Molecular Phylogeny of Microorganisms
"a pleasure to read" (Curr. Issues Mol. Biol.)
"very informative ... I would recommend this book" (Microbiology Today)
"outstanding book" (Intl. Microbiol.)
"I strongly recommend the book" (J Plant Physiol)
"comprehensive" (Fungal Diversity)
Caister Academic Press
Aharon Oren and R. Thane Papke
Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Israel and Department of Molecular and Cell Biology, University of Connecticut, USA (respectively)
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A proper understanding of the diversity, systematics and nomenclature of microbes is increasingly important in many branches of biological science. The molecular approach to phylogenetic analysis, pioneered by Carl Woese in the 1970s and leading to the three-domain model (Archaea, Bacteria, Eucarya), has revolutionized our thinking about evolution in the microbial world. The technological innovation of modern molecular biology and the rapid advancement in computational science have led to a flood of nucleic acid sequence information, bioinformatic tools and phylogenetic inference methods. Phylogenetic analysis has long played a central role in microbiology and the emerging fields of comparative genomics and phylogenomics require substantial knowledge and understanding of phylogenetic analysis and computational methods.
In this book, leading scientists from around the world explore current concepts in molecular phylogeny and their application with respect to microorganisms. The authors describe the different approaches applied today to elucidate the molecular phylogeny of prokaryotes (and eukaryotic protists) and review current phylogenetic methods, techniques and software tools. Topics covered include: a historical overview, computational tools, multilocus sequence analysis, 16S rRNA phylogenetic trees, rooting of the universal tree of life, applications of conserved indels, lateral gene transfer, endosymbiosis and the evolution of plastids.
This book is an ideal introduction to molecular phylogeny for all microbiologists and is an essential review of current concepts for experts in the field. A recommended text for all microbiology laboratories.
"describes very nicely the different approaches to apply molecular phylogeny, encountering the difficulties with the present phylogenomic species concept. This book ... addresses the most interesting issues in relation to molecular phylogeny ... Anyone, who is interested in microbial phylogeny, surely will enjoy reading this book. The hardcover, format and contents of the book make it a pleasure to read." from Curr. Issues Mol. Biol.
"This book provides a timely assessment of current concepts in the molecular phylogeny of microbes ... very informative both in defining the terms used by the authors, introducing each subject and also in providing good well-referenced reviews ... a mine of useful information and it gives some clear explanations of (to me) quite difficult concepts ... I would recommend this book to all microbiologists with an interest in molecular phylogeny." from Microbiology Today
"obligatory reading for all microbiologists to understand the essential concepts of microbial systematics and the present tree of live in our planet." from International Microbiology (2010) 13: 219-220
"I strongly recommend the book for the private book case of scientists ... and to the university libraries" from Journal of Plant Physiology
"a neat little hard back book with reasonable size print which is a comprehensive account of the molecular phylogeny in the Prokaryotes ... All bioscience students at ay level should read this book ... should be available in all university and public libraries" from Fungal Diversity (2010) 45: 345-356
Table of contents
1. Concepts About Phylogeny of Microorganisms: A Historical Overview
When at the end of the 19th century information began to accumulate about the diversity within the bacterial world, scientists started to include the bacteria in phylogenetic schemes to explain how life on Earth may have developed. Some of the early phylogenetic trees of the prokaryote world were morphology-based; others were based on the then-current ideas on the presumed conditions on our planet at the time that life first developed. Around 1950 many leading microbiologists had become pessimistic with respect to the possibility of ever reconstructing bacterial phylogeny. The concept of the prokaryote-eukaryote dichotomy did little to clarify phylogenetic relationships. The developing technology of nucleic acid sequencing, together with the recognition that sequences of building blocks in informational macromolecules (nucleic acids, proteins) can be used as 'molecular clocks' that contain historical information, led to the development of the three-domain model (Archaea - Bacteria - Eucarya) in the late 1970s, primarily based on small subunit ribosomal RNA sequence comparisons. The information currently accumulating from complete genome sequences of an ever increasing number of prokaryotes now once more will lead of modifications of our views on microbial phylogeny.
