Molecular Systematics Of Plants Ii: DNA Sequencing

Book Description

In the five years since the publication of Molecular Systematics of Plants, the field of molecular systematics has advanced at an astonishing pace. This period has been marked by a volume of new empirical data and advances in theoretical and analytical issues related to DNA. Comparative DNA sequencing, facilitated by the amplification of DNA via the polymerase chain reaction (PCR), has become the tool of choice for molecular systematics. As a result, large portions of the Molecular Systematics of Plants have become outdated.
Molecular Systematics of Plants II summarizes these recent achievements in plant molecular systematics. Like its predecessor, this completely revised work illustrates the potential of DNA markers for addressing a wide variety of phylogenetic and evolutionary questions. The volume provides guidance in choosing appropriate techniques, as well as appropriate genes for sequencing, for given levels of systematic inquiry. More than a review of techniques and previous work, Molecular Systematics of Plants II provides a stimulus for developing future research in this rapidly evolving field.
Molecular Systematics of Plants II is not only written for systematists (faculty, graduate students, and researchers), but also for evolutionary biologists, botanists, and paleobotanists interested in reviewing current theory and practice in plant molecular systematics.

Customer Reviews:

Review from the Journal of Botony.......2002-08-06

"The success of Molecular Systematics of Plants, which is the precursor of this volume, is indicated by the fact that my paperback copy has recently split down the spine after seven years of hard consultation...Molecular Systematics of Plants II, although having the same editors and a similar title, is emphatically not a second edition. It is a completley different book, surveying the extraordinary developments in plant molecular systematics during the 1990's which have been based upon comparative DNA sequencing...The editors and authors deserve congratulations for the excellence of this book...I suspect the chapters in this book will provide the backbone of the burgeoning discipline of molecular systematics for the next few year."
- by R.T. Pennington

State of the art.......2001-07-30

Compiled by top practioners in the field, this is the reference to have for those engaged in sequencing DNA in the modern plant taxonomy lab.

For those not engaged in sequencing DNA this is a good book not to have.

A essential Book.......2000-12-17

The book of Pamela Soltis and collaborators is essential to who wishes to know more concerning about of Systematic Filogenetic Vegetable. In the plants, the filogenetics processes are based on molecular data, due the difficulties of work just basing itself on morphology. Complementing the first edition, this book becomes indispensable to all the studious of Botanical Systematics.

Plant Symantics: A Phylogenetic Approach

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Second edition
PHYLOGENY AND NIRVANA
A essential book
a college text
On modern plant taxonomy

Plant Symantics: A Phylogenetic Approach
Walter S. Judd
Manufacturer: Sinauer
ProductGroup: Book
Binding: Hardcover

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ASIN: 0878934030

Book Description

Plant Systematics: A Phylogenetic Approach, Second Edition is an introductory text that incorporates phylogenetic principles and methods throughout—from the careful explanation of phylogenetic methods and principles in the initial two chapters to the taxonomic survey of vascular plant families in the last two chapters.

Orders and families are recircumscribed to represent monophyletic groups, largely following the most recent classification of the Angiosperm Phylogeny Group. The sources of taxonomic evidence are discussed, including morphology, anatomy, embryology, chromosomes, palynology, secondary plant compounds, proteins, and DNA. Molecular taxonomic methods are fully presented, and throughout the book reference is made to the results of recent studies, both molecular and morphological. A chapter on the history of plant classification puts current systematic methods in a historical context. Issues relating to variation in plant populations and species, including discussion of speciation, species concepts, polyploidy, hybridization, breeding systems, and introgression are carefully considered. Botanical nomenclature and field and herbarium methods are discussed in two appendices. New to the Second Edition are a chapter presenting an overview of the phylogeny of the green plants (with an emphasis on the vascular plants), a detailed glossary of botanical and biological terms, and coverage of 16 additional families of vascular plants. All chapters have been thoroughly updated, taking into account recent taxonomic methods and hypotheses.

The text is copiously illustrated, using in large part the informative analytical drawings developed as part of the Generic Flora of the Southeastern United States project. The text is accompanied by a much expanded CD-ROM, containing over 2,200 color photos illustrating the diagnostic characters of (and variability within) the vascular plant families covered in the text, including many images showing floral and fruit dissections.

