Phylogenetic Trees Made Easy: A How-To Manual, Second Edition (with CD-Rom)

Book Description

Phylogenetic Trees Made Easy helps beginners get started in creating phylogenetic trees from protein or nucleic acid sequence data. Although aimed at molecular and cell biologists who may not be familiar with phylogenetic or evolutionary theory, it also serves students who may be familiar with phylogenetic theory but are unfamiliar with the tools used to apply that theory. The reader is led, step by step, through identifying sequences that are homologous to a sequence of interest, downloading these sequences from databases, creating multiple alignments, and using several different methods to construct trees. "Learn More" boxes present background on the various concepts and methods, and an accompanying CD and Website provide files needed for working through the tutorials in the text. Key changes to the Second Edition include:

* discussion and screen shots updated to reflect current software versions
* all software discussed available for Macintosh, PC, and UNIX platforms
* detailed discussion of PAUP* for both Macintosh and Windows
* inclusion of PHYLIP as an alternative to PAUP*
* addition of "Advanced Topics," including constructing deep phylogenies from protein structure comparisons, ancestral sequence reconstruction, and measuring positive selection as evidence of adaptive evolution Every copy of the Second Edition includes a CD with current Windows and Macintosh beta versions of PAUP*. These time-limited versions will allow semester-length use of this popular software, giving students hands-on experience in tree-building as they work through the text.

Customer Reviews:

Excellent but.......2007-10-04

Buy this if you must but there is a third edition. They complement each other to some extent but the third edition is more useful as it is more up to date and even slimmer and yet more powerful in that it totally obviates the need to pour over Paup. Here is a good treatment of Paup. Wonderful for beginners.

Average customer rating:

Very Good Book
Definitive resource in fish systematics
THE world reference for a classification of fishes
worst drawings ever
Great book, shame about the price.

Fishes of the World
Joseph S. Nelson
Manufacturer: Wiley
ProductGroup: Book
Binding: Hardcover

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The Diversity of Fishes
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Sharks of the World (Princeton Field Guides)

ASIN: 0471250317

Book Description

"Of all the literature I use while preparing field guides for the Food and Agriculture Organization of the United Nations, Nelson's Fishes of the World is, by far, the one I refer to most often. [This] book is a standard reference . . . I continue to use it extensively in the ichthyology courses I teach, particularly in laboratory sessions."
-Kent E. Carpenter Old Dominion University

"Fishes of the World is a unique and essential resource for anyone seriously interested in the diversity and evolution of fishes. The family accounts provide quick summaries of current knowledge on all groups of living fishes and many key fossil taxa. It is a required work for every student in my laboratory."
-William E. Bemis Kingsbury Director of Shoals Marine Laboratory, Cornell University

"Only classics are known by the single name of their author, and certainly [Nelson's book] has for four editions been such a book for all those who seek an accessible, up-to-date, readable reference on fish classification. Once again, Nelson presents a balanced view of the sometimes tumultuous, but ever-exciting, study of the phylogenetic relationships and classification of fishes. In doing so, Nelson makes an excellent case for organismal biology, highlighting the many and varied morphological characters we use to diagnose fish taxa and differentiate among the 515 families of living species."
-Lynne R. Parenti Curator of Fishes and Research Scientist, National Museum of Natural History, Smithsonian Institution

Fishes of the World, Fourth Edition is the updated edition of a true classic in the field. A unique presentation of a modern, cladistically based classification of all the major living and fossil fish groups, this indispensable reference helps scientists and others identify and classify specimens, make familial connections, understand the evolution of fishes, and springboard into further research.

The taxonomy of fishes presented includes the anatomical characteristics, distribution, common and scientific names, and phylogenetic relationships for all 515 families of living fishes. Packed with representative species drawings and information on phylogentic relationships, this informative Fourth Edition features:
* Both fossil and extant species
* More than 500 illustrations
* Fully vetted scientific and common names
* An extensive bibliography

Customer Reviews:

Very Good Book.......2007-10-03

Very good book. It came very fast too...
I was really after it for my work....
It is considered reference for all ichthyologists.
My favorite!

Definitive resource in fish systematics.......2007-09-08

I just received and looked over the Fourth Edition of Nelson's book. It is the most widely-accepted resource for fish classification. Specific points in the classification, as Nelson acknowledges, are subjects of debate and research. Nelson himself seems to take the classical approach of emphasizing morphological (as opposed to molecular) traits in his classification. However, the collection and organization of up-to-date references on the various fish groups in this book is without parallel and this makes the book hugely valuable. Two reasons in addition to cost for the use of drawing as opposed to photos to picture the fishes in this book are economy of space, and ability to convey fossil fishes in a similar manner to existing species. I'm glad that I bought it!

