal evolution model
- 21.5 Concluding remarks
- Acknowledgments
- Glossary of specialized terms and abbreviations
- References
- Chapter 22. Genomic research of ancient pathogens in Central Asia
- Abstract
- 22.1 Introduction
- 22.2 Methodological aspects of ancient DNA studies
- 22.3 Studies of ancient pathogens circulating in Central Asia
- 22.4 Studies of ancient pathogens circulating in Central Asia
- 22.5 Conclusions
- Acknowledgments
- References
- Chapter 23. Subspecific nomenclature of the Cryptococcus neoformans/gattii complex and the predominant clonal evolution model
- Abstract
- 23.1 Introduction
- 23.2 Clonality and population structure in the Cryptococcus neoformans/gattii complex
- 23.3 Cryptococcus neoformans/gattii complex and the predominant clonal evolution model
- 23.4 Widespread multilocus genotypes
- 23.5 Linkage disequilibrium
- 23.6 Widespread genetic clustering (near-clades*)
- 23.7 Russian doll patterns
- 23.8 Species concept, nomenclature, and the Cryptococcus neoformans/gattii complex near-clades
- 23.9 Conclusion: the Cryptococcus neoformans/gattii complex: a paradigmatic predominant clonal evolution case
- 23.10 “Evolutionary twins” can artefactually appear as different merely due to different scientific traditions
- Glossary of specialized terms and abbreviations
- References
- Chapter 24. Phylogenomics of Mycobacterium leprae
- Abstract
- 24.1 Introduction
- 24.2 Application of whole-genome sequencing for bacterial phylogeny
- 24.3 Genomics of Mycobacterium leprae
- 24.4 Phylogenomics and strain diversity of Mycobacterium leprae
- 24.5 Mycobacterium lepromatosis: newly discovered leprosy pathogen
- 24.6 Reservoirs of Mycobacterium leprae and Mycobacterium lepromatosis
- 24.7 Conclusion
- Acknowledgments
- References
- Index
- Edition: 1
- Published: May 17, 2024
- Imprint: Academic Press
- No. of pages: 612
- Language: English
- Paperback ISBN: 9780323998864
- eBook ISBN: 9780323913096
IM
Igor Mokrousov
ES