Post date: Jun 17, 2015 4:33:22 PM
Some of the Ne estimates reported below are off. First and most importantly, Frank and I discovered that the two L2 and L3 samples were likely from different sub-lines, which were separated for an unknown number of generations (but after the reversion lines were created). This explains the low Ne for these lines, they were low because the number of generations I assumed were wrong. The generation times between reversion and non-reversion lines were also a bit off (because generation times differed between these lines). The corrected numbers are below.
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_L1-F100.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L1-F100.txt
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_L1-F91.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L1-F91.txt
varne -a in_p_L1-F91.txt -b in_p_L1-F100.txt -l 51371 -t 9 -n 2000 -x 1000
Reading input from files: in_p_L1-F91.txt and in_p_L1-F100.txt
Estimating effective population size
hat{Ne} = 398.931
median of posterior = 399.121
50% credible intervals = 390.967, 407.637
90% credible intervals = 380.08, 419.164
95% credible intervals = 376.767, 423.335
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_L1R-F35.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L1R-F35.txt
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_L1R-F46.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L1R-F46.txt
varne -a in_p_L1R-F35.txt -b in_p_L1R-F46.txt -l 51371 -t 11 -n 2000 -x 1000
Reading input from files: in_p_L1R-F35.txt and in_p_L1R-F46.txt
Estimating effective population size
hat{Ne} = 533.235
median of posterior = 532.95
50% credible intervals = 522.561, 543.597
90% credible intervals = 508.694, 561.352
95% credible intervals = 502.294, 565.04
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_L2R-F35.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L2R-F35.txt
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_L2R-F45.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L2R-F45.txt
varne -a in_p_L2R-F35.txt -b in_p_L2R-F45.txt -l 51371 -t 10 -n 2000 -x 1000
Reading input from files: in_p_L2R-F35.txt and in_p_L2R-F45.txt
Estimating effective population size
hat{Ne} = 513.463
median of posterior = 512.947
50% credible intervals = 502.735, 523.581
90% credible intervals = 488.057, 539.132
95% credible intervals = 483.943, 543.954
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_L3R-F35.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L3R-F35.txt
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_L3R-F45.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L3R-F45.txt
varne -a in_p_L3R-F35.txt -b in_p_L3R-F45.txt -l 51371 -t 10 -n 2000 -x 1000
Reading input from files: in_p_L3R-F35.txt and in_p_L3R-F45.txt
Estimating effective population size
hat{Ne} = 763.39
median of posterior = 762.297
50% credible intervals = 745.103, 784.679
90% credible intervals = 716.382, 817.927
95% credible intervals = 706.177, 829.263
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_M-13.txt | perl -p -i -e 's/^(\S+)/\1 96/' > in_p_M-13.txt
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_M-14.txt | perl -p -i -e 's/^(\S+)/\1 96/' > in_p_M-14.txt
varne -a in_p_M-13.txt -b in_p_M-14.txt -l 51371 -t 14 -n 2000 -x 1000
Reading input from files: in_p_M-13.txt and in_p_M-14.txt
Estimating effective population size
hat{Ne} = 1148.99
median of posterior = 1149.62
50% credible intervals = 1123.63, 1176.76
90% credible intervals = 1087.35, 1217.33
95% credible intervals = 1077.37, 1229.79
############### other combos for deeper Ne #####################
varne -a in_p_L1-F100.txt -b in_p_L1R-F46.txt -l 51371 -t 84 -n 2000 -x 1000
Reading input from files: in_p_L1-F100.txt and in_p_L1R-F46.txt
Estimating effective population size
hat{Ne} = 455.686
median of posterior = 455.48
50% credible intervals = 451.919, 459.812
90% credible intervals = 446.442, 465.695
95% credible intervals = 444.347, 467.46
varne -a in_p_L2-F87.txt -b in_p_L2R-F45.txt -l 51371 -t 84 -n 2000 -x 1000
Reading input from files: in_p_L2-F87.txt and in_p_L2R-F45.txt
Estimating effective population size
hat{Ne} = 437.546
median of posterior = 437.459
50% credible intervals = 434.442, 440.681
90% credible intervals = 429.531, 445.337
95% credible intervals = 428.258, 447.258
varne -a in_p_L3-F85.txt -b in_p_L3R-F45.txt -l 51371 -t 85 -n 2000 -x 1000
Reading input from files: in_p_L3-F85.txt and in_p_L3R-F45.txt
Estimating effective population size
hat{Ne} = 936.981
median of posterior = 937.103
50% credible intervals = 928.785, 944.867
90% credible intervals = 915.826, 958.653
95% credible intervals = 912.73, 962.286