Catalog Description:

A comprehensive survey of the theory and methodology of systematics as they are applied today to all groups of organisms, with a practical experience in the acquisition and analysis of systematic data.

This course was last offered Fall 1994. Depending upon demand, we hope to be able to offer this course again Fall 2000. If you are interested in taking this course, please contact Stephen Downie.

Introduction:

Systematics is the exciting and ever-changing discipline which treats the kinds and the diversity of organisms and of any and all relationships which exist among them. As such this field deals with the processes and the products of evolutionary change and with the ways in which the evolutionary relationships of these products can best be understood and classified. Any comparative study, be it behavioral, biochemical or biogeographical, should have at its base an understanding of the systematic relationships of the organisms being compared. Attempts to understand the origins of the biological diversity within ecosystems or aimed at the conservation of this diversity should have a strong systematic component. This course will provide a comprehensive survey of the theory and methodology of systematics as they are applied today to ALL groups of organisms. The course is directed at those students interested in studies of evolutionary biology, biodiversity, conservation biology, and/or systematics. Some of the topics that will be considered include: species concepts and mechanisms of speciation, the major contemporary schools of taxonomy, methodologies of phylogeny estimation, the systematic significance of patterns of geographical distribution, considerations of molecular evolution as applied to systematic studies, the formation and use of research collections and nomenclature.

Prerequisites:

Biology 121 and a course in evolutionary biology and systematics (such as Plant Biology 260 [Systematics of Flowering Plants], Entomology 302 [Classification and Evolutionary History of Insects], or Ecology, Ethology and Evolution 232 [Comparative Vertebrate Anatomy]), or consent of instructor.

Credit:

4 hours or 1 unit

Time & Place:

Lecture: Mon., Wed. & Fri., 11 a.m.-12, 408 Natural History Building
Lab: Mon., OR Wed. OR Fri., 1-4, 323 and 423 Natural History Building

Instructors:

Textbooks:

These are the books we have required students to use in the past:

Mayr, E. and P.D. Ashlock. 1991. Principles of Systematic Zoology. 2nd ed. New York: McGraw Hill, Inc.
Quicke, D. L. J. 1993. Principles and Techniques of Contemporary Taxonomy. New York: Chapman and Hall.

Supplemental Readings:

A number of books and photocopies of recent journal papers will be placed on reserve in the Biology Library. These materials will expand on topics discussed in lecture and lab and will help the students prepare their final lab presentations.

Grading:

The final grade (of 100 points) will be determined based on the following:

• Mid-term lecture examination (includes laboratory material) 25 points
• Final lecture examination (comprehensive but emphasizing last half of course; includes laboratory material) 40 points
• Laboratory presentation (each student will be required to present and lead a 45-min discussion at end of semester) 10 points
• Laboratory project write-up (due at end of semester) 25 points

Lecture Syllabus:

Week 1
Course introduction; The science of systematics

Week 2
Groups, ranking, and the historical development of classifications
Artificial, phenetic, evolutionary and cladistic approaches to classification
Identification and keys

Week 3
LABOR DAY. NO CLASS.

Week 4
Taxonomic treatment of allopatric variation
The reproductive biology of organisms (1): The population properties of sexual reproduction
The reproductive biology of organisms (2): Non-sexual modes of reproduction

Week 5
Reproductive isolating mechanisms
Species concepts (1)
Species concepts (2)

Week 6
Hybridization and introgression
Polyploidy
Modes of speciation

Week 7
Principles and criteria
Taxonomic Evidence (1): Characters and character states
Taxonomic Evidence (2): The sources of taxonomic characters

Week 8
Phenetics
Evolutionary Taxonomy
Cladistics

Week 9
Cladistics (2)
Turning dendrograms into classifications

Week 10
Molecular evolution (2): Mitochondrial and chloroplast (organellar) genomes
MID-TERM LECTURE EXAMINATION
Molecular evolution (3): Organellar genomes continued

Week 11
Molecular evolution (4): The status of the molecular "clock" hypothesis
Molecular evolution (5): Copy multiplicities revealed by Cot analyses
Molecular evolution (6): Gene duplication, the origin of gene families, exon shuffling and the orthology/paralogy problem

Week 12
Molecular evolution (7): The evolution of transposable sequences
Phylogeny estimation (1): Distance data
Phylogeny estimation (2): Maximum-parsimony (and compatibility) algorithms

Week 13
Phylogeny estimation (3): Maximum-likelihood algorithms
Phylogeny estimation (4): Cladogram reliabilities
Molecules versus morphology: Conflict or compromise?

