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Table 1 Simulation results for a population with constant size and standard microsatellite mutations

From: High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study

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

  1. 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).