Skip to main content
SpringerLink
Log in

Phylogenetics of HIV

  • Chapter
Computational and Evolutionary Analysis of HIV Molecular Sequences

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Adachi J., Hasegawa, M. 1996a. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42: 459–468.

    Google Scholar 

  • Adachi J., Hasegawa, M. 1996b. MOLPHY version 2.3: programs for molecular phylogenetics based in maximum likelihood. Comput. Sci. Monogr. 28: 1–150.

    Google Scholar 

  • Akaike, H. 1974. A new look at the statistical model identification. IEEE Trans. Autom. Contr. 19: 716–723.

    Google Scholar 

  • Bonhoeffer, S., Holmes, E. C. and Nowak, M. A. 1995. Causes of HIV diversity. Nature 376: 125.

    Google Scholar 

  • Bremer, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: 795–803.

    Google Scholar 

  • Brown, W. M., Prager, E. M., Wang, A. and Wilson, A. C. 1982. Mitochondrial sequences of primates: tempo and mode of evolution. J. Mol. Evol. 18: 225–239.

    Google Scholar 

  • Bull, J. J., Huelsenbeck, J. P., Cunningham, C. W., Swofford, D. L. and Waddell, P. J. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42: 384–397.

    Google Scholar 

  • Castelloe, J. and Templeton, A. R. 1994. Root probabilities for intraspecific gene trees under neutral coalescent theory. Mol. Phylogenet. Evol. 3: 102–113.

    Google Scholar 

  • Cornelissen, M., Kampingam, G., Zorgdrager, F. and Goudsmit, J. 1996. Human immunodeficiency virus type 1 subtypes defined by env show high frequency of recombinant gag genes. The UNAIDS Network for HIV Isolation and Characterization. J. Virol. 70: 8209–8212.

    Google Scholar 

  • Crandall, K. A. 1994. Intraspecific cladogram estimation: Accuracy at higher levels of divergence. Syst. Biol. 43: 222–235.

    Google Scholar 

  • Crandall, K. A. 1995. Intraspecific phylogenetics: Support for dental transmission of human immunodeficiency virus. J. Virol. 69: 2351–2356.

    Google Scholar 

  • Crandall, K. A. (ed.). 1999. Molecular Evolution of HIV. The Johns Hopkins University Press, Baltimore, MD.

    Google Scholar 

  • Crandall, K. A., Kelsey, C. R., Imamichi, H., Lane, C. H. and Salzman, N. P. 1999a. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol. Biol. Evol. 16: 372–382.

    Google Scholar 

  • Crandall, K. A. and Templeton, A. R. 1993. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134: 959–969.

    Google Scholar 

  • Crandall, K. A. and Templeton, A. R. 1996. Applications of intraspecific phylogenetics, In New Uses for New Phylogenies (Harvey, P. H., Leigh Brown, A. J., Maynard Smith, J. and Nee, S., eds). Oxford University Press, Oxford, England.

    Google Scholar 

  • Crandall, K. A. and Templeton, A. R. 1999. Statistical methods for detecting recombination, In The Evolution of HIV (Crandall, K. A., ed.) The Johns Hopkins University Press, Baltimore, MD.

    Google Scholar 

  • Crandall, K. A., Templeton, A. R. and Sing, C. F. 1994. Intraspecific phylogenetics: problems and solutions, In Models in Phylogeny Reconstruction (Scotland, R. W., Siebert, D. J. and Williams, D. M, eds.) Clarendon Press, Oxford, England.

    Google Scholar 

  • Crandall, K. A., Vasco, D., Posada, D. and Imamichi, H. 1999b. Advances in understanding the evolution of HIV. AIDS 13:S39–S47.

    Google Scholar 

  • Cunningham, C. W. 1997. Can three incongruence tests predict when data should be combined? Mol. Biol. Evol. 14: 733–740.

    Google Scholar 

  • Cunningham, C. W., Zhu, H. and Hillis, D. M. 1998. Best-fit maximum-likelihood models for phylogenetic inference: empirical tests with known phylogenies. Evolution 52: 978–987.

    Google Scholar 

  • de Queiroz, A. 1993. For consensus (sometimes). Syst. Biol. 42: 368–372.

    Google Scholar 

  • Eddy, S. 1998. HMMER: profile hidden Markov models for biological sequence analysis. 2.1.1. Department of Genetics, Washington University, St. Louis.

    Google Scholar 

  • Efron, B., Tibshirani, R. J. 1993. An Introduction to the Bootstrap. Chapman and Hall, New York.