2. Methods and Programs for Calculation of Phylogenetic Relationships from Molecular Sequences
Jongsik Chun and Soon Gyu Hong
The purpose of phylogenetic analysis is to understand the past evolutionary path of organisms. Even though we will never know for certain the true phylogeny of any organism, phylogenetic analysis provides best assumptions, thereby providing a framework for various disciplines in microbiology. Due to the technological innovation of modern molecular biology and the rapid advancement in computational science, accurate inference of the phylogeny of a gene or organism seems possible in the near future. There has been a flood of nucleic acid sequence information, bioinformatic tools and phylogenetic inference methods in public domain databases, literature and worldwide web space. Phylogenetic analysis has long played a central role in basic microbiology, for example in taxonomy and ecology. In addition, more recently emerging fields of microbiology, including comparative genomics and phylogenomics, require substantial knowledge and understanding of phylogenetic analysis and computational skills to handle the large-scale data involved. In this chapter we will review major steps in phylogenetic analysis and introduce relevant computer software tools with respect to their accuracy, efficiency and availability.
3. Multilocus Sequence Analysis and Bacterial Species Phylogeny Estimation
This chapter presents a review of critical factors that have to be considered and evaluated in multilocus sequence analysis (MLSA) in order to make robust estimates of bacterial species phylogenies. The theoretical arguments in favor of the conditional data combination will be presented. I will briefly review criteria for marker selection, and will provide practical advice on the computational aspects, potential pitfalls, and software choices available for each step in a MLSA. For this purpose, a detailed case study using atpD, glnII, recA and rpoB sequences of symbiotic root nodule bacteria of the genus Bradyrhizobium will be presented. I will discuss and illustrate the use of phylogenetic congruence analysis, and a strategy to evaluate the additivity of the phylogenetic signals in the different partitions. The importance of using multiple isolates per species/lineage, proper model selection and thorough tree searches to get a good estimate of a multispecies phylogeny will be emphasized. Maximum likelihood and Bayesian phylogeny estimation using supermatrices are thoroughly discussed and critically compared with the new, concatenation-independent, Bayesian Estimation of Species Trees (BEST) algorithm, which is based on the multispecies coalescent.
4. Molecular Phylogeny of Microorganisms: Is rRNA Still a Useful Marker?
The introduction of comparative rRNA sequence analysis certainly represents a major milestone in the history of microbiology. The current taxonomy of prokaryotes as well as modern probe and chip based identification methods are mainly based upon rRNA derived phylogenetic conclusions. The significance of single gene based phylogenetic inference was evaluated by including alternative global markers such as elongation and initiation factors, RNA polymerase subunits, DNA gyrases, heat shock and recA proteins. Although the comparative analyses are hampered by the generally low phylogenetic information content, and different resolution power, and multiple copies of the individual markers, the domain and prokaryotic phyla concept is globally supported.
5. The Phyla of Prokaryotes, Cultured and Uncultured
There is no official classification of prokaryotes. For the higher taxa there even is no official nomenclature: the rules of the International Code of Nomenclature of Prokaryotes do not cover taxa above the rank of class. The most commonly accepted division of the prokaryotes in two "subkingdoms" or "domains" (Bacteria and Archaea) and the classification of their species with validly published names in respectively 27 and 2 "phyla" or "divisions" (as of November 2009) is primarily based on 16S rRNA sequence comparisons. This type of classification was adopted in the latest edition of Bergey's Manual of Systematic Bacteriology. Alternative classifications have been proposed as well, based e.g. on the structure of the cell wall. Some 16S rRNA sequence-based phyla unite prokaryotes of similar physiological properties (for example Cyanobacteria, Chlorobi, Thermotogae); others (Euryarchaeota, Proteobacteria, Flavobacteria) contain organisms with highly disparate lifestyles. Some phyla based on deep 16S rRNA lineages are currently represented by one or a few species only. Environmental genomics/metagenomics approaches suggest existence of many more phyla based on the deep lineages of 16S rRNA gene sequences recovered. To obtain the organisms harboring these sequences and to study their properties is a major challenge of microbiology today.
