Supplementary Material

Supplementary Material for:

The Origins of Sexually Transmitted HIV Among Men Who Have Sex with Men

David M. Butler, Wayne Delport, Sergei L. Kosakovsky Pond, Malcolm K. Lakdawala, Pok Man Cheng, Susan J. Little, Douglas D. Richman, Davey M. Smith*

*To whom correspondence should be addressed. E-mail: davey{at}ucsd.edu

Published 10 February 2010, Sci. Transl. Med. 2, 18re1 (2010)
DOI: 10.1126/scitranslmed.3000447

This PDF file includes:

  • Table S1. Genetic differentiation between compartments.
  • Table S2. Estimated divergence times of compartments.
  • Table S3. Number of purifying (dN/dS < 1) and positive (dN/dS > 1) selection sites.
  • Table S4. Inferred substitutions along transmission branches for pairs A, E, and F (panel A) and along pretransmission branches for all pairs A to K (panel B).
  • Table S5. Marginal likelihoods, estimated as the harmonic mean of the sampled likelihoods in Bayesian MCMC analysis.
  • Fig. S1. Maximum likelihood phylogenetic tree of viral sequences from a source who infected multiple partners at two independent time points.
  • Fig. S2. Posterior distributions of parameters sampled during Bayesian MCMC analyses.
  • Fig. S3. Site-specific nonsynonymous (dN) and synonymous (dS) rates of substitution.
  • References

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