Figure 4. Phylogenetic relationship between ERV-Fc sequences.
Maximum likelihood amino acid trees of (A) Gag (B) Pol and (C) TM generated using the LG substitution matrix. In each panel, HERV-H and HERV-W sequences were included as outgroups. Boostrap confidence values of nodes are depicted by colored spheres. In order to save space, a distance of approximately 0.6 was removed from the HERV-W outgroup branch in the Gag phylogeny (A), as indicated by the broken line.
DOI: http://dx.doi.org/10.7554/eLife.12704.011
Figure 4—source data 1. Full-length ERV-Fc Gag alignment.
The phylogeny shown in Figure 4A is based on this alignment excluding the p12 region (as described in the Materials and methods).
elife-12704-fig4-data1.zip (8.1KB, zip)
DOI: 10.7554/eLife.12704.012
Figure 4—source data 2. ERV-Fc CA alignment.
elife-12704-fig4-data2.zip (3.2KB, zip)
DOI: 10.7554/eLife.12704.013
Figure 4—source data 3. Full-length ERV-Fc Pol alignment.
The phylogeny shown in Figure 4B is based on this alignment.
elife-12704-fig4-data3.zip (12.9KB, zip)
DOI: 10.7554/eLife.12704.014
Figure 4—source data 4. ERV-Fc RT alignment.
elife-12704-fig4-data4.zip (2.5KB, zip)
DOI: 10.7554/eLife.12704.015
Figure 4—source data 5. Full-length ERV-Fc Env sequences, including all recovered open reading frames.
elife-12704-fig4-data5.zip (11.7KB, zip)
DOI: 10.7554/eLife.12704.016
Figure 4—source data 6. ERV-Fc TM alignment.
The phylogeny shown in Figure 4C is based on this alignment.
elife-12704-fig4-data6.zip (2.8KB, zip)
DOI: 10.7554/eLife.12704.017
Figure 4—source data 7. Alignment of ERV-Fc Pol including both inferred and strict consensus sequences.
The phylogeny shown in Figure 4—figure supplement 1 is derived from this alignment.
elife-12704-fig4-data7.zip (13.1KB, zip)
DOI: 10.7554/eLife.12704.018
Figure 4—figure supplement 1. Inferences made in deriving ERV-Fc consensus sequences do not significantly affect phylogenetic relationships.
A ML phylogeny, generated via RAxML, comparing the relationship between our inferred Pol sequences and strict consensus sequences. HERV-H and HERV-W sequences were included as outgroups. Boostrap confidence values of nodes are depicted by colored spheres. HERV, human endogenous retrovirus; ML, maximum likelihood.