Journal of Biogeography
SUPPORTING INFORMATION
Origin and history of the Dahomey Gap separating West and Central
African rain forests: insights from the phylogeography of the legume tree
Distemonanthus benthamianus
Boris B. DEMENOU, Rosalía PIÑEIRO and Olivier J. HARDY
Appendix S1. Microsatellite amplification protocol and primers details.
Appendix S2. Summary statistics of ABC tests; PP and Posterior value computation.
Appendix S3. Demographic analyses of nSSR data of Distemonanthus
benthamianus, Posterior probability, Posterior distributions of demographic
parameters, Bias and Confidence in parameter estimates obtained with first priors
and second priors on effective population sizes.
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Appendix S1. Microsatellite amplification protocol and primers details.
Amplification was optimized in three multiplex reactions (Abis, Bbis and Cbis)
(Debout et al. 2011, modified in this study, see Table S1) with a total reaction volume
of 18 μL, 10 μL and 18 μL, respectively. PCRs included 2 µL of template DNA (10–100
ng), 10 µL (Abis, Cbis) or 5µL (Bbis) of Qi Multiplex (QI multiplex contains
HotStarTaq DNA Polymerase, QIAGEN Multiplex PCR Buffer with 6 mM MgCl2, and
dNTP Mix); 2 µL (Abis, Bbis) or 4 µL (Cbis) of primer Mix (0,4 µL of each primer (10
µM)) and 4 µL (Abis), 1µL (Bbis) and 2 µL (Cbis) of H2O. The forward primer at the
5’ end, was labelled with 6-FAM, NED, VIC, and PET. The cycling profile for PCR
included an initial step of 15 min at 95°C followed by 30 cycles of 30 s at 94°C, 90 s at
62°C-0.3°C/cycle and 30 s at 72°C, followed again by 5 cycles of 30 s at 94°C, 90 s at
53° and 30 s at 72°C, followed by a final incubation at 72 °C for 10 min.
PCR products were run on an ABI 3730 (Applied Biosystems, Lennik, Netherlands)
with 12 μL HiDi and 0.3 μL of 500 LIZ mixed with 1 µL of PCR products. The
resulting electropherograms were automatically scored with Genemapper 3.7
(Applied Biosystems) by creating panels and bin sets defining all allele sizes in a
locus, and subsequently manually corrected.
References:
Debout, G. D., Doucet, J-L. & Hardy, O.J. (2011) "Population history and gene
dispersal inferred from spatial genetic structure of a Central African timber tree,
Distemonanthus benthamianus (Caesalpinioideae)." Heredity, 106, 88-99.
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Table S1: Primer sequences, annealing temperatures and polymorphism statistics
for 11 microsatellite loci in the five gene pools of Distemonanthus benthamianus.
Repeat motif is listed 5' to 3' with respect to the forward primer (F), Ta: lower
annealing temperature, Natot: total number of allele size variants.
Locus
(multiplex)
dis054 a
dis92 a
dis125 a
dis127 a
dis138 a
dis112 b
dis130 b
dis069 c
dis103 c
dis116 c
dis140 c
Gen Bank
accession
Nos
FJ654554
KT763468 *
FJ654559
FJ654561
FJ654562
KT763469 *
KT763470 *
FJ654555
FJ654557
FJ654558
FJ654563
Primer sequence (5' to 3')
F 3:
TATTCTTGGAATTAAACGGC
R:
TTATTGATCTGCCTTTTTCC
F4:
ACCTAACCCGTGGAATGAAG
R:
GCTCGTCCTCTTCTGGTCC
F 3:
GCCAGTCACAGAGGGGTAAT
R:
AGGAAAACATTTATTTGGGCT
F4:
AAATGCCCTTATGTCTTGCC
R:
GAAGATTGAGGCATTTGTTGG
F2:
AAGTCAGTTGACCCTGTAGG
R:
ATGACTAATCTGTTGGTGGG
F4:
CCTTTTCCTCTGCTATTCTC
R:
GAAACATTACAGGGATGGC
F 3:
CTTATTTGGAGAGAGAGGAG
R:
CACAAAATCTAAGGTGAGC
F1:
GAGCAGATAAACATTAGCAG
R:
GTATTTGGTAGGATTTCTGG
F2:
CAGAGATAAGAAAAGAATAAGC
R:
AATGAAGTTGGCTGTTTTAC
F4:
GTGTTGGAGCAGAGCGGTG
R:
GCAAGGCAGTGACACGACTC
F4:
TATTTGTGTCTTTTCTTTGC
R:
TATTTGGGTGAGTGTTTTG
Repeat motif in
library
Ta (°C)
Na
tot
51.9
8
259-271