Customer Reviews:

Second edition.......2003-06-09

The second edition (2002) has been much expanded (from 464 to 576 pages) and has been adjusted to keep up with the (headlong) developments in this field. It also includes more descriptions of families.

In some ways the book has not changed. The same illustrations were used giving it the same look. It remain an introductory book, that although set up along the lines of a systembook is only of limited use as such, since coverage is far from complete. The Appendix on "Botanical nomenclature" is still a soft spot. Not only is the (badly) erroneous bit on the naming of cultivated plants still there, but the slanted view of the ICBN has worsened (the ICBN even being called "Linnaean"!) and the PhyloCode is plugged.

However this remains the foremost textbook for those wanting a start in plant taxonomy, a field that is changing ever more rapidly.

PHYLOGENY AND NIRVANA.......2001-11-29

Several colleagues have recently adopted, or plan to adopt the new textbook by JUDD, W. S., CAMPBELL, C. S., KELLOGG, E. A. & STEVENS, P. F. 1999. Plant systematics, a phylogenetic approach. ISBN 0-87893-404-9, for teaching vascular plant taxonomy. The book has some very useful introductory chapters on modern tools, which provide students with an insight on the applications of phytochemistry, mollecular biology and confection of cladograms.
Surely plant (and other) systematics bear on a traditional use of systems which have inherent flaws, given the tremendous diversity os species (or whatever you can call the final taxa) they deal with. The limitations of a patchy fossil record render phylogenetic approaches, however tempting their confection may be for a plant scientist in his search of a broader understanding, a kind of Nirvana that can never be completely conquered. We can know with some accuracy how long ago currently fossilized plants lived, but anyone familiar with the concept of convergence can hardly attribute affinities to a leaf imprint not attached to a flower or vice versa. Oddly enough, some of these concerns are addressed in Chapter 1 of the book, which is not consistent with the classification system proposed [since a large number of smaller but very important families was left out].
On p. 3 the book addresses the theory-neutral approach and clearly states it's intent to go further - into Phylogenetic interpretations. Conversely the most exhaustive numeric study of all species in a single extant genus, using all characters one can securely split into states, will shed light on their similarities, providing just another elegant and often valuable way to organize data, such as a cladogram. Distinguishing similarities reflecting true affinities from those brought about by convergence remains a cumbersome task which shall always rely on traditional methods.
The comment on p. 6 says: "We do not know the actual phylogeny of any nontrivial group of organisms [what would a trivial one be?], but instead must infer phylogenies from the data available to us." I have trouble agreeing with this point of view, since available data is admittedly patchy and often inconsistent. Paths in the true cladogram of evolution can not be retraced based on assumptions. We only have access to the dense upper surface of the crown, while the gross remainder of the tree's branches and trunk are obstructed from view. No matter from which angle one looks at it, Phylogeny draws on a generous dose of guesswork. On the practical purpose of classification, I cannot but paraphrase CRONQUIST (1988:12), one of the traditional taxonomists excommunicated in this book: "In taxonomy, consistency must always be secondary to the primary objective of recognizing natural groups on the basis of all available information".
Fitting the entire universe of traditional knowledge and current advances of plant systematics into a comprehensive book for students at any level poses obvious problems: How does one cope with limited space to organize the maelstrom of data? Our minds need to create categories in order to control storage and retreival of information. Obviously some omitting is inevitable, but at least the general idea of diversity must come across. In that sense I am especially intrigued by the comment by Michael Donoghue in the foreword "Students will readily appreciate the desirability of abandoning ranks altogether."
Following one of the modern trends, some groups of plants in the book's system, (for ex. used for Orchids in Dahlgren's treatment) are named using formal taxonomic rank, while other are not. If a group is recognized as separate, why not give it a rank? One inherent function of ranks is providing a common language - the only method of sharing knowledge currently used by humans. It must be recognized that the way in which ranks are currently applied is not problem-free: why must there be a defined number of them, let's say, between family and species? Rather than eliminating ranks, we should create new ways to apply them and see them.
No matter how deeply modern views have shifted, we can never entirely erase nor replace the results presented in old publications. Students need to know and understand important footsteps in 2 centuries of botanical investigation, which have paved the way toward current advances. We can now add new characters from an arsenal of chemical and mollecular data, ecological observations and a substantially improved matrix of geographic data. Regardless of academic rank, we are all students with a mission to discover and organize information and convey knowledge, not to ignore, misplace or ommit data. How can a student fit families like the Acanthochlamydaceae, Acoraceae, Boryaceae, Burmanniaceae, Corsiaceae, Costaceae, Didieraceae, Epacridaceae, Lemnaceae, Velloziaceae or Xyridaceae into such a system, when they are not even in the alphabetical index?
A good system must account for every component as best it can. Misplacing taxa (implicitly considered the most common flaw of traditional classifications) is still better than making-believe that odd parts don't exist. The argument of producing a textbook for undergraduate courses does not justify the omission of important plant families. Students deserve to start out at least with a complete set of families and the tools to recognize them. Even a great job of organizing a mere subset of information has very limited practical value, especially if Phylogeny is one of its main goals. Some of the smaller families which were left out are very important from both the taxonomic and the phytogeographic perspectives. Despite some hardships such as dichotomic keys starting with presence or absence of betalains, Cronquist's system remains the most recent comprehensive reference guide to the diversity of flowering plant families, simple enough to be used at the undergraduate level.
Though data from modern sources, such as molecular and chemical, are used in the introductory chapters, it is not quite clear how this data was usen in confecting the classification by JUDD et al., and there is no way of knowing whether the new system proposed shall hold its consistency after all omitted families of vascular plants are included in the data.

