Post date: Jun 28, 2016 5:19:55 PM
I used VarNe to estimate variance effective population sizes from the ML allele frequencies (see Ne subdirectory). Note that I assumed a census size of 3000, but results were nearly identical over a range of census sizes.
cut -f 3 -d " " ../AlleleFreqs/outp_BCR-13.txt | perl -p -i -e 's/^(\S+)/\1 98/' > in_p_BCR-13.txt
cut -f 3 -d " " ../AlleleFreqs/outp_BCR-15.txt | perl -p -i -e 's/^(\S+)/\1 82/' > in_p_BCR-15.txt
## cor = 0.98
varne -a in_p_BCR-13.txt -b in_p_BCR-15.txt -l 10096 -t 2 -n 3000 -x 1000
hat{Ne} = 126.595
median of posterior = 127.636
50% credible intervals = 120.38, 134.666
90% credible intervals = 111.494, 146.422
95% credible intervals = 107.966, 149.685
cut -f 3 -d " " ../AlleleFreqs/outp_BNP-13.txt | perl -p -i -e 's/^(\S+)/\1 98/' > in_p_BNP-13.txt
cut -f 3 -d " " ../AlleleFreqs/outp_BNP-15.txt | perl -p -i -e 's/^(\S+)/\1 98/' > in_p_BNP-15.txt
## cor = 0.98
varne -a in_p_BNP-13.txt -b in_p_BNP-15.txt -l 10096 -t 2 -n 3000 -x 1000
hat{Ne} = 94.4437
median of posterior = 94.4892
50% credible intervals = 90.7003, 99.2823
90% credible intervals = 85.43, 106.334
95% credible intervals = 84.1676, 108.244
cut -f 3 -d " " ../AlleleFreqs/outp_BTB-13.txt | perl -p -i -e 's/^(\S+)/\1 98/' > in_p_BTB-13.txt
cut -f 3 -d " " ../AlleleFreqs/outp_BTB-15.txt | perl -p -i -e 's/^(\S+)/\1 102/' > in_p_BTB-15.txt
## cor = 0.98
varne -a in_p_BTB-13.txt -b in_p_BTB-15.txt -l 10096 -t 2 -n 3000 -x 1000
hat{Ne} = 136.911
median of posterior = 136.728
50% credible intervals = 129.201, 144.509
90% credible intervals = 119.814, 155.722
95% credible intervals = 116.716, 160.33
cut -f 3 -d " " ../AlleleFreqs/outp_GNP-13.txt | perl -p -i -e 's/^(\S+)/\1 98/' > in_p_GNP-13.txt
cut -f 3 -d " " ../AlleleFreqs/outp_GNP-15.txt | perl -p -i -e 's/^(\S+)/\1 102/' > in_p_GNP-15.txt
## cor = 0.99
varne -a in_p_GNP-13.txt -b in_p_GNP-15.txt -l 10096 -t 2 -n 3000 -x 1000
hat{Ne} = 124.788
median of posterior = 124.431
50% credible intervals = 117.827, 131.836
90% credible intervals = 108.906, 143.276
95% credible intervals = 106.564, 145.944
cut -f 3 -d " " ../AlleleFreqs/outp_MRF-13.txt | perl -p -i -e 's/^(\S+)/\1 96/' > in_p_MRF-13.txt
cut -f 3 -d " " ../AlleleFreqs/outp_MRF-15.txt | perl -p -i -e 's/^(\S+)/\1 100/' > in_p_MRF-15.txt
varne -a in_p_MRF-13.txt -b in_p_MRF-15.txt -l 10096 -t 2 -n 3000 -x 1000
hat{Ne} = 108.314
median of posterior = 109.054
50% credible intervals = 103.612, 115.602
90% credible intervals = 96.3506, 124.931
95% credible intervals = 93.2123, 127.025
cut -f 3 -d " " ../AlleleFreqs/outp_PSP-13.txt | perl -p -i -e 's/^(\S+)/\1 98/' > in_p_PSP-13.txt
cut -f 3 -d " " ../AlleleFreqs/outp_PSP-15.txt | perl -p -i -e 's/^(\S+)/\1 76/' > in_p_PSP-15.txt
## cor = 0.98
varne -a in_p_PSP-13.txt -b in_p_PSP-15.txt -l 10096 -t 2 -n 3000 -x 1000
hat{Ne} = 105.585
median of posterior = 105.449
50% credible intervals = 99.9358, 111.039
90% credible intervals = 93.0791, 121.223
95% credible intervals = 91.5099, 124.506
cut -f 3 -d " " ../AlleleFreqs/outp_RNV-13.txt | perl -p -i -e 's/^(\S+)/\1 98/' > in_p_RNV-13.txt
cut -f 3 -d " " ../AlleleFreqs/outp_RNV-14.txt | perl -p -i -e 's/^(\S+)/\1 94/' > in_p_RNV-14.txt
## cor = 0.98
varne -a in_p_RNV-13.txt -b in_p_RNV-14.txt -l 10096 -t 1 -n 3000 -x 1000
hat{Ne} = 70.9757
median of posterior = 71.0336
50% credible intervals = 67.0002, 75.8032
90% credible intervals = 61.5135, 83.7423
95% credible intervals = 59.8147, 85.7763
cut -f 3 -d " " ../AlleleFreqs/outp_USL-13.txt | perl -p -i -e 's/^(\S+)/\1 98/' > in_p_USL-13.txt
cut -f 3 -d " " ../AlleleFreqs/outp_USL-15.txt | perl -p -i -e 's/^(\S+)/\1 100/' > in_p_USL-15.txt
varne -a in_p_USL-13.txt -b in_p_USL-15.txt -l 10096 -t 2 -n 3000 -x 1000
hat{Ne} = 123.493
median of posterior = 123.133
50% credible intervals = 117.339, 130.867
90% credible intervals = 108.791, 142.579
95% credible intervals = 106.408, 146.753