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Computer Lab in Molecular Systematics
Biol. 402 - Prof. Eernisse
California State University, Fullerton
Biol. 402 Section 01, Schedule # 18872
MoWe 11:00-11:50 and We 1:00 to 3:50, MH289
Fall, 2011
Tentative Discussions Outline and Readings
All reading assignments will be from PTME text (below left)
or supplied as pdfs or hand-outs and will be linked by week in the schedule below.
The second and third texts below have been used in the past and some reading assignments will come from them.
PageBook

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WEEK DATE LECTURE TOPIC ASSIGNMENT
1

Aug    22
Aug    24

Introduction to course: Molecular systematics
Understanding trees

 None (TITANium: NCBI assignment - due 8/24)
Understanding Trees (pp. 121-128) and browse PTME Chs. 1&2 (for Lab 1)
2 Aug    29
Aug    31		 Understanding trees (cont.)
Molecular systematics		 Understanding Trees (pp. 128-137)
None
3 Sep    5
Sep    7		 Labor Day
Molecular systematics (cont.)
NO CLASS
NCBI Assignment
4 Sep    12
Sep    14		 Multiple sequence alignment algorithms (Clustal W Online Help)
Phylogenies (cont.) and lab prep. (PAUP*)
 PTME Chs. 4 & 5 (no quiz)
Page &Holmes: Ch. 2
5 Sep    19
Sep    21		 Substitutions and Indels
Molecular evolution (cont.; Li pp. 21-34)		 Li pp. 1-11, 21-34, skim pp. 12-20
Li pp. 21-34 (cont.)
6 Sep    26
Sep    28		 Simulating molecular evolution (Literature Exercise)
Phylogenetic trees, distances, parsimony criterion		 PTME Chs. 6 & 8
PTME Chs. 6 & 8
7 Oct    3
Oct    5		 Maximum Likelihood/Bayesian Inference
Review 		PTME Chs. 9 & 10
None (Lab: Lit. Ex. Presentations)
8 Oct    10
Oct    12 		Midterm I
Upcoming Class Project background
TBA
9 Oct    17
Oct    19 		Primer design for molecular systematics TBA
TBA
10 Oct    24
Oct    26 		Species problems, hybrids, introgression
Hybrid zones, speciation by hybridization
 TBA
McGuire et al. 2007
11 Oct    31
Nov    2 		Open Lab
Species phylogenies
Avise pp. 401-421
Avise pp. 401-421
12 Nov    7
Nov    9

Phylogeography and Macroevolution
Maximum Likelihood

 Avise pp. 422-443 (P&H Ch. 6)
Swofford & Sullivan, pp. 196-204
13 Nov    14
Nov    16		 TBA - Review and work on final projects
Midterm II

TBA
TBA
14 Nov    21-25
 Fall Break
 No Class
15 Nov    28
Nov    30		 Primary literature article - TBA
High-level phylogeny of animals (Paleobiology article)
 TBA
Peterson 2005 (+ skim Avise pp. 443-452)
16 Dec    5
Dec    7		 Final project presentations
Final Project Presentations

TBA
TBA
Finals Dec 12-16

FINAL PROJECT WRITE-UPS DUE MONDAY DEC. 12
(No Final Exam)

  Turn in to MH282 by 5 p.m.
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