A essential book.......2001-11-06

The book of W. Judd is essential to all Botany student and studious of Systematics and General Botanical. For the ones that still feel difficulties in the comprehension of the concepts of Phylogenetic Systematics, the clear text and explanative allows a very clear vision of the whole process. The approach of the initial chapters, mostly of the chapter 2 is too much elucidative, allowing to the reader if involve with the study themes, learning simultaneously all vision of the phylogenetic systematic current. It is a book that can't miss in shelf of any botanist or studous of plants.

a college text.......2001-08-02

Dr. Judd is an amazing lecturer and has provided an excellent pictorial CD along with the textbook. While this book is used as as a college text I often refer to it when discussing plants in general.

On modern plant taxonomy.......2001-07-14

There seems to be a pretty universal agreement that this is the book to have for those who want to keep up with what is happening in modern plant systematics. It is a wonderfully concise text that clearly states principles and gives good practical examples. Also it gives a good overview of the main groups in the APG-system (based on three genes combined with more traditional taxonomical characters). The conciseness is also, in a way, its weak point. It leaves out much that traditionally belongs in basic taxonomy texts, so that it is dubious how well this work is suited as an introduction to plant taxonomy. The many plant groups that are not treated detract from its usefulness as "system book". Another quibble is that the illustrations (line drawings) are all borrowed from other sources, so that style and quality varies.

Techniques in Molecular Systematics and Evolution

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Techniques in Molecular Systematics and Evolution
Gonzalo Giribe
Manufacturer: Birkhäuser Basel
ProductGroup: Book
Binding: Paperback

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Accessories:

ASIN: 376436257X

Book Description

The amount of information that can be obtained by using molecular techniques in evolution, systematics and ecology has increased exponentially over the last ten years. The need for more rapid and efficient methods of data acquisition and analysis is growing accordingly. This manual presents some of the most important techniques for data acquisition developed over the last years. The choice and justification of data analysis techniques is also an important and critical aspect of modern phylogenetic and evolutionary analysis and so a considerable part of this volume addresses this important subject. The book is mainly written for students and researchers from evolutionary biology in search for methods to acquire data, but also from molecular biology who might be looking for information on how data are analyzed in an evolutionary context. To aid the user, information on web-located sites is included wherever possible. Approaches that will push the amount of information which systematics will gather in the

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Molecular Systematics of Plants

