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Population Genetic Software

ECL 290 Winter 2007
Course offered through Ecology Graduate Group Jan-Mar 2007

Instructors: Holly Ernest, Bernie May, and John Eadie

Syllabus

course objectives (pdf)

software websites (pdf)

course questions (pdf)

Week 1: Introduction to different types of markers
Josh Hull, Molly Stephens, and Rachel Schwartz
AFLP powerpoint (pdf) Molly Stephens
Microsatellite data and analysis (pdf) Josh Hull
Week 2: Review of key population genetic concepts
Ann T. Chang, Elizabeth Long, Adam Wentzell, and Jennifer Kurushima
Handout on key population genetic concepts (pdf) Elizabeth Long
Fstats powerpoint (pdf) Elizabeth Long
Hardy-Weinberg and linkage disequilibrium powerpoint (pdf) Ann Chang
Notes of frequentist, maximum likelihood, and Bayesian statistics (pdf) Jessica Petersen
Allele numbers and frequencies powerpoint (pdf) Jennifer Kurushima
Genetic Distance powerpoint (pdf) Adam Wentzell
Week 3: Getting Started with a data set (Part 1)
Renate Eberl and Lindsay Clark
Using NTSYS-pc for Principal Coordinate Analysis of dominant data (pdf) Molly Stephens
Whichloci powerpoint (pdf) Lindsay Clark
Whichloci handout (pdf) Lindsay Clark
Microsatellite toolkit and CONVERT handout (pdf) Renate Eberl
Getting started with a data set powerpoint (pdf) Renate Eberl
Week 4: Getting started with a data set: Genepop on the Web and GDA

(Part 2) Rachel Simmons and Mandi Finger

http://genepop.curtin.edu.au/

Robertson, Alan and Hill, William G. 1984.  Deviations from Hardy-Weinberg proportions: sampling variances and use in estimation of inbreeding coefficients.  Genetics 107:703-718.

GDA user's guide (pdf)

Weir, B.S. and C. Clark Cockerham 1984. Estimating F-statistics for the Analysis of Population Structure.  Evolution 38:1358-1370.

Rice, William R. 1989. Analyzing Tables of Statistical Tests. Evolution 43:223-225.

Week 5: Getting started with the data set: Genepop on the Web and Fstat

(Part 3) Andrea Drauch and Joana Fernandes

Genepop and Fstat handout (pdf) Andrea Drauch

Week 6: Using STRUCTURE Kraig Kraft and Sarah Brown, Jason Sexton

STRUCTURE handout (pdf)

STRUCTURE powerpoint (pdf)

Choosing a K:

log likelihood (pdf)

delta K and Evano's ad hoc statistic (pdf)

Testing STRUCTURE with complex population structures using simulated data handout (pdf)

EASYPOP software:http://www.unil.ch/dee/page36926_fr.html

Week 7: GENETIX  Ann T. Chang, Philip Lavretsky, and Annabelle Kleist

GENETIX handout (pdf)

GENETIX powerpoint (pdf)

Using FCA (Factorial Correspondence Analysis) powerpoint (pdf) Annabelle Kleist

Week 8: Geneclass and Assignment testing

Geneclass and assignment testing powerpoint (pdf) Catarina Ginja

Assignment testing applications (and misapplications) powerpoint (pdf) Catarina Ginja

Week 9: Kinship analysis and relatedness Jennifer Kurushima, Beverly Ajie

Relatedness powerpoint (pdf)

SPAGeDi handout (pdf)

ML-Relate handout (pdf)

K-coefficients handout (pdf)

Week 10: Parentage analysis Mariah Meek and Jessica Petersen

Parentage analysis powerpoint (pdf) Mariah Meek and Jessica Petersen

CERVUS powerpoint (pdf) Mariah Meek

Comparison between CERVUS and ML-Relate powerpoint (pdf) Jessica Petersen

CERVUS handout (pdf)