Book Chapter

An Introduction to Phylogenetics and Its Molecular Aspects

Sonderegger, Bernhard Pascal, Bittar, Gabriel Jîvasattha

2009

Overview

The following sections are included: Introduction Homology and Homoplasy: Look-alikes are Not Necessarily Closely Related Characters and Their States Homology — A Phylogenetic Hypothesis Ancestral or Derived — Qualifying the State of a Character Homoplasy — Pitfall in Phylogenetics Molecular Phylogenetics Gene Duplication vs. Speciation, Paralogy vs. Orthology Sequence Alignment — A Homology Hypothesis Evolutionary Time Evolutionary distance and the course of time Time and time again: paleontology and molecular evolution Micromutations and the molecular clock Tree Reconstitution The Tree Graph Model — Transmission of Phylogenetic Information Numerical Taxonomic Phenetics (NTP) The neighbor joining algorithm A common NTP artefact Cladistic Maximum Parsimony (CMP) Methods Symplesiomorphy, synapomorphy, and autapomorphy Cladistic maximum parsimony (CMP) and character compatibility (CC) methods CMP common artefacts Probabilistic Methods Searching for an Optimal Tree in a Large, Populated Space The number of possible phylogenetic trees The branch-and-bound algorithm Heuristic methods in tree reconstruction A rapid maximum likelihood method: RAxML Creating consensus trees Estimating tree robustness Recommended, Acceptable, and Unacceptable Groupings of Taxons Paraphylon — Acceptable with caveat Convergence and reversion polyphylons — Unacceptable Uses of Phylogenetics in Molecular Biology Prediction of Gene Function Advanced Phylogenetic Analyses and New Directions Phylogenetics Resources References

• Publisher: WORLD SCIENTIFIC
• Subject: SECTION III PHYLOGENETICS AND EVOLUTIONARY BIOINFORMATICS
• ISBN: 9789812838773, 9812838775, 9789814468695, 9789812838780, 9812838783, 981446869X