8[GT]-11n-3[AT]-5n4[AT]
56.3
8
206-232
(TG)6(AG)8
55.1
5
154-162
50
13
241-269
(TA)4(CA)2(CCCA)3(CA)
6-TA(TACA)7(CA)6(TA)4
51.9
12
156-198
4[CA]-20bp-4[TA]25bp-8[TC]5[AC]
50.7
5
188-198
18[GA]-6n-3[GA]
47.2
17
200-240
(AC)11(GT)2-ATGTAT
46.9
14
165-195
(TC)2
46.9
25
222-283
(CA)20
50
16
274-301
49.2
15
137-173
(TC)2-ACTC(TCCC)3(TC)7(CA)8(TA)
Size range (bp)
3
(CA)13
(TG)9 (TA)2
5' fluorochrome labels. 1: PETTM, 2: HEXTM, 3: NEDTM, 4: 6FAMTM. a: multiplex 1, b: multiplex 2, c: multiplex 3, *
Additional loci described in this study.
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Table S2: Primer sequences, annealing temperatures and polymorphism statistics
for 11 microsatellite loci in five gene pools of Distemonanthus benthamianus. n:
number of gene copies analysed (twice the number of individuals). Na: number of
allele size variants. HO: observed proportion of heterozygous individuals. HE:
expected heterozygosity. Null: estimated proportion of null alleles according to
software INest.
Gene pool wLG
n
Na
dis054
140
5
dis92
140
6
dis125
140
5
dis127
140
8
dis138
140
10
dis112
140
4
dis130
140
13
dis069
140
12
dis103
140
20
dis116
132
14
dis140
140
9
Ho/He
0.357 /
0.312
0.743 /
0.728
0.371 /
0.367
0.657 /
0.762
0.571 /
0.678
0.571 /
0.630
0.386 /
0.883
0.614 /
0.767
0.814/
0.903
0.636 /
0.785
0.657 /
0.760
Gene Pool nLG
Null
n
Na
0
190
3
0
192
6
0.012
192
4
0.053
192
10
0.019
192
10
0.044
190
4
0.288
190
10
0.073
192
10
0.029
190
12
0.071
180
12
0.046
190
8
Ho/He
0.158/
0.165
0.552 /
0.613
0.208 /
0.238
0.833 /
0.799
0.896 /
0.812
0.663 /
0.661
0.379 /
0.774
0.781 /
0.803
0.874 /
0.849
0.744 /
0.773
0.800 /
0.830
Gene pool sLG
Null
n
Na
0.011
152
5
0.015
154
4
0.036
154
4
0.004
154
6
0.005
154
9
0
154
4
0.213
152
12
0
154
5
0.013
154
17
0.016
132
13
0.006
154
6
Ho/He
0.223 /
0.240
0.584 /
0.658
0.104 /
0.101
0.533 /
0.541
0.753 /
0.700
0.636 /
0.657
0.303 /
0.839
0.156 /
0.149
0.805 /
0.847
0.727 /
0.743
0.546 /
0.555
Gene pool DG
Null
n
Na
0.013
62
3
0.041
66
3
0
66
3
0.015
66
5
0
66
3
0.007
66
3
0.366
66
4
0
66
5
0.003
64
4
0.015
60
5
0.007
62
5
Ho/He
0.387/
0.533
0.303 /
0.492
0.485 /
0.475
0.818 /
0.702
0.424 /
0.491
0.455 /
0.523
0.091 /
0.346
0.303 /
0,721
0.656 /
0.716
0.233 /
0.584
0.387 /
0.537
Gene pool UG
Null
n
Na
0.097
116
6
0.142
116
3
0
116
3
0
116
8
0.005
116
5
0.062
116
2
0.252
114
9
0.232
116
7
0.029
108
3
0.225
100
11
0.113
112
12
Ho/He
0.328 /
0.426
0.431 /
0.576
0.293 /
0.383
0.638 /
0.690
0.483 /
0.529
0.018 /
0.018
0.368 /
0.799
0.379 /
0.618
0.296 /
0.294
0.440 /
0.683
0.500 /
0.735
wLG, western Lower Guinea; nLG, northern Lower Guinea; sLG, southern Lower Guinea; DG, Dahomey Gap; UG, Upper Guinea
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Journal of Biogeography
Null
0.005
0.008
0
0
0
0
0.165
0.028
0
0.031
0.033
Appendix S2. Summary statistics and parameters settings of approximate Bayesian
computation tests
Summary statistics used for ABC tests
For each gene pool: mean number of alleles, mean gene diversity (Nei 1987), mean
allele size variance, and mean M index (Excoffier et al., 2005) across loci. For two
sample statistics, we added FST (Weir & Cockerham, 1984), the pairwise (δμ)2
(Goldstein et al., 1995), the mean index of classification (two samples) (Rannala &
Moutain, 1997; Pascual et al., 2007), and the shared allele distance (Chakraborty &
Jin, 1993). As prior for the microsatellite mutation model we used the default values
provided by DIYABC 2.0.4: the mean microsatellite mutation rate across loci was
specified as Mean μ∼ Log [10-5–10-3].
