Abstract
A new method to estimate within-species gene genealogies was used to establish linkages among individuals associated with the Florida dental human immunodeficiency virus transmission case. Phylogenetic relationships were estimated from 103 nucleotide sequences from the V3 region of the env gene representing the Florida dentist, eight of his seropositive patients, and many local controls. The cladogram estimation procedure supports linkages among individuals within the previously described dental clade, whereas local controls and other patients form independent networks or are outliers in the main network, indicating more distant evolutionary relationships. A nested statistical analysis also indicates significant cohesion of the dental clade group.
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- Crandall K. A., Templeton A. R. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics. 1993 Jul;134(3):959–969. doi: 10.1093/genetics/134.3.959. [DOI] [PMC free article] [PubMed] [Google Scholar]
- DeBry R. W., Abele L. G., Weiss S. H., Hill M. D., Bouzas M., Lorenzo E., Graebnitz F., Resnick L. Dental HIV transmission? Nature. 1993 Feb 25;361(6414):691–691. doi: 10.1038/361691a0. [DOI] [PubMed] [Google Scholar]
- Hillis D. M., Huelsenbeck J. P., Cunningham C. W. Application and accuracy of molecular phylogenies. Science. 1994 Apr 29;264(5159):671–677. doi: 10.1126/science.8171318. [DOI] [PubMed] [Google Scholar]
- Hillis D. M., Huelsenbeck J. P. Support for dental HIV transmission. Nature. 1994 May 5;369(6475):24–25. doi: 10.1038/369024a0. [DOI] [PubMed] [Google Scholar]
- Ou C. Y., Ciesielski C. A., Myers G., Bandea C. I., Luo C. C., Korber B. T., Mullins J. I., Schochetman G., Berkelman R. L., Economou A. N. Molecular epidemiology of HIV transmission in a dental practice. Science. 1992 May 22;256(5060):1165–1171. doi: 10.1126/science.256.5060.1165. [DOI] [PubMed] [Google Scholar]
- Roff D. A., Bentzen P. The statistical analysis of mitochondrial DNA polymorphisms: chi 2 and the problem of small samples. Mol Biol Evol. 1989 Sep;6(5):539–545. doi: 10.1093/oxfordjournals.molbev.a040568. [DOI] [PubMed] [Google Scholar]
- Sabino E. C., Shpaer E. G., Morgado M. G., Korber B. T., Diaz R. S., Bongertz V., Cavalcante S., Galvão-Castro B., Mullins J. I., Mayer A. Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals from Brazil. J Virol. 1994 Oct;68(10):6340–6346. doi: 10.1128/jvi.68.10.6340-6346.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sing C. F., Haviland M. B., Templeton A. R., Zerba K. E., Reilly S. L. Biological complexity and strategies for finding DNA variations responsible for inter-individual variation in risk of a common chronic disease, coronary artery disease. Ann Med. 1992 Dec;24(6):539–547. doi: 10.3109/07853899209167008. [DOI] [PubMed] [Google Scholar]
- Sing C. F., Haviland M. B., Zerba K. E., Templeton A. R. Application of cladistics to the analysis of genotype-phenotype relationships. Eur J Epidemiol. 1992 May;8 (Suppl 1):3–9. doi: 10.1007/BF00145343. [DOI] [PubMed] [Google Scholar]
- Templeton A. R., Boerwinkle E., Sing C. F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics. 1987 Oct;117(2):343–351. doi: 10.1093/genetics/117.2.343. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Templeton A. R., Crandall K. A., Sing C. F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics. 1992 Oct;132(2):619–633. doi: 10.1093/genetics/132.2.619. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Templeton A. R., Sing C. F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics. 1993 Jun;134(2):659–669. doi: 10.1093/genetics/134.2.659. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zharkikh A., Li W. H. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Mol Biol Evol. 1992 Nov;9(6):1119–1147. doi: 10.1093/oxfordjournals.molbev.a040782. [DOI] [PubMed] [Google Scholar]
- Zharkikh A., Li W. H. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: II. Four taxa without a molecular clock. J Mol Evol. 1992 Oct;35(4):356–366. doi: 10.1007/BF00161173. [DOI] [PubMed] [Google Scholar]