Molecular Evolution: A Phylogenetic Approach

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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Good overview of molecular evolution studies but a bit outdated.......2006-03-16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 But it's a bit outdated (Bayesian analysis not covered).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.

Phylogenetic Analysis of Morphological Data (Smithsonian Series in Comparative Evolutionary Biology) (Smithsonian Series in Comparative Evolutionary Biology)

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Phylogenetic Analysis of Morphological Data (Smithsonian Series in Comparative Evolutionary Biology) (Smithsonian Series in Comp

Phylogenetic Analysis of Morphological Data (Smithsonian Series in Comparative Evolutionary Biology) (Smithsonian Series in Comparative Evolutionary Biology)
Wiens Jj
Manufacturer: Smithsonian
ProductGroup: Book
Binding: Paperback

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ASIN: 1560988169

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.

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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
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Binding: Paperback

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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.

Phylogenetic Patterns and the Evolutionary Process: Method and Theory in Comparative Biology

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Phylogenetic Patterns and the Evolutionary Process: Method and Theory in Comparative Biology
Niles Eldredge , and Joel Cracraft
Manufacturer: Columbia University Press
ProductGroup: Book
Binding: Paperback

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Phylogenetic Analysis of DNA Sequences
Michael M. Miyamoto , and Joel Cracraft
Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Hardcover

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Book Description

With increasing frequency, systematic and evolutionary biologists have turned to the techniques of molecular biology to complement their traditional morphological and anatomical approaches to questions of the historical relationship and descent among groups of animals and plants. In particular, the comparative analysis of DNA sequences is becoming a common and important focus of research attention today. The objective of this volume is to survey the emerging field of molecular systematics of DNA sequences, and to appraise the strengths and limitations of the different approaches yielded by these techniques. The contributors are an internationally recognized group of investigators from different schools and disciplines who critically address a diversity of crucial questions about DNA systematics, including DNA sequence data acquisition, phylogenetic inference, congruence and consensus problems, limitations of molecular data, and the integration of molecular and morphological data sets. The work will interest all botanists and zoologists involved in systematics, taxonomy, and evolution.

Phylogenetic Perspectives on the Vertebrate Immune System (Advances in Experimental Medicine and Biology)

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Phylogenetic Perspectives on the Vertebrate Immune System (Advances in Experimental Medicine and Biology)

Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 0306464314

Book Description

This volume describes the evolution of immune systems and covers new molecular information concerning the development of recognition, immunoglobulins, and cytokines. Invertebrates and lower vertebrates contribute to a more complete understanding and clarification of the immune/inflammatory response in higher animals. Chapters detail the major areas of immunology and encourage a more extensive development of invertebrate models as useful and unique in modern immunological and industrial laboratories. In addition, chapters focus on mechanisms of development and immunodefenses in protostome and deuterostome and lower vertebrates. There is a strong emphasis on evolutionary cell biology, phylogenetic inferences, and the evolution of recognition and regulatory systems.

Phylogenetic Relationships Among Advanced Snakes: A Molecular Perspective (University of California Publications in Zoology)

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Phylogenetic Relationships Among Advanced Snakes: A Molecular Perspective (University of California Publications in Zoology)
John E. Cadle
Manufacturer: University of California Press
ProductGroup: Book
Binding: Paperback

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Book Description

This monograph addresses questions concerning the evolutionary history of advanced snakes using molecular phylogenetic data. Viperids are the sister group of the other clades examined. Atractaspis may share a lineage with elapids. The study concludes that, because of sampling problems, many generalizations concerning snake evolution derived from the fossil record, particularly those about the age of lineages, are probably in error.

Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists

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good orientation
Step-by-step instruction with downloadable input data files
MrBayes and Paup* manual

Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists
Barry G. Hall
Manufacturer: Sinauer Associates
ProductGroup: Book
Binding: Paperback

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Customer Reviews:

good orientation.......2004-07-26

I've been looking around for a good introduction to bioinformatics software for some months now. I have only read 37 pages, but that was worth the purchase price and I am enthusiastic about reading on. Hall does a very nice job of explaining the uses of Blast and ClustalX, differentiating among the various versions and showing how protein analysis differs from DNA analysis. (His focus is proteins.) He takes you step by step through an analysis and explains the information available on the screen at each step. He tells you how to manage the resulting input and results files, and he even explains choices of penalties for gaps. All very clear.

Step-by-step instruction with downloadable input data files.......2004-01-21

What I liked about this slim book is that, as in Chapter 1, it first provides you with data files with which you can build phylogenetic trees, then guides you through step by step. Also, I liked its concise overview about phylogenetics.

However, Chapter 2 does not come with such data files. It only provides you with templates. Why?

Also what you should be aware before ordering this book is that the explanations on this book assume that you;
(1) have a copy of PAUP (which is not a free software), and;
(2) are running PAUP on Mac OS.