Posterior probability and posterior value computation
The most- likely scenario was evaluated by comparing posterior probabilities using
logistic regression, with a 1% subset of the closest simulated data. The goodness of fit
of the scenario was assessed by the option ‘‘model checking’’ with principal
component analysis (PCA) in DIYABC, which measures the discrepancy between
model and real data. Confidence in the most likely scenario choice and accuracy of
parameter estimates were evaluated by generating 500 simulated data sets (pseudoobserved datasets) based on known parameter values (‘true values’) under a given
scenario. The posterior distribution of demographic parameters was estimated from
the 1% best simulated data sets using local linear regression and a logit
transformation of parameters. Confidence in parameter estimates was evaluated by
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Journal of Biogeography
comparing the posterior distribution of parameters from these pseudo-observed
datasets with the true values using the average relative mean bias (the difference
between the estimated and the true value divided by the true value, averaged over
simulations), and the ‘factor 2’ (the proportion of estimated values falling within the
interval between 50% and 200% of the ‘true’ value).
References:
Chakraborty, R. & Jin, L. (1993) A unified approach to study hypervariable polymorphisms:
statistical considerations of determining relatedness and population distances. EXS. 67,
153-175.
Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York, 512
pp.
Excoffier, L., Estoup A. & Cornuet, J.M. (2005) Bayesian analysis of an admixture model with
mutations and arbitrarily linked markers. Genetics 169, 1727-1738.
Goldstein, D.B., Linares, A.R., Cavalli-Sforza, L.L. & Feldman, M.W. (1995) An evaluation of
genetic distances for use with microsatellite loci. Genetics 139, 463-471.
Pascual, M., Chapuis, M.P., Mestres, F., Balanya ́, J., Huey, R.B., Gilchrist, G.W., Serra, L. &
Estoup, A. (2007) Introduction history of Drosophila subobscura in the New World : a
microsatellite based survey using ABC methods. Mol. Ecol., 16, 3069-3083.
Rannala, B., & Mountain, J. L. (1997) Detecting immigration by using multilocus genotypes.
Pro. Nat. Acad. Sci. USA 94, 9197-9201.
Weir,B.S. & Cockerham, C.C. (1984) Estimating F-statistics for the analysis of population
structure. Evolution 38: 1358-1370.
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Journal of Biogeography
Appendix S3. Demographic analyses of nSSR data of Distemonanthus
benthamianus, Posterior probability, Posterior distributions of demographic
parameters, Bias and Confidence in parameter estimates.
Table S3: Tests with first priors (Ne: 1,000 to 50,000 and Nx :10 – 500) on four
models (A) DEMOGRAPHIC EVENT MODEL: Decline, bottleneck and/or expansion
from the Pleistocene (1 Ma-1 yr BP) to the present; (B) NARROW TIME MODELS:
decline, bottleneck and/or expansion during/after the Pleistocene (1 Ma-1 yr BP) to
the present; (C) ORIGIN MODELS: from UG, LG or Admixture and (D)
ADMIXTURE MODELS: Pre-PGP (1 Ma-190 ka), Last interglacial (LIG, 130-115 ka)
or African Holocene humid period (AHP, 10–4 ka)admixture with small size or big
size following by reduction of size.
