Phylogenetic analysis of Tanzanian NHP <i>TPE</i> samples.
<p>NHP <i>TPE</i> genomes from Tanzanian isolates used were either finished genomes (n = 9, shown in bold) or partially determined (draft sequences, <b>n</b> = 13), as well as completely sequenced genomes from African, Indonesian, and Polynesian <i>TPE</i> s...
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2025
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| Summary: | <p>NHP <i>TPE</i> genomes from Tanzanian isolates used were either finished genomes (n = 9, shown in bold) or partially determined (draft sequences, <b>n</b> = 13), as well as completely sequenced genomes from African, Indonesian, and Polynesian <i>TPE</i> strains isolated from humans [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0012887#pntd.0012887.ref028" target="_blank">28</a>–<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0012887#pntd.0012887.ref031" target="_blank">31</a>]. TPA strains Nichols and SS14 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0012887#pntd.0012887.ref032" target="_blank">32</a>] were used as an outgroup. The evolutionary history was inferred using the Maximum likelihood and HKY+G model [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0012887#pntd.0012887.ref026" target="_blank">26</a>]. All positions containing gaps and missing data were eliminated (complete deletion option). There were 1,981 variable sites in the original dataset. There were 385,875 positions in the final dataset (35% of the whole genome (1,093 kb)). Bootstrap support (1000 replicates) is shown next to the branches. The scale corresponds to the number of substitutions per nucleotide. The geographical and species origin of isolates is shown next to the tree. Finished genomes are shown in bold.</p> |
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