THE world reference for a classification of fishes.......2006-04-20

This is the fourth, long awaited, edition of Fishes of the World.
Since the 2nd edition, it is THE reference for a STABLE PRACTICAL classification of all fishes of the world.
The work done by J. Nelson in the background is enormous, because for each node of the hierarchy are discussed and referenced the concurrent alternatives recently published, and is explained the choice made between them (so that one can appreciate the diversity of opinions, and the work remaining to be done).
Apart from the price that we can always find too expensive (and I am quite sure that he does not pay the author's efforts), the reviews of the previous edition missed 3 points:
- The book does not claim to give an overview of the biology and ecology of fishes, nor to give thorough illustrations of the diversity of fishes. The outlines are extremely useful to memorise the global shape of families and subfamilies. Ok, the 4th edition could have been complete in this area ...
- The book provides a management classification that is close enough of the last validated advances of research. Saying that it is not uptodate is a clear misunderstanding of what this book is useful for. In particular, it does not endorse the last published phylogeny (and by the way, a phylogeny is not a classification) if work clearly still needs to be done to establish and disseminate a new view: it tries to point out the most evidenced status of the classification, but presenting the alternatives: the people in need of one reliable classification can use it as such, the people closer to the edge of research can go further and use the information from the references given.
- I don't know any book in mammals, birds, snakes, lezards, turtles, amphibians that synthesizes the same amount of REFERENCED information, where there are altogether less species involved than in fishes! But sure, many of them have beautiful images ...
Thanks Joe.

worst drawings ever.......2003-01-22

For a book in this price range, we all want more. I have been doing fish illustrations in Environmental Biology of Fishes and some other journals. Dr. Nelson, you should contact me, we need to talk!!

Great book, shame about the price........2002-04-24

Comprehensive coverage makes this a great first reference. Most listings cite further in depth references. Published in 1994 it is probably due to be updated. The worst aspect of this book is the price. Get your library to buy it.

Plant Systematics: A Phylogenetic Approach

Average customer rating:

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

Plant Systematics: A Phylogenetic Approach
Christopher S. Campbell , Elizabeth A. Kellogg , Peter F. Stevens , and Michael J. Donoghue
Manufacturer: Sinauer Associates
ProductGroup: Book
Binding: Hardcover

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Plant Identification Terminology: An Illustrated Glossary
Plant Systematics
Guide to Flowering Plant Families
Botanical Latin
Flowering Plant Families of the World

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.

Evolutionary Pathways in Nature: A Phylogenetic Approach

Average customer rating:

Great, but a little elementary

Evolutionary Pathways in Nature: A Phylogenetic Approach
John C. Avise
Manufacturer: Cambridge University Press
ProductGroup: Book
Binding: Paperback

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Molecular Ecology
The Tree of Life: A Phylogenetic Classification (Harvard University Press Reference Library)
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ASIN: 0521674174

Book Description

Reconstructing phylogenetic trees from DNA sequences has become a popular exercise in many branches of biology, and here the well-known geneticist John Avise explains why. Molecular phylogenies provide a genealogical backdrop for interpreting the evolutionary histories of many other types of biological traits (anatomical, behavioral, ecological, physiological, biochemical and even geographical). Guiding readers on a natural history tour along dozens of evolutionary pathways, the author describes how creatures ranging from microbes to elephants came to possess their current phenotypes. Essential reading for college students, professional biologists and anyone interested in natural history and biodiversity, this book is packed with fascinating examples of evolutionary puzzles from across the animal kingdom; how the toucan got its enormous bill, how reptiles grow back lost limbs and why Arctic fish don't freeze.

Customer Reviews:

Great, but a little elementary .......2006-11-06

This a great book, well put together and an easy read. I would suggest it for those who are not familiar with phylogenetics. Otherwise it is a bit simplified for those who know and understand most of the concepts already. perfect for an undergraduate level class or advanced high school students.