UG, Upper Guinea; LG, Lower Guinea; PGP, penultimate glacial period, DG,
Dahomey Gap.
Table S3-A. DEMOGRAPHIC EVENT MODEL
GENE POOL : Western LG
Chosen scenario(s) : 4
Number of simulated data sets : 999485
Number of selected data sets : 9994
Parameter mean median mode q025 q050 q250 q750 q950
-----------------------------------------------------------------------------------------------------Ne
29000 28500 6890 8840 18800 39600 48000
t0
2650
2050 1140
312
482 1180 3620 6870
N1
306
320
484
51
78
210
416
484
t1
4290
3880 2650
680 1020 2410 5880 8970
µmic_1 0.0005 0.0005 0.0002 0.0001 0.0002 0.0003 0.0008 0.0010
pmic_1
0.2260 0.2350 0.3000 0.1130 0.1230 0.1840 0.2740 0.2980
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
q975
49000
7780
492
9460
0.0010
0.3000
0.0000
Mean
Bias
0.291
1.015
0.934
0.178
0.304
0.08
12.132
Factor
2
0.864
0.778
0.754
0.906
0.788
0.998
0.336
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GENE POOL : Northern LG
Chosen scenario(s) : 4
Number of simulated data sets : 999957
Number of selected data sets : 9999
Parameter mean median mode q025 q050 q250 q750 q950
-----------------------------------------------------------------------------------------------------Ne
12900
9070 3580 1900 2360 4850 17500 36800
t0
3310
2840 1750
321
565 1580 4710 7600
N1
302
318
485
42
69
200
415
484
t1
5330
5290 5480
849 1340 3390 7300 9380
µmic_1 0.0005 0.0005 0.0002 0.0001 0.0001 0.0003 0.0008 0.0010
pmic_1
0.2240 0.2330 0.3000 0.1130 0.1230 0.1830 0.2710 0.2970
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
q975
42600
8280
492
9690
0.0010
0.3000
0.0000
Mean
Bias
0.364
0.666
0.786
0.225
0.325
0.105
11.477
Factor
2
0.822
0.77
0.744
0.908
0.816
0.99
0.34
GENE POOL : Southern LG
Chosen scenario(s) : 4
Number of simulated data sets : 1000831
Number of selected data sets : 10008
Parameter mean median mode q025 q050 q250 q750 q950
-----------------------------------------------------------------------------------------------------Ne
28600 29100 40300 5680 7690 18400 39300 47600
t0
1620
1090
528
140
204
565 2180 4930
N1
298
314
481
39
62
194
412
483
t1
3890
3320 1800
559
772 1870 5500 8810
µmic_1 0.0005 0.0004 0.0001 0.0001 0.0001 0.0002 0.0007 0.0009
pmic_1
0.2250 0.2340 0.3000 0.1150 0.1250 0.1860 0.2700 0.2950
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
q975
48800
5980
492
9450
0.0010
0.2990
0.0000
Mean
Bias
Factor
2
0.469
0.553
0.776
0.25
0.303
0.089
11.302
0.822
0.782
0.728
0.912
0.842
0.998
0.312
GENE POOL : DG
Chosen scenario(s) : 2
Number of simulated data sets : 999277
Number of selected data sets : 9992
Parameter mean median mode q025 q050 q250 q750 q950
-----------------------------------------------------------------------------------------------------N1
391
408
494
192
232
341
457
492
t1
1810
1080
372
87
143
484 2310 6510
Ne
16300 12100 2350 1630 2040 5530 24700 43000
µmic_1 0.0006 0.0006 0.0007 0.0002 0.0002 0.0004 0.0008 0.0009
pmic_1
0.2130 0.2180 0.3000 0.1090 0.1150 0.1670 0.2630 0.2930
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
q975
496
8030
46300
0.0010
0.2980
0.0000
Mean
Bias
Factor
2
0.345
0.614
1.064
0.344
0.109
22.231
0.834
0.802
0.782
0.802
0.996
0.206
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Journal of Biogeography
GENE POOL : UG
Chosen scenario(s) : 4
Number of simulated data sets : 999634
Number of selected data sets : 9996
Parameter mean median mode q025 q050 q250 q750 q950
-----------------------------------------------------------------------------------------------------Ne