    Google Scholar 

  • Eriksson, T. 1998. AUTODECAY. 4.0. Bergius Foundation, Royal Swedish Academy of Sciences, Stockholm.

    Google Scholar 

  • Faith, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40: 366–375

    Google Scholar 

  • Faith, D. P. and Trueman, J. W. H. 1996. When the topology-dependent permutation test (T-PTP) for monophyly returns significant support for monophyly, should that be equated with (a) rejecting a null hypothesis of nonmonophyly, (b) rejecting a null hypothesis of “no structure”, (c) failing to falsify a hypothesis of monophyly, or (d) none of the above? Syst. Biol. 45: 580–586.

    Google Scholar 

  • Farris, J. S., Källersjö, M., Kluge, A. G. and Bult, C. 1994. Testing significance of incongruence. Cladistics 10:315–320.

    Google Scholar 

  • Felsenstein, J. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22: 240–249.

    Google Scholar 

  • Felsenstein, J. 1984. Distance methods for inferring phylogenies: a justification. Evolution 38: 16–24

    Google Scholar 

  • Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.

    Google Scholar 

  • Felsenstein, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22:521–565.

    Google Scholar 

  • Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package). 3.5c. Department of Genetics, University of Washington, Seattle.

    Google Scholar 

  • Fisher, A. G., Ensoli, B., Looney, D., Rose, A., Gallo, R. C., Saag, M. S., Shaw, G. M., Hahn, B. H. and Wong-Staal, F. 1988. Biologically diverse molecular variants within a single HIV-1 isolate. Nature 334: 444–447.

    Google Scholar 

  • Fitch, W. 1971. Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20: 406–416.

    Google Scholar 

  • Fu, Y. X. and Li, W. H. 1993. Statistical tests of neutrality of mutations. Genetics 133: 693–709.

    Google Scholar 

  • Galtier, N. and Gouy, M. 1998. Inferring pattern and process: maximum likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15: 871–879.

    Google Scholar 

  • Galtier, N., Gouy, M. and Gautier, C. 1996. SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phytogeny. Computer Applications in Biosciences 12: 543–548.

    Google Scholar 

  • Gao, F., Robertson, D. L., Morrison, S. G., Hui, H., Craig, S., Decke, J., Fultz, P. N., Girard, M., Shaw, G. M., Hahn, B. H. and Sharp, P. M. 1996. The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. J. Virol. 70:7013–7029.

    Google Scholar 

  • Gaut, B. S. and Weir, B. S. 1994. Detecting substitution-rate heterogeneity among regions of a nucleotide sequence. Mol. Biol. Evol. 11: 620–629.

    Google Scholar 

  • Goldman, N. 1990. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses. Syst. Zool. 39: 345–361.

    Google Scholar 

  • Goldman, N. 1993a. Simple diagnostic statistical tests of models for DNA substitution. J. Mol. Evol. 37: 650–661.

    Google Scholar 

  • Goldman, N. 1993b. Statistical tests of models of DNA substitution. J. Mol. Evol. 36: 182–198.

    Google Scholar 

  • Goldman, N., Thorne, J. L. and Jones, D. T. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149: 445–458.

    Google Scholar 

  • Goldman, N. and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11: 725–736.

    Google Scholar 

  • Goloboff, P. A. 1997. NONA. 1.5. S. M. de Tucumón: Fundacidón e Instituto Miguel Lillo, Argentina.

    Google Scholar 

  • Grantham, R. 1974. Amino acid difference formula to help explain protein evolution. Science 185: 862–864.

    Google Scholar 

  • Grassly, N. C. and Rambaut, A. 1997. Treevolve: a program to simulate the evolution of DNA sequences under different population dynamic scenarios. 1.3. Wellcome Centre for Infectious Disease, Department of Zoology, Oxford University, Oxford, UK.

    Google Scholar 

  • Groenink, M., Fouchier, R. A. M., de Goede, R. E. Y., de Wolf, F., Gruters, R. A., Cupyers, H. T. M., Hisman, H. G. and Tersmette, M. 1991. Phenotypic heterogeneity in a panel of infectious molecular human immunodeficiency virus type 1 clones derived from a single individual. J. Virol. 65: 1968–1975.

    Google Scholar 

  • Gu, X. and Li, W-H. 1992. Higher rates of amino acid substitution in rodents that in humans. Mol. Phylogenet. Evol. 1: 211–214.

