SUPPORTING INFORMATION
0.8
0.6
0.0
0.2
0.4
Pi or Theta
1.0
1.2
1.4
true pi
true theta
estimated pi
estimated theta
0
20
40
60
80
100
Chromosome Sampling Depth
Figure S1. True and estimated values of  and w as a function of the chromosome
sampling depth for  =  = 0.01/bp. Light gray regions show the 95% bootstrap
percentile confidence intervals (1000 simulations) for simulations with
recombination, and dark gray regions are from simulations without recombination.
In the absence of recombination, true values of summary statistics vary more as a
function of the chromosome sampling depth and estimated values are lower.
0.0110
0.101
0.100
1.1
0.099
0.0105
1.0
0.097
0.0100
0.098
0.9
0.0095
0.096
Pi or Theta
0.8
0.095
0.7
C
0.0090
B
0.6
0.094
A
0
20
40
60
80
100
0
20
40
60
80
100
0
20
40
60
80
Chromosome Sampling Depth Cuttoff
Figure S2. Mean values of e (solid red) and e (solid blue) for loci with different
sampling depth cutoffs (i.e. loci that have at least the specified number of sampled
chromosomes with intact recognition sequences). Dashed lines represent the true
simulation average for  (red) and  (blue). A. ==0.01/bp, B. ==0.001/bp, C.
==0.0001/bp. Since 100bp sequences were analyzed, averages on the y-axis are
100 times greater than the per bp parameter values.
100
0.4
Proportion
0.1 0.2 0.3
0.0
1
10
20
30
40
50
60
70
80
90
100
70
80
90
100
Proportion
0.0 0.2 0.4 0.6 0.8 1.0
Chromosome Sampling Depth
1
10
20
30
40
50
60
Chromosome Sampling Depth
Figure S3. Chromosome sampling depth proportions for the standard (red) and
double digest (blue) RADseq protocols. The upper graph shows sampling depths for
==0.01/bp and the lower graph for ==0.001/bp.
1.5
1.0
0.0
0.5
Pi
0
20
40
60
80
100
Chromosome Sampling Depth
Figure S4. True  (solid lines) and estimated  (dashed lines) vary as a function of
chromosome sampling depth for the standard (blue) and double-digest (red)
RADseq protocols. Dotted lines represent the true simulation averages of . Loci
with higher chromosome sampling depths (i.e. near 100) have true and estimated
values of  that are below the true simulation average, especially for the doubledigest RADseq protocol.
1.1
0
20
40
60
80
0.9
0.7
0.8
Pi or Theta
1.0
1.1
1.0
0.9
0.8
0.7
B
0.6
Pi or Theta
0.6
A
100
0
20
80
100
20
40
60
CSDC
80
0.100
0.110
0
0.090
Pi or Theta
0.100
0.090
D
0.080
C
0.080
Pi or Theta
60
CSDC
0.110
CSDC
40
100
0
20
40
60
80
100
CSDC
Figure S5. Mean values of e (solid red) and e (solid blue) for loci with different
sampling depth cutoffs (CSDC, i.e. loci that have at least the specified number of
sampled chromosomes with intact recognition sequences). Dashed lines represent
the true simulation average for  (red) and  (blue). A. Standard RADseq with
==0.01/bp, B. double digest RADseq with ==0.01/bp, C. standard RADseq with
==0.001/bp, D. double digest with ==0.001/bp. Since 100bp sequences were
analyzed, averages on the y-axis are 100 times greater than the per bp parameter
values.
B
C
Density
1.0
2
Density
0.0
0
0
5
0.5
1
10
Density
15
1.5
3
20
2.0
4
25
A
0.0
0.2
0.4
0.6
0.8
1.0
0.0
Fst
0.2
0.4
0.6
0.8
1.0
0.0
0.2
0.4
Fst
0.6
0.8
1.0
Fst
0
20
40
60
80
100
Chromosome Sampling Depth Cutoff
1.0
0.8
0.2
0.4
0.6
B
0.0
Proportion of False Positives or False Negatives
1.0
0.8
0.2
0.4
0.6
A
0.0
Proportion of False Positives or False Negatives
Figure S6. Distribution of estimated Fst when all haplotypes are sampled (blue)
versus the true distribution (black), for Nm=10 (A), Nm=1 (B), and Nm=0.1 (C).
0
20
40
60
80
100
Chromosome Sampling Depth Cutoff
Figure S7. Proportion of estimated  (red), w (blue), or D (purple) 5% outlier loci
that are false positives (solid lines) or false negatives (dashed lines) relative to the
true distribution for different chromosome sampling depth cutoffs. A. Standard
RADseq protocol. B. Double digest protocol.