Week 14
Biogeography [Q: 12.2]

Week 15
Taxonomic publications and literature
The rules of nomenclature (1)
The rules of nomenclature (2)

Week 16
The rules of nomenclature (3)
The role of systematics in studies of biodiversity and in conservation planning [Q: 13.2]
Downie's Research Program

Laboratory Syllabus:

Unless otherwise indicated, all laboratories will be held or initiated in Room 323 Natural History Building. There will be three sections (either Monday, Wednesday or Friday) from 1-4 pm. Computing facilities available for our use are in room 423 NHB. All labs are designed for providing much hands-on experience in observing, collecting and analyzing systematic data. The laboratory exercises are also designed to facilitate discussions among class participants.

• Week 1 No lab this week.

• Week 2 Characters, character states and classifications: Exercise using inanimate objects as taxa to simulate the systematic procedures of character and character state analysis; compilation of a data matrix; and construction of classifications which reflect the "relationships" among the taxa. The data matrix will be used to construct a key to facilitate the identification of the taxa.

• Week 3 Generation of a character-state matrix: Applied case studies involving either Camin's Caminalcules or Wagner's Dendrogrammaceae. Selecting and scoring characters; generation of a data matrix to be used in subsequent numerical analyses.

• Week 4 Wagner's groundplan divergence method (WGDM) of phylogenetic analysis: A manual method of parsimony analysis. Selection of characters and character states, and determination of character polarity.

• Week 5 WGDM cladograms, laboratory projects, and introduction to MacIntosh computers. Class discussion of student-constructed cladograms and pitfalls of inferring evolutionary hypotheses manually. Discussion of laboratory projects and student presentations; and an introduction to microcomputers.

• Week 6 Introduction to MacClade (I): Interactive software for exploring phylogeny and analyzing character state evolution. Introduction to the tree and data editor windows; importing files; and simple tree manipulation.

• Week 7 MacClade (II): Character transformation types (Fitch, Wagner, Camin- Sokal; and Dollo parsimony) character weighting; character exclusion; basic tree and character statistics; charting; and entering project data into MacClade.

• Week 8 Introduction to numerical phenetics, distance methods and PHYLIP I: A summary of distance-based methods of phylogenetic reconstruction using manual and computer methods.

• Week 9 Introduction to Phylogenetic Analysis Using Parsimony (PAUP I): Introducing the basic organization and capabilities of PAUP. Accessing the program; importing a data matrix; finding the most parsimonious trees using the various algorithms; and saving trees.

• Week 10 The analysis of molecular data: Aligning sequences; searching for trees using PAUP; weighting characters using MacClade; and a discussion of sequence depositories.

• Week 11 PAUP II: Coping with multiple trees; bootstrapping; forcing monophyly; specifying character types; user-defined trees; constructing a data matrix for PHYLIP analysis; and generating random trees.

• Week 12 Phylogeny Inference Package (PHYLIP) II: Programs for distance and character-state data; making consensus trees; DNA sequence programs; and maximum likelihood.

• Week 13 Museums and Herbaria: Tours of local facilities. Systematic collections; curating of collections, locations of type specimens, arrangement of collections; and taxonomic publications.

• Week 14 Student Presentations (1): Since the laboratory of Week 5, the students have had opportunity to analyse either their own research data or data obtained from literature. In doing so, they have obtained much hands-on experience in observing, collecting and analyzing systematic data using modern methods. During this and the next two labs, each student is required to give a 30-40 minute presentation of the results of their work.

• Week 15 Student Presentations (2)

• Week 16 Student Presentations (3)