User:Tara K. Luckau/Notebook/Team ConGen/2011/08/18

Tara's Lab Notebook

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Meeting with Andy Bohonak Politics of Academia clarify - authorship (including if I don't publish by a certain time), data ownership, sample ownership, lab notebooks make paper trail ... happy email SDSU form fills out with authorship, etc ... might be a good excuse to being it up verify Mendelian inheritance - high priority pregnant females, have babies (watch Rosemary's baby) maybe keep offspring alive screen mom and babies find out likelihood that a clutch all has same father will allow to see if that marker has weird null allele things Duplicate data To find error rate of data (in extraction, PCR, analysis, etc) In text, able to say "total sample size was 300 individuals per species, of which 30 were repeated 3 times, 50 repeated twice; 2 errors found, traceable to such-and-such a process, giving error rate of 1.5%" for this project, not necessary to repeat all the way back to extraction Spatial Scale gotta get: more consistent distances across roads more points across same road Literature search Lots of pop gen papers at spatial scale Software STRUCTURE - easy quick, do it with prelim data! CREATE - formats microsat data for STRUCTURE, etc. Playing with Structure software Structure 2.3.3 for MacOS spent 4 or 5 hours playing around with Structure, just trying to get it to work Here's what I learned today, so I don't forget! Formatting Data MS Excel first column is sample names (structure term = "Label") second column is population designation (structure term = "PopData", in integer form) 1 = green cluster 2 = blue cluster 3 = red cluster third column is location designation (structure term = "LocData", in integer form) 1 = Camp Pendleton 2 = Rancho Jamul / Hollenbeck 3 = Point Loma / Cabrillo National Monument 4 = Santa Ysabel Open Space Preserve 5 = Torrey Pines State Natural Reserve first row is marker names (structure term = "Marker Name") since diploid, leave an extra column for the second allele between markers MS Word copy data from Excel, Paste Special into Word as Unformatted Text Save As ... Plain Text (.txt) File Conversion: Latin-US (DOS), CR/LF Structure New Project File: New Project Step 1 Name the project: whatever you want Select directory: make a folder for all Structure projects to be saved in Choose data file: browse to the .txt file you just made (from Excel and Word) Step 2, 3, 4 -- -- Run Project Parameter Set: New... Run Length: 10,000 and 10,000 is a good place to start Ancestry Model: Admixture is appropriate for the ConGen project Allele Frequency Model: run both Correlated and Independent correlated: frequencies in the different populations are likely to be similar, due to migration or shared ancestry; improves clustering for closely related populations (subtle structure), but may increase the risk of overestimating K independent: we expect allele frequencies in different populations to be reasonably different from each other; works well for many data sets (strong structure) Advanced: unclick "Compute probability of data (for estimating K)" to make program run faster Parameter Set: Run do several iterations where K=? that pretty graphic that's in all the papers: in the left-hand pane, select the run you want (K=?) in the right-hand pane, click Bar plot: Show, then group by PopID TA-DA!