Journal of Biogeography
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Older than the islands: origin and diversification of Galápagos leaf-toed geckos
(Phyllodactylidae: Phyllodactylus) by multiple colonizations
Omar Torres-Carvajal, Charles W. Barnes, María J. Pozo-Andrade,
Washington Tapia and Gabriela Nicholls
Appendix S1 Genetic variation among island and mainland samples of
Phyllodactylus included in this study.
Based on the gene region with the largest number of parsimony-informative sites, sequence variation among species was assessed with maximum-likelihood-corrected distances,
which were obtained in PAUP* (Swofford, 2003) under the same model-selection strategy
explained in the Materials and Methods section.
The percentage of parsimony informative sites was quantified in three data matrices: (1) the complete data matrix used in concatenated tree estimation analyses, (2) the
same matrix after excluding island taxa, and (3) the same matrix as in (1) after excluding
mainland taxa.
Table S1 summarizes the patterns of variation and phylogenetic signal for all the
included genes. As expected, mitochondrial gene regions (mtDNA) were much more informative than nuclear DNA (nDNA) regions, even when mainland or island taxa were excluded (Fig. S1). Percentage values of parsimony-informative sites vary from 26.27% to
52.91% for mtDNA genes, and from 1.75% to 9.54% for nDNA gene regions. Among the
mtDNA genes, ND4 was the most informative region, followed by 16S and 12S–tRNAVal,
even though 16S was more than twice as long as the other two regions. Among the nuclear
gene regions, RAG1 was the most informative region, followed by RAG2 and PDC; ACM4
and BDNF showed the lowest percentages of parsimony-informative sites (Table S1).
Interspecific ND4 sequence divergence within Phyllodactylus ranged from 0.00 to
0.33 (mean = 0.22 ± 0.04 SD; Table S2), and was different when mainland and island samples were analysed separately (Fig. S2). There were only two distance values of zero,
between one sample of P. galapagensis from Santiago and each of two samples of P. galapagensis from Pinzón, which might be due to recent movement of individuals between
Santiago and Pinzón; all other values were above 0.04. Sequence divergence was significantly lower among Galápagos taxa (0.00–0.26; mean = 0.14 ± 0.06 SD) than among mainland taxa (0.14–0.27; mean = 0.23 ± 0.03 SD) (t-test: t = −26.66, d.f. = 399.21, P < 0.0001).
Among Galápagos taxa, P. darwini showed the greatest genetic distinctness, with
distance values of 0.23–0.26 from other species in the archipelago (Table S2). Interspecific
distances among other species were 0.12–0.16, except for those from P. galapagensis to
P. baurii from Floreana and P. barringtonensis (0.06–0.09 and 0.08–0.11, respectively). The
distances among populations of P. galapagensis from Santa Cruz, Isabela, Pinzón and
Santiago were 0–0.08 (Table S2).
Table S1 Genetic variability for mitochondrial and nuclear gene regions used in this study for three data sets: all taxa, mainland taxa and
Galápagos taxa. Number of aligned nucleotides (nt), selected model under the Bayesian information criterion and numbers of variable
(VS) and parsimony-informative sites (PIS) are indicated for each partition. Percentage of PIS in each gene region is indicated in
parentheses.
All taxa
Gene region
Mitochondrial
12S–tRNAVal
16S
ND4
Nuclear
ACM4
BDNF
CMOS
PDC
RAG1
RAG2
Total
nt
Selected model
590 TIM2+I+G
1455 012342+I+G+F
601 TIM3+I+G
383
630
390
399
304
384
5136
HKY
K80+I
TrNef+G
K80+G
TrN
TPM3uf
VS
PIS
Mainland taxa
VS
Island taxa
PIS
VS
PIS
274
728
345
212 (35.93%)
587 (40.34%)
318 (52.91%)
252
692
332
183 (31.02%)
540 (37.11%)
296 (49.25%)
169
439
258
155 (26.27%)
415 (28.52%)
255 (42.43%)
34
30
46
59
50
41
13 (3.39%)
19 (3.02%)
26 (6.66%)
24 (6.02%)
29 (9.54%)
25 (6.51%)
33
24
40
56
40
35
10 (2.61%)
12 (1.90%)
23 (5.90%)
21 (5.26%)
21 (6.91%)
19 (4.95%)
8
11
17
17
21
14
8 (2.09%)
11 (1.75%)
14 (3.59%)
17 (4.26%)
18 (5.92%)
13 (3.39%)
1662
1311
1561
1184
954
906
Table S2 ND4 genetic distances among species or island populations of Phyllodactylus from Galápagos: (1) P. darwini; (2) P. leei; (3)
‘P. baurii’ from Española; (4) P. baurii from Floreana; (5) P. barringtonensis; (6) P. galapagensis from Santa Cruz; (7) P. galapagensis
from Isabela; (8) P. galapagensis from Pinzón; (9) P. galapagensis from Santiago.
1
2
3
4
5
6
7
8
2
3
4
5
6
7
8
9
0.25–0.26
—
—
—
—
—
—
—
0.25–0.26
0.15–0.16
—
—
—
—
—
—
0.24
0.15
0.14
—
—
—
—
—
0.24
0.15
0.13–0.14
0.12–0.13
—
—
—
—
0.23–0.26
0.12–0.14
0.12–0.13
0.06–0.08
0.08–0.10
—
—
—
0.24–0.26
0.12–0.14
0.13–0.15
0.07–0.09
0.09–0.10
0.05–0.07
—
—
0.24–0.25
0.14
0.14
0.09
0.11
0.06–0.08
0.05–0.07
—
0.24–0.25
0.13–0.14
0.13–0.14
0.08–0.09
0.10–0.11
0.04–0.08
0.05–0.07
0.00–0.07
60
50
40
30
All
Mainland
20
Island
10
0
-tR
S
12
al
V
A
N
S
16
N
D
4
AC
4
M
BD
N
F
M
C
S
O
C
PD
R
1
AG
2
AG
R
Figure S1 Informativeness of three mitochondrial (12S–tRNAVal, 16S and ND4) and
six nuclear (ACM, BDNF, CMOS, PDC, RAG1 and RAG2) loci in mainland and island
species of Phyllodactylus included in this study.
Figure S2 Box plots of maximum-likelihood-corrected ND4 genetic distances among
species of Phyllodactylus from the Galápagos Islands (G), mainland South America
(M), and between the two groups.