Hi @plyons! The default tree view for SARS-CoV-2 on Nextstrain shows a “time tree” where each tip is plotted on the x-axis by its collection date and the internal nodes indicate the inferred time that ancestral strains circulated based on the observed collection dates and phylogenetic structure. In this layout, you will rarely see tips plotted on top of ancestral nodes. For example, here is the zoomed-in view of the Alpha clade in our global build:
You can change this default view to show a “divergence tree” by selecting the “divergence” button in the left navigation bar under the “Branch Length” section. In this divergence tree view of the same clade, we see tips and internal nodes plotted on the x-axis by the number of mutations they have relative to the root sequence of the tree.
Here we see that several tips fall on top of internal nodes indicating that these tips and the ancestral strain represented by the internal node have the exactly same genotype. If we added new strains to this tree with identical sequences to other strains, the new strains would be plotted at the same position on the x-axis as the other identical strains (with a slightly different y-axis position due to the “rectangular” phylogenetic tree layout).
Identical strains in this view can also appear as polytomies where the observed strains differ by genotype from their inferred ancestor but all observed strains are identical. I’ve highlighted two such polytomies in the following tree for New Zealand strains where two pairs of strains share a nucleotide mutation at 17009 (yellow tips) and then a sibling pair of strains share a mutation at 29296 (blue tips at the same x-axis position):
The “divergence view” of the tree is generally more helpful than the “time” view when discussing genetic relationships between strains or clades.
Let us know if this doesn’t fully address your original question, though, or if you have further questions about these views.