DNA extraction - I used the techniques that I developed for Qiagen DNA extraction kits
Microsatellites - I used the PCR & microsatellite techniques outlined on the Genetic Protocols web site
Analysis - The following programs were used for various aspects of this research segment:
• STRUCTURE - tells you the most likely number of groups (K) of populations, subpopulations, and leks in the region of interest. It can also be used as a form of the assignment test to look for dispersal between subpopulations and unique leks (if you have them).
• GenAlEx - I only use this program to create Arlequin & Genepop files (I've had bad experiences using the actual calculation functions)
• GENEPOP - the best overall program for calculating genetic diversity - I use it to look for HW and linkage disequilibrium and to calculate He, Ho, pairwise Fst, and Fst-based isolation by distance
• FSTAT - Allelic Richness calculations & pairwise Fst significance testing. It also has the nifty option of calculating a variety of genetic diversity measures for multiple populations, subpopulations, or groups at once and then determining if all of those values are significantly different from one another.
• BOTTLESIM - Simulates what should happen genetically happen in a population given historic genetic data and population counts
• NeESTIMATOR - Estimates effective population size given genetic data
• BOTTLENECK - Tests for a genetic bottleneck