Special Reports

Mobile DNA in Old World Monkeys: A Glimpse Through the Rhesus Macaque Genome

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Science  13 Apr 2007:
Vol. 316, Issue 5822, pp. 238-240
DOI: 10.1126/science.1139462
  • Fig. 1.

    Phylogenetic tree of retroviruses based on full-length Pol proteins. Common infectious retroviruses and endogenous retroviruses, present in fish, birds, mammals (nonprimate), and primates, were included in the analysis. Color identifications for each group are shown in the upper right corner. Asterisks and circles show deep-rooted branches with >95 and >75% bootstrap values, respectively. The ERVs identified in this study that invaded the OWM genome horizontally (i.e., through external germline infection) are indicated with red letters. For all ERVs shown in blue letters, the original insertion occurred in the common ancestor of humans and rhesus macaques (i.e., vertically) and is present in both genomes. All ERVs indicated with blue letters also generated new insertions in the OWM lineage. The scale bar indicates 10% divergence in the amino acid sequence.

  • Fig. 2.

    Median-joining network of OWM-specific L1 subfamilies. Subfamilies are represented by circles, with the circle size symbolizing the relative size of each subfamily. The length of the lines corresponds to the number of substitutions. The scale of a single substitution is shown in the upper left corner. Broken lines indicate segments not drawn to scale. Gray circles represent the subfamilies belonging to the L1CER-3 lineage, which include an 18–base pair (bp) duplication in their 3′ untranslated region (3′UTR), and green-edged circles contain intact full-length L1 elements. The dashed line and red arrow represent two alternative pathways for the origin of the L1CER-4 subfamily. The subfamilies in the blue and pink ovals share the same diagnostic mutations but do not share the 18-bp duplication. My, million years.

  • Fig. 3.

    Median-joining network of OWM-specific Alu subfamilies. Subfamilies are represented by circles. The length of the lines corresponds to the number of substitutions, and the scale of a single substitution is shown in the upper left corner. Broken lines indicate segments not drawn to scale. Gray circles represent all subfamilies belonging to the AluYRb lineage containing a 12-bp deletion. Red-edged circles denote the youngest Alu subfamily within each lineage, and the blue-edged circle indicates the AluY subfamily consensus sequence.

Additional Files


  • Mobile DNA in Old World Monkeys: A Glimpse Through the Rhesus Macaque Genome
    Kyudong Han, Miriam K. Konkel, Jinchuan Xing, Hui Wang, Jungnam Lee, Thomas J. Meyer, Charles T. Huang, Erin Sandifer, Kristi Hebert, Erin W. Barnes, Robert Hubley, Webb Miller, Arian F. A. Smit, Brygg Ullmer, Mark A. Batzer

    Supporting Online Material

    This supplement contains:
    Materials and Methods
    SOM Text
    Figs. S1 and S2
    Tables S1 to S7
    References
    Source Code

    This file is in Adobe Acrobat PDF format.

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