Read Ebook {PDF EPUB} Microbial Phylogeny and Evolution Concepts and Controversies by Jan Sapp Jan Sapp (editor) Jan Sapp opens with a history of the study of microbes, which he divides into four eras: germ theory, molecular genetics, molecular phylogenetics based on small subunit ribosomal DNA, and analyses based on full bacterial genomes. Norman Pace covers the large scale structure of the Tree of Life and the division into Bacteria, Archaea, and Eucarya. And Wolfgang Ludwig and Karl-Heinz Schleifer focus on the phylogeny of the bacteria: phyla and many subgroups are well supported, though their relationships are not. Two papers — W. Ford Doolittle's "If the Tree of Life Fell, Would We Recognize the Sound?" and William Martin's "Woe is the Tree of Life" — argue for a dominant role for horizontal gene transfer (HGT). Most of the other papers attribute much less weight to HGT, but Kurland's "Paradigm Lost" is a vehement attack on claims for its ubiquity and consequences. Carl Woese argues that HGT dominated only very early on, and that a kind of annealing happened as replication systems improved and passed through a "Darwinian threshold"; the earliest evolution involved cells rather than genomes. Radhey Gupta suggests that approaches to phylogeny using distinctive insertions and deletions (indels) produce robust trees and evidence for a stable core of genes and proteins that is minimally affected by factors such as HGT. He also argues that the eukaryotic cell evolved from symbiosis between a gram-negative bacterium and an Archaea, in an aerobic environment dominated by antibiotic-producing organisms. James Lake et al. argue for eukaryotic origins from a symbiosis between something like a purple sulfur bacteria and an eocyte, linked by hydrogen and sulfur metabolism. They suggest HGT is widespread and significant, but not so much so as to prevent construction of a meaningful Tree of Life. Some endosymbiotic events are less controversial. The origin of mitochondria as alpha-proteobacteria is now accepted, but Michael Gray considers further questions about their evolution. And John Archibald and Patrick Keeling give an account of the origin and evolution of plastids, with one primary endosymbiotic event followed by multiple secondary and even tertiary endosymbioses. Hannah Melnitsky, Frederick Rainey and Lynn Margulis present a karyomastigont model for the origin of eukaryotes, involving symbiosis between a Thermoplasma -like archaebacteria and a spirochete, and compare it to alternatives. And Michael Dolan looks at the origin of the microtubule cytoskeleton and the relationship of tubulin to the prokaryotic protein FtsZ. A couple of papers are peripheral to the central debates. Harold Morowitz and others offer a biochemists' perspective on evolution, finding robust patterns in intermediate metabolism and arguing for a phenotype-first approach. And John Werren looks at how vertically transmitted parasites can influence host reproduction, focusing on the bacteria Wolbachia , which manipulates eukaryote hosts through cytoplasmic incompatibility and sex- ratio control. All up Microbial Phylogeny and Evolution is a fascinating collection, covering some of the most exciting topics in the history of life. Jan Sapp. Jan Anthony Sapp (born June 12, 1954) is a Canadian historian of biology at York University, Canada. [1] His writings focus especially on evolutionary biology beyond the traditional neo-Darwinian framework, and emphasize the fundamental importance of symbiosis and horizontal gene transfer in heredity and evolution. He is also known for his writing on the coral reef crisis, focusing in detail on the outbreaks of crown of thorns starfish and coral bleaching. [2] Contents. Career 1 Bibliography 2 Recent publications 3 References 4 External links 5. Career. Sapp was born in Halifax, Nova Scotia. He completed his BSc hons (Biology) at Dalhousie University in 1976 before earning his MSc and Phd at the Institut d’histoire et de sociopolitique des sciences, at L'Université de Montréal in 1984. [3] [4] He subsequently held an appointment at the University of Melbourne for eight years, where he also served as chair of the Department of History and Philosophy of Science. [4] He was Andrew Mellon Fellow at the Rockefeller University, 1991-92. [4] He held the Canada Research Chair (tier 1) in the History of the Biological Sciences at l’Université du Québec à Montréal from 2001-2003 [5] before returning to York