    Google Scholar 

  • Hahn, B. H., Shaw, G. M., Taylor, M. E., Redfield, R. R., Markham, P. D., Salahuddin, S. Z., Wong-Staal, F., Gallo, R. C., Parks, E. S. and Parks, W. P. 1986. Genetic variation in HTLV-III/LAV over time in patients with AIDS or at risk for AIDS. Science 232: 1548–1553.

    Google Scholar 

  • Hall, P. and Martin, M. A. 1988. On bootstrap resampling and iteration. Biometrika 75: 661–671.

    Google Scholar 

  • Hartmann, M. and Golding, B. G. 1998. Searching for substitution rate heterogeneity. Mol. Phy. Evol. 9: 64–71.

    Google Scholar 

  • Hasegawa, M. 1990. Phylogeny and molecular evolution in primates. Jpn. J. Genet. 65: 243–266.

    Google Scholar 

  • Hasegawa, M., Kishino, K. and Yano, T. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160–174.

    Google Scholar 

  • Hein, J. 1990. Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci. 98: 185–200.

    Google Scholar 

  • Hey, J., and Wakeley, J. 1997. A coalescent estimator of the population recombination rate. Genetics 145: 833–846.

    Google Scholar 

  • Hillis, D. M. 1999. Phylogenetics and the study of HIV, In The Evolution of HIV (Crandall, K. A., ed.) Johns Hopkins University Press, Baltimore, MD.

    Google Scholar 

  • Hillis, D. M., Bull, J. J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42: 182–192.

    Google Scholar 

  • Hillis, D. M., Huelsenbeck, J. P. and Cunningham, C. W. 1994. Application and accuracy of molecular phylogenies. Science 264: 671–677.

    Google Scholar 

  • Hillis, D. M., Mable, B. K. and Moritz, C. 1996. Applications of molecular systematics: The state of the field and a look to the future, In Molecular Systematics, (Hillis, D. M., Moritz, C. and Mable, B. K., eds.) Sinauer Associates, Sunderland, MA.

    Google Scholar 

  • Holland, J. J., De la Torre, J. C. and Steinhauer, D. A. 1992. RNA virus populations as quasispecies. Curr. Top. Microbiol. Immunol. 176: 1–20.

    Google Scholar 

  • Holmes, E. C., Pybus, O. G. and Harvey, P. H. 1999. The molecular population dynamics of HIV-1, In The Evolution of HIV, (Crandall, K. A., ed.) The Johns Hopkins University Press, Baltimore, MD.

    Google Scholar 

  • Holmes, E. C., Zhang, L. Q., Simmonds, P., Ludlam, C. A. and Leigh Brown, A. J. 1992. Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc. Natl Acad. Sci. USA 89: 4835–4839.

    Google Scholar 

  • Hudson, R. R., Kreitman, M. and Aguade, M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153–159.

    Google Scholar 

  • Huelsenbeck, J. 1995. The Siminator: a program for simulating data under the HKY85 model of DNA substitution with gamma distributed rates among sites. 2.0. Department of Integrative Biology, University of California at Berkeley, Berkely, CA.

    Google Scholar 

  • Huelsenbeck, J. P. and Bull, J. J. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45: 92–98.

    Google Scholar 

  • Huelsenbeck, J. P., Bull, J. J. and Cunningham, W. 1996a. Combining data in phylogenetic analysis. Trend Ecol. Evol. 11: 152–158.

    Google Scholar 

  • Huelsenbeck, J. P. and Crandall, K. A. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28: 437–466.

    Google Scholar 

  • Huelsenbeck, J. P., Hillis, D. M. and Jones, R. 1996b. Parametric bootstrapping in molecular phylogenetics: applications and performance, In Molecular Zoology: Advances, Strategies, and Protocols, (Ferraris, J. D. and Palumbi, S. R., eds.) Wiley-Liss, New York, NY.

    Google Scholar 

  • Huelsenbeck, J. P. and Rannala, B. 1997. Phylogenetic methods come of age: testing hypothesis in a evolutionary context. Science 276: 227–232.

    Google Scholar 

  • Hughes, A. L. and Nei, M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167–170.

    Google Scholar 

  • Ina, Y. 1995. New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J. Mol. Evol. 40: 190–226.

    Google Scholar 

  • Jukes, T. H. and Cantor, C. R. 1969. Evolution of protein molecules, In Mammalian Protein Metabolism, (Munro, H. M., ed.) Academic Press, New York, NY.

