How to read a phylogenetic tree

Phylogenetic dendrograms, or trees, provide information about the inferred evolutionary relationships between viruses. The example shown in the figure is a phylogenetic tree for 10 viral isolates from different individuals whose genome sequences have been determined. The horizontal dimension of the tree represents the amount of genetic change, and the scale (0.07) is the number of changes divided by the length of the sequence (in some trees this may be expressed as % change). The blue circles, called nodes, represent putative ancestors of the sampled viruses. Therefore, the branches represent chains of infections that have led to sampled viruses. The vertical distances have no significance. The tree in the figure is rooted, which means that we know the common ancestor of all the sampled viruses.

A rooted tree gives the order of branching from left to right: virus A existed before B, although the unit of time might not be known. The numbers next to each node represent the measure of support; these are computed by a variety of statistical approaches including “bootstrapping” and “Bayesian posterior probabilities.” A value close to 1 indicates strong evidence that sequences to the right of the node cluster together better than any other sequences. Often there is no known isolate corresponding to the root of the tree; in this case, an arbitrary root may be estimated, or the tree will be unrooted. In these cases, it can no longer be assumed that the order of ancestors proceeds from left to right. Phylogenetic trees can also be constructed by grouping sampled viruses by host of isolation. Such an arrangement sometimes.

makes it possible to identify the animal source of a human virus. Circular forms, such as a radial format tree, are often displayed when the root is unknown. Trees relating nucleic acid sequences depict the relationships as if sampled and intermediary sequences were on a trajectory to the present sequences. This deduction is an oversimplification, because any intermediate that was lost during evolution will not be represented in the tree. In addition, any recombination or gene exchange by coinfection with similar viral genomes will scramble ordered lineages

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