University where he has been a professor since 1992. Bibliography. Sapp, Jan (2009). The New Foundations of Evolution: On the Tree of Life . Oxford ; New York: Oxford University Press. [6] Microbial Phylogeny and Evolution: Concepts and Controversies . Jan Sapp (ed.). Oxford University Press, USA. 2005. Sapp, Jan (2003). Genesis: The Evolution of Biology . Oxford: New York : Oxford University Press. Sapp, Jan (1999). What is Natural? : Coral Reef Crisis . New York: Oxford University Press. Sapp, Jan (1994). Evolution by Association: A History of Symbiosis . New York: Oxford University Press. Sapp, Jan (1990). Where the Truth Lies: Franz Moewus and the Origins of Molecular Biology . Cambridge [England] ; New York: Cambridge University Press. Sapp, Jan (1987). Beyond the Gene: Cytoplasmic Inheritance and the Struggle for Authority in Genetics . Monographs on the history and philosophy of biology. New York: Oxford University Press. Recent publications. Gilbert, S. F.; Sapp, J.; Tauber, A. I. (2012). "A symbiotic view of life: We have never been individuals". The Quarterly review of biology 87 (4): 325–341. Sapp, Jan (April 2012). "Race Finished". American Scientist 100 (2). p. 164. Sapp, Jan (2012). "Evolution Replayed". BioScience 62 (7): 693–694. Sapp, Jan (2012-10-22). "Too Fantastic for Polite Society". In Dorion Sagan (ed.). Lynn Margulis: the life and legacy of a scientific rebel (1 ed.). Vermont: Chelsea Green Publishing. pp. 54–67. Sapp, Jan (2012). "Horizontal Gene Transfer and the Tree of Life". In Joseph Seckbach (ed.). Genesis - In The Beginning . Cellular Origin, Life in Extreme Habitats and Astrobiology 22 . Dordrecht: Springer Netherlands. pp. 743–755. Sapp, Jan (2011). "Lamarckian Leaps in the Microbial World". In Snait Gissis and Eva Jablonka (ed.). Transformations of Lamarckism: from subtle fluids to molecular biology . Cambridge, Mass.: MIT Press. pp. 271–283. Sapp, J. (2010). "On the Origin of Symbiosis". In Joseph Seckbach and Martin Grube (ed.). Symbioses and Stress . Cellular Origin, Life in Extreme Habitats and Astrobiology 17 . Dordrecht: Springer Netherlands. pp. 3‒18. Sapp, J. (2010). "Saltational symbiosis". Theory in Biosciences 129 (2–3): 125–133. References. ^ "Jan Sapp". York University: Graduate Program in Biology . Retrieved 2013-02-14 . ^ Verner, Brent. "What Is Natural?: Jan Sapp". Oxford University Press . Retrieved 2013-02-14 . ^ Ailie Smith; Ann McCarthy (2010-07-27). "Provenance: Dr Jan Anthony Sapp". The University of Melbourne - Guide to the Records of Dr Jan Sapp Regarding the Briggs Affair . Retrieved 2013-02-14 . ^ a b c Symbioses and Stress: Joint Ventures in Biology . Joseph Seckbach (ed.). Springer. 2010-01-01. ^ Sévigny, Judith; Claire Deschênes; Monique Frize; Safaa Mohamed (2003-03-07). "Canada Research Chairs Compilation". Ottawa, Canada: Canada Research Chairs Secretariat. p. 36. ^ Byrnes, W. Malcolm (January–February 2010). by Jan Sapp" The New Foundations of Evolution "Review: . American Scientist . External links. Biography pages at York University: Department of Biology. WorldCat VIAF: 2547085 LCCN: n86088524. All articles with unsourced statements Articles with unsourced statements from February 2013 WorldHeritage articles with VIAF identifiers WorldHeritage articles with LCCN identifiers VIAF not on Wikidata 1954 births Canada Research Chairs Historians of science Living people York University faculty All stub articles Canadian scientist stubs Canadian historian stubs History of science stubs Geneticist and evolutionary biologist stubs. Help improve this article. About Us Privacy Policy Contact Us. Copyright © World Library Foundation. All rights reserved. eBooks from Project Gutenberg are sponsored by the World Library Foundation, a 501c(4) Member's Support Non-Profit Organization, and is NOT affiliated with any governmental agency or department. Microbial Phylogeny and Evolution: Concepts and Controversies. I remember finding the Science magazine with the illustrations from the Haemophilus influenzae genome paper on the cover ( Fleischmann et al., 1995) in the library during my undergraduate project work. It was an exciting time: in the molecular evolution class we had learned that most questions and controversies regarding microbial evolution and phylogeny could be answered, if only we had enough sequence data. A little over 10 years have passed since this first complete bacterial genome was published, and what have we learned in that