The Tree of Life: A Phylogenetic Classification (Harvard University Press Reference Library)

Average customer rating:

Thorough phylogenetic classification of life on Earth
Awesome reference

The Tree of Life: A Phylogenetic Classification (Harvard University Press Reference Library)
Guillaume Lecointre , and Hervé Le Guyader
Manufacturer: Belknap Press
ProductGroup: Book
Binding: Hardcover

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Evolutionary Pathways in Nature: A Phylogenetic Approach
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The Third Domain

ASIN: 0674021835

Book Description

Did you know that you are more closely related to a mushroom than to a daisy? That crocodiles are closer to birds than to lizards? That dinosaurs are still among us? That the terms "fish," "reptiles," and "invertebrates" do not indicate scientific groupings? All this is the result of major changes in classification, whose methods have been totally revisited over the last thirty years.

Modern classification, based on phylogeny, no longer places humans at the center of nature. Groups of organisms are no longer defined by their general appearance, but by their different individual characteristics. Phylogeny, therefore, by showing common ancestry, outlines a tree of evolutionary relationships from which one can retrace the history of life.

This book diagrams the tree of life according to the most recent methods of classification. By showing how life forms arose and developed and how they are related, The Tree of Life presents a key to the living world in all its dazzling variety.

Customer Reviews:

Thorough phylogenetic classification of life on Earth.......2007-09-07

"The Tree of Life" is a thorough modern phylogenetic classification of life on this planet. This book is great for anyone interested in how different organisms are really related, from single-celled organisms up to humans and our close relatives. Anyone who has ever thought it strange that we should group turtles, crocodilians and dinosaurs together as "reptiles", but exclude birds (and mammals), will likely be interested in this book. The book is comprehensive, detailed, and well illustrated, and remarkably well-priced.

This book covers the whole range of life on Earth, though primates and other mammalian groups are given far more thorough treatment than bacteria and archaeans. Each section provides a description of the distinguishing features of the relevant group, with examples of some of the members, information on the fossil record, and plenty of illustrations.

The main drawback with such a work is, of course, that the field is changing rapidly and it is close to impossible to ever be fully up-to-date. Another minor, but slightly annoying, problem is that a number of errors have crept into the English translation, so, for example, "Pliocene" appears as "Pilocene" in many places in the book.*

Nonetheless, the scope of "The Tree of Life", the detailed description and the abundant illustrations make this an invaluable reference work for those interested in biological classification.

*Note: I assume that these errors are absent from the original French text.

Awesome reference.......2006-12-18

This book is truly a work of art in layout, design and presentation of line drawings and scientific content. It is one of the best scientific presentations I have seen and anyone remotely interested in this subject needs to check this excellent reference.

Molecular Evolution: A Phylogenetic Approach

Average customer rating:

would not recommend
Good overview of molecular evolution studies but a bit outdated
Nice figures
Trees and more trees
Handy read

Molecular Evolution: A Phylogenetic Approach
Roderic D. Page , and Edward C. Holmes
Manufacturer: Blackwell Publishing Limited
ProductGroup: Book
Binding: Paperback

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ASIN: 0865428891

Customer Reviews:

would not recommend.......2007-03-26

We use this book in the class and most of us don't like it. The book just doesn't do a good job explaining many things. Unless you are an expert in the field or at least have prior experience I would not recommend you this book.

Good overview of molecular evolution studies but a bit outdated.......2006-03-16

If you're not familiar with DNA sequences analysis and inferring phylogenies, this book is a must read (as far as I know the only introduction book to the field). But it's a bit outdated (Bayesian analysis not covered).

Nice figures.......2004-01-08

I'm new to molecular evolution and have been confused with various terms and concepts (e.g., cladogram vs. phylogram vs. dendrogram, plesiomorphy vs. apomorphy vs. autapomorphy vs. synapomorphy vs. homoplasy, etc.). Reading other books that try to explain these concepts mostly in words only added more confusion.

Every page in this book contains highly illustrative figures that accompanies well written text. Of course, not all sections are not immediately clear to understand, and I would need to read other books as well.

If you are new to molecular evolution, start with this book along with any other books that may suit your particular need.

Trees and more trees.......2000-11-27

Although molecular phylogenetic analysis can be extremely complex, this reference provides an introduction to the subject that is straightforward to read. The reference begins with consideration of trees, which are structures used to model actual evolutionary relationships between genes or entire lifeforms. It then provides an introduction to molecular and population genetics. Coding as well as noncoding DNA (tandem repeats, transposable elements, retroviruses, spacer DNA) is considered. The reference then considers how genetic change can be measured, followed by how we can deduce molecular phylogenies. The validity of the molecular clock is then considered, along with a discussion of the neutralist-selectionist debate. The reference finally considers how different phylogenies can be combined to determine actual phylogeny, reconciled trees, and rates of diversification.