So, if you are running PAUP on Windows/UNIX and do not have any access to Mac, you probably don't want to buy this book. PAUP manual should better serve you.

MrBayes and Paup* manual.......2003-09-28

I picked up this book because I was trying to learn MrBayes on my own with little success. With new versions of MrBayes, this book is already out of date and I encountered some frustration with my Nexus code being wrong, but between the help function, a lot of trial and error, and Hall's book I managed to successfully analyze my data using Bayesian analysis! I highly recommend it for the "cookbook" appeal-- software like PAUP and MrBayes can be difficult to learn on your own, and it's nice to have someone explain it step by step. I would have liked some instruction on saturation curves, but the book is fairly complete otherwise. MacClade is not mentioned, probably because it is more user-friendly than the programs included. PTME has been criticized for some incorrect statements in the book regarding theory, but I would expect students to use this book for practice more than theory. Overall, a great little manual to have on the shelf.

Phylogenetic analysis of the Malvadendrina clade (Malvaceae s.l.) based on plastid DNA sequences [An article from: Organisms Diversity & Evolution]

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Phylogenetic analysis of the Malvadendrina clade (Malvaceae s.l.) based on plastid DNA sequences [An article from: Organisms Diversity & Evolution]
R. Nyffeler , C. Bayer , W.S. Alverson , A. Yen , and Whit
Manufacturer: Elsevier
ProductGroup: Book
Binding: Digital
ASIN: B000RR4ONK

Book Description

This digital document is a journal article from Organisms Diversity & Evolution, published by Elsevier in 2005. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser.

Description:
Phylogenetic relationships within Malvaceae s.l., a clade that includes the traditional families Bombacaceae, Malvaceae s.str., Sterculiaceae, and Tiliaceae, have become greatly clarified thanks to recent molecular systematic research. In this paper, we use DNA sequences of four plastid regions (atpB, matK, ndhF, and rbcL) to study relationships within Malvadendrina, one of the two major clades of Malvaceae s.l. The four data sets were generally in agreement, but five terminal taxa manifested highly unexpected affinities in the rbcL partition, and the non-coding sequences of the trnK intron were found to provide limited phylogenetic information for resolving relationships at the base of Malvadendrina. The remaining data strongly support the existence of six major clades within Malvadendrina: Brownlowioideae, Dombeyoideae, Helicteroideae, Malvatheca (comprising Bombacoideae and Malvoideae), Sterculioideae, and Tilioideae. These data also resolve the placement of two problematic taxa: Nesogordonia (in Dombeyoideae) and Mortoniodendron (in Tilioideae). The relationships among the six clades are not definitively resolved, but the best-supported topology has Dombeyoideae as sister to the remainder of Malvadendrina (posterior probability PP=80%) and Sterculioideae as sister to Malvatheca (PP=86%). This early branching position of Dombeyoideae is supported by similarities in floral characters between members of that clade and outgroup taxa in Byttnerioideae. Similarly, the sister-group relationship of Sterculioideae and Malvatheca receives support from androecial characteristics, like subsessile or sessile anthers and an absence of staminodes, shared by these two clades.

The phylogenetic characteristics of three different 28S rRNA gene regions in Encarsia (Insecta, Hymenoptera, Aphelinidae) [An article from: Organisms Diversity & Evolution]

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The phylogenetic characteristics of three different 28S rRNA gene regions in Encarsia (Insecta, Hymenoptera, Aphelinidae) [An article from: Organisms Diversity & Evolution]
S. Schmidt , F. Driver , and P. De Barro
Manufacturer: Elsevier
ProductGroup: Book
Binding: Digital
ASIN: B000RR976Y

Book Description

This digital document is a journal article from Organisms Diversity & Evolution, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser.

Description:
Two expansion segments of the large ribosomal subunit (28S-D2 and 28S-D3) and the ribosomal first internal transcribed spacer (ITS-1) were sequenced to investigate the potential of each region for defining species limits and for inferring phylogenetic relationships within the aphelinid genus Encarsia (Hymenoptera, Chalcidoidea). Alignment of the ITS-1 region was complicated by the presence of high levels of length polymorphism. Secondary-structure models of the ITS-1 molecule are proposed which led to an improved alignment and the inclusion of some highly polymorphic sequences. The additional information obtained from the secondary-structure models can provide a justification for the exclusion of hypervariable regions from the phylogenetic analysis. The D3 region is the most conserved, ITS-1 the most variable of the three gene regions investigated. Phylogenetic analyses suggest the D2 region to be most suitable not only for inferring relationships, but also for taxonomic and diagnostic purposes at species level. The ITS-1 region is best suited for inferring relationships between closely related species or among populations of the same species. The combined analysis using all three regions led to a better tree and a reduced number of equally most parsimonious trees. See also Electronic Supplement at: http://www.senckenberg.de/odes/06-07.htm

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