Skip to main content
Journal cover image

Different models, different trees: the geographic origin of PTLV-I.

Publication ,  Journal Article
Kelsey, CR; Crandall, KA; Voevodin, AF
Published in: Mol Phylogenet Evol
November 1999

Using nucleotide sequences from three genomic regions of the human and simian T-cell lymphotropic virus type I (HTLV-I/STLV-I)-consisting of 69 sequences from a 140-bp segment of the pol region, 98 sequences from a 503-bp segment of the LTR, and 154 sequences from a 386-bp segment of the env region-we tested two hypotheses concerning the geographic origin and evolution of STLV-I and HTLV-I. First, we tested the assumption of equal rates of evolution along STLV-I and HTLV-I lineages using a likelihood ratio test to ascertain whether current levels of genomic diversity can be used to determine ancestry. We demonstrated that unequal rates of evolution along HTLV-I and STLV-I lineages have occurred throughout evolutionary time, thus calling into question the use of pairwise distances to assign ancestry. Second, we constructed phylogenetic trees using multiple phylogenetic techniques to test for the geographic origin of STLV-I and HTLV-I. Using the principle of likelihood, we chose a statistically justified model of evolution for each data set. We demonstrated the utility of the likelihood ratio test to determine which model of evolution should be chosen for phylogenetic analyses, revealing that using different models of evolution produces conflicting results, and neither the hypothesis of an African origin nor the hypothesis of an Asian origin can be rejected statistically. Our best estimates of phylogenetic relationships, however, support an African origin of PTLV for each gene region.

Duke Scholars

Published In

Mol Phylogenet Evol

DOI

ISSN

1055-7903

Publication Date

November 1999

Volume

13

Issue

2

Start / End Page

336 / 347

Location

United States

Related Subject Headings

  • Simian T-lymphotropic virus 1
  • Repetitive Sequences, Nucleic Acid
  • Phylogeny
  • Models, Genetic
  • Likelihood Functions
  • Humans
  • Human T-lymphotropic virus 1
  • Geography
  • Genes, pol
  • Genes, env
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Kelsey, C. R., Crandall, K. A., & Voevodin, A. F. (1999). Different models, different trees: the geographic origin of PTLV-I. Mol Phylogenet Evol, 13(2), 336–347. https://doi.org/10.1006/mpev.1999.0663
Kelsey, C. R., K. A. Crandall, and A. F. Voevodin. “Different models, different trees: the geographic origin of PTLV-I.Mol Phylogenet Evol 13, no. 2 (November 1999): 336–47. https://doi.org/10.1006/mpev.1999.0663.
Kelsey CR, Crandall KA, Voevodin AF. Different models, different trees: the geographic origin of PTLV-I. Mol Phylogenet Evol. 1999 Nov;13(2):336–47.
Kelsey, C. R., et al. “Different models, different trees: the geographic origin of PTLV-I.Mol Phylogenet Evol, vol. 13, no. 2, Nov. 1999, pp. 336–47. Pubmed, doi:10.1006/mpev.1999.0663.
Kelsey CR, Crandall KA, Voevodin AF. Different models, different trees: the geographic origin of PTLV-I. Mol Phylogenet Evol. 1999 Nov;13(2):336–347.
Journal cover image

Published In

Mol Phylogenet Evol

DOI

ISSN

1055-7903

Publication Date

November 1999

Volume

13

Issue

2

Start / End Page

336 / 347

Location

United States

Related Subject Headings

  • Simian T-lymphotropic virus 1
  • Repetitive Sequences, Nucleic Acid
  • Phylogeny
  • Models, Genetic
  • Likelihood Functions
  • Humans
  • Human T-lymphotropic virus 1
  • Geography
  • Genes, pol
  • Genes, env