Figure S1.

TM3 Log Likelihood
0.000012
0.00001
Log Likelihood
0.000008
0.000006
0.000004
0.000002
0
0
20000
40000
60000
80000
100000
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Ne
(A) Fernandina Ne=116,130 (CI = 298 – 120,000); upper bound Ne=120,000
TM3 Log Likelihood
0.0016
0.0014
0.0012
Log Likelihood
0.001
0.0008
0.0006
0.0004
0.0002
0
0
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400
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800
Ne
(B) San Cristóbal Ne=960 (CI = 73 – 1,000); upper bound Ne=1,000
1000
1200
TM3 Log Likelihood
0.0001
0.00009
0.00008
Log Likelihood
0.00007
0.00006
0.00005
0.00004
0.00003
0.00002
0.00001
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0
2000
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Ne
(C) Floreana Ne=770 (CI = 0 – 16,000); upper bound Ne=16,000
TM3 Log Likelihood
0.0001
0.00009
0.00008
Log Likelihood
0.00007
0.00006
0.00005
0.00004
0.00003
0.00002
0.00001
0
0
2000
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Ne
(D) Genovesa Ne=783 (CI = 0 – 15,000); upper bound Ne=15,000
12000
14000
16000
TM3 Log Likelihood
0.03
0.025
Log Likelihood
0.02
0.015
0.01
0.005
0
0
50
100
150
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Ne
(E) Marchena Ne=40 (CI = 21 – 86); upper bound Ne=1000
TM3 Log Likelihood
0.00025
Log Likelihood
0.0002
0.00015
0.0001
0.00005
0
0
1000
2000
3000
4000
Ne
(F) Pinta Ne=2,036 (CI = 0– 6000); upper bound Ne=6000
5000
6000
7000
TM3 Log Likelihood
0.0004
0.00035
0.0003
Log Likelihood
0.00025
0.0002
0.00015
0.0001
0.00005
0
0
500
1000
1500
2000
2500
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3500
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4500
Ne
(G) Santiago Ne=3,657 (CI = 18 – 4000); upper bound Ne= 4000
TM3 Log Likelihood
0.00012
0.0001
Log Likelihood
0.00008
0.00006
0.00004
0.00002
0
0
2000
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6000
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12000
Ne
(H) Santa Cruz (Camaño) Ne=12,011 (CI = 59 – 13,000); upper bound Ne=13,000
14000
TM3 Log Likelihood
0.00007
0.00006
Log Likelihood
0.00005
0.00004
0.00003
0.00002
0.00001
0
0
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Ne
(I) Española Ne=18,120 (CI = 0 – 21,000); upper bound Ne=21,000
TM3 Log Likelihood
0.000035
0.00003
Log Likelihood
0.000025
0.00002
0.000015
0.00001
0.000005
0
0
5000
10000
15000
20000
25000
30000
Ne
(J) Isabela Ne=37,523 (CI = 0 – 40,000); upper bound Ne=40,000
35000
40000
45000
TM3 Log Likelihood
0.0001
0.00009
0.00008
Log Likelihood
0.00007
0.00006
0.00005
0.00004
0.00003
0.00002
0.00001
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0
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Ne
(K) Santa Fé Ne=15,006 (CI = 409 – 16,000); upper bound Ne=16,000
14000
16000
18000