time? This is where Microbial Phylogeny and Evolution: Concepts and Controversies tries to fit in. It is apparent that the main focus is on controversies: the book is heavily biased towards areas of dispute. About half of the chapters are devoted to lateral gene transfer and the possibility of a true phylogeny for microbes, and the other half are about the origin of eukaryotes and their organelles and the role of symbioses in the process. As a consequence, there is a lack of coverage of many new insights from microbial genomics. For example, the concept of gene loss in intracellular parasites and symbionts ( Ochman and Moran, 2001) is completely absent from the book. Although this approach limits the book's value as an overview of the fields of microbial evolution and phylogeny, it leaves plenty of space for detailed discussions of a few of the controversial issues. In the introductory chapter, “The Bacterium's Place in Nature,” the editor puts microbial phylogeny and evolution into a historical context. A lot of thought has indeed been devoted to these subjects since the rise of microbiology in the second part of the 19th century, and for me it was refreshing to read about the various ideas on bacterial phylogeny that have been entertained in the past. The remaining 14 chapters in the book are devoted to current knowledge and hypotheses; and just by reading the table of contents it is evident that the editor successfully has compiled a set of coauthors that guarantee that the focus is on controversial issues. This is both a strength and a weakness: some issues are well covered, with the different viewpoints represented, whereas other issues falsely may appear as established as they are represented by only one viewpoint. A large part of the book is devoted to discussions about the occurrence of genetic exchange between distantly related microbial organisms, an evolutionary phenomenon known as lateral (or horizontal) gene transfer (LGT or HGT). This has been a hot topic ever since sequence data from completed prokaryotic genome projects accumulated in the late 1990s, when it became obvious that phylogenies based on different genes in the genomes give contradictory results. Although all researchers agree that gene transfers do occur during microbial evolution, the frequency of occurrence and the impact on the possibility of reconstructing a universal tree are a matter of vigorous debate. At the end of the last decade, Ford Doolittle challenged the field by asking what the meaning of a universal tree would be if genetic material is constantly exchanged between its branches ( Doolittle, 1999). Much of the writing about gene transfer since then has focused either on defending or attacking this view (for example, Gogarten et al., 2002; Kurland et al., 2003). This debate is well documented in the book, with many of the key individuals represented in the author list, and different extreme views are presented in the various chapters. As a consequence, it is difficult to get a balanced view of the various roles of LGT in microbial phylogeny and evolution by reading the different chapters. Fortunately, LGT is an area of intensive ongoing research. Two recent reports indicate that a subset of genes in the genomes is maintained and inherited vertically, whereas a different set of genes is transmitted between genomes via gene transfers, which creates the large genetic diversity observed in prokaryotes ( Beiko et al., 2005; Lerat et al., 2005). These results suggest that a universal tree based on genomic data indeed is possible, in principle. However, it remains to be seen whether the number of genes that can be identified as vertically inherited is large enough to create a phylogenetic signal with sufficient historical information to be robust against phylogenetic artefacts. An early attempt to take advantage of the availability of complete genome data to create a universal tree identified only 14 genes that are useful for phylogenetic purposes among the 45 genomes that were analyzed ( Brown et al., 2001); and the number of such genes is expected to decrease with the number of included taxa. Sadly, efforts like these to recreate microbial phylogeny based on information from whole genomes are not well covered in the book. This is also a controversial subject in microbial phylogeny, and it would have been appropriate to have included a few chapters discussing the various approaches (see Snel et al., 2005, for a recent