Book contents
- Frontmatter
- Contents
- Preface
- Acknowledgments
- 1 The Central Dogma
- 2 RNA Secondary Structure
- 3 Comparing DNA Sequences
- 4 Predicting Species: Statistical Models
- 5 Substitution Matrices for Amino Acids
- 6 Sequence Databases
- 7 Local Alignment and the BLAST Heuristic
- 8 Statistics of BLAST Database Searches
- 9 Multiple Sequence Alignment I
- 10 Multiple Sequence Alignment II
- 11 Phylogeny Reconstruction
- 12 Protein Motifs and PROSITE
- 13 Fragment Assembly
- 14 Coding Sequence Prediction with Dicodons
- 15 Satellite Identification
- 16 Restriction Mapping
- 17 Rearranging Genomes: Gates and Hurdles
- A Drawing RNA Cloverleaves
- B Space-Saving Strategies for Alignment
- C A Data Structure for Disjoint Sets
- D Suggestions for Further Reading
- Bibliography
- Index
11 - Phylogeny Reconstruction
Published online by Cambridge University Press: 05 June 2012
- Frontmatter
- Contents
- Preface
- Acknowledgments
- 1 The Central Dogma
- 2 RNA Secondary Structure
- 3 Comparing DNA Sequences
- 4 Predicting Species: Statistical Models
- 5 Substitution Matrices for Amino Acids
- 6 Sequence Databases
- 7 Local Alignment and the BLAST Heuristic
- 8 Statistics of BLAST Database Searches
- 9 Multiple Sequence Alignment I
- 10 Multiple Sequence Alignment II
- 11 Phylogeny Reconstruction
- 12 Protein Motifs and PROSITE
- 13 Fragment Assembly
- 14 Coding Sequence Prediction with Dicodons
- 15 Satellite Identification
- 16 Restriction Mapping
- 17 Rearranging Genomes: Gates and Hurdles
- A Drawing RNA Cloverleaves
- B Space-Saving Strategies for Alignment
- C A Data Structure for Disjoint Sets
- D Suggestions for Further Reading
- Bibliography
- Index
Summary
The urge to record or to reconstruct “family trees” seems to be a strong one in many different areas of human activity. Animal breeders have an obvious interest in pedigrees, linguists have grouped human languages into families descended from a common (and in many cases unattested) ancestor, and, when several manuscripts of the same text have been recovered, biblical scholars have tried to piece together which ones served as sources for which others. Even before the advent of the theory of evolution, naturalists attempted to discern the “Divine Plan” by assigning each known organism to its correct place in a system of nesting categories known as a taxonomy.
More modern biologists have tried to reconstruct the course of evolution by building trees reflecting similarities and differences in relevant features or characters of various species. Whereas early work relied upon morphological features such as shape of leaf or fruit for classification, most recent efforts focus on less subjective molecular features. In this chapter, we develop a program for constructing the evolutionary tree – or phylogeny – that best accounts for the differences observed in a multiple sequence alignment.
Parsimonious Phylogenies
Broadly speaking, there are two approaches to reconstructing the phylogeny of a group of species. One approach first reduces the similarities and differences among the n species to n(n – 1)/2 numerical scores; it then finds the phylogeny that optimizes a certain mathematical function of those scores.
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- Information
- Genomic PerlFrom Bioinformatics Basics to Working Code, pp. 155 - 172Publisher: Cambridge University PressPrint publication year: 2002