18600 15300 8380 3540 4250 8810 26300 43700
t0
1850
1370 1050
246
335
806 2520 4880
N1
282
295
399
28
45
170
399
478
t1
6140
6240 8480 1860 2270 4250 8130 9610
µmic_1 0.0004 0.0004 0.0002 0.0001 0.0001 0.0002 0.0006 0.0009
pmic_1
0.2100 0.2120 0.2740 0.1110 0.1190 0.1670 0.2560 0.2910
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
q975
46900
5650
490
9820
0.0010
0.2960
0.0000
Mean
Bias
Factor
2
0.489
1.072
0.865
0.188
0.317
0.059
14.100
0.770
0.778
0.746
0.922
0.782
0.996
0.306
Table S3-B. NARROW TIME MODELS
GENE POOL : Western LG
Chosen scenario(s) : 3
Number of simulated data sets : 999597
Number of selected data sets : 9995
Parameter mean median mode q025 q050 q250 q750 q950
-----------------------------------------------------------------------------------------------------Ne
26700 25800 20300 7580 9140 17000 35900 46600
t5
1250
1250 1220 1200 1210 1220 1270 1300
N1
242
226
168
60
77
147
330
454
t4
1690
1700 1850 1420 1440 1580 1810 1880
µmic_1 0.0006 0.0006 0.0010 0.0002 0.0002 0.0004 0.0008 0.0010
pmic_1
0.2150 0.2210 0.3000 0.1090 0.1160 0.1680 0.2650 0.2960
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
q975
Mean
Bias
Factor
2
48200
1300
477
1890
0.0010
0.3000
0.0000
0.285
-0.000
0.386
0.006
0.208
0.059
14.827
0.854
1.000
0.848
1.000
0.888
0.998
0.274
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Journal of Biogeography
GENE POOL : Northern LG
Chosen scenario(s) : 3
Number of simulated data sets : 999192
Number of selected data sets : 9991
Parameter mean median mode q025 q050 q250 q750 q950
-----------------------------------------------------------------------------------------------------Ne
13300
9680 6520 2370 2860 5580 17800 36600
t5
1250
1250 1270 1200 1210 1230 1270 1290
N1
298
300
333
84
108
206
392
477
t4
1640
1630 1560 1410 1420 1520 1750 1870
µmic_1 0.0005 0.0005 0.0003 0.0001 0.0001 0.0003 0.0008 0.0010
pmic_1
0.2070 0.2090 0.3000 0.1060 0.1130 0.1580 0.2580 0.2930
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
q975
Mean
Bias
Factor
2
42100
1300
488
1880
0.0010
0.2980
0.0000
0.275
0.000
0.298
0.003
0.228
0.130
13.591
0.826
1.000
0.842
1.000
0.886
0.992
0.276
q975
Mean
Bias
Factor
2
48600
1300
443
1890
0.0009
0.2990
0.0000
0.305
0.000
0.340
0.003
0.210
0.102
12.794
0.826
1.000
0.846
1.000
0.888
0.996
0.254
GENE POOL : Southern LG
Chosen scenario(s) : 3
Number of simulated data sets : 999274
Number of selected data sets : 9992
Parameter mean median mode q025 q050 q250 q750 q950
-----------------------------------------------------------------------------------------------------Ne
27100 26800 18500 6860 8670 17600 36500 47000
t5
1250
1250 1200 1200 1200 1220 1270 1290
N1
186
164
100
38
49
101
251
403
t4
1690
1710 1870 1430 1450 1580 1810 1880
µmic_1 0.0004 0.0003 0.0002 0.0001 0.0001 0.0002 0.0005 0.0008
pmic_1
0.2160 0.2210 0.3000 0.1100 0.1180 0.1700 0.2650 0.2950
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
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Journal of Biogeography
GENE POOL : DG
Chosen scenario(s) : 4
Number of simulated data sets : 1001089
Number of selected data sets : 10010
Mean
Bias
Parameter mean
median mode q025 q050 q250 q750 q950 q975
-----------------------------------------------------------------------------------------------------N1
391
399
446
243
264
342
449
489
495 0.066
t6
393
367
250
207
215
277
492
647
674 0.059
Ne
8770
6400 3660 1780 2150 3950 10900 24300 30300 0.472
0.000 0.000 0.000 0.000 0.000 0.000 0.001
µmic_1
0.0005 0.0005
2
1
1
3
7
9