review). Instead we get several chapters dealing with the universal tree based on phylogenies of single genes, such as the small subunit ribosomal RNA and other components of the translational machinery, despite the fact that most of the workers in this field have given up on such approaches. The identification of LGT as a mechanism in microbial genome evolution has rationalized many previously unexplained observations. For example, virulence traits, metabolic properties, and the spread of antibiotic resistance have been assigned to gene transfer events ( Ochman et al., 2000); and in an ambitious effort, Boucher and coworkers showed that LGT probably has played a major role in the evolution of many phenotypic traits in prokaryotes, such as photosynthesis, nitrogen fixation, and sulfate reduction ( Boucher et al., 2003). As a researcher working on the role of LGT in the diversification process of microbes, I would have appreciated some coverage of these aspects in the book, in addition to the impact of the phenomenon on the possibility of a true microbial phylogeny. After all, a universal tree of life relating all organisms appears meaningless if it is not used to understand the evolutionary process behind the biological diversity observed in the microbial world. The remainder of the book is mostly devoted to symbiosis and its role in the origin of eukaryotes and eukaryotic organelles. Two well-balanced and informative chapters that review the current understanding of the origin of mitochondria and plastids are included, which is refreshing after the opinionated and often data-poor chapters on phylogeny and gene transfer. We also get several chapters dealing with the origin of the eukaryotic cell itself, a topic at least as controversial as the role of gene transfer in microbial evolution. The familiar hypotheses are offered one by one: the genetic annealing model is presented by Woese, Martin promotes his hydrogen hypothesis, Gupta maintains that the eukaryotes arose from a long- term symbiosis between a gram-negative eubacterium and an archaeon, Lake and coworkers take their chance to market their eocyte model for the origin of eukaryotes, and Melnitsky, Rainey, and Margulis argue that their karyomastigont model explains more known facts than any other alternative. These theories have been presented elsewhere, and the authors present little new data here to support their own hypothesis. However, the origin of eukaryotes remains a central unanswered question in biology, and it is really nice to have these alternative hypotheses compiled in a single book. It is interesting, although somewhat disappointing, to see that these competing theories are able to coexist in the presence of a huge amount of genome data. The reason, I would say, is that each hypothesis is designed to explain its own set of observations, and that the number of unexplained similarities and differences between prokaryotes and eukaryotes remains large. Hopefully, comparative genomics in combination with cell biology will identify which of these observations are informative about the origin of eukaryotes, and which may be explained by other means. For example, such studies have shown that the ancestor of all eukaryotes already had mitochondria ( Embley et al., 2003), a piece of knowledge that has to be taken into account by any theory of the origin of eukaryotes. If you are interested in learning about the available competing hypotheses for the origin of eukaryotes, then this book is definitely for you. I would also recommend it to anyone who would like to have the debate over the influence of LGT on microbial phylogeny nicely compiled into a single source, with the cautionary note that you should not expect to get any up-to-date review of the knowledge of phylogeny, or any deeper understanding of the mechanisms and biological consequences of gene transfer events. However, this is definitely not a book to pick up to check what a decade of microbial genomics has contributed to science. In fact, if it is read with this intention, it could lead to the false impression that we molecular evolutionists have spent a decade just arguing over controversial issues, resulting in minimal advancement in science! Nevertheless, Microbial Phylogeny and Evolution: Concepts and Controversies is a fascinating read if you are interested in how science proceeds and how the process is influenced by the personalities of the key individuals in the field.