TABLE S1. Results of the Bayesian inference analyses by partition, the number of
generations the chains were run (values in millions), the number of generations discarded as the
burn-in period, and the marginal log likelihood (lnL) scores of each run based on bootstrapped
values (see text).
_______________________________________________________________________
Data
No. generations
Partition
Burn-in
Marginal lnL
_______________________________________________________________________
BRCA1
16.8
none
1,678,700
–52,054.793
BRCA1
35.9
codon
3,596,600
–51,884.078
GHR
21.5
none
2,146,800
–26,052.013
GHR
33.3
codon
3,332,700
–25,722.724
IRBP
20.7
none
2,070,800
–31,216.657
IRBP
23.5
codon
2,353,200
–29,633.921
RAG1
28.4
none
2,842,200
–39,427.366
RAG1
30
codon
3,000,000
–39,105.281
Concatenated
11.1
none
1,110,100
–147,388.717
Concatenated
15
codon
1,501,900
–146,670.543
Concatenated
15.1
gene
1,510,700
–146,836.256
Concatenated
19.4
gene & codon 1,940,500
–146,839.924
_______________________________________________________________________
FIGURE S1. Biogeographic regions used in ancestral-state estimations. Colors of
biogeographic regions correspond to those in Figure 5.
FIGURE S2. Maximum-likelihood phylogram of the BRCA1 gene reconstructed with the
general time reversible (GTR) plus invariable sites (I) and gamma distributed rates ()
(GTR+I+) substitution model. Values at nodes represent Bayesian posterior probabilities
greater than 50%.
FIGURE S3. Maximum-likelihood phylogram of the GHR gene reconstructed with the
GTR+I+ substitution model. Values at nodes represent Bayesian posterior probabilities greater
than 50%.
FIGURE S4. Maximum likelihood phylogram of the IRBP gene reconstructed with the
GTR+I+ substitution model. Values at nodes represent Bayesian posterior probabilities greater
than 50%. Grey vertical bars denote clades with inconsistent reconstructions among all gene
trees.
FIGURE S5. Maximum-likelihood phylogram of the RAG1 gene reconstructed with the
GTR+I+ substitution model. Values at nodes represent Bayesian posterior probabilities greater
than 50%. Grey vertical bars denote clades with inconsistent reconstructions among all gene
trees.
FIGURE S6. Time-calibrated subsampled tree from the Beast analysis and diversificationrate shifts from the Medusa analysis. Nodes 1–8 are supported with a corrected Akaike
information criterion cutoff of 6.5–8, and nodes 1–9 by a cutoff of 4–6.4. Letters in squares at
nodes represent biogeographic transitions. Af, Africa; NA, North America; SA, South America;
S, Sahul; A, Southeast Asia; EA, Eurasia; M, Madagascar. The number following the
biogeographic transition corresponds to the chronological order of colonizations.