Handy read.......2000-03-25

This book is very well written and a handy tool for anyone who is new to molecular evolution. Nice diagrams and concise chapters. The authors know how to break up the sometimes demanding ideas into appropriate bites. Perfect for grad students and senior undergrads.

The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny

Average customer rating:

Nicely combine theory and practice
very good and very practical

The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny

Manufacturer: Cambridge University Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 052180390X

Book Description

The Phylogenetic Handbook is a broad introduction to the theory and practice of nucleotide and amino acid phylogenetic analysis. As an unique feature of this book, each chapter contains an extensive practical section, in which step-by-step exercises on real data sets introduce the most widely used phylogeny software including CLUSTAL, PHYLIP, PAUP*, DAMBE, TREE-PUZZLE, TREECON, SplitsTree, TreeView, SimPlot, MEGA2, PAML and BOOTSCANNING. The book provides a strong background in basic topics: the use of sequence databases, alignment algorithms, tree-building methods, estimation of genetic distances, and testing models of evolution.

Download Description

The Phylogentic Handbook is a broad introduction to the theory and practice of nucleotide and amino acid phylogenetic analysis. As an unique feature of this book, each chapter contains an extensive practical section, in which step-by-step exercises on real data sets introduce the most widely used phylogeny software including CLUSTAL, PHYLIP, PAUP*, DAMBE, TREE-PUZZLE, TREECON, SplitsTree, TreeView, SimPlot, and BOOTSCANNING. The book provides a strong background in basic topics: the use of sequence databases, alignment algorithms, tree-building methods, estimation of genetic distances, and testing models of evolution.

Customer Reviews:

Nicely combine theory and practice.......2005-11-22

I came across this book while doing some phylogenetic analysis and found it very useful.

The first two chapters give some background information on molecular evolution and sequence databases, as well as a downloadable dataset used throughout the book.

The real business starts from chapter 3--multiple sequence alignment (MSA). Problems and algorithms of MSA are briefly reviewed. Here you know how CLUSTALW and T-Coffee work. The presentation of the progressive alignment used in CLUSTALW is especially clear. However, other popular programs are not metioned, probably they are not available or not widely used at the time when the book was written. I recommend PROCONS and MUSCLE for protein alignment and DIALIGN-T for both dna and protein alignment. Check them out.

Chapter 4 reviews nucleotide substitution model, concise and not much math on continuous-time Markov chain(CTMC). A chart shows the relationship between popular models including GTR, TN93, HKY85, F84, F81, K80 and JC. I like it. To know more details of CTMC of these models, however, you need to consult other books. Exercises using PHYLIP and DAMBE can be found.

One someone have the sequence aligned, and genetic/evolutionary distance between them adjusted using say JC, she/he is ready to jump to the next chapter 5 -- Phylogeny Inferrence based on distance methods. Here the outdated UPGMA, mainstream NJ and Fitch-Morgoliash methods are presented by examples, effectively cleaning the fog before these ACRONYM. Bootstrapping and Jacknifing, the two methods for assessing quality of phylogeny, are briefly explained, then progress to exercise using PHYLIP.

The next two chapters are maximum-likelihood with TREE-PUZZLE, and Parimony* (* means MP+ML+Distance) in PAUP*.

Working on dna or protein sequences sometimes can mean a whole lot of difference, these topics are dealt in chapter 8--Phylogenetic analysis using protein sequences and chapter 9--analysis of nucleotide sequences using TREECON.

If you only need to get the tree, you can stop here. The remainign chapters either deal with dN/dS, detecting recomination, or centered on particular software packages including SplitsTree,LAMARC and DAMBE(A heavily used package in this book another is PHYLIP).

Overall, the book is comprehensive, well balanced between practice and theory. Though contributed by different authors, the two editors seamlessly wave these chapters into a nice book. Bravo to them!

My only concern is book does not cover many widely-used programs, but we, the arduous tree constructors, can find them out by ourselves, do we?

very good and very practical.......2005-10-19

it is very convenient and handy for a junior student.

