Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards
Article first published online: 28 MAY 2013
© 2013 John Wiley & Sons Ltd
Volume 22, Issue 13, pages 3495–3510, July 2013
How to Cite
Welton, L. J., Siler, C. D., Oaks, J. R., Diesmos, A. C. and Brown, R. M. (2013), Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards. Molecular Ecology, 22: 3495–3510. doi: 10.1111/mec.12324
- Issue published online: 26 JUN 2013
- Article first published online: 28 MAY 2013
- Manuscript Accepted: 19 MAR 2013
- Manuscript Revised: 17 MAR 2013
- Manuscript Received: 4 APR 2012
- NSF Biotic Surveys and Inventories. Grant Number: DEB 0743491
- NSF. Grant Number: DEB 0804115
- Fulbright and Fulbright-Hayes Fellowships
- University of Kansas Biodiversity Institute
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. 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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