0 0.278
0.121 0.104 0.109 0.146 0.247 0.291 0.296
pmic_1
0.1960 0.1930
0
0
0
0
0
0
0 0.118
0.000 0.000 0.000 0.000 0.000 0.000 0.000
snimic_1
0.0000 0.0000
0
0
0
0
0
0
0 18.560
Factor
2
0.958
0.984
0.786
0.822
0.994
0.190
GENE POOL : UG
Chosen scenario(s) : 3
Number of simulated data sets : 998855
Number of selected data sets : 9988
Parameter mean median mode q025 q050 q250 q750 q950
-----------------------------------------------------------------------------------------------------Ne
16000 12800 6250 3050 3760 7480 21600 39800
t5
1250
1250 1210 1200 1200 1220 1270 1290
N1
115
94
53
16
21
52
155
285
t4
1690
1710 1860 1430 1450 1590 1810 1880
µmic_1 0.0005 0.0004 0.0003 0.0002 0.0002 0.0003 0.0006 0.0009
pmic_1
0.1940 0.1920 0.1420 0.1050 0.1100 0.1460 0.2410 0.2870
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
q975
Mean
Bias
Factor
2
44200
1300
350
1890
0.0009
0.2930
0.0000
0.264
0.001
0.395
0.010
0.226
0.106
14.778
0.842
1.000
0.826
1.000
0.890
0.992
0.250
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Journal of Biogeography
Table S3-C. ORIGIN MODELS
Chosen scenario(s) : 6
Number of simulated data sets : 999044
Number of selected data sets : 9990
Parameter mean median mode q025 q050 q250 q750 q950
-----------------------------------------------------------------------------------------------------N1
26300 25400 22800 8350 10200 18400 33800 45100
N2
345
362
492
105
142
271
437
487
N3
7710
5590 3320 1890 2180 3690 8880 21700
t0
142
110
98
21
28
71
162
388
r
0.34
0.29
0.04
0.02
0.03
0.14
0.50
0.85
t1
4980
4730 3510 1320 1660 3240 6640 9010
Ne
4640
3580 1650 1130 1250 2170 5900 11700
µmic_1 0.0002 0.0002 0.0001 0.0001 0.0001 0.0001 0.0003 0.0006
pmic_1
0.2080 0.2100 0.3000 0.1090 0.1160 0.1590 0.2580 0.2940
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
q975
47400
493
29300
492
0.92
9470
14200
0.0007
0.3000
0.0000
Mean
Bias
Factor
2
0.116
0.101
0.108
0.398
0.968
0.888
0.964
0.800
0.158
0.168
0.272
0.057
6888
0.928
0.882
0.864
0.998
0.364
Table S3-D. ADMIXTURE MODELS
Chosen scenario(s) : 6
Number of simulated data sets : 999633
Number of selected data sets : 9996
Parameter mean median mode
q025
q050
q250
q750
-----------------------------------------------------------------------------------------------------N1
33100 33700 31500 12900 15700 25400 41600
N2
200
190
169
77
88
142
242
N3
23100 21700 15600
4420
5870 13300 31800
tad6
74
75
95
43
45
60
88
r
0.3140 0.2940 0.2630 0.0513 0.0798 0.2000 0.4010
ted36
1230
1230
1250
1150
1160
1190
1260
Ne1
24600 24000
3990
2180
3230 12100 36900
Ne3
21700 20100
1080
1380
1910
8460 33700
tbd36
1650
1650
1710
1410
1430
1530
1770
Ne2
23200 21200 12300
3420
4770 11900 33700
Ne5
5020
2280
1260
1060
1110
1480
4650
ts
5440
5210
4480
1980
2320
3730
7050
Ne
5800
4660
2710
1180
1350
2740
7590
µmic_1
0.0002 0.0001 0.0001 0.0001 0.0001 0.0001 0.0002
pmic_1
0.2180 0.2250 0.3000 0.1120 0.1200 0.1720 0.2670
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
q950
48300
359
45100
98
0.6210
1290
47400
46600
1870
46600
20400
9210
14000
0.0004
0.2980
0.0000
q975
49200
412
47500
99
0.7220
1300
48700
48300
1890
48300
29500
9610
16600
0.0005
0.3000
0.0000
12
Journal of Biogeography
Table S4: Tests with second set of priors (Ne: 10 to 10,000 and Nx :10 – 2,000) on
two models (A) DEMOGRAPHIC EVENT MODEL: Decline. bottleneck and/or
expansion from the Pleistocene (1 Ma-1 yr BP) to the present; (B) NARROW TIME
MODELS: decline. bottleneck and/or expansion during/after the Pleistocene (1 Ma-1
yr BP) to the present.