Manufacturer: Springer
ProductGroup: Book
Binding: Paperback

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ASIN: 0412022419

Book Description

The application of molecular techniques is rapidly transforming the study of plant systematics. The precision they offer enables researchers to classify plants that have not been subject to rigorous classification before and thus allows them to obtain a clearer picture of evolutionary relationships. Plant Molecular Systematics is arranged both conceptually and phylogenetically to accommodate the interests not only of general systematists, but also those of people interested in a particular plant family. The first part discusses molecular sequencing; the second reviews restriction site analysis and the sequencing of mitochondrial DNA. A third section details the analysis of ribosomal DNA and chloroplast DNA. The following section introduces model studies involving well-studied families such as the Onagraceae, Compositae and Leguminosae. The book concludes with a section addressing theoretical topics such as data analysis and the question of morphological vs. molecular data.

Avian Molecular Evolution And Systematics

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Indispensable for Avian molecular biologists

Avian Molecular Evolution And Systematics
DAVID P. MINDELL
Manufacturer: Academic Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 0124983154

Book Description

The use of DNA and other biological macromolecules has revolutionized systematic studies of evolutionary history. Methods that use sequences of nucleotides and amino acids are now routinely used as data for addressing evolutionary questions that, although not new questions, have defied description and analysis. The world-renowned contributors use these new methods to unravel particular aspects of the evolutionary history of birds. Avian Molecular Evolution and Systematics presents an overview of the theory and application of molecular systematics, focusing on the phylogeny and evolutionary biology of birds. New, developing areas in the phylogeny of birds at multiple taxonomic areas are covered, as well as methods of analysis for molecular data, evolutionary genetics within and between bird populations, and the application of molecular-based phylogenies to broader questions of evolution.

Key Features
* Contains authoritative contributions from leading researchers
* Discusses the utility of different molecular markers for questions of avian evolution, involving populations and higher-level taxa
* Applies molecular-based phylogenies of birds and molecular population genetics data to broad questions of organismal and molecular evolution.
* Compares and contrasts molecular and morphological data sets

Customer Reviews:

Indispensable for Avian molecular biologists.......2000-03-25

'Avian Molecular Evolution and Systematics' provides students and researches alike with an unparalleled review of avian molecular techniques in sytematics and phylogenetics. David P. Mindell has compiled an authoritative collection of contributions from ornithologists and molecular biologists that cover both theoretical and practical applications. The chapters trace the theory behind the altered gene order of avian mtDNA and provide informative reviews of the utility of mtDNA genes in systematics, phylogeny, phylogeography and deciphering patterns of avian evolution. In addition to covering mtDNA a chapter is included on the theory and application of microsatellites, a relatively new technique to molecular biology. It is however unfortunate that there are not more avian microsatellite examples besides that which covers relatedness between cooperative displaying male manakins. However the author does include other applications of microsatellite data (quantitative gene flow and genetic variation) using gray seals and bighorn sheep as examples. This book ends with a chapter on ancient DNA that reviews some of the more commonly used extraction procedures for ancient DNA and again provides examples covering systematics and paleoecology. Although the chapters do cover some molecular procedures the book does not serve as a laboratory guideline to working with avian DNA, rather it covers the more interesting theoretical aspects of avian speciation and evolution. In general 'Avian Molecular Evolution and Systematics' is indispensable for the avian molecular biologist who is interested in phylogenetics, systematics and the evolution of behavior.

Molecular Identification, Systematics, and Population Structure of Prokaryotes

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Molecular Identification, Systematics, and Population Structure of Prokaryotes
Erko, Ed. Stackerbrandt
Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 3540231552

Book Description

Systematic biology has a far wider application than merely the provision of a reliable classification scheme for new strains. With the framework of the hierarchic system stabilizing, genomes, noncoding regions, and genes and their products can now be evaluated in an evolutionary context. This book summarizes recent developments in the molecular characterization of cultured and as-yet uncultured prokaryotes, emphasizing the strengths and weaknesses of individual approaches. The chapters of the book are compiled to stimulate students to enter the field of bacterial diversity, presenting a broad spectrum of fascinating multifaceted disciplines that illuminate the paths to ecosystem functioning, communication within communities, symbiosis, life in extreme environments, astrobiology, and more.

