Post date: Sep 16, 2013 9:40:13 PM
I created two sets of 'populations' or groups for the 3 population test. Set A is less finely divided than set B. Here are the f-3 results for each:
parameter file: paramfile
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
DIR: ./
SSS: lycaeidesA
indivname: lycaeidesA.ind
snpname: lycaeidesA.snp
genotypename: lycaeidesA.geno
popfilename: f3_tests_setA
## qp3Pop version: 204
nplist: 13
number of blocks for block jackknife: 21
snps: 15075
Source 1 Source 2 Target f_3 std. err Z SNPs
result: anna mel alp -0.021266 0.002711 -7.844 13304
result: anna mel idas -0.039625 0.002265 -17.493 14556
result: anna mel long -0.033923 0.001787 -18.984 14671
result: anna mel warn -0.057609 0.002049 -28.116 14048
result: anna idas ricei 0.026423 0.002924 9.035 10159
result: anna mel ricei 0.067377 0.004529 14.877 10252
result: anna idas cave 0.034304 0.002981 11.508 11203
result: anna mel cave 0.013093 0.003837 3.412 11338
result: idas mel long -0.023021 0.000616 -37.379 14589
result: idas mel dubs -0.028078 0.000644 -43.607 14273
result: long mel dubs -0.009547 0.000411 -23.212 14330
result: idas mel subl 0.054061 0.002191 24.677 14061
result: idas mel warn 0.042328 0.001512 27.993 14674
##end of qp3Pop
parameter file: paramfile
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
DIR: ./
SSS: lycaeidesB
indivname: lycaeidesB.ind
snpname: lycaeidesB.snp
genotypename: lycaeidesB.geno
popfilename: f3_tests_setB
## qp3Pop version: 204
nplist: 38
number of blocks for block jackknife: 21
snps: 15075
Source 1 Source 2 Target f_3 std. err Z SNPs
result: mele anna melw 0.045640 0.002357 19.367 13161
result: anna melw mtr 0.080464 0.008592 9.365 8261
result: anna mele mtr 0.095055 0.008641 11.001 8476
result: anna melw csp -0.037466 0.002797 -13.397 10741
result: anna mele csp -0.019428 0.003151 -6.166 10848
result: anna melw srnv -0.002078 0.003107 -0.669 12577
result: anna mele srnv 0.022080 0.003282 6.727 12652
result: anna melw whit 0.025304 0.003042 8.318 11341
result: anna mele whit 0.055150 0.003424 16.107 11678
result: anna mele idasynp -0.049763 0.002190 -22.724 14062
result: anna mele idasstb -0.028749 0.003363 -8.549 11727
result: anna idasn idasstb 0.021204 0.001932 10.974 11176
result: anna mele idasn -0.015260 0.003583 -4.259 12773
result: anna mele long -0.043579 0.001961 -22.218 14588
result: anna mele warn -0.064350 0.002345 -27.443 13957
result: anna idasn ricei 0.019129 0.003049 6.274 9685
result: anna mele ricei 0.066127 0.004818 13.725 10148
result: anna mele warn -0.064350 0.002345 -27.443 13957
result: mele anna warn -0.064350 0.002345 -27.443 13957
result: anna idasn warn 0.014331 0.001682 8.520 13880
result: anna idasn cave 0.036178 0.003193 11.331 10632
result: anna mele cave 0.007565 0.004022 1.881 11104
result: idasynp mele long -0.021465 0.000548 -39.155 14481
result: idasynp melr long -0.017283 0.000464 -37.213 14438
result: idasynp mele melr -0.018260 0.000616 -29.657 13948
result: idasynp mele dubs -0.028884 0.000632 -45.676 13898
result: idasynp melr dubs -0.021742 0.000498 -43.630 13645
result: long mele dubs -0.011254 0.000479 -23.515 14170
result: idasynp mele subl 0.058903 0.002034 28.956 13354
result: idasynp melr subl 0.061719 0.001917 32.203 12917
result: idasn mele warn 0.025430 0.001711 14.859 14278
result: idasn mele long -0.038906 0.000863 -45.076 14450
result: idasn melr long -0.029282 0.000709 -41.275 14433
result: idasn mele melr -0.023626 0.000682 -34.666 13666
result: idasn mele dubs -0.044056 0.000988 -44.581 13593
result: idasn melr dubs -0.031591 0.000766 -41.265 13460
result: idasn mele subl 0.030674 0.002181 14.063 12438
result: idasn melr subl 0.039561 0.002019 19.591 12205
result: melr long dubs -0.008202 0.000332 -24.698 13808
##end of qp3Pop
I switched source 1 and target for group A and all f-3 statistics were positive (this is rather encouraging). Note the files codesA.txt and codesB.txt tell which sampling localities are included in each 'population'. This output was generated with the following command: qp3Pop -p paramfile > f3out_set*.txt