UG, Upper Guinea; LG, Lower Guinea; DG, Dahomey Gap.
Table S4-A. DEMOGRAPHIC EVENT MODEL
GENE POOL : Western LG
Chosen scenario(s) : 4
Number of simulated data sets : 998808
Number of selected data sets : 9988
Parameter mean median mode
q025
q050
q250
q750
q950
q975
-----------------------------------------------------------------------------------------------------Ne
7530
7610
9720
4450
4890
6400
8820
9760
9890
t0
2310
1610
188
69
130
639
3410
6810
7740
N1
1180
1220
1500
180
290
790
1600
1920
1960
t1
4930
4690
2360
623
925
2610
7230
9390
9700
µmic_1 0.0006 0.0006 0.0010 0.0002 0.0003 0.0005 0.0008 0.0010 0.0010
pmic_1
0.2440 0.2560 0.3000 0.1260 0.1430 0.2140 0.2840 0.3000 0.3000
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
GENE POOL : Northern LG
Chosen scenario(s) : 4
Number of simulated data sets : 999021
Number of selected data sets : 9990
Parameter mean median mode
q025
q050
q250
q750
q950
q975
-----------------------------------------------------------------------------------------------------Ne
5530
5130
4400
2180
2480
3800
7230
9450
9720
t0
2890
2270
19
47
108
816
4540
7620
8330
N1
1190
1240
1460
179
294
807
1620
1920
1960
t1
5760
5880
8800
862
1350
3630
8070
9650
9830
µmic_1 0.0006 0.0006 0.0004 0.0001 0.0002 0.0004 0.0008 0.0010 0.0010
pmic_1
0.2320 0.2420 0.3000 0.1180 0.1320 0.1990 0.2750 0.2970 0.3000
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
13
Journal of Biogeography
GENE POOL : Southern LG
Chosen scenario(s) : 4
Number of simulated data sets : 1000098
Number of selected data sets : 10000
Parameter mean median mode
q025
q050
q250
q750
q950
q975
-----------------------------------------------------------------------------------------------------Ne
7660
7870
9900
4300
4750
6450
9090
9830
9920
t0
1330
706
89
26
46
248
1810
4830
6090
N1
864
785
412
78
135
439
1250
1820
1900
t1
4600
4210
2140
620
885
2280
6740
9300
9640
µmic_1 0.0005 0.0005 0.0003 0.0001 0.0002 0.0003 0.0007 0.0009 0.0010
pmic_1
0.2440 0.2560 0.3000 0.1260 0.1450 0.2140 0.2840 0.3000 0.3000
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
GENE POOL : DG
Chosen scenario(s) : 2
Number of simulated data sets : 1000940
Number of selected data sets : 10009
Parameter mean median mode
q025
q050
q250
q750
q950
q975
-----------------------------------------------------------------------------------------------------N1
906
811
634
313
371
582
1170
1750
1870
t1
2950
2100
702
223
336
1040
4240
8340
9130
Ne
5870
6060
8740
924
1450
3870
8040
9620
9800
µmic_1 0.0005 0.0005 0.0003 0.0001 0.0002 0.0003 0.0007 0.0009 0.0010
pmic_1
0.2120 0.2180 0.2630 0.1080 0.1170 0.1690 0.2600 0.2920 0.2960
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
GENE POOL : UG
Chosen scenario(s) : 4
Number of simulated data sets : 1000819
Number of selected data sets : 10008
Parameter mean median mode
q025
q050
q250
q750
q950
q975
-----------------------------------------------------------------------------------------------------Ne
6790
6970
9550
2830
3280
5200
8530
9710
9850
t0
1510
1100
372
115
173
575
1990
4370
5470
N1
519
410
164
30
51
201
716
1410
1640
t1
6350
6530
9700
1880
2370
4560
8330
9680
9840
µmic_1 0.0005 0.0005 0.0003 0.0001 0.0002 0.0003 0.0007 0.0009 0.0010
pmic_1
0.2200 0.2270 0.3000 0.1130 0.1230 0.1790 0.2670 0.2960 0.3000
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
14