    Google Scholar 

  • Kelsey, C. R., Crandall, K. A. and Voevodin, A. F. 1999. Different models, different trees: The geographic origin of PTLV-I. Mol. Phylogenet. Evol. 10: 336–347.

    Google Scholar 

  • Kimura, M. 1977. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267: 275–276.

    Google Scholar 

  • Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111–120.

    Google Scholar 

  • Kishino, H. and Hasegawa, M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol, Evol. 29: 170–179.

    Google Scholar 

  • Kjer, K. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs. Mol. Phylogenet. Evol. 4: 314–330.

    Google Scholar 

  • Kluge, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38: 7–25.

    Google Scholar 

  • Korber, B., Theiler, J. and Wolinsky, S. 1998. Limitations of a molecular clock applied to the considerations of the origin of HI V-1. Science 280: 1868–1871.

    Google Scholar 

  • Krushkal, J. and Li, W.-H. 1999. Use of phylogenetic inference to test an HIV transmission hypothesis, In Molecular Evolution of HIV, (Crandall, K. A., ed.) The Johns Hopkins University Press, Baltimore, MD.

    Google Scholar 

  • Kumar, S., Tamura, K. and Nei, M. 1993. MEGA: Molecular Evolutionary Genetics Analysis. 1.01. The Pennsylvania State University, University Park, PA

    Google Scholar 

  • Lai, S., Page, J. B. and Lai, H. 1995. HIV results in the frame. Paradox remains [letter]. Nature 375: 196–197; discussion 198.

    Google Scholar 

  • Langley, C. H. and Fitch, W. 1974. An estimation of the constancy of the rate of molecular evolution. J. Mol. Evol. 3: 161–177.

    Google Scholar 

  • Leigh Brown, A. 1994. Methods of evolutionary analysis of viral sequences, In The Evolutionary Biology of Viruses, (Morse, S. S., ed.) Raven Press, Ltd., New York.

    Google Scholar 

  • Leigh Brown, A. J. and Holmes, E. C. 1994. Evolutionary biology of human inmunodeficiency virus. Annu. Rev. Ecol. Syst. 25: 127–165.

    Google Scholar 

  • Leitner, T., Escanilla, D., Marquina, S., Wahlberg, J., Brostrom, C., Hansson, H. B., Uhlen, M. and Albert, J. 1995. Biological and molecular characterization of subtype D, G, and A/D recombinant HIV-1 transmissions in Sweden. Virology 209: 136–146.

    Google Scholar 

  • Leitner, T., Kumar, S. and Albert, J. 1997. Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J. Virol. 71: 4761–4770.

    Google Scholar 

  • Lewis, P. O. 1998. A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Mol. Biol. Evol. 15: 277–283.

    Google Scholar 

  • Lewontin, R. C. 1989. Inferring the number of evolutionary events from DNA coding sequences. Mol. Biol. Evol. 6: 15–32.

    Google Scholar 

  • Li, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96–99.

    Google Scholar 

  • Li, W.-H. 1997. Molecular Evolution. Sinauer Associates, Inc., Sunderland, MA.

    Google Scholar 

  • Li, W.-H., Tanimura, M. and Sharp, P. M. 1988. Rates and dates of divergence between AIDS virus nucleotide sequences. Mol. Biol. Evol. 5: 313–330.

    Google Scholar 

  • Lio, P., Goldman, N., Thorne, J. L. and Jones, D. T. 1998. PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics 14: 726–733.

    Google Scholar 

  • Lole, K. S., Bollinger, R. C., Paranjape, R. S., Gadkari, D., Kulkarni, S. S., Novak, N. G., Ingersoll, R., Sheppard, H. W. and Ray, S. C. 1998. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73: 152–160.

    Google Scholar 

  • Louwagie, J. J., McCutchan, F., Brennan, T., Peeters, M., Brennan, T., Sanders-Buell, E., Eddy, G., van der Groen, G., Fransen, K., Bershy-Damet, M., Deleys, R. and Burke, D. 1993. Phylogenetic analysis of gag genes from seventy international HIV-1 isolates provides evidence for multiple genotypes. AIDS 7: 769–780.

    Google Scholar 

  • Maddison, W. P. and Maddison, D. R. 1994. MacClade: Analysis of phylogeny and character evolution. Sinauer Associates, Sunderland, MA.

    Google Scholar 

  • Martins, E. 1997. COMPARE: phylogenetic analysis of comparative data. 4.1. Department of Biology, University of Oregon, Eugene, OR.