Phylogenetics (Oxford Lecture Series in Mathematics and Its Applications, 24)

Average customer rating:

Good, for the dedicated reader

Phylogenetics (Oxford Lecture Series in Mathematics and Its Applications, 24)
Charles Semple , and Mike Steel
Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Hardcover

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Inferring Phylogenies
Mathematics of Evolution and Phylogeny
Computational Molecular Evolution (Oxford Series in Ecology and Evolution)
Computational Genome Analysis: An Introduction (Statistics for Biology & Health)
Evolutionary Dynamics: Exploring the Equations of Life

ASIN: 0198509421

Book Description

'Phylogenetics' is the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics. It is a flourishing area of intereaction between mathematics, statistics, computer science and biology. The main role of phylogenetic techniques lies in evolutionary biology, where it is used to infer historical relationships between species. However, the methods are also relevant to a diverse range of fields including epidemiology, ecology, medicine, as well as linguistics and cognitive psychology This graduate-level book, based on the authors lectures at The University of Canterbury, New Zealand, focuses on the mathematical aspects of phylogenetics. It brings together the central results of the field (providing proofs of the main theorem), outlines their biological significance,and indicates how algorithms may be derived. The presentation is self-contained and relies on discrete mathematics with some probability theory. A set of exercises and at least one specialist topic ends each chapter. This book is intended for biologists interested in the mathematical theory behind phylogenetic methods, and for mathematicians, statisticians, and computer scientists eager to learn about this emerging area of discrete mathematics. 'Phylogenetics' in the 24th volume in the Oxford Lecture Series in Mathematics and its Applications. This series contains short books suitable for graduate students and researchers who want a well-written account of mathematics that is fundamental to current to research. The series emphasises future directions of research and focuses on genuine applications of mathematics to finance, engineering and the physical and biological sciences.

Customer Reviews:

Good, for the dedicated reader.......2004-02-18

Starting with genes, proteins, or other biological traits, phylogenetics is about describing relationships between them. Phylogenetics tries to estimate "family trees" given only the family members visible today - exact lineage is guesswork, since the parents, grandparents, and shared heritage can never be known.

This book offers deep analysis of one family of techniques for deducing possible trees. It gives a very thorough, formal description of ways to examine and resolve different sources of information, or to determine that they can not be resolved. It offers minute analysis of ways to take subsets of the whole family, analyze the subsets, then merge the subset conclusions together, as much as possible. It also addresses the statistical character of the tree-building problem. The reader who masters this material has a powerful set of tools for phylogenetic analysis.

That reader must be truly dedicated, though. The first two chapters read like mathematical graph theory (because they are). The next few chapters are also highly mathematical, but offer a bit more biological insight. I'm not a mathematician, so I find this book tough going. The graph-theoretic conclusions give wonderful insight into combining information from multiple traits and in noting points of conflict. It takes me a while, though, to unwind the formal notation enough to attach biological meaning to it. There are a few helpful statistical analyses, but they could be missed - the more familiar kinds of statistics are hidden among the combinatorics and tree perturbations. Later chapters revisit familiar topics like parsimony and Markov models, but with theoretical depth that's hard to find elsewhere.

Within the whole gamut of phylogenetic techniques now used, this book addresses only one range. Within that range, however, Semple and Steel have done a fine job of showing the theory behind those techniques. I value the insights that this book brings. Even so, it's not always easy to dislodge those insights from the solid slabs of proofs in which they are embedded. I appreciate the demonstration of NP-completeness of specific problems, but I can't always apply that knowledge to the biology I want to address.

Book Description

New methodological developments in morphological phylogenetics---including approaches for analyzing ontogenetic data, fossils, morphometric characters, intraspecific variation, and hybrid taxa---are summarized in this book. The actual practice of morphological phylogenetics is also evaluated, especially in regard to its controversial use in the study of the evolution of morphological characters.

Customer Reviews:

Phylogenetic Analysis of Morphological Data (Smithsonian Series in Comparative Evolutionary Biology) (Smithsonian Series in Comp.......2006-10-29

That's an important book for the users of morphological data in phylogenetic analisys. Problems and methods are explained in the several articles of the book.

Average customer rating:

clear reading for beginners
Molecular Evolution and Phylogenetics by Masatoshi Nei, Sudhir Kumar
A valuable addition
OK, until something better comes along
Top in its Field

Molecular Evolution and Phylogenetics
Masatoshi Nei , and Sudhir Kumar
Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Paperback

Biochemistry | Biological Sciences | Science | Subjects | Books

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Similar Items:

Phylogenetic Trees Made Easy: A How-to Manual, Third Edition
Inferring Phylogenies
The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny
Fundamentals of Molecular Evolution
Molecular Evolution: A Phylogenetic Approach

ASIN: 0195135857

Book Description

During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.

