Hi, I'm new to Phylogenetics. How do i draw interpretations & evaluate the attached Phylogeny tree?
For example,
- what are the types of information that can be derived from this phylogenetic tree?
- what are the interpretations that can be made on the virus isolated from singapore?
- what can i hypothesized about the ancestral strain of this virus?
Thank you.
In a phylogenetic tree, the vertical lines simply space the sequences in the analysis and mean nothing. It is the horizontal lines and branching patterns that have significance. The numbers at each node are called "bootstrap values." These range from 0 to 100, and the closer to 100 the value is at a particular node, the more statistically reliable is that specific bifurcation (branching pattern). The length of the horizontal connecting lines represents evolutionary distance based on differences in the sequences used in the analysis. To estimate distance, you can add up the horizontal branches connecting one sequence to another, and then compare this length to the scale bar, which at 0.05, represents a 5% difference in sequence identity.
The tree has 99% and 100% bootstrap support for there being two major clades or "sub-subtypes" within the Dengue 2 serotype sequences used here. One is represented by two African sequences and the other clade or group is represented by sequences of viruses from Kenya and Asia. The "rooting" of this tree seems misleading, and would probably be better drawn with no root, or with a midpoint root half way between the two clades. The Singapore virus is clearly in the Kenya/Asia clade.
To get a feeling for how distant those two Dengue-2 subclades are from each other, you would want to add in sequences from Dengue-1, Dengue-3 and Dengue-4 serotypes. These would also serve as a good "outgroup" to the Dengue-2 which you are interested in.
The attached paper makes it clear that the Senegal/Burkina Faso clade in your tree is the African "sylvatic" or primate lineage of Dengue 2 while the other clade is the human lineage. At least one of your sequences (KX821510 from Kenya) is just a tiny 512 base region of the capsid gene, and this can cause problems with the entire tree depending on how the phylogenetic tree building is done. Complete genomes of hundreds of Dengue-2 isolates are available, so it may be better to use only the longer sequences. I am attaching an alignment and a neighbor-joining tree built from it.
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