Post date: Jun 15, 2015 10:31:19 PM
I wrote a program (varne) to estimate the variance effective population size from temporal allele frequency change (see Jorde & Ryman 2007). I ran this on the seed beetle genetic data. The commands and results are below. Note that the values for L2 and L3 are quite low, but that the rest make sense. This is consistent with the lower allele frequency correlations within L2 and L3 and with a pca plot based on population allele frequencies (/labs/evolution/projects/cmaclentil/popgen/popPcPlot.pdf). Why?
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_L2-F78.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L2-F78.txt
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_L2-F87.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L2-F87.txt
varne -a in_p_L2-F78.txt -b in_p_L2-F87.txt -l 51371 -t 9 -n 2000 -x 1000
Reading input from files: in_p_L2-F78.txt and in_p_L2-F87.txt
Estimating effective population size
hat{Ne} = 70.698
median of posterior = 70.7217
50% credible intervals = 69.9834, 71.4052
90% credible intervals = 69.003, 72.3941
95% credible intervals = 68.7211, 72.7776
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_L3-F76.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L3-F76.txt
cut -f 1 -d "," /home/zgompert/labs/evolution/projects/cmaclentil/popgen/popfreqs/p_L3-F85.txt | perl -p -i -e 's/^(\S+)/\1 80/' > in_p_L3-F85.txt
varne -a in_p_L3-F76.txt -b in_p_L3-F85.txt -l 51371 -t 9 -n 2000 -x 1000
Reading input from files: in_p_L3-F76.txt and in_p_L3-F85.txt
Estimating effective population size
hat{Ne} = 60.7393
median of posterior = 60.7191
50% credible intervals = 60.2326, 61.2706
90% credible intervals = 59.5856, 62.0127
95% credible intervals = 59.3807, 62.3011
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 13 -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} = 1066.92
median of posterior = 1069.18
50% credible intervals = 1042.33, 1093.69
90% credible intervals = 1010.4, 1131.02
95% credible intervals = 1000.38, 1145.4