Customer Reviews:

clear reading for beginners.......2007-10-05

this book is realy straightforward, very well-written and really explains the oncept in a very clear way. Excellent choice for non-specialists.

Molecular Evolution and Phylogenetics by Masatoshi Nei, Sudhir Kumar.......2007-03-09

Overall it is a good and complete book on Molecular Evolution, and basic DNA analysis techniques.

A valuable addition.......2003-11-26

I don't look for any one book to answer all my questions. This one carries its weight, though, and maybe a bit more.

The first section gives the clearest and most detailed description of nucleotide sequence comparisons I've seen. I'm no biologist, but it really got me thinking about some new ways to talk about substitution matrices.

The bulk of the book covers what I hoped for originally: phylogenetic trees. The authors choose an unusual approach - it doesn't quite meet the authors' initial promise of math-minimization, but doesn't climb too far up the ivory tower, either. I find it a very practical, usable level of presentation. I'd be nervous about going beyond their formulas, since the math for real understanding isn't all there. Still, the phylogeny discussion covers a lot of material, and covers it well enough for me to write programs about most of it.

The final section addresses population genetics. I have nothing against population genetics, it just never seemed to point where I'm headed. Nei and Kumar corrected my mis-impression. Population gentics is the background model, the null hypothesis, behind the functions that score population differences. It really shows what happens when the tree of life branches out.

The book has some minor weaknesses. It emphasizes nucleotide sequences at the expense of peptides; I can't fault an author for writing what they want as opposed to what I want. On page one, the authors decline an intensely mathematical approach. By page 25, they're up to Poisson and gamma distances. The typography make the section breaks into a "Where's Waldo" experience. Nei's favorite author, based on citations, is Nei. Well, false modesty is no virtue. This book seems authoritative and Nei seems to be an authority, maybe not just in Nei's opinion.

This book really has given me a lot more to work with than most. Education isn't cheap these days, and this book is very educational. I just hope no one asks me to lend it any time soon.

OK, until something better comes along.......2003-02-20

Nei and Kumar's "Molecular Evolution and Phylogenetics" is basically an updated version of Nei's 1987 "Molecular Evolutionary Genetics" book. Accordingly, attention is shifted to reviewing many recent advances in methods of phylogenetic inference with an obvious bias towards distance methods, particularly those which the senior author devised. In fairness, they give decent coverage to the more popular parsimony and likelihood methods as well. The great strength of the book is the number of real examples used to illustrate properties of the methods, and their focus on statistical methodology without miring the reader in detailed mathematics. The disappointment is that while breadth of coverage is tolerable, depth is lacking. Expanding their views on the shortcomings of likelihood in choosing tree topology and likelihood ratio-tests in choosing models of sequence evolution would have been most enlightening, particularly as these issues have been brushed lightly aside by phylo-likelihoodists. Other methods (Hadamard transformations, Bayesian phylogenetic inference) were absent altogether. Further the chapter on molecular clocks was disappointing--old 1980s controversies were rehashed, while there was nothing on methods that relax the assumption of rate constancy while still allowing divergences to be dated. Admittedly some of this is very new and research is ongoing, but there isn't even a hint of these developments in this chapter. Another plus though is the addition of a chapter on inferring ancestral states of molecular sequences.

Unlike Molecular Evolutionary Genetics, far too little of the book is devoted to methods at the population level, and what is there again smacks of state-of-the-art 15-20 years ago. I was hoping for much more coverage of microsatellite and AFLP data. There was very little for either, while now rarely-used RFLPs were given extensive coverage.

In short, this book was too short, particularly for the price, and I almost gave it 3 stars rather than 4. However, if you are a phylogeneticist, you will probably want to have this book on your shelf. A lighter introduction for the uninitiated would be Rod Page's "Molecular Evolution" or Graur and Li's "Fundamentals of Molecular Evolution". However, my hopes for a good comprehensive text and reference on phylogenetic methods now rest on publication of Joseph Felsenstein's "Inferring Phylogenies".

Top in its Field.......2000-09-21

This book is an excellent text and reference for both graduate students and faculty. It covers several topics in molecular evolution and phylogenetic analysis, as the title suggests. It stands as a unique contribution because the authors explain the mathematical and conceptual framework of a given topic in molecular evolution or phylogenetic analysis and give subsequent examples to show how various analytical methods can be applied to the study of that topic. In that context, the explanation of concepts was exceptionally clear, which made it easy to understand potentially difficult subject matter. This book is highly recommended to those wishing to study the analysis of genes and proteins in an evolutionary framework.

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