Article first published online: 8 APR 2014
© 2014 John Wiley & Sons Ltd
Volume 23, Issue 8, pages 2072–2092, April 2014
How to Cite
Luo, S.-J., Zhang, Y., Johnson, W. E., Miao, L., Martelli, P., Antunes, A., Smith, J. L. D. and O'Brien, S. J. (2014), Sympatric Asian felid phylogeography reveals a major Indochinese–Sundaic divergence. Molecular Ecology, 23: 2072–2092. doi: 10.1111/mec.12716
- Issue published online: 8 APR 2014
- Article first published online: 8 APR 2014
- Accepted manuscript online: 14 MAR 2014 12:03PM EST
- Manuscript Accepted: 21 FEB 2014
- Manuscript Revised: 19 FEB 2014
- Manuscript Received: 22 OCT 2013
- NIH Intramural Program (2000–2009)
- NIH Pre-Doctoral (2000–2003) and Post-Doctoral (2007–2009) Fellowships
- UMN Doctoral Dissertation Fellowship (2005–2006)
- National Natural Science Foundation of China . Grant Number: NSFC No. 31271320
- Center for Life Sciences at PKU
- ERDF through COMPETE . Grant Numbers: PEst-C/MAR/LA0015/2013, PTDC/AAC-AMB/121301/2010, FCOMP-01-0124-FEDER-019490
- Russian Ministry of Science Mega-Grant . Grant Number: 11.G34.31.0068
Appendix S1 Supplementary Methods, Tables and Figures.
Table S1 Samples included in this study, with geographic origins, sources, names and genetic information.
Table S2 Summary of wild cat specimens used in this study.
Table S3 Mitochondrial (mtDNA) and nuclear loci used in this study.
Table S4 Summary of mtDNA and Y haplotypes of the individuals used in the partitioned phylogenetic analyses.
Table S5 Summary of variable sites in the nuclear DNA segments within felid species.
Table S6 Results of mismatch distribution and estimates of Tajima's D and Fu's Fs of the mtDNA sequences in each felid population: Indochinese Prionailurus bengalensis, Sundaic P. bengalensis, Indochinese P. viverrinus and Indochinese Pardofelis temminckii.
Fig. S1 MtDNA phylogenetic relationships (1792 bp) among Prionailurus spp. and Pardofelis spp. estimated in paup with maximum-likelihood method.
Fig. S2 Phylogenetic relationships (2154 bp) among Y-chromosome haplotypes of Prionailurus spp., Pardofelis spp. and Panthera spp. estimated in paup with maximum-likelihood method.
Fig. S3 Phylogenetic relationships among mtDNA haplotype (1792 bp) of Prionailurus spp. estimated in paup with maximum parsimony (MP), minimum evolution (ME) and maximum-likelihood (ML) methods (the MP tree is shown).
Fig. S4 Phylogenetic relationships among mtDNA haplotypes (1220 bp) of Pardofelis spp. estimated in paup with maximum parsimony (MP), minimum evolution (ME) and maximum-likelihood (ML) methods (without missing data).
Fig. S5 Cumulative AWTY plots for diagnostics of output from mrbayes analyses with mitochondrial haplotypes, with 25% as the fraction of burn-in.
Fig. S6 AWTY bivariate plot of the split frequencies for comparison between paired Bayesian MCMC simulations from mrbayes analyses with mitochondrial haplotypes, with 25% as the fraction of burn-in.
Fig. S7 Mismatch distribution analyses of mtDNA sequences.
Fig. S8 Phylogenetic analysis and TMRCA estimates in Prionailurus spp. and Pardofelis spp. based on 3946-bp combined mtDNA and Y-chromosome haplotypes.
|mec12716-sup-0002-AppendixS2.nex||application/nex||92K||Appendix S2 MtDNA sequence alignment for Fig. 2(A), Fig. 5(A) and Fig S1.|
|mec12716-sup-0003-AppendixS3.nex||application/nex||32K||Appendix S3 Y-chromosome sequence alignment for Fig. 3, Fig. 5(B) and Fig. S2.|
|mec12716-sup-0004-AppendixS4.nex||application/nex||273K||Appendix S4 PLP1 sequence alignment for Fig. 4.|
|mec12716-sup-0005-AppendixS5.nex||application/nex||170K||Appendix S5 Combined mtDNA and Y chromosome sequence alignment for Fig. S8.|
|mec12716-sup-0006-AppendixS6.tre||application/tre||43K||Appendix S6 Phylogenetic tree file for Fig. 5(A).|
|mec12716-sup-0007-AppendixS7.tre||application/tre||14K||Appendix S7 Phylogenetic tree file for Fig 5(B).|
|mec12716-sup-0008-AppendixS8.tre||application/tre||38K||Appendix S8 Phylogenetic tree file for Fig. S8(B).|
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