Biology Reference
In-Depth Information
CHAPTER 12
Molecular Systematics and the
Evolution of Arthropods
Chapter Outline
12.1 Overview 522
12.2 Introduction 523
12.3 Controversies in Molecular Systematics and Evolution
527
12.3.1
Molecular versus Morphological Traits
527
12.3.2
The Molecular Clock
528
12.3.3
The Neutral (or Nearly Neutral) Theory of Evolution
530
12.3.4 Homology and Similarity 531
12.4 Molecular Methods for Molecular Systematics and Evolution
531
12.4.1
Protein Electrophoresis
533
12.4.2
Molecular Cytology
535
12.4.3
Restriction Fragment Length Polymorphism (RFLP) Analysis
536
12.4.4
DNA and Genome Sequencing
537
12.4.5
Fragment Analyses of Genomic DNA
538
12.5 Targets of DNA Analysis
538
12.5.1 Mitochondria 539
12.5.1.1
The Barcode of Life Project
542
12.5.2
Ribosomal RNA
544
12.5.3
Satellite DNA
546
12.5.4 Introns 546
12.5.5
Nuclear Protein-Coding Genes
546
12.5.6
Rare Genomic Changes
546
12.5.7 MicroRNAs 547
12.6 Steps in Phylogenetic Analysis of DNA Sequence Data
549
12.6.1
Gene Trees or Species Trees
549
12.6.2
Rooted or Unrooted Trees
549
12.6.3
Tree Types
549
12.6.4
Project Goals and Appropriate DNA Sequences
551
12.6.5
Sequence Comparisons with BLAST
553
12.6.6
Aligning Sequences
556
12.6.7
Constructing Phylogenies
556
12.6.8 Artifacts 561
12.6.9
Software Packages
562
