Inferring Phylogenies
Phylogenies (evolutionary trees) are basic to thinking about and analyzing differences between species. Statistical, computational, and algorithmic work on them has been ongoing for four decades, with great advances in understanding. Yet no book has summarized this work until now. Inferring Phylogenies explains clearly the assumptions and logic of making inferences about phylogenies, and using them to make inferences about evolutionary processes. It is an essential text and reference for anyone who wants to understand how phylogenies are reconstructed and how they are used.

As phylogenies are inferred with various kinds of data, this book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.

Inferring Phylogenies is intended for graduate-level courses, assuming some knowledge of statistics, mathematics (calculus and fundamental matrix algebra), molecular sequences, and quantitative genetics.
1101662240
Inferring Phylogenies
Phylogenies (evolutionary trees) are basic to thinking about and analyzing differences between species. Statistical, computational, and algorithmic work on them has been ongoing for four decades, with great advances in understanding. Yet no book has summarized this work until now. Inferring Phylogenies explains clearly the assumptions and logic of making inferences about phylogenies, and using them to make inferences about evolutionary processes. It is an essential text and reference for anyone who wants to understand how phylogenies are reconstructed and how they are used.

As phylogenies are inferred with various kinds of data, this book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.

Inferring Phylogenies is intended for graduate-level courses, assuming some knowledge of statistics, mathematics (calculus and fundamental matrix algebra), molecular sequences, and quantitative genetics.
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Inferring Phylogenies

Inferring Phylogenies

by Joseph Felsenstein
Inferring Phylogenies

Inferring Phylogenies

by Joseph Felsenstein

Overview

Phylogenies (evolutionary trees) are basic to thinking about and analyzing differences between species. Statistical, computational, and algorithmic work on them has been ongoing for four decades, with great advances in understanding. Yet no book has summarized this work until now. Inferring Phylogenies explains clearly the assumptions and logic of making inferences about phylogenies, and using them to make inferences about evolutionary processes. It is an essential text and reference for anyone who wants to understand how phylogenies are reconstructed and how they are used.

As phylogenies are inferred with various kinds of data, this book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.

Inferring Phylogenies is intended for graduate-level courses, assuming some knowledge of statistics, mathematics (calculus and fundamental matrix algebra), molecular sequences, and quantitative genetics.

Product Details

ISBN-13: 9780878931774
Publisher: Sinauer Associates is an imprint of Oxford University Press
Publication date: 09/04/2003
Edition description: New Edition
Pages: 580
Product dimensions: 9.04(w) x 7.06(h) x 0.94(d)

About the Author

Joe Felsenstein is Professor in the Department of Genome Sciences at the University of Washington, Seattle, where he has taught for more than thirty years. He earned a B.S. (Honors) in Zoology from the University of Wisconsin, Madison, and a Ph.D. in Zoology from the University of Chicago. Dr. Felsenstein is the author of the widely used PHYLIP package of programs for inferring phylogenies. He served as President of the Society for the Study of Evolution in 1993 and has received numerous awards, including: election to membership in the American Academy of Arts and Sciences (1992); the Sewall Wright Award, American Society of Naturalists (1993; election to membership in the National Academy of Sciences (1999); and the Weldon Memorial Prize, Oxford University (2000). His work has ranged from theoretical evolutionary genetics to statistical methods for inferring phylogenies. His current research interests include the development of coalescent-based Markov Chain Monte Carlo methods of computing likelihoods for models of evolution within species, and development of statistical methods for inferences about quantitative characters within and between species.

Table of Contents

1. Parsimony methods

2. Counting evolutionary changes

3. How many trees are there?

4. Finding the best tree by heuristic search

5. Finding the best tree by branch and bound

6. Ancestral states and branch lengths

7. Variants of parsimony

8. Compatibility

9. Statistical properties of parsimony

10. A digression on history and philosophy

11. Distance matrix methods

12. Quartets of species

13. Models of DNA evolution

14. Models of protein evolution

15. Restriction sites, RAPDs, AFLPs, and microsatellites

16. Likelihood methods

17. Hadamard methods

18. Bayesian inference of phylogenies

19. Testing models, trees, and clocks

20. Bootstrap, jackknife, and permutation tests

21. Paired-sites tests

22. Invariants

23. Brownian motion and gene frequencies

24. Quantitative characters

25. Comparative methods

26. Coalescent trees

27. Likelihood calculations on coalescents

28. Coalescents and species trees

29. Alignment, gene families, and genomics

30. Consensus trees and distances between trees

31. Biogeography, hosts, and parasites

32. Phylogenies and paleontology

33. Tests based on tree shape

34. Drawing trees

35. Phylogeny software
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