|
Ne
|
Vk
|
Ne/Nc
|
He(SD)
|
K (SD)
|
Fis(SD)
|
M-ratio (SD)
|
%P
|
FPR
|
|---|
| | | | | | | | |
M-ratioft
|
M-ratiosim
|
Het excess
|
MSVAR
|
|---|
|
50
| | | | | | | | | | | |
| |
2
|
1
|
0.11 (0.17)
|
1.53 (0.59)
|
0.00 (0.09)
|
1.00 (0.03)
|
48
|
0.01
|
0.02
|
0.01
|
0.00
|
| |
40
|
0.1
|
0.07 (0.14)
|
1.30 (0.52)
|
-0.03 (0.12)
|
1.00 (0.00)
|
27
|
0.0
|
0.04
|
0.02
|
0.00
|
| |
400
|
0.01
|
0.05 (0.14)
|
1.24 (0.45)
|
-0.01 (0.11)
|
1.00 (0.03)
|
23
|
0.01
|
0.04
|
0.10
|
0.00
|
| |
2000
|
0.002
|
0.07 (0.13)
|
1.25 (0.35)
|
-0.15 (0.17)
|
0.97 (0.06)
|
25
|
0.00
|
0.17
|
0.11
|
0.00
|
|
500
| | | | | | | | | | | |
| |
2
|
1
|
0.44 (0.16)
|
3.08 (0.72)
|
-0.02 (0.12)
|
1.00 (0.03)
|
100
|
0.0
|
0.09
|
0.04
|
0.00
|
| |
40
|
0.1
|
0.42 (0.20)
|
2.74 (0.81)
|
-0.07 (0.21)
|
0.98 (0.07)
|
96
|
0.03
|
0.36
|
0.32
|
0.62
|
| |
400
|
0.01
|
0.43 (0.23)
|
2.91 (1.10)
|
-0.17 (0.29)
|
0.87 (0.18)
|
89
|
0.21
|
1.00
|
0.53
|
0.97
|
| |
2000
|
0.002
|
0.44 (0.21)
|
3.17 (1.20)
|
-0.19 (0.31)
|
0.71 (0.21)
|
88
|
0.43
|
1.00
|
0.54
|
1.00
|
|
2500
| | | | | | | | | | | |
| |
2
|
1
|
0.71 (0.06)
|
6.3 (1.3)
|
0.01 (0.05)
|
0.95 (0.08)
|
100
|
0.0
|
0.03
|
0.06
|
0.06
|
| |
40
|
0.1
|
0.69 (0.1)
|
5.7 (1.8)
|
-0.08 (0.11)
|
0.89 (0.13)
|
100
|
0.07
|
0.51
|
0.20
|
0.66
|
| |
400
|
0.01
|
0.64 (0.09)
|
4.5 (1.2)
|
-0.19 (0.13)
|
0.82 (0.15)
|
99
|
0.35
|
1.00
|
0.39
|
0.99
|
| |
2000
|
0.002
|
0.61 (0.12)
|
4.2 (1.4)
|
-0.20 (0.12)
|
0.69 (0.18)
|
99
|
0.49
|
1.00
|
0.42
|
1.00
|
|
5000
| | | | | | | | | | | |
| |
2
|
1
|
0.76 (0.08)
|
7.70 (1.60)
|
-0.016 (0.08)
|
0.94 (0.09)
|
100
|
0.0
|
0.05
|
0.07
|
0.14
|
| |
40
|
0.1
|
0.72 (0.09)
|
6.06 (1.76)
|
-0.11 (0.17)
|
0.81 (0.19)
|
100
|
0.23
|
0.93
|
0.22
|
0.97
|
| |
400
|
0.01
|
0.66 (0.13)
|
4.80 (1.51)
|
-0.22 (0.16)
|
0.68 (0.23)
|
100
|
0.50
|
1.00
|
0.40
|
1.00
|
| |
2000
|
0.002
|
0.67 (0.11)
|
4.90 (1.66)
|
-0.24 (0.14)
|
0.66 (0.20)
|
99
|
0.58
|
1.00
|
0.43
|
1.00
|
- Mean values of summary statistics (with standard deviations) across 100 replicates are given. The last four columns report the rate of false positives (FPR = type I error) estimated as the fraction of replicates with an M-ratio smaller than the commonly used threshold of 0.68 (M-ratioft), with a M-ratio smaller and the critical value computed by simulation using the same parameter θ = 4N
e
μ used to generate the data (M-ratiosim), where a significant (P< 0.05) heterozygoty excess was detected using the program BOTTLENECK, and where a significant difference between ancestral and current population size is detected by MSVAR, respectively. N
e
= effective population size; N
c
= census population size; H
e
= expected heterozygosity; F = inbreeding coefficient, estimated as 1-H
o
/H
e
, where H
o
is the observed heterozygosity; M = M-ratio; %P = fraction of replicates producing a polymorphic locus; the starting values, in the log10 scale, for the mean and variance of the prior distributions in MSVAR, are as follows: ancestral size (3,1), current size (3,1), mutation rate ( -3.3,1), time since the decline (2,0.5); means and variances (and their means and variances) of the hyperprior distributions used in MSVAR are as follows: ancestral size (3,1,0,0.5), current size (3,1,0,0.5), mutation rate (-3.3,0.25,0,0.5), time since the decline (2,0.5,0,0.5).