Telling the Evolutionary Time: Molecular Clocks and the Fossil Record (SYSTEMATICS ASSOCIATION SPECIAL VOLUMES)

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Telling the Evolutionary Time: Molecular Clocks and the Fossil Record (SYSTEMATICS ASSOCIATION SPECIAL VOLUMES)
Phillip C. J., Ed. Donoghue
Manufacturer: CRC Press
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Binding: Hardcover

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Morphology, Shape and Phylogeny (Systematics Association Special Volume)

ASIN: 0415275245

Book Description

Determining the precise timing for the evolutionary origin of groups of organisms has become increasingly important as scientists from diverse disciplines attempt to examine rates of anatomical or molecular evolution and correlate intrinsic biological events to extrinsic environmental events. Molecular clock analyses indicate that many major groups are twice as old, or more, than a literal reading of the fossil record attests, implying that the fossil record is incomplete. Few paleontologists agree that the fossil record is inadequate, arguing instead that our understanding of the molecular clock is far from ideal. Telling the Evolutionary Time: Molecular Clocks and the Fossil Record represents a discussion between molecular biologists and paleontologists, in which they investigate the significance of competing sources of data, explain the nature of molecular clocks and the fossil record, and strive to develop compromise models that incorporate contradictory opinions. These are presented as a series of case studies dealing with many of the most important groups of complex organisms, such as protists, land plants, flowering plants, complex animals, chordates, vertebrates, tetrapods, and modern birds. Bringing fresh insight and various perspectives to a complicated argument, this book assembles all sides of the debate into one comprehensive text. It is a significant volume for research scientists and advanced students across the field of evolutionary biology.

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A classic
simply brilliant
What is Molecular Phylogenetics?
review of Molecular Systematics

Molecular Systematics
David M. Hillis
Manufacturer: Sinauer Associates
ProductGroup: Book
Binding: Paperback

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ASIN: 0878932801

Book Description

Within the past decade, molecular systematic methods have been applied in most fields of biology to provide an evolutionary framework whenever comparisons are made among individuals, populations, or higher taxa. The first edition of Molecular Systematics became a standard reference for this vigorous field by describing each aspect of the planning, execution, and analysis of a molecular systematic study. The new edition updates and expands this coverage, and includes considerable information on new molecular techniques and methods of analysis.

Molecular Systematics includes chapters on sampling design, the collection and storage of tissues, each of the major molecular techniques, and intraspecific and phylogenetic analysis. The sampling chapters describe how to plan a study and how to collect, transport, and store the appropriate tissues for each study. The techniques chapters cover principles, assumptions, applications, limitations, and protocols for isozyme electrophoresis, molecular cytogenetics, DNA hybridization, the polymerase chain reaction, restriction site and fragment analysis, and nucleic acid sequencing and alignment. Advantages and disadvantages of alternative approaches are discussed for each technique, and recent developments (such as new methods of fluorescent in situ hybridization, rapid screening methods for detecting DNA sequence variation, automated sequencing methods, new approaches for PCR, and microsatellite analyses) are detailed. Three additional chapters cover the rationale and methodology of molecular data analysis at both the population and interspecific levels, and provide information on using and obtaining the relevant computer programs (including the many programs available for free across the Internet). The chapter on phylogenetic analysis has been considerably expanded to include the latest developments in maximum likelihood analysis, spectral analysis, methods for reconstructing reticulating networks, corrections for complex models of sequence evolution, and methods for assessing confidence in phylogenetic results. The book also includes discussion of processes of molecular evolution, experimental molecular studies, molecular simulations, the molecular meaning of homology, and limitations and applications of the molecular clock hypothesis.

This edition of Molecular Systematics will provide new insights and is an important reference work for established investigators, as well as a comprehensive introduction for newcomers to the field.

Customer Reviews:

A classic.......2005-03-25

To date there is no substitute for this book. In my grad student molecular lab, this has been the most frequently permanently "borrowed" book. (And you know who you are, so please return my copy...?)

The range of the book is broad, it has done everything from help me troubleshoot PCRs early in my career to learn the theory involved in my analysis methods. It is getting a little old but still incredibly useful.

