Appendix S1 Specimen voucher numbers, identification and geographic location of samples for this study.

Appendix S2 Description of *BEAST methodology for inferring BP&P starting topologies.

Appendix S3 Description of BP&P species delimitation methodology.


Fig. S1 Mitochondrial (left) and concatenated nuclear (right) maximum likelihood phylogenetic estimates. Only bootstrap support >70% is indicated.

Fig. S2 Individual maximum likelihood gene trees for the four nuclear loci sampled. Only bootstrap support >70% is indicated.

Fig. S3 Mitochondrial and nuclear (ND1–ND2, DGL-α, L52, L74, PRLR) statistical haplotype networks inferred by TCS (Clement et al. 2000).

Fig. S4 Distance-based (neighbour-joining) nuclear haplotype network as inferred by the NeighborNet algorithm of splitstree. Input standardized distance matrix created with the program pofad.

Fig. S5 Distruct visualization (Rosenberg 2004) visualization of structure analyses and summarized geographic distribution of major Varanus demes (Pritchard et al. 2000) for K = 6 populations.

Fig. S6 Bayesian estimates of the Varanus salvator Complex species tree as inferred by the program *beast.

Fig. S7 Recognized major faunal regions and island groups of the Philippines, including distributions of Varanus species.


Table S1 Individual loci, original publications and polymerase chain reaction (PCR) thermal profiles for each. Annealing temperature was varied to improve amplification for problematic samples.

Table S2 Loci and associated primers sequenced for this study. Thermal profiles for PCR and cycle sequencing reactions vary only by annealing temperature (55–58º) across primers and samples.

Table S3 Estimated models of evolution by data partition, as inferred by jmodeltest. Final models selected by AIC and applied for partitioned, model-based analyses.

Table S4 Summary of results among loci for tests of neutrality using Tajima's D (Tajima 1989).

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