I will post relevant data sets here by Wednesday of the respective week
Lab 1 - genotyping error and data checking
Software Microchecker: Manual, Paper
Software Pedant: Manual, Paper, Poster
Lab Handout, Lecture Slides
Data: A sample of 96 brown rockfish from Point Heyer, Vashon Island, scored at 4 microsatellite loci.
Lab 2 - Statistical tests
The two Excel files are only there for your entertainment - you only need the four input files below
- Sock02.xls: Excel spreadsheet with microsatellite and SNP data for four sockeye populations.
- Sock02all.xls: The same data in an Excel spreadsheet with Microsatellite Toolkit run already, that is, all the input files are in here.
- S02mic: Microsatellite input file for Genepop
- S02SNP: SNP input file for Genepop
- SNPs.dat: SNP input file for FSTAT
- Micros.dat: Microsatellite input file for FSTAT
Lab 3 - Estimation of population differentiation: FST, AMOVA, genetic distances
- FSTAT: has an extensive help file that explains methods
- Arlequin: general purpose program, but here used for AMOVAs (Analysis of Molecular Variance)
- SPSS: general statistics software
- Sock0203: same sockeye data as above, but for two years (2002, 2003). Prepare your own input files.
Lab 4 - Power analysis and correction for multiple tests
POWSIM - make sure you got the newest version (should be dates 12/1/2006)
Excel Spreadsheet - save to your computer. PopTools version of the same
Lab 5 - Relatedness
Lab5.zip - compressed file with lab handout, data files and spreadsheet
- Likelihood based inference of parentage using co-dominant markers. Includes powerful simulations allowing for genotyping error. Original version was published in 1998, but this is a new version (2006) that removed some of the earlier problems. The website provides a brief overview of the basic methods in the program, while the Help file is a more in depth description - both are very good
- Java application that does many analyses previously only available in KINSHIP on the Mac platform. Primarily used for pedigree relationship reconstruction and kin group assignments using genetic markers
Lab 6 - Effective population size
Spreadsheet with data: Ne.xls
Input file for Bottleneck: Forks3BY.txt
input files for Ne-estimator: ForksNe99.txt, ForksNe02.txt, ForksNe05.txt
- Ne Estimator
- Uses various methods to estimate effective population size. Can be integrated with three other programs, TM3 (Bayesian), McLeeps (multilocus maximum likelihood) and a method allowing immigration (MLNE).
- Program to detect recent population bottlenecks from genetic data
Lab 7 - Assignment methods
- contains lab handout, Excel sheet of data, input files for GeneClass and Structure and the paper on Forks Creek Assignment by yours truly.
Lab 8 - Landscape Genetics
Excel spreadsheet with data
Background to the data:
The Tumut fragmentation study
Paper: Peakall et a. 2003
Lab 9 - Selection
FDist2 - download
input files: all years, 2002, 2003, 2004
Lab 10 - Thanksgiving
Lab 11 - Phylogeography
Phylogeography.zip: data files for Mega, DNASP and Automated Nested Clade Analysis.
Originating paper: Piertney et al. 2005