    Google Scholar 

  • McDonald, J. H. and Kreitman, M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652–654.

    Google Scholar 

  • Messier, W. and Stewart, C.-B. 1997. Episodic adaptive evolution of primate Iysozymes. Nature 385: 151–154.

    Google Scholar 

  • Mickevich, M. F. and Farris, J. S. 1981. The implications of congruence in Menidia. Syst Zool 30: 351–370.

    Google Scholar 

  • Miller, R. G. 1966 Simultaneous Statistical Inference. McGraw-Hill, New York.

    Google Scholar 

  • Mindell, D. P. 1996. Positive selection and rates of evolution in immunodeficiency viruses from humans and chimpanzees. Proc. Natl Acad. Sci. USA 93: 3284–3288.

    Google Scholar 

  • Miyamoto, M. M. and Fitch, W. M. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44: 64–76.

    Google Scholar 

  • Miyata, T. and Yasunaga, T. 1980. Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitution from homologous nucleotide sequences and its application. J. Mol. Evol. 16: 23–36.

    Google Scholar 

  • Moriyama, E. N., Ina, Y., Ikeo, K., Shimizu, M. and Gojobori, T. 1991. Mutation pattern of human immunodeficiency virus gene. J. Mol. Evol. 32: 360–363.

    Google Scholar 

  • Muse, S. 1999. Modeling the molecular evolution of HIV sequences, In The Evolution of HIV, (Crandall, K. A., ed.) Johns Hopkins University Press, Baltimore, MD.

    Google Scholar 

  • Muse, S. V. 1996. Estimating synonymous and nonsynonymous substitution rates. Mol. Biol. Evol. 13: 105–114.

    Google Scholar 

  • Muse, S. V. 2000. HYPHY: hypothesis testing using phylogenies. Beta 1.0. Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, NC

    Google Scholar 

  • Muse, S. V. and Gaut, B. S. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11: 715–724.

    Google Scholar 

  • Muse, S. V. and Weir, B. S. 1992. Testing for equality of evolutionary rates. Genetics 132: 269–276.

    Google Scholar 

  • Nei, M. 1996. Phylogenetic analysis in molecular evolutionary genetics. Ann. Rev. Genet. 30: 371–403.

    Google Scholar 

  • Nei, M. and Gojobori, T. 1986. Simple method for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418–426.

    Google Scholar 

  • Nielsen, R. 1997. The ratio of replacement to silent divergence and tests of neutrality. J. Evol. Biol. 10: 217–231.

    Google Scholar 

  • Nielsen, R. and Yang, Z. 1998. Likelihood methods for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929–936.

    Google Scholar 

  • Nixon, K. C. and Carpenter, J. M. 1996. On simultaneous analysis. Cladistics 12: 221–241.

    Google Scholar 

  • Nowak, M. and Bangham, C. R. M. 1996. Population dynamics of inmune responses to persistent viruses. Science 272: 74–79.

    Google Scholar 

  • Olsen, G. J., Matsuda, H., Hagstrom, R. and Overbeek, R. 1994. Fast DNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosciences 10: 41–48.

    Google Scholar 

  • Page, R. D. M. 1993. COMPONENT. 2.0. Natural History Museum, London, UK

    Google Scholar 

  • Pamilo, P. and Bianchi, N. O. 1993. Evolution of the Zfx and Zfy genes: rates and interdependence between genes. Mol. Biol. Evol. 10: 271–281.

    Google Scholar 

  • Pedersen, A.-M. K., Wiuf, C. and Christiansen, F. B. 1998. A codon-based model designed to describe lentiviral evolution. Mol. Biol. Evol. 15: 1069–1081.

    Google Scholar 

  • Penny, D. and Hendy, M. D. 1985. The use of tree comparison metrics. Syst. Zool. 34: 75–82.

    Google Scholar 

  • Penny, D. and Hendy, M. D. 1986. Estimating the reliability of evolutionary trees. Mol Biol. Evol. 3: 403–417.

    Google Scholar 

  • Penny, D., Hendy, M. D. and Steel, M. A. 1992. Progress with methods for constructing evolutionary trees. Trends Ecol Evol 7: 73–79.

    Google Scholar 

  • Penny, D, Lockhart, P. J., Steel, M. A. and Hendy, M. D. 1994. The role of models in reconstructing evolutionary trees, In Models in Phylogenetic Reconstruction, (Scotland, R. W., Siebert, D. J. and Williams, D. M., eds.) Clarendon Press, Oxford.