An update to my earlier post:
By the way, since my book has been "borrowed," I just looked up the price to re-purchase one. As of 26 August 06, the price is over $200.00. That is enough to give a graduate student a heart attack.

Dr. Hillis, any plans for another edition? Help...

simply brilliant.......2004-05-15

Hillis gets down to the nitty gritty right away in this information packed book. The text is very readable and he goes into some detail on the methods used to reconstruct phylogenies from sequence data. He pulls no punches in describing the weaknesses and strengths of each method, and further offers insight as to where the field is headed and what we can expect in future analyses as genomic and EST databases become ever larger.

In short, this is a detailed overview of using sequence data to test evolutionary hypotheses. It is an essential part of your bookshelf as an evolutionary biologist. Highly recommend!

What is Molecular Phylogenetics?.......2002-10-08

This book does not tell anything about sequence alignment.
Except this 'little problem' it is a good book anyway.
But do you think that sequence alignment is not an important issue in molecular phylogenetics?

review of Molecular Systematics.......2000-06-22

Molecular Systematics is the best general text on population and evolutionary genetics I have read. It provides sufficient depth to give adequate understanding of molecular phylogenetics and molecular population genetics data for most purposes. The broad research behind the work makes it an excellent starting point for finding journal articles on specific subjects within this field. The only drawback to the book is that it is five years old and the field is quite fast moving. Hopefully a new edition will appear shortly.

Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics (SYSTEMATICS ASSOCIATION SPECIAL VOLUMES)

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Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics (SYSTEMATICS ASSOCIATION SPECIAL VOLUMES)
Robert P Ed. Hirt
Manufacturer: CRC Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 0415299047

Book Description

The recent revolution in molecular biology has spread through every field of biology including systematics and evolution. Researchers can now analyze the genomes of different species relatively quickly, and this is generating a great deal of data and theories about relationships between taxa as well as how they originated and diversified. Organelles, Genomes and Eukaryote Phylogeny covers recent developments in the field of "deep level" phylogenetic inference of eukaryotes, especially with respect to the origin and evolution of eukaryotic cells and their organelles. It focuses on interpretation of data derived from molecular and cell biology, genome sequencing with respect to the timing and mechanism of eukaryogenesis, and the endosymbiotic events leading to mitochondria and plastids. As ideas that prevailed for twenty years are being revised, updated, or abandoned in the face of more sophisticated analysis of molecular sequence data, this book will prove relevant to all students and professionals working in molecular systematics, comparative genomics, and cell biology.

Introduction to Computational Biology: And Evolutionary Approach

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try the enclosed GUI program

Introduction to Computational Biology: And Evolutionary Approach
Bernhard Haubold
Manufacturer: Birkhauser
ProductGroup: Book
Binding: Hardcover

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Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

ASIN: 3764367008

Book Description

Analysis of molecular sequence data is the main subject of this introduction to computational biology. There are two closely connected aspects to biological sequences: (i) their relative position in the space of all other sequences, and (ii) their movement through this sequence space in evolutionary time. Accordingly, the first part of the book deals with classical methods of sequence analysis: pairwise alignment, exact string matching, multiple alignment, and hidden Markov models. In the second part evolutionary time takes center stage and phylogenetic reconstruction, the analysis of sequence variation, and the dynamics of genes in populations are explained in detail. In addition, the book contains a computer program with a graphical user interface that allows the reader to experiment with a number of key concepts developed by the authors.

This textbook is intended for students enrolled in courses in computational biology or bioinformatics as well as for molecular biologists, mathematicians, and computer scientists.

Customer Reviews:

try the enclosed GUI program.......2006-10-14

For some readers, the best attraction of the book is the GUI program that lets you quickly experiment and apply the main ideas. The text is very interdisciplinary, written for diverse audiences, spanning biology, computer science and mathematics. Some aspects of the book may perhaps be too mathematical for some biology readers. Say the Hidden Markov Models, for example. But if you keep at it, you should get able to get the gist of the models. Which is another reason for the usefulness of the GUI. Essentially, so long as you understand the basic math ideas, the GUI lets you sidestep the grotty details and focus on applying the overall models.

It could also be that the book is suitable for a university course. The chapter exercises and accompanying answers are useful, in this regard.

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