Journal of Biogeography
Table S4-B. NARROW TIME MODELS
GENE POOL : Western LG
Chosen scenario(s) : 3
Number of simulated data sets : 999741
Number of selected data sets : 9997
Parameter mean median mode
q025
q050
q250
q750
q950
q975
-----------------------------------------------------------------------------------------------------Ne
7530
7630
7170
4400
4860
6360
8840
9780
9880
t5
1250
1250
1210
1200
1200
1220
1270
1290
1300
N1
632
477
214
79
102
237
907
1680
1840
t4
1680
1700
1890
1420
1440
1570
1810
1880
1890
µmic_1
0.0007 0.0007 0.0010 0.0002 0.0003 0.0005 0.0008 0.0010 0.0010
pmic_1
0.2380 0.2480 0.3000 0.1220 0.1370 0.2060 0.2800 0.3000 0.3000
snimic_1
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
GENE POOL : Northern LG
Chosen scenario(s) : 3
Number of simulated data sets : 998768
Number of selected data sets : 9987
Parameter mean median mode
q025
q050
q250
q750
q950
q975
-----------------------------------------------------------------------------------------------------Ne
5680
5360
4090
2360
2660
3960
7360
9440
9690
t5
1250
1250
1200
1200
1200
1220
1270
1290
1300
N1
834
735
388
125
163
398
1220
1800
1900
t4
1660
1670
1790
1420
1430
1540
1790
1880
1890
µmic_1 0.0005 0.0005 0.0003 0.0002 0.0002 0.0003 0.0007 0.0010 0.0010
pmic_1
0.2270 0.2360 0.3000 0.1150 0.1270 0.1900 0.2710 0.2960 0.2990
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
15
Journal of Biogeography
GENE POOL : Southern LG
Chosen scenario(s) : 3
Number of simulated data sets : 998663
Number of selected data sets : 9986
Parameter mean median mode
q025
q050
q250
q750
q950
q975
-----------------------------------------------------------------------------------------------------Ne
7580
7850
9640
4020
4510
6320
9030
9820
9910
t5
1250
1250
1210
1200
1200
1220
1270
1290
1300
N1
301
154
55
27
34
76
355
1170
1490
t4
1680
1700
1820
1420
1440
1570
1810
1880
1890
µmic_1 0.0005 0.0004 0.0003 0.0001 0.0002 0.0003 0.0006 0.0009 0.0010
pmic_1
0.2370 0.2480 0.3000 0.1210 0.1360 0.2040 0.2790 0.3000 0.3000
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
GENE POOL : DG
Chosen scenario(s) : 4
Number of simulated data sets : 999266
Number of selected data sets : 9992
Parameter mean median mode
q025
q050
q250
q750
q950
q975
-----------------------------------------------------------------------------------------------------N1
670
592
498
285
320
453
799
1310
1510
t6
443
436
308
214
228
321
564
671
685
Ne
5320
5100
4570
1460
1810
3420
7170
9330
9630
µmic_1 0.0004 0.0004 0.0002 0.0001 0.0001 0.0002 0.0006 0.0009 0.0009
pmic_1
0.2040 0.2070 0.2510 0.1060 0.1130 0.1560 0.2540 0.2910 0.2960
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
GENE POOL : UG
Chosen scenario(s) : 3
Number of simulated data sets : 999677
Number of selected data sets : 9996
Parameter mean median mode
q025
q050
q250
q750
q950
q975
-----------------------------------------------------------------------------------------------------Ne
6500
6520
6750
2830
3310
4930
8150
9590
9800
t5
1250
1250
1210
1200
1200
1220
1270
1290
1300
N1
171
85
26
15
18
43
176
661
1050
t4
1690
1710
1870
1420
1450
1590
1810
1880
1890
µmic_1 0.0005 0.0005 0.0004 0.0002 0.0002 0.0003 0.0007 0.0009 0.0010
pmic_1
0.2130 0.2170 0.3000 0.1110 0.1190 0.1670 0.2610 0.2950 0.2990
snimic_1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
16
Journal of Biogeography