but in practical terms it is useful to have a tree-like map, because it allows you to assess the phylogenetic distance between two groups.
That works as long as a virus doesn't transfer genes from one species to the next and thus invalidates the tree structure.
It depends on your goal. What a lot of non-biologists don't realize is that the ladder keeps going after species down through subspecies and beyond. In terms of bacteria, which do undergo horizontal gene transfer, we generally refer to them by their strain in addition to their species. The strain tells you where you got the culture, and, in lab settings, what it's used for. CAMP Staphylococcus aureus is used for the CAMP test, for example -- because you know where the strain comes from, you can be reasonably confident that it will behave like other bacteri...
If it's worth saying, but not worth its own post (even in Discussion), then it goes here.
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