    Google Scholar 

  • Posada, D. and Crandall, K. A. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14: 817–818.

    Google Scholar 

  • Prager, E. M. and Wilson, A. C. 1988. Ancient origin of lactalbumin from Iysozyme: Analysis of DNA and amino acid sequences. J. Mol. Evol. 27: 326–335.

    Google Scholar 

  • Rambaut, A. and Grassly, N. C. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosciences 13: 235–238.

    Google Scholar 

  • Robertson, D. L., Hahn, B. H. and Sharp, P. M. 1995a. Recombination in AIDS viruses. J. Mol. Evol. 40: 249–259.

    Google Scholar 

  • Robertson, D. L., Sharp, P. M., McCutchan, F. E. and Hahn, B. H. 1995b. Recombination in HIV-1. Nature 374: 124–126.

    Google Scholar 

  • Robinson, D. F. and Foulds, L. R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53: 131–147.

    Google Scholar 

  • Robinson, M., Gouy, M., Gautier, C. and Mouchiroud, D. Sensitivity of the relative-rate test to taxonomic sampling. Mol. Biol Evol. 15: 1091–1098.

    Google Scholar 

  • Rodrigo, A. G., Kelly-Borges, M., Bergquist, P. R. and Bergquist, P. L. 1993. A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. New Zealand J. Bot. 31: 257–268.

    Google Scholar 

  • Rodríguez, F., Oliver, J. F., Marín, A. and Medina, J. R. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142: 485–501.

    Google Scholar 

  • Rozas, J. and Rozas, R. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174–175.

    Google Scholar 

  • Rzhetsky, A. and Nei, M. 1992. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9: 945–967.

    Google Scholar 

  • Rzhetsky, A. and Nei, M. 1993. METREE: program package for inferring and testing minimum evolution trees. 1.2. Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, University Park, PA

    Google Scholar 

  • Rzhetsky, A. and Nei, M. 1995. Tests of applicability of several substitution models for DNA sequence data. Mol. Biol. Evol. 12: 131–151.

    Google Scholar 

  • Sabino, E. C., Shpaer, E. G., Morgado, M. G., Korber, B. T. M., Diaz, R., Bongertz, V., Cavalcante, S., Galvao-Castro, B., Mullins, J. I. and Mayer, A. 1994 Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals from Brazil. J. Virol. 68: 6340–6346.

    Google Scholar 

  • Salminen, M. O., Carr, J. K., Burke, D. S. and McCutchan, F. E. 1996. Identification of breakpoints in intergenotypic recombinants of HIV-1 by bootscanning. AIDS Res. Hum. Retroviruses 11: 1423–1425.

    Google Scholar 

  • Sanderson, M. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14: 1218–1231.

    Google Scholar 

  • Sanderson, M. J. and Doyle, J. J. 1992. Reconstruction of organismal and gene phylogenies from data on multigene families: Concerted evolution, homoplasy, and confidence. Syst. Biol. 41: 4–17.

    Google Scholar 

  • Sarich, V. M. and Wilson, A. C. 1973. Generation time and genomic evolution in primates. Science 179: 1144–1447.

    Google Scholar 

  • Schneider, S., Kueffer, J.-M., Roessli, D. and Excofier, L. 1997. Arlequin: A software for population genetic data analysis. 1.1. Genetics and Biometry Lab, Dept. of Anthropology, University of Geneva.

    Google Scholar 

  • Seibert, S. A., Howell, C. Y., Hughes, M. K. and Hughes, A. L. 1995. Natural selection on the gag, pol, and env, genes of human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 12: 803–813.

    Google Scholar 

  • Seiller-Moiseiwitsch, F., Margolin, B. H. and Swanstrom, R. 1994. Genetic variability of the human immunodeficiency virus: statistical and biological issues. Annu. Rev. Genet. 28: 559–596.

    Google Scholar 

  • Sharp, P. M., Robertson, D. L., Gao, F. and Hahn, B. H. 1994. Origins and diversity of human immunodeficiency viruses. AIDS 8: S27–S42.

    Google Scholar 

  • Sharp, P. M., Robertson, D. L. and Hahn, B. H. 1995, Cross-species transmission and recombination of AIDS viruses. Phil. Trans. R. Soc. Land. B 349: 41–47.

    Google Scholar 

  • Sharp, P. M., Robertson, D. L. and Hahn, B. H. 1996. Cross-species transmission and recombination of ‘AIDS’viruses. In New Uses for New Phylogenies, (Harvey, P. H., Leigh Brown, A. J., Smith, J. M. and Nee, S, eds.) Oxford University Press, Oxford.