6. Rooting the Tree of Life
Defining the evolutionary relationships between groups of organisms is a major part of modern-day microbiology. With the continuing dramatic increase in the availability of genomic data, these techniques have been extended to describing an all-encompassing "tree of life". However, identifying the location of the root of this tree corresponding to the most recent common ancestor is a challenging and distinct problem that has yet to be solved. To date, many investigations have proposed various roots, using a wide diversity of biological data and techniques. A survey of the most promising of these models illustrates the difficulty faced in reaching a scientific consensus on the issue, as well as the additional philosophical complications posed by our emerging understanding of the role of horizontal gene transfer in genome evolution.
7. Applications of Conserved Indels for Understanding Microbial Phylogeny
Radhey S. Gupta
Comparative analysis of genome sequences is leading to discovery of large numbers of novel molecular markers that are proving very helpful in understanding many important aspects of microbial phylogeny. Of these molecular markers, the conserved inserts or deletions (indels) in protein sequences provide particularly useful means for identifying different groups of microbes in clear molecular terms and for understanding how they have branched off from a common ancestor. This chapter provides an overview of the utility of conserved indels and other novel molecular markers (viz. lineage-specific proteins) for understanding microbial phylogeny at different phylogenetic depths with specific examples. Genetic and biochemical studies of these markers should also lead to identification of novel properties that are unique to different groups of microbes.
8. Construction and Deconstruction: Influence of Lateral Gene Transfer on the Evolution of the Tree of Life
Efforts to construct the tree of life take their conceptual motivation from Charles Darwin's theory of evolution. Until the advent of molecular biology, however, a universal tree of life was well beyond the scope of the data and methods of traditional organismal phylogeny. The rapid development of these methods and bodies of genetic sequence from the 1970s onwards resulted in major reclassifications of life and revived ambitions to represent all organismal lineages by one true tree of life. Subsequent realization of the significance of lateral gene transfer and other non-vertical processes has subtly reconceptualized and reoriented attempts to construct this universal phylogeny. This chapter sets out these shifts of construction, deconstruction and reconstruction, with an eye towards understanding the future of the tree of life.
9. Horizontal Gene Transfer and the Formation of Groups of Microorganisms
David Williams, Cheryl P. Andam and J. Peter Gogarten
In this chapter, we discuss the impact of gene transfer on the formation of groups of organisms. We begin by discussing the obvious: gene transfer can make it more difficult to define and determine relationships. In those cases where many genes have been transferred between preferred partners, the majority of genes in a genome may reflect gene acquisition, and as a consequence, if a coherent signal is detected, one nevertheless might not be sure that the signal is due to organismal shared ancestry. In the second part of this chapter we will focus on two positive aspects of gene transfer. The presence of a particular transferred gene was shown, in several cases, to constitute a shared derived character useful in classification. Gene transfer can put together new metabolic pathways that open up new ecological niches, and consequently, the transfer of an adaptive gene might create a new group of organisms.
10. Endosymbiosis and the Evolution of Plastids
Christopher E. Lane and Dion G. Durnford
Photosynthesis is one of the most successful energy production strategies on the planet and has been co-opted numerous times throughout evolutionary history via the uptake and retention of photosynthetic cells by non-photosynthetic eukaryotic heterotrophs. Whereas the result of this process is clear, what is not settled is the mode and tempo of plastid movement among eukaryotes, particularly plastids of red algal derivation. Recent changes in our understanding of the relationships between eukaryotic supergroups have only served to complicate the picture further. In this chapter we summarize current information on the evolution of plastids with a particular focus on relationships among photosynthetic eukaryotes, the process of endosymbiogenesis and the variation in ways plastids have been modified to suit the light harvesting needs of their hosts. The understanding of all of these factors is an active field of continued research that will undoubtedly lead to further discoveries in the coming years.
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(EAN: 9781904455677 9781912530724 Subjects: [bacteriology] [microbiology] [molecular microbiology] [genomics] [bioinformatics] [molecular biology] )