Sample Collection - Birds were captured using walk-in funnel traps, night-lighting, and rocket nets. Plucked feathers were collected from adult
sage-grouse as part of research projects in Bighorn County, Montana and Sheridan County, Wyoming (2003-2006), Campbell County, Wyoming (2003-2004), and Johnson County,
Wyoming (2004-2006).
DNA extraction - I used the techniques that I developed for Qiagen DNA extraction kits - see link in side bar
Microsatellites - I used the PCR & microsatellite techniques outlined on the Genetic Protocols web site - see link in side bar
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).
• Colony - finds highly related individuals to exclude them from the STRUCTURE analysis
• 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.
• Arlequin - AMOVA & can be used for pairwise Fst significance testing
• Relatedness - all relatedness analyses
• R - Mantel tests & Partial Mantel tests