    Google Scholar 

  • Siepel, A. C., Halpern, A. L., Macken, C. and Korber, B. T. M. 1995. A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res. Hum. Retroviruses 11: 1413–1416.

    Google Scholar 

  • Siepel, A. C. and Korber, B. K. 1995. Scanning the data base for recombinant HIV-1 genomes, In Human Retroviruses and AIDS 1995: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences., (Myers, G., Korber, B., Hahn, B., Jeang, K.-T., Mellors, J., McCutchan, F., Henderson, L., Pavlakis, G. and Theoretical Biology and Biophysics Group LANL, Los Alamos, NM., eds.) Theoretical Biology and Biophysics Group, Los Alamos National Labora-tory, Los Alamos, NM.

    Google Scholar 

  • Simon, F., Mauclere, P., Roques, P., Loussert-Ajaka, I., Müller-Trutwin, M. C., Saragosti, S., Georges-Courbot, M. C., Barre-Sinoussi, F. and Brun-Vezinet, F. 1998. Identification of a new human immunodeficiency virus type 1 distinct from group M and group O. Nature Medicine 4: 1032–1037.

    Google Scholar 

  • Sitnikova, T., Rzhetsky, A. and Nei, M. 1995. Interior-branch and bootstrap tests of phylogenetic trees. Mol. Biol. Evol. 12: 319–333.

    Google Scholar 

  • Steel, M. A., Cooper, A. C. and Penny, D. 1996. Confidence intervals for the divergence time of two clades. Syst. Biol. 45: 127–134.

    Google Scholar 

  • Steel, M. A. and Penny, D. 1993. Distributions of tree comparison metrics — some new results. Syst. Biol. 42: 126–141.

    Google Scholar 

  • Strimmer, K. and Haeseler, Av. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964–969.

    Google Scholar 

  • Sullivan, J. and Swofford, D. L. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenies. Journal of Mammalian Evolution 4: 77–86.

    Google Scholar 

  • Swofford, D. L. 1991. When are phylogeny estimates from molecular and morphological data incongruent? In Phylogenetic analysis of DNA sequences, (Miyamoto, M. M. and Cracraft, J., eds.) Oxford University Press, New York, Oxford.

    Google Scholar 

  • Swofford, D. L. 1998. PAUP * Phylogenetic analysis using parsimony and other methods. 4.0 beta. Sinauer Associates, Sunderland, MA

    Google Scholar 

  • Swofford, D. L., Olsen, G. J., Waddell, P. J. and Hillis, D. M. 1996a. Phylogenetic Inference, In Molecular Systematics, (Hillis, D. M., Moritz, C. and Mable, B. K., eds.) Sinauer Associates, Inc., Sunderland, MA.

    Google Scholar 

  • Swofford, D. L., Thorne, J. L., Felsenstein, J. and Wiegmann, B. M. 1996b. The topology-dependent permutation test for monophyly does not test for monophyly. Syst. Biol. 45: 575–579.

    Google Scholar 

  • Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.

    Google Scholar 

  • Tajima, F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135: 599–607.

    Google Scholar 

  • Tavaré, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences, In Lectures on Mathematics in the Life Sciences, (Miura, R. M., ed.) Amer. Math. Soc., Providence, RI.

    Google Scholar 

  • Templeton, A. R. 1983a. Convergent evolution and nonparametric inferences from restriction data and DNA sequences. In Statistical Analysis of DNA Sequence Data, (Weir, B. S., ed.) Marcel Dekker, Inc., New York.

    Google Scholar 

  • Templeton, A. R. 1983b. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37: 221–244.

    Google Scholar 

  • Templeton, A. R., Crandall, K. A. and Sing, C. F. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619–633.

    Google Scholar 

  • Templeton, A. R. and Sing, C. F. 1993. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134: 659–669.

    Google Scholar 

  • Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. and Higgins, D. G. 1997, The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876–4882.

    Google Scholar 

  • Thorne, J., Kishino, H. and Painter, I. S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15: 1647–1657.

    Google Scholar 

  • Thorne, J. L., Goldman, N. and Jones, D. T. 1996. Combining protein evolution and secondary structure. Mol. Biol Evol. 13: 666–673.

    Google Scholar 

  • Thorne, J. L., Kishino, H. and Felsenstein, J. 1991. An evolutionary model for the maximum likelihood alignment of sequence evolution. J. Mol. Evol. 33: 114–124.

    Google Scholar 

  • Thorne, J. L., Kishino, H. and Felsenstein, J. 1992. Inching toward reality: an improved likelihood model of sequence evolution. J. Mol. Evol. 34: 3–16.

    Google Scholar 

  • Uyenoyama, M. K. 1995. A generalized least-squares estimate for the origin of sporophytic self-incompatibility. Genetics 139: 975–992.

    Google Scholar 

  • Vartanian, J.-P., Meyerhans, A., Åsjo, B. and Wain-Hobson, S. 1991. Selection, recombination, and GÆA hypermutation of human immunodeficiency virus type 1 genomes. J. Virol. 65: 1779–1788.

    Google Scholar 

  • Weiller, G. F., McClure, M. A. and Gibbs, A. J. 1995. Molecular phylogenetic analysis, In Molecular Basis of Virus Evolution, (Gibbs, A., Calisher, C. H. and García Arenal, F., eds.) Cambridge University Press, Cambridge.

    Google Scholar 

  • Wheeler, W. 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12: 1–9.

    Google Scholar 

  • Whelan, S. and Goldman, N. 1999. Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics. Mol. Biol. Evol. 16: 1292–1299.

    Google Scholar 

  • Wu, C.-I. and Li, W.-H. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl Acad. Sci. USA 82: 1741–1745.

    Google Scholar 

  • Yamaguchi, Y. and Gojobori, T. 1997. Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc. Natl Acad. Sci. USA 94: 1264–1269.

    Google Scholar 

  • Yang, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10. 1396–1401.

    Google Scholar 

  • Yang, Z. 1994a. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39: 105–111.

    Google Scholar 

  • Yang, Z. 1994b. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39: 306–314.

    Google Scholar 

  • Yang, Z. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42: 587–596.

    Google Scholar 

  • Yang, Z. 1997. Applications Note: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosciences 13: 555–556.

    Google Scholar 

  • Yang, Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15: 568–573.

    Google Scholar 

  • Yang, Z., Goldman, N. and Friday, A. 1994. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11: 316–324.

    Google Scholar 

  • Yang, Z., Goldman, N. and Friday, A. 1995a. Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst. Biol. 44: 384–399.

    Google Scholar 

  • Yang, Z., Kumar, S. and Net, M. 1995b. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141: 1641–1650.

    Google Scholar 

  • Yang, Z. and Nielsen, R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol. 46: 409–418.

    Google Scholar 

  • Yang, Z., Nielsen, R. and Masami, H. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15: 1600–1611.

    Google Scholar 

  • Yokoyama, S., Chung, L. and Gojobori, T. 1988. Molecular evolution of the human immunodeficiency and related viruses. Mol. Biol. Evol. 5: 237–251.

    Google Scholar 

  • Zharkikh, A. and Li, W.-H. 1992a. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Mol. Biol. Evol. 9: 1119–1147.

    Google Scholar 

  • Zharkikh, A. and Li, W.-H. 1992b. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: II. Four taxa without a molecular clock, J. Mol. Evol. 35: 356–366.

    Google Scholar 

  • Zharkikh, A. and Li, W.-H. 1995. Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique. Mol. Phylogenet. Evol. 4: 44–63.

    Google Scholar 

  • Zhu, T., Wang, N., Carr, A., Wolinsky, S. and Ho, D. D. 1995. Evidence for coinfection by multiple strains of human immunodeficiency virus type 1 subtype B in an acute seroconvertor. J. Virol. 69: 1324–1327

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Zoology, Brigham Young University, Provo, UT, 84602, USA

    David Posada & Keith A. Crandall

  2. Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA

    David M. Hillis

Authors
  1. David Posada
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Keith A. Crandall
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. David M. Hillis
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. University of Auckland, Auckland, New Zealand

    Allen G. Rodrigo

  2. University of Washington, Washington, USA

    Gerald H. Learn Jr.

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Kluwer Academic Publishers

About this chapter

Cite this chapter

Posada, D., Crandall, K.A., Hillis, D.M. (2002). Phylogenetics of HIV. In: Rodrigo, A.G., Learn, G.H. (eds) Computational and Evolutionary Analysis of HIV Molecular Sequences. Springer, Boston, MA. https://doi.org/10.1007/0-306-46900-6_7

Download citation

  • DOI: https://doi.org/10.1007/0-306-46900-6_7

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-0-7923-7994-2

  • Online ISBN: 978-0-306-46900-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation